diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..f5a0417 --- /dev/null +++ b/.gitignore @@ -0,0 +1,5 @@ +*.out +*.pyc +*.tar +*.tar.gz +dataset/* \ No newline at end of file diff --git a/README.md b/README.md new file mode 100644 index 0000000..832c6e6 --- /dev/null +++ b/README.md @@ -0,0 +1,7 @@ +![SINGA banner and concept](img/SINGA.png) + +## SINGA - Molecular Sampling with Protein-Ligand INteractions aware Generative Adversarial Network + +### This project is under progress. Coming soon. + +Developer: OON Yu Yang, Project Officer (Computational Biology/Biochemistry) at School of Biological Sciences, Nanyang Technological University Singapore \ No newline at end of file diff --git a/autodock_vina/LICENSE b/autodock_vina/LICENSE new file mode 100644 index 0000000..d645695 --- /dev/null +++ b/autodock_vina/LICENSE @@ -0,0 +1,202 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/autodock_vina/bin/vina b/autodock_vina/bin/vina new file mode 100755 index 0000000..d5c555a Binary files /dev/null and b/autodock_vina/bin/vina differ diff --git a/autodock_vina/bin/vina_split b/autodock_vina/bin/vina_split new file mode 100644 index 0000000..0300b2c Binary files /dev/null and b/autodock_vina/bin/vina_split differ diff --git a/config/config.yml b/config/config.yml new file mode 100644 index 0000000..230bd8d --- /dev/null +++ b/config/config.yml @@ -0,0 +1,57 @@ +autodock: + executable: ./autodock_vina/bin/vina + num_modes: 9 + seed: 1 + +dataset: + name: pl + path: ./dataset/crossdocked_pocket10 + split: ./dataset/split_by_name.pt + +featuriser: + interaction_cutoff: 4.0 + sasa_cutoff: 4.0 + symbol_radius_path: ./config/symbol_radius.json + +general: + MAX_INT: 2147483647 + seed: 1 + +pymeshSkippedComplex: +- 4nrt +- 1hqh +- 1uy9 +- 4bpi +- 6n4b +- 5twl +- 5hdz +- 3bgl +- 4mdq +- 3rv9 +- 4j9a +- 4ctk +- 2y06 +- 2chz +- 6e7w +- 2wkt +- 3udj +- 5a5v +- 1jik +- 2a5u +- 4ayw +- 3dpd +- 2bb7 +- 5myn +- 5nkk +- 1zkk +- 2r3y +- 6e7s +- 5un1 +- 5i94 +- 6e7x +- 1hqf +- 4p7s +- 2xm8 +- 6mu1 +- 1uyi + diff --git a/config/symbol_radius.json b/config/symbol_radius.json new file mode 100644 index 0000000..524c360 --- /dev/null +++ b/config/symbol_radius.json @@ -0,0 +1,105 @@ +{ + "H" : 1.10, + "C" : 1.70, + "N" : 1.55, + "O" : 1.52, + "P" : 1.80, + "S" : 1.80, + "SE": 1.90, + "F" : 1.47, + "CL": 1.75, + "BR": 1.83, + "I" : 1.98, + "LI": 1.81, + "BE": 1.53, + "NA": 2.27, + "MG": 1.73, + "K" : 2.75, + "CA": 2.31, + "RB": 3.03, + "SR": 2.49, + "CS": 3.43, + "BA": 2.68, + "FR": 3.48, + "RA": 2.83, + "SC": 2.11, + "TI": 1.95, + "V" : 1.06, + "CR": 1.13, + "MN": 1.19, + "FE": 1.26, + "CO": 1.13, + "NI": 1.63, + "CU": 1.40, + "ZN": 1.39, + "Y" : 1.61, + "ZR": 1.42, + "NB": 1.33, + "MO": 1.75, + "TC": 2.00, + "RU": 1.20, + "RH": 1.22, + "PD": 1.63, + "AG": 1.72, + "CD": 1.58, + "HF": 1.40, + "TA": 1.22, + "W" : 1.26, + "RE": 1.30, + "OS": 1.58, + "IR": 1.22, + "PT": 1.75, + "AU": 1.66, + "HG": 1.55, + "AL": 1.84, + "GA": 1.87, + "IN": 1.93, + "SN": 2.17, + "TL": 1.96, + "PB": 2.02, + "BI": 2.07, + "PO": 1.97, + "B" : 1.92, + "SI": 2.10, + "GE": 2.11, + "AS": 1.85, + "SB": 2.06, + "TE": 2.06, + "AT": 2.02, + "HE": 1.40, + "NE": 1.54, + "AR": 1.88, + "KR": 2.02, + "XE": 2.16, + "RN": 2.20, + "LA": 1.83, + "CE": 1.86, + "PR": 1.62, + "ND": 1.79, + "PM": 1.76, + "SM": 1.74, + "EU": 1.96, + "GD": 1.69, + "TB": 1.66, + "DY": 1.63, + "HO": 1.61, + "ER": 1.59, + "TM": 1.57, + "YB": 1.54, + "LU": 1.53, + "AC": 2.12, + "TH": 1.84, + "PA": 1.60, + "U" : 1.86, + "NP": 1.71, + "PU": 1.67, + "AM": 1.66, + "CM": 1.65, + "BK": 1.64, + "CF": 1.63, + "ES": 1.62, + "FM": 1.61, + "MD": 1.60, + "NO": 1.59, + "LR": 1.58 +} \ No newline at end of file diff --git a/config/symbol_radius.metadata b/config/symbol_radius.metadata new file mode 100644 index 0000000..bef8622 --- /dev/null +++ b/config/symbol_radius.metadata @@ -0,0 +1,16 @@ +/* + METADATA + ======== + symbol_radius.json + + Taken from: + + Mantina et al. "Consistent van der Waals Radii for + the Whole Main Group". J. Phys. Chem. A, 2009, 113 (19), pp + 5806–5812. + + Many of these elements, if they occur in a PDB file, should + probably rather be skipped than used in a SASA calculation, and + ionization will change the effective radius. + +*/ \ No newline at end of file diff --git a/config/train.yml b/config/train.yml new file mode 100644 index 0000000..a4c8d48 --- /dev/null +++ b/config/train.yml @@ -0,0 +1,80 @@ +dataset: + name: pl + path: ./dataset/crossdocked_vina10 + split: ./dataset/split_by_name.pt + +model: + name: singa + +train: + seed: 1 + use_apex: False + batch_size: 8 + num_workers: 8 + pin_memory: True + max_iters: 500000 + val_freq: 5000 + pos_noise_std: 0.1 + max_grad_norm: 100.0 + optimizer: + type: adam + lr: 2.e-4 + weight_decay: 0 + beta1: 0.99 + beta2: 0.999 + scheduler: + type: plateau + factor: 0.6 + patience: 8 + min_lr: 1.e-5 + transform: + mask: + type: mixed + min_ratio: 0.0 + max_ratio: 1.1 + min_num_masked: 1 + min_num_unmasked: 0 + p_random: 0.15 + p_bfs: 0.6 + p_invbfs: 0.25 + contrastive: + num_real: 20 + num_fake: 20 + pos_real_std: 0.05 + pos_fake_std: 2.0 + edgesampler: + k: 8 + +PLInteraction: + nonpolar: + 6: 1.7 + 9: 1.47 + 17: 1.75 + 35: 1.85 + 53: 1.98 + hbond_dist_cut: 3.5 + hbond_angle_cut: 180.0 + hbond_dist_bound: 2.5 + hbond_angle_bound: 90.0 + hphob_dist_cut: 4.0 + hphob_dist_bound: 1.25 + contact_scale_cut: 1.75 + contact_scale_opt: 1.25 + sbridge_dist_cut: 5.0 + sbridge_dist_bound: 3.25 + sbridge_resonance: True + pistack_dist_cut: 6.5 + pistack_dist_bound: 3.8 + pistack_angle_cut: 90.0 + pistack_angle_boundL 60.0 + pication_dist_cut: 6.5 + pication_dist_bound: 4.3 + pication_angle_cut: 90.0 + pication_angle_bound: 30.0 + xbond_dist_cut: 5.0 + xbond_dist_bound: 3.5 + xbond_angle_cut: 150.0 + xbond_angle_bound: 135.0 + acceptor_metal_dist_cut: 4.0 + pimetal_dist_cut: 5.0 + diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..492029e --- /dev/null +++ b/environment.yml @@ -0,0 +1,346 @@ +name: SINGA +channels: + - pytorch-nightly + - nvidia + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1=conda_forge + - _openmp_mutex=4.5=2_kmp_llvm + - anyio=3.7.1=pyhd8ed1ab_0 + - argon2-cffi=21.3.0=pyhd8ed1ab_0 + - argon2-cffi-bindings=21.2.0=py310h5764c6d_3 + - asttokens=2.2.1=pyhd8ed1ab_0 + - async-lru=2.0.3=pyhd8ed1ab_0 + - attrs=23.1.0=pyh71513ae_1 + - babel=2.12.1=pyhd8ed1ab_1 + - backcall=0.2.0=pyh9f0ad1d_0 + - backports=1.0=pyhd8ed1ab_3 + - backports.functools_lru_cache=1.6.5=pyhd8ed1ab_0 + - beautifulsoup4=4.12.2=pyha770c72_0 + - biopython=1.81=py310h1fa729e_0 + - blas=1.0=mkl + - bleach=6.0.0=pyhd8ed1ab_0 + - boost=1.74.0=py310h7c3ba0c_5 + - boost-cpp=1.74.0=h75c5d50_8 + - bottleneck=1.3.7=py310h0a54255_0 + - brotlipy=0.7.0=py310h7f8727e_1002 + - bzip2=1.0.8=h7b6447c_0 + - c-ares=1.19.1=hd590300_0 + - ca-certificates=2023.5.7=hbcca054_0 + - cached-property=1.5.2=hd8ed1ab_1 + - cached_property=1.5.2=pyha770c72_1 + - cairo=1.16.0=hb05425b_5 + - certifi=2023.5.7=pyhd8ed1ab_0 + - cffi=1.15.1=py310h5eee18b_3 + - cftime=1.6.2=py310hde88566_1 + - charset-normalizer=2.0.4=pyhd3eb1b0_0 + - colorama=0.4.6=pyhd8ed1ab_0 + - cryptography=39.0.1=py310h9ce1e76_2 + - cuda-cudart=12.1.105=0 + - cuda-cupti=12.1.105=0 + - cuda-libraries=12.1.0=0 + - cuda-nvrtc=12.1.105=0 + - cuda-nvtx=12.1.105=0 + - cuda-opencl=12.2.53=0 + - cuda-runtime=12.1.0=0 + - curl=8.1.2=h409715c_0 + - cycler=0.11.0=pyhd8ed1ab_0 + - debugpy=1.5.1=py310h295c915_0 + - decorator=5.1.1=pyhd8ed1ab_0 + - defusedxml=0.7.1=pyhd8ed1ab_0 + - entrypoints=0.4=pyhd8ed1ab_0 + - exceptiongroup=1.1.2=pyhd8ed1ab_0 + - executing=1.2.0=pyhd8ed1ab_0 + - fasteners=0.17.3=pyhd8ed1ab_0 + - ffmpeg=4.2.2=h20bf706_0 + - filelock=3.9.0=py310h06a4308_0 + - flit-core=3.9.0=pyhd8ed1ab_0 + - fontconfig=2.14.1=hef1e5e3_0 + - freetype=2.10.4=hca18f0e_2 + - giflib=5.2.1=h0b41bf4_3 + - glib=2.69.1=he621ea3_2 + - gmp=6.2.1=h295c915_3 + - gmpy2=2.1.2=py310heeb90bb_0 + - gnutls=3.6.15=he1e5248_0 + - greenlet=2.0.1=py310h6a678d5_0 + - griddataformats=1.0.1=pyhd8ed1ab_0 + - gsd=2.9.0=py310h278f3c1_0 + - hdf4=4.2.15=h9772cbc_5 + - hdf5=1.12.2=nompi_h4df4325_101 + - icu=70.1=h27087fc_0 + - idna=3.4=py310h06a4308_0 + - importlib-metadata=6.8.0=pyha770c72_0 + - importlib_metadata=6.8.0=hd8ed1ab_0 + - importlib_resources=6.0.0=pyhd8ed1ab_1 + - intel-openmp=2023.1.0=hdb19cb5_46305 + - ipykernel=6.15.0=pyh210e3f2_0 + - ipython=8.14.0=pyh41d4057_0 + - ipywidgets=8.0.7=pyhd8ed1ab_0 + - jbig=2.1=h7f98852_2003 + - jedi=0.18.2=pyhd8ed1ab_0 + - jinja2=3.1.2=py310h06a4308_0 + - jpeg=9e=h0b41bf4_3 + - json5=0.9.14=pyhd8ed1ab_0 + - jsonschema=4.18.0=pyhd8ed1ab_0 + - jsonschema-specifications=2023.6.1=pyhd8ed1ab_0 + - jupyter-lsp=2.2.0=pyhd8ed1ab_0 + - jupyter_client=8.3.0=pyhd8ed1ab_0 + - jupyter_core=5.3.1=py310hff52083_0 + - jupyter_events=0.6.3=pyhd8ed1ab_0 + - jupyter_server=2.7.0=pyhd8ed1ab_0 + - jupyter_server_terminals=0.4.4=pyhd8ed1ab_1 + - jupyterlab=4.0.2=pyhd8ed1ab_0 + - jupyterlab_pygments=0.2.2=pyhd8ed1ab_0 + - jupyterlab_server=2.23.0=pyhd8ed1ab_0 + - jupyterlab_widgets=3.0.8=pyhd8ed1ab_0 + - keyutils=1.6.1=h166bdaf_0 + - kiwisolver=1.4.4=py310h6a678d5_0 + - krb5=1.20.1=h81ceb04_0 + - lame=3.100=h7b6447c_0 + - lcms2=2.12=h3be6417_0 + - ld_impl_linux-64=2.38=h1181459_1 + - lerc=3.0=h295c915_0 + - libaec=1.0.6=hcb278e6_1 + - libcublas=12.1.0.26=0 + - libcufft=11.0.2.4=0 + - libcufile=1.7.0.149=0 + - libcurand=10.3.3.53=0 + - libcurl=8.1.2=h409715c_0 + - libcusolver=11.4.4.55=0 + - libcusparse=12.0.2.55=0 + - libdeflate=1.8=h7f8727e_5 + - libedit=3.1.20191231=he28a2e2_2 + - libev=4.33=h516909a_1 + - libffi=3.4.4=h6a678d5_0 + - libgcc-ng=13.1.0=he5830b7_0 + - libgfortran-ng=13.1.0=h69a702a_0 + - libgfortran5=13.1.0=h15d22d2_0 + - libiconv=1.17=h166bdaf_0 + - libidn2=2.3.4=h5eee18b_0 + - libnetcdf=4.8.1=nompi_h21705cb_104 + - libnghttp2=1.52.0=h61bc06f_0 + - libnpp=12.0.2.50=0 + - libnsl=2.0.0=h7f98852_0 + - libnvjitlink=12.1.105=0 + - libnvjpeg=12.1.1.14=0 + - libopenblas=0.3.23=pthreads_h80387f5_0 + - libopus=1.3.1=h7b6447c_0 + - libpng=1.6.39=h753d276_0 + - libsodium=1.0.18=h36c2ea0_1 + - libsqlite=3.42.0=h2797004_0 + - libssh2=1.11.0=h0841786_0 + - libstdcxx-ng=13.1.0=hfd8a6a1_0 + - libtasn1=4.19.0=h5eee18b_0 + - libtiff=4.3.0=h6f004c6_2 + - libunistring=0.9.10=h27cfd23_0 + - libuuid=2.38.1=h0b41bf4_0 + - libvpx=1.7.0=h439df22_0 + - libwebp=1.2.4=h11a3e52_1 + - libwebp-base=1.2.4=h5eee18b_1 + - libxcb=1.15=h0b41bf4_0 + - libxml2=2.9.14=h22db469_4 + - libxslt=1.1.35=h8affb1d_0 + - libzip=1.9.2=hc929e4a_1 + - libzlib=1.2.13=hd590300_5 + - llvm-openmp=16.0.6=h4dfa4b3_0 + - lz4-c=1.9.3=h9c3ff4c_1 + - markupsafe=2.1.1=py310h7f8727e_0 + - matplotlib-base=3.4.3=py310h23f4a51_2 + - matplotlib-inline=0.1.6=pyhd8ed1ab_0 + - mdanalysis=2.5.0=py310hff15622_1 + - mistune=3.0.0=pyhd8ed1ab_0 + - mkl=2023.1.0=h6d00ec8_46342 + - mkl-service=2.4.0=py310h5eee18b_1 + - mkl_fft=1.3.6=py310h1128e8f_1 + - mkl_random=1.2.2=py310h1128e8f_1 + - mmtf-python=1.1.3=pyhd8ed1ab_0 + - mpc=1.1.0=h10f8cd9_1 + - mpfr=4.0.2=hb69a4c5_1 + - mrcfile=1.4.3=pyhd8ed1ab_0 + - msgpack-python=1.0.5=py310hdf3cbec_0 + - nbclient=0.8.0=pyhd8ed1ab_0 + - nbconvert-core=7.6.0=pyhd8ed1ab_0 + - nbformat=5.9.1=pyhd8ed1ab_0 + - ncurses=6.4=h6a678d5_0 + - nest-asyncio=1.5.6=pyhd8ed1ab_0 + - netcdf4=1.6.0=nompi_py310h0a86a1f_103 + - nettle=3.7.3=hbbd107a_1 + - networkx=2.8.4=py310h06a4308_1 + - nglview=3.0.6=pyhba93850_0 + - notebook-shim=0.2.3=pyhd8ed1ab_0 + - numexpr=2.8.4=py310h85018f9_1 + - numpy-base=1.25.0=py310hb5e798b_0 + - openbabel=3.1.1=py310h154a6b4_3 + - openblas=0.3.23=pthreads_h855a84d_0 + - openh264=2.1.1=h4ff587b_0 + - openssl=3.1.1=hd590300_1 + - overrides=7.3.1=pyhd8ed1ab_0 + - packaging=23.1=pyhd8ed1ab_0 + - pandas=1.5.3=py310h1128e8f_0 + - pandocfilters=1.5.0=pyhd8ed1ab_0 + - parso=0.8.3=pyhd8ed1ab_0 + - patsy=0.5.3=pyhd8ed1ab_0 + - pbr=5.11.1=pyhd8ed1ab_0 + - pcre=8.45=h9c3ff4c_0 + - pexpect=4.8.0=pyh1a96a4e_2 + - pickleshare=0.7.5=py_1003 + - pillow=9.4.0=py310h6a678d5_0 + - pip=23.1.2=py310h06a4308_0 + - pixman=0.40.0=h36c2ea0_0 + - pkgutil-resolve-name=1.3.10=pyhd8ed1ab_0 + - platformdirs=3.8.1=pyhd8ed1ab_0 + - plip=2.2.1=pyhd8ed1ab_0 + - pooch=1.7.0=pyha770c72_3 + - prolif=1.1.0=pyhd8ed1ab_0 + - prometheus_client=0.17.1=pyhd8ed1ab_0 + - prompt-toolkit=3.0.39=pyha770c72_0 + - prompt_toolkit=3.0.39=hd8ed1ab_0 + - psutil=5.9.5=py310h1fa729e_0 + - pthread-stubs=0.4=h36c2ea0_1001 + - ptyprocess=0.7.0=pyhd3deb0d_0 + - pure_eval=0.2.2=pyhd8ed1ab_0 + - pycairo=1.24.0=py310hda9f760_0 + - pycparser=2.21=pyhd3eb1b0_0 + - pyedr=0.7.1=pyhd8ed1ab_0 + - pygments=2.15.1=pyhd8ed1ab_0 + - pyopenssl=23.0.0=py310h06a4308_0 + - pyparsing=3.1.0=pyhd8ed1ab_0 + - pysocks=1.7.1=py310h06a4308_0 + - python=3.10.12=hd12c33a_0_cpython + - python-dateutil=2.8.2=pyhd8ed1ab_0 + - python-fastjsonschema=2.17.1=pyhd8ed1ab_0 + - python-json-logger=2.0.7=pyhd8ed1ab_0 + - python_abi=3.10=3_cp310 + - pytng=0.3.0=py310hc908c09_0 + - pytorch=2.1.0.dev20230711=py3.10_cuda12.1_cudnn8.9.2_0 + - pytorch-cuda=12.1=ha16c6d3_5 + - pytorch-mutex=1.0=cuda + - pytz=2023.3=pyhd8ed1ab_0 + - pyyaml=6.0=py310h5eee18b_1 + - pyzmq=25.1.0=py310h6a678d5_0 + - rdkit=2022.03.2=py310h1c297d8_0 + - readline=8.2=h5eee18b_0 + - redo=2.0.4=pyh9f0ad1d_0 + - referencing=0.29.1=pyhd8ed1ab_0 + - reportlab=3.6.12=py310h5eee18b_0 + - requests=2.29.0=py310h06a4308_0 + - rfc3339-validator=0.1.4=pyhd8ed1ab_0 + - rfc3986-validator=0.1.1=pyh9f0ad1d_0 + - rpds-py=0.8.10=py310hcb5633a_0 + - scikit-learn=1.3.0=py310hf7d194e_0 + - seaborn=0.12.2=hd8ed1ab_0 + - seaborn-base=0.12.2=pyhd8ed1ab_0 + - send2trash=1.8.2=pyh41d4057_0 + - setuptools=67.8.0=py310h06a4308_0 + - six=1.16.0=pyh6c4a22f_0 + - sniffio=1.3.0=pyhd8ed1ab_0 + - soupsieve=2.3.2.post1=pyhd8ed1ab_0 + - spyrmsd=0.5.2=pyhd8ed1ab_0 + - sqlalchemy=2.0.18=py310h2372a71_0 + - sqlite=3.41.2=h5eee18b_0 + - stack_data=0.6.2=pyhd8ed1ab_0 + - statsmodels=0.14.0=py310h278f3c1_1 + - sympy=1.11.1=py310h06a4308_0 + - tbb=2021.8.0=hdb19cb5_0 + - terminado=0.17.1=pyh41d4057_0 + - threadpoolctl=3.1.0=pyh8a188c0_0 + - tidynamics=1.1.2=pyhd8ed1ab_0 + - tinycss2=1.2.1=pyhd8ed1ab_0 + - tk=8.6.12=h1ccaba5_0 + - tomli=2.0.1=pyhd8ed1ab_0 + - torchaudio=2.1.0.dev20230711=py310_cu121 + - torchtriton=2.1.0+3c400e7818=py310 + - torchvision=0.16.0.dev20230711=py310_cu121 + - tornado=6.3.2=py310h2372a71_0 + - tqdm=4.65.0=pyhd8ed1ab_1 + - traitlets=5.9.0=pyhd8ed1ab_0 + - typing_extensions=4.7.1=pyha770c72_0 + - typing_utils=0.1.0=pyhd8ed1ab_0 + - tzdata=2023c=h04d1e81_0 + - urllib3=1.26.16=py310h06a4308_0 + - wcwidth=0.2.6=pyhd8ed1ab_0 + - webencodings=0.5.1=py_1 + - websocket-client=1.6.1=pyhd8ed1ab_0 + - wheel=0.38.4=py310h06a4308_0 + - widgetsnbextension=4.0.8=pyhd8ed1ab_0 + - x264=1!157.20191217=h7b6447c_0 + - xorg-libxau=1.0.11=hd590300_0 + - xorg-libxdmcp=1.1.3=h7f98852_0 + - xz=5.2.6=h166bdaf_0 + - yaml=0.2.5=h7b6447c_0 + - zeromq=4.3.4=h9c3ff4c_1 + - zipp=3.16.0=pyhd8ed1ab_1 + - zlib=1.2.13=hd590300_5 + - zstd=1.5.2=h8a70e8d_1 + - pip: + - absl-py==1.4.0 + - aiohttp==3.8.5 + - aiosignal==1.3.1 + - alabaster==0.7.13 + - astunparse==1.6.3 + - async-timeout==4.0.3 + - biopandas==0.4.1 + - cachetools==5.3.1 + - dgl==1.1.1 + - docutils==0.20.1 + - easydict==1.10 + - flatbuffers==23.5.26 + - freesasa==2.2.0.post3 + - frozenlist==1.4.0 + - fsspec==2023.6.0 + - gast==0.4.0 + - gensim==4.3.1 + - google-auth==2.22.0 + - google-auth-oauthlib==1.0.0 + - google-pasta==0.2.0 + - grpcio==1.56.0 + - h5py==3.9.0 + - imagesize==1.4.1 + - joblib==1.3.1 + - keras==2.13.1 + - libclang==16.0.0 + - lightning-utilities==0.9.0 + - lxml==4.9.3 + - markdown==3.4.3 + - mpmath==1.2.1 + - multidict==6.0.4 + - node2vec==0.4.6 + - numpy==1.24.3 + - numpydoc==1.5.0 + - oauthlib==3.2.2 + - oddt==0.7 + - opencadd==0+unknown + - opt-einsum==3.3.0 + - parmed==4.1.0 + - protobuf==4.23.4 + - pyasn1==0.5.0 + - pyasn1-modules==0.3.0 + - pytorch-lightning==2.0.6 + - requests-oauthlib==1.3.1 + - rsa==4.9 + - scipy==1.11.1 + - smart-open==6.3.0 + - snowballstemmer==2.2.0 + - spektral==1.3.0 + - sphinx==7.1.0 + - sphinxcontrib-applehelp==1.0.4 + - sphinxcontrib-devhelp==1.0.2 + - sphinxcontrib-htmlhelp==2.0.1 + - sphinxcontrib-jsmath==1.0.1 + - sphinxcontrib-qthelp==1.0.3 + - sphinxcontrib-serializinghtml==1.1.5 + - tensorboard==2.13.0 + - tensorboard-data-server==0.7.1 + - tensorflow==2.13.0 + - tensorflow-estimator==2.13.0 + - tensorflow-io-gcs-filesystem==0.32.0 + - termcolor==2.3.0 + - torch-geometric==2.3.1 + - torch-scatter==2.1.1 + - torchmetrics==1.0.3 + - torchsummary==1.5.1 + - typing-extensions==4.5.0 + - werkzeug==2.3.6 + - wrapt==1.15.0 + - yarl==1.9.2 diff --git a/example/1m7y_1m7y.pkl b/example/1m7y_1m7y.pkl new file mode 100644 index 0000000..517a077 Binary files /dev/null and b/example/1m7y_1m7y.pkl differ diff --git a/example/2o98_2o98.pkl b/example/2o98_2o98.pkl new file mode 100644 index 0000000..32a3dfc Binary files /dev/null and b/example/2o98_2o98.pkl differ diff --git a/example/7cff_ligand.sdf b/example/7cff_ligand.sdf new file mode 100644 index 0000000..dddb0cd --- /dev/null +++ b/example/7cff_ligand.sdf @@ -0,0 +1,509 @@ +7cff + PyMOL2.5 3D 0 + + 17 15 0 0 0 0 0 0 0 0999 V2000 + 16.8060 32.7500 -6.6890 Zn 0 0 0 0 0 0 0 0 0 0 0 0 + 7.0410 42.0840 22.2730 Mg 0 0 0 0 0 0 0 0 0 0 0 0 + -3.4960 29.8920 12.4250 N 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3570 30.7740 12.1000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7340 31.9610 11.2340 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.4140 31.4900 10.0470 N 0 0 0 0 0 0 0 0 0 0 0 0 + -4.2760 30.3360 10.1810 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.7090 30.1630 11.6370 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.3450 32.2330 8.8000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.7030 33.7050 8.9910 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.7440 33.8270 9.9380 O 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0470 28.5320 12.1320 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.1490 28.0430 13.2590 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.6480 28.7330 14.8490 S 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5390 29.4650 15.4490 O 0 0 0 0 0 0 0 0 0 0 0 0 + -3.7740 29.6490 14.6570 O 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0130 27.6330 15.7350 O 0 0 0 0 0 0 0 0 0 0 0 0 + 3 4 1 0 0 0 0 + 3 8 1 0 0 0 0 + 3 12 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 1 0 0 0 0 + 6 7 1 0 0 0 0 + 6 9 1 0 0 0 0 + 7 8 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 12 13 1 0 0 0 0 + 13 14 1 0 0 0 0 + 14 15 1 0 0 0 0 + 14 16 2 0 0 0 0 + 14 17 2 0 0 0 0 +M END +> +HEADER TRANSPORT PROTEIN 25-JUN-20 7CFF +TITLE STRUCTURE OF THE THERMOSTABILIZED TRANSMEMBRANE DOMAIN OF THE +TITLE 2 BACTERIAL CNNM/CORC FAMILY MG2+ TRANSPORTER IN COMPLEX WITH MG2+ +COMPND MOL_ID: 1; +COMPND 2 MOLECULE: HEMOLYSIN; +COMPND 3 CHAIN: A; +COMPND 4 SYNONYM: CORC; +COMPND 5 ENGINEERED: YES; +COMPND 6 MUTATION: YES +SOURCE MOL_ID: 1; +SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS PARVATIENSIS; +SOURCE 3 ORGANISM_TAXID: 456163; +SOURCE 4 GENE: AV541_07030; +SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; +SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 +KEYWDS TRANSPORTER, TRANSPORT PROTEIN +EXPDTA X-RAY DIFFRACTION +AUTHOR Y.HUANG,F.JIN,M.HATTORI +REVDAT 2 10-MAR-21 7CFF 1 TITLE +REVDAT 1 24-FEB-21 7CFF 0 +JRNL AUTH Y.HUANG,F.JIN,Y.FUNATO,Z.XU,W.ZHU,J.WANG,M.SUN,Y.ZHAO,Y.YU, +JRNL AUTH 2 H.MIKI,M.HATTORI +JRNL TITL STRUCTURAL BASIS FOR THE MG 2+ RECOGNITION AND REGULATION OF +JRNL TITL 2 THE CORC MG 2+ TRANSPORTER. +JRNL REF SCI ADV V. 7 2021 +JRNL REFN ESSN 2375-2548 +JRNL PMID 33568487 +JRNL DOI 10.1126/SCIADV.ABE6140 +REMARK 2 +REMARK 2 RESOLUTION. 2.00 ANGSTROMS. +REMARK 3 +REMARK 3 REFINEMENT. +REMARK 3 PROGRAM : PHENIX 1.18.2_3874 +REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN +REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, +REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, +REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, +REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, +REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, +REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT +REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART +REMARK 3 +REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 +REMARK 3 +REMARK 3 DATA USED IN REFINEMENT. +REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 +REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.27 +REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 +REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 +REMARK 3 NUMBER OF REFLECTIONS : 15683 +REMARK 3 +REMARK 3 FIT TO DATA USED IN REFINEMENT. +REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 +REMARK 3 R VALUE (WORKING SET) : 0.216 +REMARK 3 FREE R VALUE : 0.232 +REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 +REMARK 3 FREE R VALUE TEST SET COUNT : 785 +REMARK 3 +REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). +REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE +REMARK 3 1 49.2700 - 3.6300 0.95 2586 136 0.2317 0.2473 +REMARK 3 2 3.6300 - 2.8800 0.97 2516 132 0.2059 0.2060 +REMARK 3 3 2.8800 - 2.5200 0.97 2477 131 0.1854 0.2142 +REMARK 3 4 2.5200 - 2.2900 0.95 2430 128 0.1931 0.2101 +REMARK 3 5 2.2900 - 2.1300 0.96 2442 128 0.2178 0.2817 +REMARK 3 6 2.1300 - 2.0000 0.96 2447 130 0.2519 0.2527 +REMARK 3 +REMARK 3 BULK SOLVENT MODELLING. +REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL +REMARK 3 SOLVENT RADIUS : 1.11 +REMARK 3 SHRINKAGE RADIUS : 0.90 +REMARK 3 K_SOL : NULL +REMARK 3 B_SOL : NULL +REMARK 3 +REMARK 3 ERROR ESTIMATES. +REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.152 +REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.245 +REMARK 3 +REMARK 3 B VALUES. +REMARK 3 FROM WILSON PLOT (A**2) : 31.18 +REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.56 +REMARK 3 OVERALL ANISOTROPIC B VALUE. +REMARK 3 B11 (A**2) : NULL +REMARK 3 B22 (A**2) : NULL +REMARK 3 B33 (A**2) : NULL +REMARK 3 B12 (A**2) : NULL +REMARK 3 B13 (A**2) : NULL +REMARK 3 B23 (A**2) : NULL +REMARK 3 +REMARK 3 TWINNING INFORMATION. +REMARK 3 FRACTION: NULL +REMARK 3 OPERATOR: NULL +REMARK 3 +REMARK 3 DEVIATIONS FROM IDEAL VALUES. +REMARK 3 RMSD COUNT +REMARK 3 BOND : 0.007 1258 +REMARK 3 ANGLE : 0.974 1707 +REMARK 3 CHIRALITY : 0.047 204 +REMARK 3 PLANARITY : 0.007 204 +REMARK 3 DIHEDRAL : 16.497 440 +REMARK 3 +REMARK 3 TLS DETAILS +REMARK 3 NUMBER OF TLS GROUPS : NULL +REMARK 3 +REMARK 3 NCS DETAILS +REMARK 3 NUMBER OF NCS GROUPS : NULL +REMARK 3 +REMARK 3 OTHER REFINEMENT REMARKS: NULL +REMARK 4 +REMARK 4 7CFF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 +REMARK 100 +REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUN-20. +REMARK 100 THE DEPOSITION ID IS D_1300017511. +REMARK 200 +REMARK 200 EXPERIMENTAL DETAILS +REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION +REMARK 200 DATE OF DATA COLLECTION : 02-NOV-18 +REMARK 200 TEMPERATURE (KELVIN) : 100 +REMARK 200 PH : 4.0 +REMARK 200 NUMBER OF CRYSTALS USED : 1 +REMARK 200 +REMARK 200 SYNCHROTRON (Y/N) : Y +REMARK 200 RADIATION SOURCE : SPRING-8 +REMARK 200 BEAMLINE : BL32XU +REMARK 200 X-RAY GENERATOR MODEL : NULL +REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M +REMARK 200 WAVELENGTH OR RANGE (A) : 1 +REMARK 200 MONOCHROMATOR : NULL +REMARK 200 OPTICS : NULL +REMARK 200 +REMARK 200 DETECTOR TYPE : PIXEL +REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M +REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS +REMARK 200 DATA SCALING SOFTWARE : XDS +REMARK 200 +REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15683 +REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 +REMARK 200 RESOLUTION RANGE LOW (A) : 49.300 +REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL +REMARK 200 +REMARK 200 OVERALL. +REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 +REMARK 200 DATA REDUNDANCY : 4.700 +REMARK 200 R MERGE (I) : NULL +REMARK 200 R SYM (I) : NULL +REMARK 200 FOR THE DATA SET : 6.9900 +REMARK 200 +REMARK 200 IN THE HIGHEST RESOLUTION SHELL. +REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 +REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 +REMARK 200 COMPLETENESS FOR SHELL (%) : NULL +REMARK 200 DATA REDUNDANCY IN SHELL : NULL +REMARK 200 R MERGE FOR SHELL (I) : NULL +REMARK 200 R SYM FOR SHELL (I) : NULL +REMARK 200 FOR SHELL : NULL +REMARK 200 +REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH +REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT +REMARK 200 SOFTWARE USED: PHASER +REMARK 200 STARTING MODEL: NULL +REMARK 200 +REMARK 200 REMARK: NULL +REMARK 280 +REMARK 280 CRYSTAL +REMARK 280 SOLVENT CONTENT, VS (%): 64.68 +REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.48 +REMARK 280 +REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MM ZNCL2, 100 MM SODIUM ACETATE (PH +REMARK 280 4.0), 40% POLYETHYLENE GLYCOL 200, LIPIDIC CUBIC PHASE, +REMARK 280 TEMPERATURE 291K +REMARK 290 +REMARK 290 CRYSTALLOGRAPHIC SYMMETRY +REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 2 +REMARK 290 +REMARK 290 SYMOP SYMMETRY +REMARK 290 NNNMMM OPERATOR +REMARK 290 1555 X,Y,Z +REMARK 290 2555 -X,-Y,Z +REMARK 290 3555 -X,Y,-Z +REMARK 290 4555 X,-Y,-Z +REMARK 290 5555 X+1/2,Y+1/2,Z +REMARK 290 6555 -X+1/2,-Y+1/2,Z +REMARK 290 7555 -X+1/2,Y+1/2,-Z +REMARK 290 8555 X+1/2,-Y+1/2,-Z +REMARK 290 +REMARK 290 WHERE NNN -> OPERATOR NUMBER +REMARK 290 MMM -> TRANSLATION VECTOR +REMARK 290 +REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS +REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM +REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY +REMARK 290 RELATED MOLECULES. +REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 +REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 +REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 +REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 +REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 +REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 +REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 +REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 +REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 28.74500 +REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.66000 +REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 +REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 28.74500 +REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.66000 +REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 +REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 28.74500 +REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 41.66000 +REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 +REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 28.74500 +REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 41.66000 +REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 +REMARK 290 +REMARK 290 REMARK: NULL +REMARK 300 +REMARK 300 BIOMOLECULE: 1 +REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM +REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN +REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON +REMARK 300 BURIED SURFACE AREA. +REMARK 350 +REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN +REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE +REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS +REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND +REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. +REMARK 350 +REMARK 350 BIOMOLECULE: 1 +REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC +REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC +REMARK 350 SOFTWARE USED: PISA +REMARK 350 TOTAL BURIED SURFACE AREA: 4050 ANGSTROM**2 +REMARK 350 SURFACE AREA OF THE COMPLEX: 15400 ANGSTROM**2 +REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 KCAL/MOL +REMARK 350 APPLY THE FOLLOWING TO CHAINS: A +REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 +REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 +REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 +REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 +REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 83.32000 +REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 +REMARK 375 +REMARK 375 SPECIAL POSITION +REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS +REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL +REMARK 375 POSITIONS. +REMARK 375 +REMARK 375 ATOM RES CSSEQI +REMARK 375 HOH A 303 LIES ON A SPECIAL POSITION. +REMARK 375 HOH A 322 LIES ON A SPECIAL POSITION. +REMARK 375 HOH A 336 LIES ON A SPECIAL POSITION. +REMARK 375 HOH A 367 LIES ON A SPECIAL POSITION. +REMARK 375 HOH A 378 LIES ON A SPECIAL POSITION. +REMARK 375 HOH A 379 LIES ON A SPECIAL POSITION. +REMARK 375 HOH A 383 LIES ON A SPECIAL POSITION. +REMARK 465 +REMARK 465 MISSING RESIDUES +REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE +REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN +REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) +REMARK 465 +REMARK 465 M RES C SSSEQI +REMARK 465 MET A 24 +REMARK 465 ALA A 25 +REMARK 465 SER A 26 +REMARK 465 PRO A 27 +REMARK 465 GLU A 184 +REMARK 465 SER A 185 +REMARK 465 SER A 186 +REMARK 465 GLY A 187 +REMARK 465 LEU A 188 +REMARK 465 GLU A 189 +REMARK 465 VAL A 190 +REMARK 465 LEU A 191 +REMARK 465 PHE A 192 +REMARK 465 GLN A 193 +REMARK 470 +REMARK 470 MISSING ATOM +REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; +REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; +REMARK 470 I=INSERTION CODE): +REMARK 470 M RES CSSEQI ATOMS +REMARK 470 GLU A 28 CG CD OE1 OE2 +REMARK 470 ASN A 29 CG OD1 ND2 +REMARK 470 LYS A 68 CG CD CE NZ +REMARK 470 ARG A 182 CG CD NE CZ NH1 NH2 +REMARK 500 +REMARK 500 GEOMETRY AND STEREOCHEMISTRY +REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT +REMARK 500 +REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. +REMARK 500 +REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE +REMARK 500 C18 OLC A 204 C1 OLC A 205 1.49 +REMARK 500 O HOH A 349 O HOH A 352 1.97 +REMARK 500 O HOH A 331 O HOH A 338 2.05 +REMARK 500 O HOH A 365 O HOH A 373 2.09 +REMARK 500 OE1 GLU A 142 O HOH A 301 2.10 +REMARK 500 O HOH A 351 O HOH A 365 2.10 +REMARK 500 O HOH A 371 O HOH A 380 2.15 +REMARK 500 O HOH A 309 O HOH A 370 2.19 +REMARK 500 +REMARK 500 REMARK: NULL +REMARK 500 +REMARK 500 GEOMETRY AND STEREOCHEMISTRY +REMARK 500 SUBTOPIC: TORSION ANGLES +REMARK 500 +REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: +REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; +REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). +REMARK 500 +REMARK 500 STANDARD TABLE: +REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) +REMARK 500 +REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- +REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 +REMARK 500 +REMARK 500 M RES CSSEQI PSI PHI +REMARK 500 ASP A 78 59.63 -146.48 +REMARK 500 GLU A 130 -63.83 -133.28 +REMARK 500 HIS A 140 37.69 -144.55 +REMARK 500 +REMARK 500 REMARK: NULL +REMARK 610 +REMARK 610 MISSING HETEROATOM +REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; +REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; +REMARK 610 I=INSERTION CODE): +REMARK 610 M RES C SSEQI +REMARK 610 OLC A 204 +REMARK 610 OLC A 205 +REMARK 610 OLC A 206 +REMARK 620 +REMARK 620 METAL COORDINATION +REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; +REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): +REMARK 620 +REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL +REMARK 620 MG A 202 MG +REMARK 620 N RES CSSEQI ATOM +REMARK 620 1 SER A 43 O +REMARK 620 2 SER A 43 OG 87.1 +REMARK 620 3 SER A 47 OG 89.8 176.7 +REMARK 620 4 ASN A 90 OD1 91.2 93.0 88.1 +REMARK 620 5 GLY A 129 O 89.1 95.8 83.1 171.2 +REMARK 620 6 GLU A 130 OE2 173.4 96.6 86.5 94.1 85.1 +REMARK 620 N 1 2 3 4 5 +REMARK 620 +REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL +REMARK 620 ZN A 201 ZN +REMARK 620 N RES CSSEQI ATOM +REMARK 620 1 GLU A 63 OE1 +REMARK 620 2 GLU A 63 OE2 58.2 +REMARK 620 3 GLU A 66 OE1 121.9 75.6 +REMARK 620 4 GLU A 66 OE2 102.8 104.0 54.1 +REMARK 620 5 HIS A 139 ND1 8.3 55.0 114.1 95.9 +REMARK 620 6 HOH A 311 O 87.2 144.7 124.6 75.4 89.8 +REMARK 620 N 1 2 3 4 5 +REMARK 800 +REMARK 800 SITE +REMARK 800 SITE_IDENTIFIER: AC1 +REMARK 800 EVIDENCE_CODE: SOFTWARE +REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 201 +REMARK 800 +REMARK 800 SITE_IDENTIFIER: AC2 +REMARK 800 EVIDENCE_CODE: SOFTWARE +REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 +REMARK 800 +REMARK 800 SITE_IDENTIFIER: AC3 +REMARK 800 EVIDENCE_CODE: SOFTWARE +REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 203 +REMARK 800 +REMARK 800 SITE_IDENTIFIER: AC4 +REMARK 800 EVIDENCE_CODE: SOFTWARE +REMARK 800 SITE_DESCRIPTION: binding site for residue OLC A 206 +REMARK 800 +REMARK 800 SITE_IDENTIFIER: AC5 +REMARK 800 EVIDENCE_CODE: SOFTWARE +REMARK 800 SITE_DESCRIPTION: binding site for residues OLC A 204 and OLC A +REMARK 800 205 +DBREF1 7CFF A 25 182 UNP A0A109QFA5_9DEIN +DBREF2 7CFF A A0A109QFA5 25 182 +SEQADV 7CFF MET A 24 UNP A0A109QFA INITIATING METHIONINE +SEQADV 7CFF ALA A 101 UNP A0A109QFA VAL 101 ENGINEERED MUTATION +SEQADV 7CFF LEU A 183 UNP A0A109QFA EXPRESSION TAG +SEQADV 7CFF GLU A 184 UNP A0A109QFA EXPRESSION TAG +SEQADV 7CFF SER A 185 UNP A0A109QFA EXPRESSION TAG +SEQADV 7CFF SER A 186 UNP A0A109QFA EXPRESSION TAG +SEQADV 7CFF GLY A 187 UNP A0A109QFA EXPRESSION TAG +SEQADV 7CFF LEU A 188 UNP A0A109QFA EXPRESSION TAG +SEQADV 7CFF GLU A 189 UNP A0A109QFA EXPRESSION TAG +SEQADV 7CFF VAL A 190 UNP A0A109QFA EXPRESSION TAG +SEQADV 7CFF LEU A 191 UNP A0A109QFA EXPRESSION TAG +SEQADV 7CFF PHE A 192 UNP A0A109QFA EXPRESSION TAG +SEQADV 7CFF GLN A 193 UNP A0A109QFA EXPRESSION TAG +SEQRES 1 A 170 MET ALA SER PRO GLU ASN PRO TRP LEU TRP ALA VAL LEU +SEQRES 2 A 170 VAL LEU LEU LEU ALA LEU SER ALA PHE PHE SER ALA SER +SEQRES 3 A 170 GLU THR ALA ILE THR THR LEU TYR PRO TRP LYS LEU LYS +SEQRES 4 A 170 GLU LEU ALA GLU SER LYS ASN GLY PRO PHE ARG LEU LEU +SEQRES 5 A 170 ALA GLU ASP ILE THR ARG PHE LEU THR THR ILE LEU VAL +SEQRES 6 A 170 GLY ASN ASN LEU VAL ASN ILE ALA ALA THR ALA LEU ALA +SEQRES 7 A 170 THR GLU LEU ALA THR GLN ALA PHE GLY SER ALA GLY VAL +SEQRES 8 A 170 GLY VAL ALA THR GLY ALA MET THR PHE LEU ILE LEU PHE +SEQRES 9 A 170 PHE GLY GLU ILE THR PRO LYS SER LEU ALA VAL HIS HIS +SEQRES 10 A 170 ALA GLU ALA ILE ALA ARG LEU ALA ALA TRP PRO ILE TYR +SEQRES 11 A 170 GLY LEU SER VAL LEU PHE TYR PRO VAL GLY ARG PHE PHE +SEQRES 12 A 170 SER LEU VAL SER GLY GLY LEU LEU ARG LEU LEU GLY LEU +SEQRES 13 A 170 GLU PRO ARG LEU GLU SER SER GLY LEU GLU VAL LEU PHE +SEQRES 14 A 170 GLN +HET ZN A 201 1 +HET MG A 202 1 +HET EPE A 203 15 +HET OLC A 204 17 +HET OLC A 205 13 +HET OLC A 206 11 +HETNAM ZN ZINC ION +HETNAM MG MAGNESIUM ION +HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID +HETNAM OLC (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE +HETSYN EPE HEPES +HETSYN OLC 1-OLEOYL-R-GLYCEROL +FORMUL 2 ZN ZN 2+ +FORMUL 3 MG MG 2+ +FORMUL 4 EPE C8 H18 N2 O4 S +FORMUL 5 OLC 3(C21 H40 O4) +FORMUL 8 HOH *84(H2 O) +HELIX 1 AA1 ASN A 29 TYR A 57 1 29 +HELIX 2 AA2 PRO A 58 SER A 67 1 10 +HELIX 3 AA3 GLY A 70 ASP A 78 1 9 +HELIX 4 AA4 ASP A 78 GLY A 110 1 33 +HELIX 5 AA5 SER A 111 GLU A 130 1 20 +HELIX 6 AA6 GLU A 130 HIS A 139 1 10 +HELIX 7 AA7 HIS A 140 LEU A 177 1 38 +LINK O SER A 43 MG MG A 202 1555 1555 2.13 +LINK OG SER A 43 MG MG A 202 1555 1555 2.27 +LINK OG SER A 47 MG MG A 202 1555 1555 2.24 +LINK OE1 GLU A 63 ZN ZN A 201 1555 1555 2.17 +LINK OE2 GLU A 63 ZN ZN A 201 1555 1555 2.34 +LINK OE1 GLU A 66 ZN ZN A 201 1555 1555 2.64 +LINK OE2 GLU A 66 ZN ZN A 201 1555 1555 2.08 +LINK OD1 ASN A 90 MG MG A 202 1555 1555 2.22 +LINK O GLY A 129 MG MG A 202 1555 1555 2.21 +LINK OE2 GLU A 130 MG MG A 202 1555 1555 2.16 +LINK ND1 HIS A 139 ZN ZN A 201 1555 4565 2.22 +LINK ZN ZN A 201 O HOH A 311 1555 1555 2.02 +CISPEP 1 TYR A 57 PRO A 58 0 1.09 +CISPEP 2 LYS A 68 ASN A 69 0 7.63 +CISPEP 3 ASN A 69 GLY A 70 0 -23.29 +SITE 1 AC1 4 GLU A 63 GLU A 66 HIS A 139 HOH A 311 +SITE 1 AC2 5 SER A 43 SER A 47 ASN A 90 GLY A 129 +SITE 2 AC2 5 GLU A 130 +SITE 1 AC3 8 THR A 80 THR A 84 GLY A 163 ARG A 164 +SITE 2 AC3 8 SER A 167 HOH A 313 HOH A 372 HOH A 375 +SITE 1 AC4 6 LEU A 168 GLY A 172 LEU A 173 ARG A 175 +SITE 2 AC4 6 LEU A 183 HOH A 303 +SITE 1 AC5 6 TRP A 33 LEU A 36 LEU A 40 LEU A 104 +SITE 2 AC5 6 ALA A 105 LEU A 124 +CRYST1 57.490 83.320 98.530 90.00 90.00 90.00 C 2 2 2 8 +ORIGX1 1.000000 0.000000 0.000000 0.00000 +ORIGX2 0.000000 1.000000 0.000000 0.00000 +ORIGX3 0.000000 0.000000 1.000000 0.00000 +SCALE1 0.017394 0.000000 0.000000 0.00000 +SCALE2 0.000000 0.012002 0.000000 0.00000 +SCALE3 0.000000 0.000000 0.010149 0.00000 + + +$$$$ diff --git a/example/7cff_protein.pdb b/example/7cff_protein.pdb new file mode 100644 index 0000000..ba750f7 --- /dev/null +++ b/example/7cff_protein.pdb @@ -0,0 +1,1178 @@ +CRYST1 57.490 83.320 98.530 90.00 90.00 90.00 C 2 2 2 1 +ATOM 1 N GLU A 28 11.742 44.085 46.478 1.00 76.85 N +ATOM 2 CA GLU A 28 12.513 44.570 45.339 1.00 73.22 C +ATOM 3 C GLU A 28 13.937 44.005 45.355 1.00 81.44 C +ATOM 4 O GLU A 28 14.913 44.747 45.498 1.00 82.48 O +ATOM 5 CB GLU A 28 12.546 46.101 45.328 1.00 65.12 C +ATOM 6 N ASN A 29 14.041 42.686 45.216 1.00 76.70 N +ATOM 7 CA ASN A 29 15.339 42.044 45.107 1.00 72.56 C +ATOM 8 C ASN A 29 15.991 42.411 43.774 1.00 77.67 C +ATOM 9 O ASN A 29 15.299 42.643 42.776 1.00 67.81 O +ATOM 10 CB ASN A 29 15.199 40.526 45.216 1.00 72.00 C +ATOM 11 N PRO A 30 17.325 42.469 43.730 1.00 81.92 N +ATOM 12 CA PRO A 30 17.988 42.801 42.457 1.00 76.85 C +ATOM 13 C PRO A 30 17.695 41.794 41.363 1.00 71.26 C +ATOM 14 O PRO A 30 17.561 42.172 40.192 1.00 66.71 O +ATOM 15 CB PRO A 30 19.476 42.815 42.834 1.00 84.11 C +ATOM 16 CG PRO A 30 19.568 41.896 44.011 1.00 82.58 C +ATOM 17 CD PRO A 30 18.293 42.113 44.783 1.00 83.88 C +ATOM 18 N TRP A 31 17.589 40.513 41.719 1.00 66.34 N +ATOM 19 CA TRP A 31 17.281 39.493 40.726 1.00 69.13 C +ATOM 20 C TRP A 31 15.923 39.744 40.083 1.00 63.11 C +ATOM 21 O TRP A 31 15.744 39.504 38.881 1.00 53.06 O +ATOM 22 CB TRP A 31 17.321 38.107 41.371 1.00 70.82 C +ATOM 23 CG TRP A 31 18.709 37.607 41.652 1.00 86.77 C +ATOM 24 CD1 TRP A 31 19.259 37.363 42.877 1.00 97.71 C +ATOM 25 CD2 TRP A 31 19.720 37.279 40.686 1.00 94.35 C +ATOM 26 NE1 TRP A 31 20.548 36.907 42.735 1.00107.82 N +ATOM 27 CE2 TRP A 31 20.856 36.848 41.401 1.00 98.32 C +ATOM 28 CE3 TRP A 31 19.776 37.311 39.288 1.00 92.09 C +ATOM 29 CZ2 TRP A 31 22.034 36.452 40.766 1.00 94.78 C +ATOM 30 CZ3 TRP A 31 20.948 36.918 38.659 1.00 90.37 C +ATOM 31 CH2 TRP A 31 22.059 36.494 39.399 1.00 90.24 C +ATOM 32 N LEU A 32 14.954 40.227 40.866 1.00 54.57 N +ATOM 33 CA LEU A 32 13.615 40.434 40.329 1.00 54.09 C +ATOM 34 C LEU A 32 13.614 41.509 39.252 1.00 48.76 C +ATOM 35 O LEU A 32 12.944 41.358 38.225 1.00 47.17 O +ATOM 36 CB LEU A 32 12.638 40.787 41.451 1.00 50.48 C +ATOM 37 CG LEU A 32 12.402 39.701 42.503 1.00 56.75 C +ATOM 38 CD1 LEU A 32 11.525 40.219 43.640 1.00 56.09 C +ATOM 39 CD2 LEU A 32 11.786 38.465 41.869 1.00 47.43 C +ATOM 40 N TRP A 33 14.376 42.585 39.451 1.00 49.56 N +ATOM 41 CA TRP A 33 14.474 43.607 38.417 1.00 51.69 C +ATOM 42 C TRP A 33 15.175 43.068 37.177 1.00 48.41 C +ATOM 43 O TRP A 33 14.840 43.457 36.054 1.00 43.74 O +ATOM 44 CB TRP A 33 15.203 44.839 38.954 1.00 51.53 C +ATOM 45 CG TRP A 33 14.462 45.525 40.048 1.00 60.20 C +ATOM 46 CD1 TRP A 33 14.819 45.589 41.366 1.00 68.06 C +ATOM 47 CD2 TRP A 33 13.226 46.243 39.931 1.00 62.00 C +ATOM 48 NE1 TRP A 33 13.884 46.305 42.074 1.00 71.82 N +ATOM 49 CE2 TRP A 33 12.897 46.719 41.217 1.00 62.12 C +ATOM 50 CE3 TRP A 33 12.368 46.532 38.864 1.00 56.06 C +ATOM 51 CZ2 TRP A 33 11.746 47.463 41.466 1.00 53.78 C +ATOM 52 CZ3 TRP A 33 11.225 47.275 39.116 1.00 56.95 C +ATOM 53 CH2 TRP A 33 10.925 47.729 40.408 1.00 54.09 C +ATOM 54 N ALA A 34 16.151 42.175 37.360 1.00 45.41 N +ATOM 55 CA ALA A 34 16.826 41.588 36.211 1.00 42.00 C +ATOM 56 C ALA A 34 15.935 40.586 35.488 1.00 44.21 C +ATOM 57 O ALA A 34 16.082 40.397 34.276 1.00 42.45 O +ATOM 58 CB ALA A 34 18.126 40.915 36.645 1.00 43.99 C +ATOM 59 N VAL A 35 15.026 39.919 36.206 1.00 39.52 N +ATOM 60 CA VAL A 35 14.083 39.038 35.525 1.00 38.02 C +ATOM 61 C VAL A 35 13.107 39.862 34.699 1.00 39.58 C +ATOM 62 O VAL A 35 12.774 39.506 33.564 1.00 35.76 O +ATOM 63 CB VAL A 35 13.352 38.131 36.532 1.00 39.34 C +ATOM 64 CG1 VAL A 35 12.110 37.494 35.887 1.00 29.88 C +ATOM 65 CG2 VAL A 35 14.294 37.050 37.048 1.00 41.53 C +ATOM 66 N LEU A 36 12.660 40.993 35.239 1.00 36.97 N +ATOM 67 CA LEU A 36 11.708 41.814 34.507 1.00 37.62 C +ATOM 68 C LEU A 36 12.359 42.454 33.281 1.00 39.68 C +ATOM 69 O LEU A 36 11.744 42.524 32.210 1.00 34.58 O +ATOM 70 CB LEU A 36 11.105 42.839 35.465 1.00 37.77 C +ATOM 71 CG LEU A 36 10.208 43.911 34.873 1.00 45.96 C +ATOM 72 CD1 LEU A 36 8.841 43.316 34.674 1.00 40.11 C +ATOM 73 CD2 LEU A 36 10.112 45.038 35.875 1.00 50.46 C +ATOM 74 N VAL A 37 13.620 42.872 33.401 1.00 38.59 N +ATOM 75 CA VAL A 37 14.370 43.319 32.232 1.00 38.36 C +ATOM 76 C VAL A 37 14.503 42.181 31.224 1.00 38.90 C +ATOM 77 O VAL A 37 14.288 42.367 30.021 1.00 34.77 O +ATOM 78 CB VAL A 37 15.745 43.872 32.653 1.00 40.37 C +ATOM 79 CG1 VAL A 37 16.720 43.812 31.494 1.00 35.84 C +ATOM 80 CG2 VAL A 37 15.609 45.287 33.190 1.00 45.05 C +ATOM 81 N LEU A 38 14.855 40.986 31.701 1.00 36.37 N +ATOM 82 CA LEU A 38 14.969 39.827 30.821 1.00 35.68 C +ATOM 83 C LEU A 38 13.672 39.569 30.065 1.00 35.89 C +ATOM 84 O LEU A 38 13.696 39.291 28.858 1.00 29.86 O +ATOM 85 CB LEU A 38 15.375 38.596 31.636 1.00 36.95 C +ATOM 86 CG LEU A 38 15.614 37.228 30.981 1.00 43.46 C +ATOM 87 CD1 LEU A 38 14.337 36.415 30.782 1.00 44.19 C +ATOM 88 CD2 LEU A 38 16.334 37.409 29.658 1.00 41.90 C +ATOM 89 N LEU A 39 12.534 39.651 30.758 1.00 30.18 N +ATOM 90 CA LEU A 39 11.250 39.386 30.118 1.00 33.27 C +ATOM 91 C LEU A 39 10.943 40.426 29.046 1.00 29.81 C +ATOM 92 O LEU A 39 10.429 40.089 27.975 1.00 30.02 O +ATOM 93 CB LEU A 39 10.146 39.345 31.178 1.00 27.59 C +ATOM 94 CG LEU A 39 10.126 38.084 32.051 1.00 31.17 C +ATOM 95 CD1 LEU A 39 9.224 38.329 33.260 1.00 32.11 C +ATOM 96 CD2 LEU A 39 9.684 36.833 31.296 1.00 27.07 C +ATOM 97 N LEU A 40 11.253 41.691 29.315 1.00 30.33 N +ATOM 98 CA LEU A 40 11.035 42.730 28.320 1.00 31.09 C +ATOM 99 C LEU A 40 11.974 42.562 27.133 1.00 32.99 C +ATOM 100 O LEU A 40 11.597 42.894 26.007 1.00 25.64 O +ATOM 101 CB LEU A 40 11.204 44.112 28.956 1.00 33.60 C +ATOM 102 CG LEU A 40 10.041 44.606 29.823 1.00 34.91 C +ATOM 103 CD1 LEU A 40 10.456 45.757 30.713 1.00 38.10 C +ATOM 104 CD2 LEU A 40 8.851 44.996 28.958 1.00 31.12 C +ATOM 105 N ALA A 41 13.189 42.046 27.363 1.00 29.94 N +ATOM 106 CA ALA A 41 14.086 41.730 26.251 1.00 31.83 C +ATOM 107 C ALA A 41 13.546 40.576 25.416 1.00 32.93 C +ATOM 108 O ALA A 41 13.628 40.602 24.180 1.00 25.43 O +ATOM 109 CB ALA A 41 15.478 41.389 26.781 1.00 34.69 C +ATOM 110 N LEU A 42 12.986 39.554 26.067 1.00 26.04 N +ATOM 111 CA LEU A 42 12.348 38.482 25.304 1.00 31.31 C +ATOM 112 C LEU A 42 11.168 39.014 24.487 1.00 29.24 C +ATOM 113 O LEU A 42 10.971 38.606 23.333 1.00 25.46 O +ATOM 114 CB LEU A 42 11.914 37.350 26.242 1.00 20.19 C +ATOM 115 CG LEU A 42 13.072 36.454 26.694 1.00 30.25 C +ATOM 116 CD1 LEU A 42 12.597 35.525 27.793 1.00 25.72 C +ATOM 117 CD2 LEU A 42 13.616 35.649 25.509 1.00 32.08 C +ATOM 118 N SER A 43 10.387 39.952 25.052 1.00 26.08 N +ATOM 119 CA SER A 43 9.260 40.547 24.314 1.00 29.24 C +ATOM 120 C SER A 43 9.726 41.297 23.069 1.00 29.71 C +ATOM 121 O SER A 43 9.021 41.323 22.050 1.00 24.72 O +ATOM 122 CB SER A 43 8.487 41.516 25.206 1.00 19.21 C +ATOM 123 OG SER A 43 7.434 42.127 24.509 1.00 23.12 O +ATOM 124 N ALA A 44 10.856 42.003 23.188 1.00 26.47 N +ATOM 125 CA ALA A 44 11.459 42.680 22.049 1.00 30.97 C +ATOM 126 C ALA A 44 11.996 41.668 21.055 1.00 28.53 C +ATOM 127 O ALA A 44 11.840 41.836 19.843 1.00 30.13 O +ATOM 128 CB ALA A 44 12.570 43.620 22.529 1.00 29.45 C +ATOM 129 N PHE A 45 12.604 40.593 21.553 1.00 30.60 N +ATOM 130 CA PHE A 45 13.073 39.538 20.666 1.00 29.31 C +ATOM 131 C PHE A 45 11.920 38.959 19.848 1.00 29.60 C +ATOM 132 O PHE A 45 12.028 38.784 18.625 1.00 25.47 O +ATOM 133 CB PHE A 45 13.766 38.448 21.482 1.00 26.55 C +ATOM 134 CG PHE A 45 14.007 37.179 20.712 1.00 28.08 C +ATOM 135 CD1 PHE A 45 15.068 37.084 19.833 1.00 28.23 C +ATOM 136 CD2 PHE A 45 13.173 36.086 20.874 1.00 32.30 C +ATOM 137 CE1 PHE A 45 15.307 35.923 19.120 1.00 33.10 C +ATOM 138 CE2 PHE A 45 13.393 34.919 20.162 1.00 28.88 C +ATOM 139 CZ PHE A 45 14.465 34.838 19.276 1.00 32.57 C +ATOM 140 N PHE A 46 10.792 38.674 20.506 1.00 25.68 N +ATOM 141 CA PHE A 46 9.664 38.085 19.788 1.00 26.09 C +ATOM 142 C PHE A 46 9.043 39.063 18.792 1.00 26.91 C +ATOM 143 O PHE A 46 8.705 38.681 17.663 1.00 26.25 O +ATOM 144 CB PHE A 46 8.620 37.602 20.782 1.00 26.21 C +ATOM 145 CG PHE A 46 9.015 36.354 21.499 1.00 25.03 C +ATOM 146 CD1 PHE A 46 9.507 35.272 20.801 1.00 26.31 C +ATOM 147 CD2 PHE A 46 8.928 36.278 22.887 1.00 25.09 C +ATOM 148 CE1 PHE A 46 9.878 34.104 21.462 1.00 27.39 C +ATOM 149 CE2 PHE A 46 9.305 35.131 23.564 1.00 26.79 C +ATOM 150 CZ PHE A 46 9.783 34.033 22.859 1.00 27.87 C +ATOM 151 N SER A 47 8.862 40.323 19.187 1.00 25.07 N +ATOM 152 CA SER A 47 8.207 41.262 18.283 1.00 26.11 C +ATOM 153 C SER A 47 9.125 41.644 17.121 1.00 25.66 C +ATOM 154 O SER A 47 8.677 41.744 15.970 1.00 20.77 O +ATOM 155 CB SER A 47 7.729 42.467 19.088 1.00 26.26 C +ATOM 156 OG SER A 47 6.782 42.035 20.049 1.00 23.63 O +ATOM 157 N ALA A 48 10.427 41.771 17.383 1.00 28.11 N +ATOM 158 CA ALA A 48 11.377 41.995 16.296 1.00 26.98 C +ATOM 159 C ALA A 48 11.396 40.814 15.333 1.00 29.64 C +ATOM 160 O ALA A 48 11.392 41.005 14.110 1.00 23.13 O +ATOM 161 CB ALA A 48 12.781 42.239 16.854 1.00 24.59 C +ATOM 162 N SER A 49 11.381 39.586 15.871 1.00 29.69 N +ATOM 163 CA SER A 49 11.391 38.402 15.021 1.00 27.70 C +ATOM 164 C SER A 49 10.152 38.345 14.149 1.00 31.34 C +ATOM 165 O SER A 49 10.240 38.023 12.955 1.00 27.15 O +ATOM 166 CB SER A 49 11.487 37.138 15.869 1.00 25.59 C +ATOM 167 OG SER A 49 12.671 37.119 16.630 1.00 29.75 O +ATOM 168 N GLU A 50 8.984 38.643 14.730 1.00 26.55 N +ATOM 169 CA GLU A 50 7.750 38.648 13.950 1.00 30.90 C +ATOM 170 C GLU A 50 7.869 39.600 12.767 1.00 31.08 C +ATOM 171 O GLU A 50 7.562 39.235 11.627 1.00 27.49 O +ATOM 172 CB GLU A 50 6.559 39.044 14.830 1.00 28.76 C +ATOM 173 CG GLU A 50 5.194 38.745 14.202 1.00 33.83 C +ATOM 174 CD GLU A 50 4.721 39.815 13.221 1.00 51.99 C +ATOM 175 OE1 GLU A 50 3.895 39.489 12.334 1.00 57.25 O +ATOM 176 OE2 GLU A 50 5.176 40.978 13.324 1.00 52.28 O1- +ATOM 177 N THR A 51 8.319 40.831 13.026 1.00 28.67 N +ATOM 178 CA THR A 51 8.417 41.807 11.953 1.00 32.70 C +ATOM 179 C THR A 51 9.463 41.389 10.933 1.00 28.29 C +ATOM 180 O THR A 51 9.219 41.451 9.725 1.00 28.09 O +ATOM 181 CB THR A 51 8.735 43.189 12.519 1.00 28.65 C +ATOM 182 OG1 THR A 51 7.653 43.605 13.348 1.00 28.92 O +ATOM 183 CG2 THR A 51 8.897 44.196 11.389 1.00 28.47 C +ATOM 184 N ALA A 52 10.635 40.945 11.399 1.00 25.67 N +ATOM 185 CA ALA A 52 11.666 40.502 10.464 1.00 31.11 C +ATOM 186 C ALA A 52 11.147 39.391 9.561 1.00 33.20 C +ATOM 187 O ALA A 52 11.358 39.415 8.343 1.00 31.54 O +ATOM 188 CB ALA A 52 12.901 40.032 11.233 1.00 34.04 C +ATOM 189 N ILE A 53 10.453 38.412 10.137 1.00 31.83 N +ATOM 190 CA ILE A 53 9.991 37.272 9.354 1.00 34.71 C +ATOM 191 C ILE A 53 8.958 37.713 8.327 1.00 33.43 C +ATOM 192 O ILE A 53 9.068 37.393 7.136 1.00 35.26 O +ATOM 193 CB ILE A 53 9.434 36.181 10.283 1.00 28.27 C +ATOM 194 CG1 ILE A 53 10.581 35.457 10.991 1.00 31.11 C +ATOM 195 CG2 ILE A 53 8.553 35.224 9.494 1.00 40.44 C +ATOM 196 CD1 ILE A 53 10.145 34.679 12.230 1.00 33.15 C +ATOM 197 N THR A 54 7.942 38.458 8.770 1.00 30.75 N +ATOM 198 CA THR A 54 6.856 38.812 7.866 1.00 33.12 C +ATOM 199 C THR A 54 7.307 39.773 6.772 1.00 34.11 C +ATOM 200 O THR A 54 6.788 39.709 5.650 1.00 32.93 O +ATOM 201 CB THR A 54 5.681 39.409 8.648 1.00 35.85 C +ATOM 202 OG1 THR A 54 6.109 40.563 9.382 1.00 34.16 O +ATOM 203 CG2 THR A 54 5.115 38.380 9.618 1.00 35.06 C +ATOM 204 N THR A 55 8.270 40.659 7.057 1.00 32.04 N +ATOM 205 CA THR A 55 8.693 41.599 6.021 1.00 37.11 C +ATOM 206 C THR A 55 9.586 40.936 4.976 1.00 40.94 C +ATOM 207 O THR A 55 9.720 41.462 3.864 1.00 40.54 O +ATOM 208 CB THR A 55 9.408 42.820 6.624 1.00 37.15 C +ATOM 209 OG1 THR A 55 10.645 42.431 7.224 1.00 40.11 O +ATOM 210 CG2 THR A 55 8.547 43.517 7.682 1.00 38.01 C +ATOM 211 N LEU A 56 10.199 39.800 5.308 1.00 35.21 N +ATOM 212 CA LEU A 56 10.935 39.034 4.318 1.00 38.18 C +ATOM 213 C LEU A 56 10.023 38.163 3.466 1.00 41.51 C +ATOM 214 O LEU A 56 10.375 37.852 2.324 1.00 39.18 O +ATOM 215 CB LEU A 56 11.989 38.165 5.008 1.00 35.98 C +ATOM 216 CG LEU A 56 13.116 38.994 5.632 1.00 32.80 C +ATOM 217 CD1 LEU A 56 14.061 38.135 6.462 1.00 33.76 C +ATOM 218 CD2 LEU A 56 13.870 39.772 4.557 1.00 38.70 C +ATOM 219 N TYR A 57 8.849 37.798 3.975 1.00 37.75 N +ATOM 220 CA TYR A 57 7.920 36.826 3.400 1.00 45.81 C +ATOM 221 C TYR A 57 7.036 37.478 2.336 1.00 48.99 C +ATOM 222 O TYR A 57 6.532 38.586 2.543 1.00 46.43 O +ATOM 223 CB TYR A 57 7.048 36.218 4.500 1.00 46.26 C +ATOM 224 CG TYR A 57 6.054 35.183 4.026 1.00 46.29 C +ATOM 225 CD1 TYR A 57 6.433 33.865 3.842 1.00 49.55 C +ATOM 226 CD2 TYR A 57 4.734 35.528 3.789 1.00 48.34 C +ATOM 227 CE1 TYR A 57 5.520 32.916 3.412 1.00 60.94 C +ATOM 228 CE2 TYR A 57 3.816 34.596 3.367 1.00 56.10 C +ATOM 229 CZ TYR A 57 4.210 33.294 3.175 1.00 60.58 C +ATOM 230 OH TYR A 57 3.285 32.366 2.750 1.00 77.82 O +ATOM 231 N PRO A 58 6.817 36.824 1.180 1.00 48.01 N +ATOM 232 CA PRO A 58 7.337 35.500 0.833 1.00 48.06 C +ATOM 233 C PRO A 58 8.564 35.510 -0.070 1.00 42.06 C +ATOM 234 O PRO A 58 9.353 34.571 -0.017 1.00 38.89 O +ATOM 235 CB PRO A 58 6.161 34.868 0.092 1.00 52.29 C +ATOM 236 CG PRO A 58 5.559 36.028 -0.653 1.00 47.33 C +ATOM 237 CD PRO A 58 5.827 37.283 0.187 1.00 47.22 C +ATOM 238 N TRP A 59 8.726 36.565 -0.871 1.00 45.49 N +ATOM 239 CA TRP A 59 9.661 36.508 -1.991 1.00 47.14 C +ATOM 240 C TRP A 59 11.111 36.498 -1.515 1.00 43.05 C +ATOM 241 O TRP A 59 11.915 35.674 -1.970 1.00 41.89 O +ATOM 242 CB TRP A 59 9.403 37.675 -2.946 1.00 46.94 C +ATOM 243 CG TRP A 59 8.111 37.562 -3.725 1.00 56.42 C +ATOM 244 CD1 TRP A 59 6.970 38.295 -3.537 1.00 54.38 C +ATOM 245 CD2 TRP A 59 7.835 36.668 -4.820 1.00 60.48 C +ATOM 246 NE1 TRP A 59 6.007 37.912 -4.441 1.00 65.77 N +ATOM 247 CE2 TRP A 59 6.510 36.917 -5.240 1.00 70.02 C +ATOM 248 CE3 TRP A 59 8.580 35.684 -5.484 1.00 56.12 C +ATOM 249 CZ2 TRP A 59 5.915 36.220 -6.296 1.00 67.14 C +ATOM 250 CZ3 TRP A 59 7.985 34.990 -6.535 1.00 52.41 C +ATOM 251 CH2 TRP A 59 6.666 35.260 -6.925 1.00 60.47 C +ATOM 252 N LYS A 60 11.476 37.402 -0.596 1.00 38.31 N +ATOM 253 CA LYS A 60 12.875 37.442 -0.175 1.00 40.62 C +ATOM 254 C LYS A 60 13.238 36.238 0.690 1.00 38.94 C +ATOM 255 O LYS A 60 14.377 35.753 0.638 1.00 37.33 O +ATOM 256 CB LYS A 60 13.176 38.744 0.558 1.00 42.44 C +ATOM 257 CG LYS A 60 14.623 38.878 1.004 1.00 40.27 C +ATOM 258 CD LYS A 60 15.571 38.877 -0.182 1.00 46.34 C +ATOM 259 CE LYS A 60 16.894 39.513 0.204 1.00 52.21 C +ATOM 260 NZ LYS A 60 17.840 39.592 -0.942 1.00 65.23 N1+ +ATOM 261 N LEU A 61 12.283 35.727 1.470 1.00 44.25 N +ATOM 262 CA LEU A 61 12.536 34.523 2.258 1.00 43.63 C +ATOM 263 C LEU A 61 12.856 33.334 1.355 1.00 43.15 C +ATOM 264 O LEU A 61 13.781 32.562 1.638 1.00 36.46 O +ATOM 265 CB LEU A 61 11.327 34.226 3.150 1.00 40.10 C +ATOM 266 CG LEU A 61 11.534 33.516 4.492 1.00 48.64 C +ATOM 267 CD1 LEU A 61 12.539 34.265 5.364 1.00 38.03 C +ATOM 268 CD2 LEU A 61 10.198 33.347 5.219 1.00 38.76 C +ATOM 269 N LYS A 62 12.114 33.174 0.254 1.00 44.65 N +ATOM 270 CA LYS A 62 12.398 32.062 -0.653 1.00 43.75 C +ATOM 271 C LYS A 62 13.793 32.183 -1.255 1.00 42.01 C +ATOM 272 O LYS A 62 14.543 31.202 -1.295 1.00 40.61 O +ATOM 273 CB LYS A 62 11.338 31.977 -1.751 1.00 43.31 C +ATOM 274 CG LYS A 62 9.923 31.805 -1.218 1.00 51.36 C +ATOM 275 CD LYS A 62 9.892 30.786 -0.077 1.00 56.71 C +ATOM 276 CE LYS A 62 8.498 30.645 0.527 1.00 68.94 C +ATOM 277 NZ LYS A 62 8.134 31.806 1.402 1.00 61.53 N1+ +ATOM 278 N GLU A 63 14.175 33.385 -1.693 1.00 41.00 N +ATOM 279 CA GLU A 63 15.502 33.592 -2.272 1.00 39.69 C +ATOM 280 C GLU A 63 16.610 33.251 -1.289 1.00 43.67 C +ATOM 281 O GLU A 63 17.602 32.606 -1.658 1.00 42.96 O +ATOM 282 CB GLU A 63 15.651 35.037 -2.748 1.00 40.60 C +ATOM 283 CG GLU A 63 14.980 35.259 -4.079 1.00 45.61 C +ATOM 284 CD GLU A 63 15.558 34.352 -5.137 1.00 39.44 C +ATOM 285 OE1 GLU A 63 16.704 34.601 -5.558 1.00 47.21 O +ATOM 286 OE2 GLU A 63 14.880 33.377 -5.522 1.00 44.94 O1- +ATOM 287 N LEU A 64 16.480 33.713 -0.045 1.00 39.11 N +ATOM 288 CA LEU A 64 17.423 33.307 0.984 1.00 42.75 C +ATOM 289 C LEU A 64 17.355 31.806 1.230 1.00 42.06 C +ATOM 290 O LEU A 64 18.380 31.181 1.499 1.00 44.79 O +ATOM 291 CB LEU A 64 17.143 34.079 2.271 1.00 43.42 C +ATOM 292 CG LEU A 64 17.340 35.591 2.108 1.00 44.56 C +ATOM 293 CD1 LEU A 64 16.668 36.356 3.241 1.00 43.99 C +ATOM 294 CD2 LEU A 64 18.821 35.938 2.000 1.00 44.75 C +ATOM 295 N ALA A 65 16.162 31.213 1.124 1.00 38.44 N +ATOM 296 CA ALA A 65 16.003 29.787 1.395 1.00 44.81 C +ATOM 297 C ALA A 65 16.646 28.913 0.322 1.00 57.92 C +ATOM 298 O ALA A 65 17.159 27.832 0.638 1.00 70.56 O +ATOM 299 CB ALA A 65 14.522 29.437 1.524 1.00 41.71 C +ATOM 300 N GLU A 66 16.616 29.339 -0.944 1.00 45.13 N +ATOM 301 CA GLU A 66 17.226 28.530 -1.999 1.00 59.08 C +ATOM 302 C GLU A 66 18.746 28.620 -1.968 1.00 67.37 C +ATOM 303 O GLU A 66 19.432 27.649 -2.314 1.00 65.01 O +ATOM 304 CB GLU A 66 16.689 28.958 -3.364 1.00 56.39 C +ATOM 305 CG GLU A 66 16.718 30.435 -3.558 1.00 53.05 C +ATOM 306 CD GLU A 66 16.790 30.826 -4.998 1.00 49.41 C +ATOM 307 OE1 GLU A 66 15.848 30.477 -5.736 1.00 47.71 O +ATOM 308 OE2 GLU A 66 17.788 31.465 -5.383 1.00 52.75 O1- +ATOM 309 N SER A 67 19.283 29.773 -1.583 1.00 72.62 N +ATOM 310 CA SER A 67 20.625 29.800 -1.036 1.00 79.94 C +ATOM 311 C SER A 67 20.602 29.185 0.367 1.00 94.16 C +ATOM 312 O SER A 67 19.545 28.986 0.970 1.00 95.81 O +ATOM 313 CB SER A 67 21.162 31.231 -1.009 1.00 75.99 C +ATOM 314 OG SER A 67 22.446 31.288 -0.413 1.00 88.77 O +ATOM 315 N LYS A 68 21.781 28.847 0.875 1.00 98.75 N +ATOM 316 CA LYS A 68 21.907 28.209 2.179 1.00 94.13 C +ATOM 317 C LYS A 68 23.107 28.844 2.870 1.00104.09 C +ATOM 318 O LYS A 68 23.943 29.465 2.209 1.00120.25 O +ATOM 319 CB LYS A 68 22.051 26.686 2.018 1.00 91.97 C +ATOM 320 N ASN A 69 23.215 28.715 4.198 1.00102.42 N +ATOM 321 CA ASN A 69 22.402 27.903 5.103 1.00 92.93 C +ATOM 322 C ASN A 69 22.263 28.694 6.411 1.00 89.42 C +ATOM 323 O ASN A 69 22.859 29.768 6.542 1.00 86.98 O +ATOM 324 CB ASN A 69 23.089 26.547 5.344 1.00 93.75 C +ATOM 325 CG ASN A 69 22.106 25.395 5.489 1.00101.83 C +ATOM 326 OD1 ASN A 69 21.161 25.261 4.708 1.00 98.84 O +ATOM 327 ND2 ASN A 69 22.318 24.563 6.507 1.00102.19 N +ATOM 328 N GLY A 70 21.437 28.240 7.352 1.00 80.39 N +ATOM 329 CA GLY A 70 20.310 27.358 7.112 1.00 71.80 C +ATOM 330 C GLY A 70 18.936 27.771 7.624 1.00 55.41 C +ATOM 331 O GLY A 70 17.958 27.080 7.334 1.00 51.56 O +ATOM 332 N PRO A 71 18.829 28.884 8.362 1.00 38.69 N +ATOM 333 CA PRO A 71 17.543 29.175 9.001 1.00 49.33 C +ATOM 334 C PRO A 71 16.450 29.537 8.013 1.00 46.37 C +ATOM 335 O PRO A 71 15.267 29.346 8.322 1.00 41.60 O +ATOM 336 CB PRO A 71 17.871 30.369 9.913 1.00 44.07 C +ATOM 337 CG PRO A 71 19.323 30.637 9.753 1.00 48.93 C +ATOM 338 CD PRO A 71 19.690 30.076 8.447 1.00 49.81 C +ATOM 339 N PHE A 72 16.805 30.067 6.839 1.00 43.70 N +ATOM 340 CA PHE A 72 15.792 30.679 5.988 1.00 36.27 C +ATOM 341 C PHE A 72 14.911 29.628 5.329 1.00 35.90 C +ATOM 342 O PHE A 72 13.704 29.842 5.162 1.00 35.41 O +ATOM 343 CB PHE A 72 16.466 31.580 4.953 1.00 39.24 C +ATOM 344 CG PHE A 72 17.136 32.785 5.556 1.00 39.09 C +ATOM 345 CD1 PHE A 72 16.396 33.742 6.224 1.00 41.84 C +ATOM 346 CD2 PHE A 72 18.503 32.953 5.460 1.00 48.50 C +ATOM 347 CE1 PHE A 72 17.009 34.853 6.783 1.00 43.32 C +ATOM 348 CE2 PHE A 72 19.123 34.056 6.013 1.00 43.95 C +ATOM 349 CZ PHE A 72 18.374 35.010 6.679 1.00 43.76 C +ATOM 350 N ARG A 73 15.492 28.489 4.945 1.00 33.81 N +ATOM 351 CA ARG A 73 14.677 27.374 4.463 1.00 46.13 C +ATOM 352 C ARG A 73 13.733 26.875 5.550 1.00 34.59 C +ATOM 353 O ARG A 73 12.554 26.611 5.289 1.00 40.17 O +ATOM 354 CB ARG A 73 15.570 26.229 3.978 1.00 44.45 C +ATOM 355 CG ARG A 73 14.837 25.169 3.181 1.00 56.76 C +ATOM 356 CD ARG A 73 15.146 23.775 3.712 1.00 67.34 C +ATOM 357 NE ARG A 73 14.162 23.345 4.707 1.00 77.94 N +ATOM 358 CZ ARG A 73 14.406 23.207 6.010 1.00 75.29 C +ATOM 359 NH1 ARG A 73 15.618 23.463 6.491 1.00 66.64 N1+ +ATOM 360 NH2 ARG A 73 13.436 22.811 6.833 1.00 56.71 N +ATOM 361 N LEU A 74 14.247 26.722 6.770 1.00 41.45 N +ATOM 362 CA LEU A 74 13.400 26.397 7.912 1.00 40.55 C +ATOM 363 C LEU A 74 12.242 27.382 8.023 1.00 36.68 C +ATOM 364 O LEU A 74 11.071 26.983 8.034 1.00 35.86 O +ATOM 365 CB LEU A 74 14.247 26.398 9.184 1.00 40.02 C +ATOM 366 CG LEU A 74 13.595 25.948 10.494 1.00 38.53 C +ATOM 367 CD1 LEU A 74 13.151 24.497 10.413 1.00 43.98 C +ATOM 368 CD2 LEU A 74 14.581 26.151 11.628 1.00 41.83 C +ATOM 369 N LEU A 75 12.557 28.681 8.051 1.00 33.66 N +ATOM 370 CA LEU A 75 11.523 29.714 8.142 1.00 36.37 C +ATOM 371 C LEU A 75 10.550 29.633 6.970 1.00 37.49 C +ATOM 372 O LEU A 75 9.330 29.628 7.164 1.00 36.01 O +ATOM 373 CB LEU A 75 12.162 31.105 8.188 1.00 35.18 C +ATOM 374 CG LEU A 75 12.947 31.575 9.419 1.00 36.92 C +ATOM 375 CD1 LEU A 75 13.594 32.905 9.107 1.00 33.58 C +ATOM 376 CD2 LEU A 75 12.066 31.687 10.662 1.00 31.09 C +ATOM 377 N ALA A 76 11.076 29.581 5.739 1.00 35.23 N +ATOM 378 CA ALA A 76 10.211 29.616 4.563 1.00 37.00 C +ATOM 379 C ALA A 76 9.241 28.443 4.546 1.00 38.21 C +ATOM 380 O ALA A 76 8.072 28.603 4.184 1.00 42.93 O +ATOM 381 CB ALA A 76 11.051 29.629 3.280 1.00 32.87 C +ATOM 382 N GLU A 77 9.697 27.262 4.962 1.00 33.63 N +ATOM 383 CA GLU A 77 8.880 26.066 4.825 1.00 41.99 C +ATOM 384 C GLU A 77 7.775 25.967 5.866 1.00 43.32 C +ATOM 385 O GLU A 77 6.790 25.259 5.634 1.00 50.65 O +ATOM 386 CB GLU A 77 9.770 24.819 4.883 1.00 50.50 C +ATOM 387 CG GLU A 77 10.606 24.624 3.616 1.00 61.63 C +ATOM 388 CD GLU A 77 11.428 23.341 3.624 1.00 75.95 C +ATOM 389 OE1 GLU A 77 11.442 22.632 4.653 1.00 79.16 O +ATOM 390 OE2 GLU A 77 12.084 23.049 2.602 1.00 86.98 O1- +ATOM 391 N ASP A 78 7.888 26.657 6.995 1.00 44.52 N +ATOM 392 CA ASP A 78 6.848 26.510 8.001 1.00 37.25 C +ATOM 393 C ASP A 78 6.651 27.826 8.743 1.00 36.65 C +ATOM 394 O ASP A 78 6.771 27.916 9.960 1.00 31.43 O +ATOM 395 CB ASP A 78 7.191 25.364 8.952 1.00 40.17 C +ATOM 396 CG ASP A 78 5.981 24.870 9.705 1.00 43.11 C +ATOM 397 OD1 ASP A 78 4.888 25.472 9.533 1.00 43.01 O +ATOM 398 OD2 ASP A 78 6.124 23.896 10.469 1.00 41.74 O1- +ATOM 399 N ILE A 79 6.297 28.869 7.996 1.00 33.65 N +ATOM 400 CA ILE A 79 6.190 30.180 8.617 1.00 34.65 C +ATOM 401 C ILE A 79 5.091 30.182 9.681 1.00 33.22 C +ATOM 402 O ILE A 79 5.190 30.904 10.670 1.00 33.27 O +ATOM 403 CB ILE A 79 5.982 31.264 7.542 1.00 38.85 C +ATOM 404 CG1 ILE A 79 6.176 32.657 8.152 1.00 37.55 C +ATOM 405 CG2 ILE A 79 4.610 31.146 6.928 1.00 43.94 C +ATOM 406 CD1 ILE A 79 5.975 33.787 7.204 1.00 49.28 C +ATOM 407 N THR A 80 4.073 29.323 9.549 1.00 30.64 N +ATOM 408 CA THR A 80 2.982 29.324 10.522 1.00 33.25 C +ATOM 409 C THR A 80 3.454 28.843 11.892 1.00 31.49 C +ATOM 410 O THR A 80 3.012 29.358 12.928 1.00 29.03 O +ATOM 411 CB THR A 80 1.830 28.449 10.027 1.00 41.05 C +ATOM 412 OG1 THR A 80 1.290 29.005 8.816 1.00 44.05 O +ATOM 413 CG2 THR A 80 0.740 28.374 11.087 1.00 32.22 C +ATOM 414 N ARG A 81 4.345 27.857 11.915 1.00 28.00 N +ATOM 415 CA ARG A 81 4.935 27.421 13.175 1.00 34.07 C +ATOM 416 C ARG A 81 5.657 28.572 13.861 1.00 28.57 C +ATOM 417 O ARG A 81 5.571 28.741 15.086 1.00 26.26 O +ATOM 418 CB ARG A 81 5.897 26.255 12.921 1.00 31.98 C +ATOM 419 CG ARG A 81 6.877 25.968 14.063 1.00 26.90 C +ATOM 420 CD ARG A 81 7.834 24.832 13.705 1.00 36.49 C +ATOM 421 NE ARG A 81 7.075 23.627 13.413 1.00 37.04 N +ATOM 422 CZ ARG A 81 6.839 22.658 14.292 1.00 40.51 C +ATOM 423 NH1 ARG A 81 7.336 22.726 15.522 1.00 37.54 N1+ +ATOM 424 NH2 ARG A 81 6.110 21.614 13.931 1.00 46.78 N +ATOM 425 N PHE A 82 6.368 29.381 13.086 1.00 28.39 N +ATOM 426 CA PHE A 82 7.161 30.438 13.695 1.00 30.99 C +ATOM 427 C PHE A 82 6.286 31.566 14.210 1.00 29.33 C +ATOM 428 O PHE A 82 6.492 32.040 15.328 1.00 25.88 O +ATOM 429 CB PHE A 82 8.206 30.939 12.708 1.00 24.92 C +ATOM 430 CG PHE A 82 9.332 29.984 12.542 1.00 29.33 C +ATOM 431 CD1 PHE A 82 9.270 28.968 11.597 1.00 31.05 C +ATOM 432 CD2 PHE A 82 10.431 30.054 13.373 1.00 30.55 C +ATOM 433 CE1 PHE A 82 10.303 28.071 11.460 1.00 33.92 C +ATOM 434 CE2 PHE A 82 11.471 29.151 13.239 1.00 34.04 C +ATOM 435 CZ PHE A 82 11.406 28.165 12.278 1.00 34.45 C +ATOM 436 N LEU A 83 5.285 31.984 13.428 1.00 27.43 N +ATOM 437 CA LEU A 83 4.431 33.086 13.861 1.00 29.87 C +ATOM 438 C LEU A 83 3.534 32.678 15.026 1.00 29.75 C +ATOM 439 O LEU A 83 3.217 33.514 15.883 1.00 26.59 O +ATOM 440 CB LEU A 83 3.600 33.589 12.684 1.00 29.19 C +ATOM 441 CG LEU A 83 4.382 34.094 11.463 1.00 31.78 C +ATOM 442 CD1 LEU A 83 3.416 34.622 10.404 1.00 32.72 C +ATOM 443 CD2 LEU A 83 5.382 35.183 11.861 1.00 33.13 C +ATOM 444 N THR A 84 3.123 31.403 15.077 1.00 25.09 N +ATOM 445 CA THR A 84 2.360 30.904 16.217 1.00 26.30 C +ATOM 446 C THR A 84 3.203 30.892 17.479 1.00 22.32 C +ATOM 447 O THR A 84 2.725 31.256 18.558 1.00 24.23 O +ATOM 448 CB THR A 84 1.851 29.486 15.931 1.00 30.73 C +ATOM 449 OG1 THR A 84 0.985 29.498 14.787 1.00 29.42 O +ATOM 450 CG2 THR A 84 1.117 28.922 17.129 1.00 27.13 C +ATOM 451 N THR A 85 4.442 30.413 17.370 1.00 23.87 N +ATOM 452 CA THR A 85 5.332 30.368 18.521 1.00 25.94 C +ATOM 453 C THR A 85 5.595 31.772 19.051 1.00 25.83 C +ATOM 454 O THR A 85 5.610 31.999 20.267 1.00 25.90 O +ATOM 455 CB THR A 85 6.638 29.672 18.127 1.00 25.89 C +ATOM 456 OG1 THR A 85 6.333 28.358 17.651 1.00 25.90 O +ATOM 457 CG2 THR A 85 7.592 29.559 19.319 1.00 24.88 C +ATOM 458 N ILE A 86 5.768 32.735 18.149 1.00 24.71 N +ATOM 459 CA ILE A 86 6.003 34.115 18.569 1.00 27.63 C +ATOM 460 C ILE A 86 4.776 34.686 19.266 1.00 22.12 C +ATOM 461 O ILE A 86 4.887 35.354 20.300 1.00 25.22 O +ATOM 462 CB ILE A 86 6.414 34.962 17.352 1.00 25.09 C +ATOM 463 CG1 ILE A 86 7.830 34.610 16.903 1.00 28.37 C +ATOM 464 CG2 ILE A 86 6.274 36.469 17.632 1.00 24.58 C +ATOM 465 CD1 ILE A 86 8.179 35.219 15.487 1.00 28.77 C +ATOM 466 N LEU A 87 3.588 34.436 18.715 1.00 26.08 N +ATOM 467 CA LEU A 87 2.353 34.877 19.353 1.00 27.36 C +ATOM 468 C LEU A 87 2.270 34.377 20.787 1.00 26.17 C +ATOM 469 O LEU A 87 2.085 35.172 21.715 1.00 25.86 O +ATOM 470 CB LEU A 87 1.141 34.374 18.571 1.00 29.98 C +ATOM 471 CG LEU A 87 -0.172 34.628 19.323 1.00 32.99 C +ATOM 472 CD1 LEU A 87 -0.554 36.081 19.171 1.00 32.73 C +ATOM 473 CD2 LEU A 87 -1.288 33.709 18.829 1.00 37.20 C +ATOM 474 N VAL A 88 2.395 33.054 20.976 1.00 19.76 N +ATOM 475 CA VAL A 88 2.352 32.460 22.315 1.00 26.17 C +ATOM 476 C VAL A 88 3.453 33.042 23.186 1.00 25.56 C +ATOM 477 O VAL A 88 3.205 33.464 24.320 1.00 22.80 O +ATOM 478 CB VAL A 88 2.469 30.925 22.240 1.00 26.91 C +ATOM 479 CG1 VAL A 88 2.545 30.285 23.657 1.00 22.81 C +ATOM 480 CG2 VAL A 88 1.330 30.335 21.453 1.00 27.02 C +ATOM 481 N GLY A 89 4.690 33.055 22.665 1.00 22.67 N +ATOM 482 CA GLY A 89 5.824 33.521 23.451 1.00 22.87 C +ATOM 483 C GLY A 89 5.734 34.993 23.818 1.00 26.71 C +ATOM 484 O GLY A 89 6.056 35.380 24.948 1.00 25.95 O +ATOM 485 N ASN A 90 5.337 35.840 22.861 1.00 21.97 N +ATOM 486 CA ASN A 90 5.234 37.273 23.136 1.00 21.27 C +ATOM 487 C ASN A 90 4.202 37.549 24.221 1.00 25.04 C +ATOM 488 O ASN A 90 4.464 38.309 25.157 1.00 22.18 O +ATOM 489 CB ASN A 90 4.884 38.048 21.855 1.00 23.14 C +ATOM 490 CG ASN A 90 5.108 39.559 21.999 1.00 26.30 C +ATOM 491 OD1 ASN A 90 6.209 40.032 22.341 1.00 26.93 O +ATOM 492 ND2 ASN A 90 4.061 40.325 21.729 1.00 31.00 N +ATOM 493 N ASN A 91 3.037 36.900 24.137 1.00 22.96 N +ATOM 494 CA ASN A 91 2.022 37.101 25.161 1.00 24.69 C +ATOM 495 C ASN A 91 2.493 36.578 26.508 1.00 26.53 C +ATOM 496 O ASN A 91 2.319 37.250 27.531 1.00 25.89 O +ATOM 497 CB ASN A 91 0.716 36.431 24.748 1.00 25.83 C +ATOM 498 CG ASN A 91 -0.116 37.304 23.831 1.00 33.12 C +ATOM 499 OD1 ASN A 91 -0.888 38.146 24.295 1.00 32.22 O +ATOM 500 ND2 ASN A 91 0.049 37.122 22.516 1.00 25.45 N +ATOM 501 N LEU A 92 3.119 35.396 26.526 1.00 24.26 N +ATOM 502 CA LEU A 92 3.586 34.836 27.789 1.00 23.04 C +ATOM 503 C LEU A 92 4.558 35.783 28.492 1.00 19.51 C +ATOM 504 O LEU A 92 4.443 36.025 29.705 1.00 22.96 O +ATOM 505 CB LEU A 92 4.232 33.464 27.546 1.00 25.61 C +ATOM 506 CG LEU A 92 5.002 32.871 28.723 1.00 23.64 C +ATOM 507 CD1 LEU A 92 4.036 32.492 29.823 1.00 26.11 C +ATOM 508 CD2 LEU A 92 5.815 31.656 28.285 1.00 22.79 C +ATOM 509 N VAL A 93 5.558 36.298 27.771 1.00 20.06 N +ATOM 510 CA VAL A 93 6.532 37.141 28.468 1.00 19.61 C +ATOM 511 C VAL A 93 5.929 38.493 28.851 1.00 23.72 C +ATOM 512 O VAL A 93 6.270 39.048 29.909 1.00 25.16 O +ATOM 513 CB VAL A 93 7.847 37.301 27.675 1.00 23.15 C +ATOM 514 CG1 VAL A 93 8.564 35.951 27.549 1.00 26.90 C +ATOM 515 CG2 VAL A 93 7.640 37.969 26.285 1.00 21.79 C +ATOM 516 N ASN A 94 5.008 39.036 28.047 1.00 23.42 N +ATOM 517 CA ASN A 94 4.376 40.307 28.421 1.00 25.77 C +ATOM 518 C ASN A 94 3.491 40.130 29.648 1.00 26.38 C +ATOM 519 O ASN A 94 3.395 41.021 30.503 1.00 22.23 O +ATOM 520 CB ASN A 94 3.544 40.860 27.263 1.00 20.15 C +ATOM 521 CG ASN A 94 4.402 41.460 26.161 1.00 27.37 C +ATOM 522 OD1 ASN A 94 5.563 41.751 26.388 1.00 25.29 O +ATOM 523 ND2 ASN A 94 3.823 41.670 24.972 1.00 23.13 N +ATOM 524 N ILE A 95 2.821 38.989 29.738 1.00 25.69 N +ATOM 525 CA ILE A 95 1.950 38.739 30.876 1.00 26.01 C +ATOM 526 C ILE A 95 2.789 38.429 32.117 1.00 26.93 C +ATOM 527 O ILE A 95 2.505 38.923 33.210 1.00 25.88 O +ATOM 528 CB ILE A 95 0.952 37.618 30.507 1.00 25.99 C +ATOM 529 CG1 ILE A 95 -0.035 38.124 29.433 1.00 23.52 C +ATOM 530 CG2 ILE A 95 0.231 37.036 31.747 1.00 23.81 C +ATOM 531 CD1 ILE A 95 -0.783 36.995 28.676 1.00 22.47 C +ATOM 532 N ALA A 96 3.878 37.671 31.948 1.00 24.54 N +ATOM 533 CA ALA A 96 4.745 37.347 33.074 1.00 23.19 C +ATOM 534 C ALA A 96 5.443 38.587 33.613 1.00 29.96 C +ATOM 535 O ALA A 96 5.641 38.712 34.828 1.00 25.97 O +ATOM 536 CB ALA A 96 5.773 36.287 32.669 1.00 21.25 C +ATOM 537 N ALA A 97 5.808 39.527 32.735 1.00 26.53 N +ATOM 538 CA ALA A 97 6.434 40.758 33.203 1.00 26.22 C +ATOM 539 C ALA A 97 5.426 41.650 33.923 1.00 28.26 C +ATOM 540 O ALA A 97 5.759 42.278 34.937 1.00 25.18 O +ATOM 541 CB ALA A 97 7.071 41.509 32.038 1.00 26.24 C +ATOM 542 N THR A 98 4.196 41.728 33.401 1.00 21.18 N +ATOM 543 CA THR A 98 3.158 42.525 34.042 1.00 24.06 C +ATOM 544 C THR A 98 2.806 41.968 35.416 1.00 27.44 C +ATOM 545 O THR A 98 2.647 42.731 36.374 1.00 25.99 O +ATOM 546 CB THR A 98 1.916 42.579 33.153 1.00 27.07 C +ATOM 547 OG1 THR A 98 2.255 43.227 31.925 1.00 26.45 O +ATOM 548 CG2 THR A 98 0.790 43.378 33.834 1.00 24.83 C +ATOM 549 N ALA A 99 2.687 40.639 35.522 1.00 26.05 N +ATOM 550 CA ALA A 99 2.401 39.995 36.801 1.00 30.89 C +ATOM 551 C ALA A 99 3.497 40.274 37.826 1.00 26.56 C +ATOM 552 O ALA A 99 3.213 40.601 38.986 1.00 24.76 O +ATOM 553 CB ALA A 99 2.234 38.486 36.591 1.00 21.76 C +ATOM 554 N LEU A 100 4.759 40.102 37.428 1.00 24.99 N +ATOM 555 CA LEU A 100 5.864 40.388 38.334 1.00 30.85 C +ATOM 556 C LEU A 100 5.870 41.859 38.733 1.00 34.98 C +ATOM 557 O LEU A 100 6.005 42.192 39.919 1.00 30.63 O +ATOM 558 CB LEU A 100 7.190 39.990 37.688 1.00 29.48 C +ATOM 559 CG LEU A 100 8.474 40.364 38.430 1.00 37.25 C +ATOM 560 CD1 LEU A 100 8.512 39.746 39.842 1.00 35.63 C +ATOM 561 CD2 LEU A 100 9.679 39.928 37.631 1.00 35.13 C +ATOM 562 N ALA A 101 5.712 42.755 37.754 1.00 30.66 N +ATOM 563 CA ALA A 101 5.658 44.186 38.049 1.00 28.09 C +ATOM 564 C ALA A 101 4.502 44.522 38.984 1.00 28.74 C +ATOM 565 O ALA A 101 4.634 45.387 39.860 1.00 25.65 O +ATOM 566 CB ALA A 101 5.537 44.983 36.747 1.00 30.19 C +ATOM 567 N THR A 102 3.362 43.848 38.823 1.00 21.07 N +ATOM 568 CA THR A 102 2.226 44.120 39.697 1.00 25.70 C +ATOM 569 C THR A 102 2.495 43.607 41.110 1.00 25.93 C +ATOM 570 O THR A 102 2.101 44.245 42.096 1.00 25.29 O +ATOM 571 CB THR A 102 0.961 43.487 39.123 1.00 27.22 C +ATOM 572 OG1 THR A 102 0.732 43.996 37.803 1.00 24.13 O +ATOM 573 CG2 THR A 102 -0.240 43.786 39.997 1.00 25.76 C +ATOM 574 N GLU A 103 3.195 42.478 41.230 1.00 27.73 N +ATOM 575 CA GLU A 103 3.604 42.017 42.551 1.00 29.24 C +ATOM 576 C GLU A 103 4.441 43.072 43.261 1.00 30.40 C +ATOM 577 O GLU A 103 4.210 43.377 44.436 1.00 31.28 O +ATOM 578 CB GLU A 103 4.382 40.706 42.453 1.00 28.84 C +ATOM 579 CG GLU A 103 5.193 40.424 43.732 1.00 41.45 C +ATOM 580 CD GLU A 103 5.413 38.955 43.968 1.00 51.67 C +ATOM 581 OE1 GLU A 103 6.219 38.378 43.207 1.00 66.93 O +ATOM 582 OE2 GLU A 103 4.787 38.383 44.904 1.00 48.63 O1- +ATOM 583 N LEU A 104 5.423 43.641 42.563 1.00 27.23 N +ATOM 584 CA LEU A 104 6.270 44.657 43.181 1.00 32.22 C +ATOM 585 C LEU A 104 5.469 45.911 43.522 1.00 33.64 C +ATOM 586 O LEU A 104 5.602 46.471 44.619 1.00 30.33 O +ATOM 587 CB LEU A 104 7.432 45.002 42.251 1.00 31.68 C +ATOM 588 CG LEU A 104 8.365 43.873 41.819 1.00 36.65 C +ATOM 589 CD1 LEU A 104 9.350 44.413 40.791 1.00 44.52 C +ATOM 590 CD2 LEU A 104 9.101 43.294 43.031 1.00 41.67 C +ATOM 591 N ALA A 105 4.609 46.352 42.599 1.00 25.63 N +ATOM 592 CA ALA A 105 3.891 47.613 42.798 1.00 27.53 C +ATOM 593 C ALA A 105 2.865 47.519 43.923 1.00 29.27 C +ATOM 594 O ALA A 105 2.695 48.474 44.690 1.00 25.90 O +ATOM 595 CB ALA A 105 3.215 48.045 41.494 1.00 27.32 C +ATOM 596 N THR A 106 2.146 46.401 44.022 1.00 24.96 N +ATOM 597 CA THR A 106 1.129 46.291 45.063 1.00 27.12 C +ATOM 598 C THR A 106 1.737 45.998 46.429 1.00 30.56 C +ATOM 599 O THR A 106 1.157 46.364 47.455 1.00 28.25 O +ATOM 600 CB THR A 106 0.107 45.213 44.714 1.00 26.97 C +ATOM 601 OG1 THR A 106 0.777 43.964 44.489 1.00 30.46 O +ATOM 602 CG2 THR A 106 -0.670 45.610 43.452 1.00 30.78 C +ATOM 603 N GLN A 107 2.888 45.341 46.466 1.00 26.02 N +ATOM 604 CA GLN A 107 3.596 45.215 47.729 1.00 34.67 C +ATOM 605 C GLN A 107 4.109 46.566 48.187 1.00 35.06 C +ATOM 606 O GLN A 107 4.100 46.858 49.393 1.00 28.56 O +ATOM 607 CB GLN A 107 4.735 44.204 47.586 1.00 35.47 C +ATOM 608 CG GLN A 107 4.223 42.772 47.490 1.00 37.90 C +ATOM 609 CD GLN A 107 5.332 41.746 47.351 1.00 43.39 C +ATOM 610 OE1 GLN A 107 6.485 42.094 47.101 1.00 49.37 O +ATOM 611 NE2 GLN A 107 4.985 40.470 47.509 1.00 40.83 N +ATOM 612 N ALA A 108 4.510 47.417 47.231 1.00 25.25 N +ATOM 613 CA ALA A 108 4.983 48.757 47.552 1.00 28.11 C +ATOM 614 C ALA A 108 3.826 49.683 47.908 1.00 33.60 C +ATOM 615 O ALA A 108 3.895 50.421 48.897 1.00 32.46 O +ATOM 616 CB ALA A 108 5.781 49.331 46.379 1.00 31.18 C +ATOM 617 N PHE A 109 2.736 49.630 47.132 1.00 28.17 N +ATOM 618 CA PHE A 109 1.727 50.679 47.143 1.00 31.32 C +ATOM 619 C PHE A 109 0.321 50.210 47.479 1.00 31.82 C +ATOM 620 O PHE A 109 -0.588 51.052 47.547 1.00 31.68 O +ATOM 621 CB PHE A 109 1.678 51.378 45.777 1.00 31.18 C +ATOM 622 CG PHE A 109 3.003 51.906 45.318 1.00 34.51 C +ATOM 623 CD1 PHE A 109 3.768 52.717 46.147 1.00 41.92 C +ATOM 624 CD2 PHE A 109 3.488 51.589 44.060 1.00 36.12 C +ATOM 625 CE1 PHE A 109 4.994 53.203 45.728 1.00 41.83 C +ATOM 626 CE2 PHE A 109 4.707 52.073 43.635 1.00 41.15 C +ATOM 627 CZ PHE A 109 5.462 52.884 44.469 1.00 40.87 C +ATOM 628 N GLY A 110 0.096 48.915 47.655 1.00 24.22 N +ATOM 629 CA GLY A 110 -1.257 48.449 47.885 1.00 28.36 C +ATOM 630 C GLY A 110 -2.069 48.385 46.598 1.00 34.54 C +ATOM 631 O GLY A 110 -1.542 48.147 45.501 1.00 30.13 O +ATOM 632 N SER A 111 -3.375 48.627 46.737 1.00 27.21 N +ATOM 633 CA SER A 111 -4.275 48.454 45.605 1.00 39.25 C +ATOM 634 C SER A 111 -4.005 49.481 44.509 1.00 38.27 C +ATOM 635 O SER A 111 -4.236 49.194 43.330 1.00 35.58 O +ATOM 636 CB SER A 111 -5.726 48.511 46.082 1.00 36.83 C +ATOM 637 OG SER A 111 -5.977 49.724 46.753 1.00 37.39 O +ATOM 638 N ALA A 112 -3.475 50.658 44.861 1.00 30.56 N +ATOM 639 CA ALA A 112 -3.084 51.609 43.823 1.00 34.60 C +ATOM 640 C ALA A 112 -1.955 51.069 42.958 1.00 32.75 C +ATOM 641 O ALA A 112 -1.725 51.578 41.853 1.00 30.16 O +ATOM 642 CB ALA A 112 -2.663 52.942 44.447 1.00 38.03 C +ATOM 643 N GLY A 113 -1.250 50.049 43.438 1.00 31.82 N +ATOM 644 CA GLY A 113 -0.177 49.466 42.662 1.00 30.66 C +ATOM 645 C GLY A 113 -0.650 48.828 41.371 1.00 32.37 C +ATOM 646 O GLY A 113 0.137 48.677 40.437 1.00 28.05 O +ATOM 647 N VAL A 114 -1.927 48.431 41.309 1.00 29.90 N +ATOM 648 CA VAL A 114 -2.476 47.869 40.075 1.00 33.19 C +ATOM 649 C VAL A 114 -2.471 48.916 38.964 1.00 30.74 C +ATOM 650 O VAL A 114 -2.126 48.620 37.815 1.00 29.91 O +ATOM 651 CB VAL A 114 -3.894 47.318 40.310 1.00 32.74 C +ATOM 652 CG1 VAL A 114 -4.509 46.845 38.980 1.00 32.34 C +ATOM 653 CG2 VAL A 114 -3.874 46.182 41.319 1.00 30.93 C +ATOM 654 N GLY A 115 -2.859 50.150 39.289 1.00 30.51 N +ATOM 655 CA GLY A 115 -2.830 51.214 38.294 1.00 33.75 C +ATOM 656 C GLY A 115 -1.417 51.654 37.969 1.00 34.76 C +ATOM 657 O GLY A 115 -1.086 51.908 36.805 1.00 33.78 O +ATOM 658 N VAL A 116 -0.565 51.738 38.991 1.00 25.41 N +ATOM 659 CA VAL A 116 0.853 52.035 38.789 1.00 31.28 C +ATOM 660 C VAL A 116 1.489 51.029 37.835 1.00 30.86 C +ATOM 661 O VAL A 116 2.211 51.403 36.906 1.00 28.64 O +ATOM 662 CB VAL A 116 1.591 52.052 40.141 1.00 33.37 C +ATOM 663 CG1 VAL A 116 3.093 52.086 39.914 1.00 32.44 C +ATOM 664 CG2 VAL A 116 1.122 53.237 41.010 1.00 31.06 C +ATOM 665 N ALA A 117 1.292 49.729 38.091 1.00 30.08 N +ATOM 666 CA ALA A 117 1.901 48.727 37.225 1.00 28.59 C +ATOM 667 C ALA A 117 1.273 48.728 35.838 1.00 28.21 C +ATOM 668 O ALA A 117 1.973 48.482 34.851 1.00 25.12 O +ATOM 669 CB ALA A 117 1.789 47.329 37.836 1.00 28.98 C +ATOM 670 N THR A 118 -0.034 48.986 35.737 1.00 24.01 N +ATOM 671 CA THR A 118 -0.640 49.064 34.414 1.00 29.57 C +ATOM 672 C THR A 118 -0.042 50.205 33.609 1.00 29.37 C +ATOM 673 O THR A 118 0.296 50.027 32.435 1.00 26.83 O +ATOM 674 CB THR A 118 -2.145 49.248 34.500 1.00 27.76 C +ATOM 675 OG1 THR A 118 -2.715 48.161 35.215 1.00 25.00 O +ATOM 676 CG2 THR A 118 -2.726 49.249 33.081 1.00 24.98 C +ATOM 677 N GLY A 119 0.070 51.395 34.217 1.00 27.02 N +ATOM 678 CA GLY A 119 0.652 52.521 33.503 1.00 27.27 C +ATOM 679 C GLY A 119 2.102 52.280 33.124 1.00 29.54 C +ATOM 680 O GLY A 119 2.493 52.449 31.968 1.00 29.52 O +ATOM 681 N ALA A 120 2.925 51.885 34.098 1.00 25.21 N +ATOM 682 CA ALA A 120 4.337 51.648 33.808 1.00 29.29 C +ATOM 683 C ALA A 120 4.540 50.533 32.782 1.00 30.65 C +ATOM 684 O ALA A 120 5.375 50.668 31.880 1.00 28.22 O +ATOM 685 CB ALA A 120 5.092 51.321 35.093 1.00 33.24 C +ATOM 686 N MET A 121 3.808 49.416 32.907 1.00 23.97 N +ATOM 687 CA MET A 121 4.063 48.286 32.020 1.00 26.95 C +ATOM 688 C MET A 121 3.526 48.528 30.620 1.00 27.12 C +ATOM 689 O MET A 121 4.117 48.052 29.648 1.00 27.34 O +ATOM 690 CB MET A 121 3.466 46.989 32.587 1.00 29.96 C +ATOM 691 CG MET A 121 4.232 46.454 33.791 1.00 27.36 C +ATOM 692 SD MET A 121 6.032 46.431 33.522 1.00 30.33 S +ATOM 693 CE MET A 121 6.206 45.087 32.342 1.00 32.31 C +ATOM 694 N THR A 122 2.426 49.266 30.494 1.00 25.11 N +ATOM 695 CA THR A 122 1.951 49.637 29.174 1.00 23.99 C +ATOM 696 C THR A 122 2.987 50.480 28.439 1.00 27.85 C +ATOM 697 O THR A 122 3.230 50.275 27.240 1.00 27.30 O +ATOM 698 CB THR A 122 0.631 50.392 29.301 1.00 27.30 C +ATOM 699 OG1 THR A 122 -0.352 49.517 29.867 1.00 26.82 O +ATOM 700 CG2 THR A 122 0.165 50.900 27.926 1.00 28.89 C +ATOM 701 N PHE A 123 3.609 51.437 29.134 1.00 26.35 N +ATOM 702 CA PHE A 123 4.675 52.201 28.497 1.00 28.45 C +ATOM 703 C PHE A 123 5.832 51.295 28.104 1.00 29.89 C +ATOM 704 O PHE A 123 6.305 51.339 26.968 1.00 29.77 O +ATOM 705 CB PHE A 123 5.212 53.310 29.396 1.00 25.87 C +ATOM 706 CG PHE A 123 6.510 53.851 28.890 1.00 31.94 C +ATOM 707 CD1 PHE A 123 6.542 54.585 27.710 1.00 36.79 C +ATOM 708 CD2 PHE A 123 7.704 53.543 29.512 1.00 35.69 C +ATOM 709 CE1 PHE A 123 7.740 55.053 27.185 1.00 37.03 C +ATOM 710 CE2 PHE A 123 8.910 54.017 28.997 1.00 43.02 C +ATOM 711 CZ PHE A 123 8.925 54.769 27.830 1.00 37.02 C +ATOM 712 N LEU A 124 6.329 50.492 29.051 1.00 24.02 N +ATOM 713 CA LEU A 124 7.508 49.671 28.776 1.00 30.43 C +ATOM 714 C LEU A 124 7.237 48.626 27.698 1.00 28.97 C +ATOM 715 O LEU A 124 8.054 48.447 26.792 1.00 31.39 O +ATOM 716 CB LEU A 124 7.992 48.990 30.054 1.00 26.90 C +ATOM 717 CG LEU A 124 8.517 49.991 31.090 1.00 35.18 C +ATOM 718 CD1 LEU A 124 8.789 49.286 32.419 1.00 38.66 C +ATOM 719 CD2 LEU A 124 9.772 50.665 30.579 1.00 30.78 C +ATOM 720 N ILE A 125 6.108 47.918 27.782 1.00 23.74 N +ATOM 721 CA ILE A 125 5.814 46.898 26.782 1.00 24.70 C +ATOM 722 C ILE A 125 5.575 47.538 25.418 1.00 27.35 C +ATOM 723 O ILE A 125 6.060 47.037 24.399 1.00 26.98 O +ATOM 724 CB ILE A 125 4.633 46.016 27.221 1.00 22.27 C +ATOM 725 CG1 ILE A 125 5.009 45.234 28.482 1.00 25.96 C +ATOM 726 CG2 ILE A 125 4.212 45.054 26.083 1.00 24.56 C +ATOM 727 CD1 ILE A 125 3.908 44.365 29.056 1.00 24.41 C +ATOM 728 N LEU A 126 4.832 48.647 25.369 1.00 26.04 N +ATOM 729 CA LEU A 126 4.599 49.308 24.090 1.00 31.75 C +ATOM 730 C LEU A 126 5.901 49.847 23.527 1.00 30.12 C +ATOM 731 O LEU A 126 6.228 49.598 22.363 1.00 26.73 O +ATOM 732 CB LEU A 126 3.574 50.437 24.232 1.00 26.06 C +ATOM 733 CG LEU A 126 2.098 50.035 24.067 1.00 27.89 C +ATOM 734 CD1 LEU A 126 1.195 51.210 24.411 1.00 26.30 C +ATOM 735 CD2 LEU A 126 1.807 49.549 22.642 1.00 28.08 C +ATOM 736 N PHE A 127 6.680 50.559 24.356 1.00 26.85 N +ATOM 737 CA PHE A 127 7.880 51.211 23.838 1.00 29.99 C +ATOM 738 C PHE A 127 8.996 50.206 23.556 1.00 29.12 C +ATOM 739 O PHE A 127 9.518 50.141 22.435 1.00 26.45 O +ATOM 740 CB PHE A 127 8.358 52.307 24.801 1.00 27.55 C +ATOM 741 CG PHE A 127 9.415 53.200 24.209 1.00 27.82 C +ATOM 742 CD1 PHE A 127 9.064 54.264 23.410 1.00 29.60 C +ATOM 743 CD2 PHE A 127 10.760 52.939 24.412 1.00 26.73 C +ATOM 744 CE1 PHE A 127 10.032 55.080 22.852 1.00 31.95 C +ATOM 745 CE2 PHE A 127 11.740 53.750 23.849 1.00 26.94 C +ATOM 746 CZ PHE A 127 11.374 54.814 23.075 1.00 28.54 C +ATOM 747 N PHE A 128 9.386 49.424 24.555 1.00 26.72 N +ATOM 748 CA PHE A 128 10.538 48.544 24.405 1.00 32.92 C +ATOM 749 C PHE A 128 10.180 47.157 23.898 1.00 26.40 C +ATOM 750 O PHE A 128 11.024 46.513 23.261 1.00 25.24 O +ATOM 751 CB PHE A 128 11.284 48.402 25.740 1.00 25.73 C +ATOM 752 CG PHE A 128 11.932 49.680 26.210 1.00 34.01 C +ATOM 753 CD1 PHE A 128 12.994 50.235 25.512 1.00 33.19 C +ATOM 754 CD2 PHE A 128 11.476 50.325 27.348 1.00 30.52 C +ATOM 755 CE1 PHE A 128 13.591 51.409 25.940 1.00 32.01 C +ATOM 756 CE2 PHE A 128 12.069 51.505 27.782 1.00 35.53 C +ATOM 757 CZ PHE A 128 13.129 52.043 27.081 1.00 30.01 C +ATOM 758 N GLY A 129 8.976 46.661 24.191 1.00 26.05 N +ATOM 759 CA GLY A 129 8.644 45.309 23.768 1.00 29.33 C +ATOM 760 C GLY A 129 7.958 45.217 22.421 1.00 30.12 C +ATOM 761 O GLY A 129 7.816 44.117 21.871 1.00 28.32 O +ATOM 762 N GLU A 130 7.516 46.359 21.877 1.00 27.34 N +ATOM 763 CA GLU A 130 6.737 46.321 20.645 1.00 31.46 C +ATOM 764 C GLU A 130 7.214 47.345 19.608 1.00 28.25 C +ATOM 765 O GLU A 130 7.711 46.965 18.543 1.00 31.72 O +ATOM 766 CB GLU A 130 5.247 46.501 20.979 1.00 28.84 C +ATOM 767 CG GLU A 130 4.664 45.411 21.950 1.00 34.95 C +ATOM 768 CD GLU A 130 4.871 43.937 21.480 1.00 35.59 C +ATOM 769 OE1 GLU A 130 4.798 43.674 20.251 1.00 37.77 O +ATOM 770 OE2 GLU A 130 5.109 43.036 22.344 1.00 28.85 O1- +ATOM 771 N ILE A 131 7.111 48.640 19.912 1.00 31.35 N +ATOM 772 CA ILE A 131 7.349 49.668 18.899 1.00 29.61 C +ATOM 773 C ILE A 131 8.823 49.728 18.518 1.00 28.20 C +ATOM 774 O ILE A 131 9.177 49.643 17.335 1.00 24.13 O +ATOM 775 CB ILE A 131 6.822 51.018 19.403 1.00 29.01 C +ATOM 776 CG1 ILE A 131 5.291 51.010 19.300 1.00 31.80 C +ATOM 777 CG2 ILE A 131 7.493 52.185 18.675 1.00 34.21 C +ATOM 778 CD1 ILE A 131 4.602 52.046 20.202 1.00 30.34 C +ATOM 779 N THR A 132 9.704 49.834 19.505 1.00 24.00 N +ATOM 780 CA THR A 132 11.134 49.887 19.192 1.00 28.61 C +ATOM 781 C THR A 132 11.642 48.637 18.492 1.00 31.36 C +ATOM 782 O THR A 132 12.375 48.774 17.488 1.00 31.23 O +ATOM 783 CB THR A 132 11.944 50.163 20.463 1.00 26.37 C +ATOM 784 OG1 THR A 132 11.595 51.452 20.983 1.00 25.63 O +ATOM 785 CG2 THR A 132 13.435 50.123 20.154 1.00 30.11 C +ATOM 786 N PRO A 133 11.341 47.409 18.940 1.00 29.83 N +ATOM 787 CA PRO A 133 11.894 46.251 18.223 1.00 26.98 C +ATOM 788 C PRO A 133 11.314 46.065 16.837 1.00 28.48 C +ATOM 789 O PRO A 133 12.029 45.602 15.942 1.00 24.01 O +ATOM 790 CB PRO A 133 11.570 45.062 19.143 1.00 27.10 C +ATOM 791 CG PRO A 133 10.442 45.543 19.999 1.00 25.94 C +ATOM 792 CD PRO A 133 10.739 46.997 20.227 1.00 29.08 C +ATOM 793 N LYS A 134 10.041 46.402 16.628 1.00 26.55 N +ATOM 794 CA LYS A 134 9.473 46.267 15.289 1.00 27.74 C +ATOM 795 C LYS A 134 10.086 47.274 14.332 1.00 35.42 C +ATOM 796 O LYS A 134 10.407 46.934 13.187 1.00 29.45 O +ATOM 797 CB LYS A 134 7.957 46.444 15.342 1.00 28.65 C +ATOM 798 CG LYS A 134 7.261 45.251 16.008 1.00 31.56 C +ATOM 799 CD LYS A 134 5.764 45.300 15.794 1.00 36.95 C +ATOM 800 CE LYS A 134 5.122 43.979 16.170 1.00 39.11 C +ATOM 801 NZ LYS A 134 5.744 42.824 15.454 1.00 36.73 N1+ +ATOM 802 N SER A 135 10.231 48.526 14.779 1.00 27.48 N +ATOM 803 CA SER A 135 10.888 49.540 13.965 1.00 29.60 C +ATOM 804 C SER A 135 12.305 49.112 13.601 1.00 33.92 C +ATOM 805 O SER A 135 12.714 49.197 12.438 1.00 30.95 O +ATOM 806 CB SER A 135 10.880 50.866 14.723 1.00 30.42 C +ATOM 807 OG SER A 135 11.991 51.643 14.349 1.00 41.42 O +ATOM 808 N LEU A 136 13.055 48.602 14.580 1.00 27.28 N +ATOM 809 CA LEU A 136 14.406 48.122 14.315 1.00 28.20 C +ATOM 810 C LEU A 136 14.418 46.966 13.309 1.00 35.63 C +ATOM 811 O LEU A 136 15.295 46.897 12.434 1.00 32.27 O +ATOM 812 CB LEU A 136 15.058 47.702 15.630 1.00 30.64 C +ATOM 813 CG LEU A 136 16.460 47.125 15.502 1.00 36.30 C +ATOM 814 CD1 LEU A 136 17.465 48.266 15.427 1.00 38.39 C +ATOM 815 CD2 LEU A 136 16.767 46.207 16.687 1.00 47.02 C +ATOM 816 N ALA A 137 13.442 46.058 13.406 1.00 28.96 N +ATOM 817 CA ALA A 137 13.461 44.856 12.582 1.00 32.22 C +ATOM 818 C ALA A 137 13.324 45.164 11.093 1.00 30.62 C +ATOM 819 O ALA A 137 13.901 44.450 10.265 1.00 25.73 O +ATOM 820 CB ALA A 137 12.357 43.890 13.028 1.00 25.41 C +ATOM 821 N VAL A 138 12.583 46.207 10.713 1.00 28.28 N +ATOM 822 CA VAL A 138 12.430 46.440 9.276 1.00 36.67 C +ATOM 823 C VAL A 138 13.772 46.782 8.640 1.00 32.83 C +ATOM 824 O VAL A 138 13.978 46.534 7.449 1.00 36.36 O +ATOM 825 CB VAL A 138 11.380 47.533 8.989 1.00 40.74 C +ATOM 826 CG1 VAL A 138 10.008 47.109 9.493 1.00 46.04 C +ATOM 827 CG2 VAL A 138 11.800 48.847 9.580 1.00 42.04 C +ATOM 828 N HIS A 139 14.698 47.317 9.404 1.00 30.41 N +ATOM 829 CA HIS A 139 16.010 47.688 8.895 1.00 37.79 C +ATOM 830 C HIS A 139 17.083 46.634 9.076 1.00 38.14 C +ATOM 831 O HIS A 139 18.165 46.818 8.677 1.00 40.87 O +ATOM 832 CB HIS A 139 16.508 48.993 9.518 1.00 34.96 C +ATOM 833 CG HIS A 139 15.526 50.099 9.456 1.00 35.75 C +ATOM 834 ND1 HIS A 139 15.371 50.900 8.355 1.00 40.83 N +ATOM 835 CD2 HIS A 139 14.623 50.520 10.354 1.00 36.65 C +ATOM 836 CE1 HIS A 139 14.405 51.757 8.577 1.00 37.41 C +ATOM 837 NE2 HIS A 139 13.932 51.542 9.781 1.00 35.06 N +ATOM 838 N HIS A 140 16.765 45.544 9.710 1.00 34.16 N +ATOM 839 CA HIS A 140 17.732 44.486 9.956 1.00 35.01 C +ATOM 840 C HIS A 140 17.048 43.134 9.871 1.00 33.95 C +ATOM 841 O HIS A 140 17.367 42.208 10.625 1.00 31.45 O +ATOM 842 CB HIS A 140 18.411 44.668 11.313 1.00 34.45 C +ATOM 843 CG HIS A 140 19.158 45.954 11.445 1.00 40.57 C +ATOM 844 ND1 HIS A 140 18.611 47.079 12.024 1.00 42.32 N +ATOM 845 CD2 HIS A 140 20.402 46.305 11.040 1.00 46.52 C +ATOM 846 CE1 HIS A 140 19.494 48.060 11.987 1.00 40.45 C +ATOM 847 NE2 HIS A 140 20.589 47.618 11.397 1.00 42.05 N +ATOM 848 N ALA A 141 16.105 43.002 8.932 1.00 32.08 N +ATOM 849 CA ALA A 141 15.221 41.841 8.926 1.00 32.80 C +ATOM 850 C ALA A 141 15.988 40.549 8.677 1.00 36.30 C +ATOM 851 O ALA A 141 15.678 39.514 9.276 1.00 29.83 O +ATOM 852 CB ALA A 141 14.123 42.026 7.877 1.00 33.63 C +ATOM 853 N GLU A 142 16.987 40.582 7.790 1.00 34.11 N +ATOM 854 CA GLU A 142 17.703 39.352 7.471 1.00 37.89 C +ATOM 855 C GLU A 142 18.552 38.883 8.642 1.00 35.83 C +ATOM 856 O GLU A 142 18.573 37.692 8.967 1.00 31.77 O +ATOM 857 CB GLU A 142 18.580 39.545 6.242 1.00 39.16 C +ATOM 858 CG GLU A 142 17.822 39.651 4.964 1.00 42.91 C +ATOM 859 CD GLU A 142 18.753 39.589 3.777 1.00 61.97 C +ATOM 860 OE1 GLU A 142 19.760 38.845 3.853 1.00 62.40 O +ATOM 861 OE2 GLU A 142 18.495 40.295 2.784 1.00 68.67 O1- +ATOM 862 N ALA A 143 19.283 39.803 9.271 1.00 31.58 N +ATOM 863 CA ALA A 143 20.115 39.411 10.396 1.00 37.98 C +ATOM 864 C ALA A 143 19.265 38.897 11.558 1.00 34.47 C +ATOM 865 O ALA A 143 19.638 37.923 12.223 1.00 30.78 O +ATOM 866 CB ALA A 143 20.985 40.590 10.831 1.00 38.23 C +ATOM 867 N ILE A 144 18.113 39.531 11.809 1.00 29.19 N +ATOM 868 CA ILE A 144 17.304 39.133 12.954 1.00 31.12 C +ATOM 869 C ILE A 144 16.653 37.777 12.704 1.00 33.82 C +ATOM 870 O ILE A 144 16.616 36.928 13.595 1.00 28.72 O +ATOM 871 CB ILE A 144 16.262 40.215 13.294 1.00 30.79 C +ATOM 872 CG1 ILE A 144 16.958 41.417 13.941 1.00 30.55 C +ATOM 873 CG2 ILE A 144 15.217 39.663 14.274 1.00 32.36 C +ATOM 874 CD1 ILE A 144 16.185 42.695 13.865 1.00 30.16 C +ATOM 875 N ALA A 145 16.121 37.559 11.499 1.00 30.14 N +ATOM 876 CA ALA A 145 15.549 36.259 11.165 1.00 29.36 C +ATOM 877 C ALA A 145 16.601 35.162 11.256 1.00 35.40 C +ATOM 878 O ALA A 145 16.328 34.074 11.773 1.00 31.77 O +ATOM 879 CB ALA A 145 14.931 36.293 9.769 1.00 30.99 C +ATOM 880 N ARG A 146 17.819 35.439 10.775 1.00 36.76 N +ATOM 881 CA ARG A 146 18.874 34.434 10.816 1.00 43.52 C +ATOM 882 C ARG A 146 19.177 34.017 12.245 1.00 41.58 C +ATOM 883 O ARG A 146 19.360 32.827 12.535 1.00 40.74 O +ATOM 884 CB ARG A 146 20.142 34.967 10.149 1.00 42.64 C +ATOM 885 CG ARG A 146 21.269 33.949 10.198 1.00 54.67 C +ATOM 886 CD ARG A 146 22.637 34.582 10.042 1.00 55.63 C +ATOM 887 NE ARG A 146 22.687 35.507 8.919 1.00 61.50 N +ATOM 888 CZ ARG A 146 22.660 35.142 7.642 1.00 67.88 C +ATOM 889 NH1 ARG A 146 22.580 33.855 7.308 1.00 65.37 N1+ +ATOM 890 NH2 ARG A 146 22.719 36.071 6.697 1.00 59.99 N +ATOM 891 N LEU A 147 19.215 34.987 13.153 1.00 36.12 N +ATOM 892 CA LEU A 147 19.595 34.723 14.531 1.00 37.72 C +ATOM 893 C LEU A 147 18.436 34.187 15.356 1.00 36.26 C +ATOM 894 O LEU A 147 18.663 33.445 16.311 1.00 33.84 O +ATOM 895 CB LEU A 147 20.147 35.998 15.173 1.00 38.18 C +ATOM 896 CG LEU A 147 21.649 36.206 14.987 1.00 52.72 C +ATOM 897 CD1 LEU A 147 22.038 37.643 15.314 1.00 56.73 C +ATOM 898 CD2 LEU A 147 22.440 35.212 15.834 1.00 61.76 C +ATOM 899 N ALA A 148 17.202 34.544 15.012 1.00 33.88 N +ATOM 900 CA ALA A 148 16.044 34.137 15.798 1.00 31.10 C +ATOM 901 C ALA A 148 15.490 32.772 15.406 1.00 31.45 C +ATOM 902 O ALA A 148 14.779 32.157 16.207 1.00 28.78 O +ATOM 903 CB ALA A 148 14.928 35.168 15.653 1.00 30.47 C +ATOM 904 N ALA A 149 15.785 32.291 14.196 1.00 27.52 N +ATOM 905 CA ALA A 149 15.073 31.128 13.662 1.00 33.13 C +ATOM 906 C ALA A 149 15.245 29.893 14.546 1.00 34.06 C +ATOM 907 O ALA A 149 14.267 29.195 14.854 1.00 27.74 O +ATOM 908 CB ALA A 149 15.544 30.827 12.246 1.00 32.23 C +ATOM 909 N TRP A 150 16.481 29.591 14.950 1.00 29.02 N +ATOM 910 CA TRP A 150 16.698 28.340 15.672 1.00 34.09 C +ATOM 911 C TRP A 150 16.187 28.416 17.110 1.00 32.46 C +ATOM 912 O TRP A 150 15.573 27.445 17.574 1.00 28.91 O +ATOM 913 CB TRP A 150 18.174 27.937 15.619 1.00 30.18 C +ATOM 914 CG TRP A 150 18.545 27.395 14.258 1.00 39.08 C +ATOM 915 CD1 TRP A 150 19.338 27.990 13.322 1.00 40.17 C +ATOM 916 CD2 TRP A 150 18.088 26.167 13.675 1.00 39.62 C +ATOM 917 NE1 TRP A 150 19.418 27.200 12.199 1.00 40.14 N +ATOM 918 CE2 TRP A 150 18.658 26.076 12.392 1.00 42.95 C +ATOM 919 CE3 TRP A 150 17.266 25.126 14.125 1.00 43.24 C +ATOM 920 CZ2 TRP A 150 18.431 24.988 11.552 1.00 46.19 C +ATOM 921 CZ3 TRP A 150 17.042 24.042 13.285 1.00 46.80 C +ATOM 922 CH2 TRP A 150 17.622 23.984 12.020 1.00 46.33 C +ATOM 923 N PRO A 151 16.391 29.523 17.848 1.00 32.85 N +ATOM 924 CA PRO A 151 15.756 29.609 19.179 1.00 31.40 C +ATOM 925 C PRO A 151 14.244 29.488 19.124 1.00 31.03 C +ATOM 926 O PRO A 151 13.639 28.836 19.983 1.00 30.90 O +ATOM 927 CB PRO A 151 16.199 30.987 19.698 1.00 32.88 C +ATOM 928 CG PRO A 151 17.456 31.273 18.998 1.00 35.58 C +ATOM 929 CD PRO A 151 17.298 30.662 17.613 1.00 29.34 C +ATOM 930 N ILE A 152 13.614 30.071 18.106 1.00 26.27 N +ATOM 931 CA ILE A 152 12.161 30.021 18.033 1.00 30.35 C +ATOM 932 C ILE A 152 11.700 28.632 17.613 1.00 26.97 C +ATOM 933 O ILE A 152 10.673 28.133 18.085 1.00 28.15 O +ATOM 934 CB ILE A 152 11.647 31.124 17.088 1.00 25.05 C +ATOM 935 CG1 ILE A 152 11.872 32.509 17.707 1.00 25.18 C +ATOM 936 CG2 ILE A 152 10.178 30.985 16.833 1.00 24.10 C +ATOM 937 CD1 ILE A 152 11.552 33.648 16.746 1.00 27.42 C +ATOM 938 N TYR A 153 12.448 27.990 16.713 1.00 26.70 N +ATOM 939 CA TYR A 153 12.161 26.608 16.356 1.00 33.14 C +ATOM 940 C TYR A 153 12.184 25.714 17.590 1.00 25.19 C +ATOM 941 O TYR A 153 11.314 24.853 17.759 1.00 25.41 O +ATOM 942 CB TYR A 153 13.167 26.121 15.320 1.00 29.77 C +ATOM 943 CG TYR A 153 12.800 24.792 14.712 1.00 39.94 C +ATOM 944 CD1 TYR A 153 11.655 24.655 13.936 1.00 39.31 C +ATOM 945 CD2 TYR A 153 13.601 23.674 14.910 1.00 42.63 C +ATOM 946 CE1 TYR A 153 11.310 23.432 13.385 1.00 43.90 C +ATOM 947 CE2 TYR A 153 13.275 22.460 14.357 1.00 48.17 C +ATOM 948 CZ TYR A 153 12.128 22.339 13.598 1.00 53.73 C +ATOM 949 OH TYR A 153 11.804 21.112 13.055 1.00 54.65 O +ATOM 950 N GLY A 154 13.167 25.916 18.465 1.00 26.80 N +ATOM 951 CA GLY A 154 13.228 25.139 19.693 1.00 30.83 C +ATOM 952 C GLY A 154 12.014 25.341 20.578 1.00 29.58 C +ATOM 953 O GLY A 154 11.445 24.375 21.097 1.00 28.89 O +ATOM 954 N LEU A 155 11.596 26.604 20.762 1.00 27.59 N +ATOM 955 CA LEU A 155 10.415 26.880 21.578 1.00 25.93 C +ATOM 956 C LEU A 155 9.158 26.328 20.937 1.00 27.81 C +ATOM 957 O LEU A 155 8.216 25.940 21.646 1.00 27.62 O +ATOM 958 CB LEU A 155 10.236 28.382 21.803 1.00 25.97 C +ATOM 959 CG LEU A 155 11.161 29.107 22.770 1.00 29.35 C +ATOM 960 CD1 LEU A 155 10.955 30.616 22.637 1.00 32.37 C +ATOM 961 CD2 LEU A 155 10.900 28.659 24.205 1.00 28.60 C +ATOM 962 N SER A 156 9.132 26.279 19.601 1.00 22.21 N +ATOM 963 CA SER A 156 7.954 25.832 18.879 1.00 27.15 C +ATOM 964 C SER A 156 7.596 24.389 19.195 1.00 31.95 C +ATOM 965 O SER A 156 6.451 23.990 18.972 1.00 32.75 O +ATOM 966 CB SER A 156 8.167 25.990 17.369 1.00 28.83 C +ATOM 967 OG SER A 156 8.922 24.908 16.853 1.00 32.26 O +ATOM 968 N VAL A 157 8.547 23.592 19.687 1.00 28.19 N +ATOM 969 CA VAL A 157 8.233 22.193 19.968 1.00 36.89 C +ATOM 970 C VAL A 157 7.166 22.106 21.041 1.00 33.68 C +ATOM 971 O VAL A 157 6.337 21.192 21.029 1.00 38.18 O +ATOM 972 CB VAL A 157 9.497 21.400 20.355 1.00 36.13 C +ATOM 973 CG1 VAL A 157 10.587 21.598 19.305 1.00 40.52 C +ATOM 974 CG2 VAL A 157 9.977 21.781 21.739 1.00 41.04 C +ATOM 975 N LEU A 158 7.128 23.081 21.943 1.00 33.45 N +ATOM 976 CA LEU A 158 6.043 23.223 22.899 1.00 37.50 C +ATOM 977 C LEU A 158 4.992 24.247 22.475 1.00 37.21 C +ATOM 978 O LEU A 158 3.792 23.975 22.592 1.00 35.40 O +ATOM 979 CB LEU A 158 6.605 23.612 24.263 1.00 33.72 C +ATOM 980 CG LEU A 158 5.511 23.944 25.269 1.00 45.73 C +ATOM 981 CD1 LEU A 158 4.928 22.671 25.866 1.00 53.37 C +ATOM 982 CD2 LEU A 158 6.062 24.855 26.343 1.00 60.04 C +ATOM 983 N PHE A 159 5.401 25.415 21.972 1.00 33.38 N +ATOM 984 CA PHE A 159 4.445 26.507 21.784 1.00 30.01 C +ATOM 985 C PHE A 159 3.536 26.283 20.585 1.00 29.32 C +ATOM 986 O PHE A 159 2.378 26.716 20.590 1.00 29.87 O +ATOM 987 CB PHE A 159 5.171 27.839 21.599 1.00 24.78 C +ATOM 988 CG PHE A 159 5.770 28.397 22.847 1.00 26.84 C +ATOM 989 CD1 PHE A 159 5.673 27.717 24.059 1.00 30.17 C +ATOM 990 CD2 PHE A 159 6.436 29.612 22.814 1.00 28.59 C +ATOM 991 CE1 PHE A 159 6.229 28.238 25.211 1.00 28.27 C +ATOM 992 CE2 PHE A 159 6.996 30.150 23.982 1.00 30.28 C +ATOM 993 CZ PHE A 159 6.892 29.451 25.179 1.00 31.92 C +ATOM 994 N TYR A 160 4.059 25.704 19.510 1.00 25.29 N +ATOM 995 CA TYR A 160 3.223 25.558 18.323 1.00 28.23 C +ATOM 996 C TYR A 160 2.102 24.567 18.564 1.00 33.02 C +ATOM 997 O TYR A 160 0.936 24.891 18.244 1.00 27.05 O +ATOM 998 CB TYR A 160 4.098 25.195 17.118 1.00 26.70 C +ATOM 999 CG TYR A 160 3.343 25.007 15.837 1.00 33.52 C +ATOM 1000 CD1 TYR A 160 2.348 25.893 15.461 1.00 30.18 C +ATOM 1001 CD2 TYR A 160 3.638 23.946 14.985 1.00 38.29 C +ATOM 1002 CE1 TYR A 160 1.659 25.732 14.267 1.00 37.10 C +ATOM 1003 CE2 TYR A 160 2.950 23.771 13.798 1.00 40.65 C +ATOM 1004 CZ TYR A 160 1.961 24.670 13.446 1.00 43.55 C +ATOM 1005 OH TYR A 160 1.277 24.510 12.261 1.00 54.20 O +ATOM 1006 N PRO A 161 2.330 23.368 19.134 1.00 32.55 N +ATOM 1007 CA PRO A 161 1.201 22.509 19.520 1.00 37.43 C +ATOM 1008 C PRO A 161 0.187 23.221 20.388 1.00 32.99 C +ATOM 1009 O PRO A 161 -1.022 23.038 20.194 1.00 32.17 O +ATOM 1010 CB PRO A 161 1.876 21.351 20.279 1.00 39.90 C +ATOM 1011 CG PRO A 161 3.223 21.236 19.648 1.00 43.76 C +ATOM 1012 CD PRO A 161 3.626 22.695 19.374 1.00 38.03 C +ATOM 1013 N VAL A 162 0.657 24.061 21.316 1.00 34.65 N +ATOM 1014 CA VAL A 162 -0.237 24.777 22.219 1.00 31.43 C +ATOM 1015 C VAL A 162 -1.114 25.757 21.451 1.00 33.02 C +ATOM 1016 O VAL A 162 -2.339 25.784 21.621 1.00 32.17 O +ATOM 1017 CB VAL A 162 0.573 25.502 23.305 1.00 34.66 C +ATOM 1018 CG1 VAL A 162 -0.254 26.623 23.934 1.00 34.76 C +ATOM 1019 CG2 VAL A 162 1.035 24.520 24.355 1.00 36.47 C +ATOM 1020 N GLY A 163 -0.496 26.600 20.624 1.00 28.82 N +ATOM 1021 CA GLY A 163 -1.270 27.563 19.864 1.00 29.89 C +ATOM 1022 C GLY A 163 -2.225 26.894 18.900 1.00 29.95 C +ATOM 1023 O GLY A 163 -3.339 27.372 18.685 1.00 30.24 O +ATOM 1024 N ARG A 164 -1.800 25.778 18.306 1.00 33.72 N +ATOM 1025 CA ARG A 164 -2.655 25.091 17.337 1.00 38.41 C +ATOM 1026 C ARG A 164 -3.862 24.457 18.017 1.00 29.62 C +ATOM 1027 O ARG A 164 -4.990 24.555 17.515 1.00 30.81 O +ATOM 1028 CB ARG A 164 -1.844 24.045 16.576 1.00 38.59 C +ATOM 1029 CG ARG A 164 -2.537 23.496 15.349 1.00 48.36 C +ATOM 1030 CD ARG A 164 -1.592 22.631 14.516 1.00 53.82 C +ATOM 1031 NE ARG A 164 -2.281 22.023 13.380 1.00 71.05 N +ATOM 1032 CZ ARG A 164 -2.601 20.732 13.291 1.00 82.68 C +ATOM 1033 NH1 ARG A 164 -2.290 19.889 14.271 1.00 71.39 N1+ +ATOM 1034 NH2 ARG A 164 -3.232 20.281 12.215 1.00 87.90 N +ATOM 1035 N PHE A 165 -3.637 23.799 19.151 1.00 31.33 N +ATOM 1036 CA PHE A 165 -4.734 23.312 19.983 1.00 33.83 C +ATOM 1037 C PHE A 165 -5.759 24.411 20.247 1.00 34.14 C +ATOM 1038 O PHE A 165 -6.950 24.249 19.949 1.00 30.26 O +ATOM 1039 CB PHE A 165 -4.174 22.781 21.300 1.00 32.30 C +ATOM 1040 CG PHE A 165 -5.214 22.141 22.186 1.00 39.20 C +ATOM 1041 CD1 PHE A 165 -5.706 20.867 21.897 1.00 35.89 C +ATOM 1042 CD2 PHE A 165 -5.702 22.810 23.287 1.00 40.02 C +ATOM 1043 CE1 PHE A 165 -6.667 20.279 22.711 1.00 45.88 C +ATOM 1044 CE2 PHE A 165 -6.657 22.226 24.112 1.00 45.13 C +ATOM 1045 CZ PHE A 165 -7.140 20.969 23.824 1.00 40.44 C +ATOM 1046 N PHE A 166 -5.299 25.547 20.792 1.00 30.27 N +ATOM 1047 CA PHE A 166 -6.170 26.701 21.034 1.00 33.35 C +ATOM 1048 C PHE A 166 -6.966 27.066 19.790 1.00 26.31 C +ATOM 1049 O PHE A 166 -8.189 27.241 19.840 1.00 28.04 O +ATOM 1050 CB PHE A 166 -5.344 27.924 21.472 1.00 29.95 C +ATOM 1051 CG PHE A 166 -4.832 27.865 22.882 1.00 33.69 C +ATOM 1052 CD1 PHE A 166 -5.062 26.764 23.683 1.00 40.85 C +ATOM 1053 CD2 PHE A 166 -4.094 28.930 23.396 1.00 35.93 C +ATOM 1054 CE1 PHE A 166 -4.574 26.725 24.989 1.00 47.50 C +ATOM 1055 CE2 PHE A 166 -3.604 28.907 24.684 1.00 39.42 C +ATOM 1056 CZ PHE A 166 -3.843 27.797 25.492 1.00 47.26 C +ATOM 1057 N SER A 167 -6.283 27.218 18.657 1.00 29.37 N +ATOM 1058 CA SER A 167 -6.989 27.688 17.474 1.00 30.89 C +ATOM 1059 C SER A 167 -8.000 26.646 16.986 1.00 26.49 C +ATOM 1060 O SER A 167 -9.112 26.993 16.571 1.00 22.98 O +ATOM 1061 CB SER A 167 -5.978 28.038 16.388 1.00 31.53 C +ATOM 1062 OG SER A 167 -6.607 28.243 15.152 1.00 47.15 O +ATOM 1063 N LEU A 168 -7.640 25.363 17.046 1.00 24.55 N +ATOM 1064 CA LEU A 168 -8.576 24.309 16.646 1.00 31.39 C +ATOM 1065 C LEU A 168 -9.787 24.277 17.565 1.00 30.34 C +ATOM 1066 O LEU A 168 -10.926 24.178 17.099 1.00 30.23 O +ATOM 1067 CB LEU A 168 -7.870 22.946 16.636 1.00 31.64 C +ATOM 1068 CG LEU A 168 -6.908 22.738 15.467 1.00 36.61 C +ATOM 1069 CD1 LEU A 168 -6.041 21.525 15.743 1.00 42.21 C +ATOM 1070 CD2 LEU A 168 -7.679 22.573 14.167 1.00 35.01 C +ATOM 1071 N VAL A 169 -9.563 24.391 18.874 1.00 27.10 N +ATOM 1072 CA VAL A 169 -10.679 24.363 19.814 1.00 30.21 C +ATOM 1073 C VAL A 169 -11.535 25.613 19.659 1.00 31.90 C +ATOM 1074 O VAL A 169 -12.769 25.551 19.732 1.00 30.63 O +ATOM 1075 CB VAL A 169 -10.163 24.214 21.253 1.00 29.13 C +ATOM 1076 CG1 VAL A 169 -11.312 24.329 22.231 1.00 32.21 C +ATOM 1077 CG2 VAL A 169 -9.424 22.884 21.432 1.00 30.16 C +ATOM 1078 N SER A 170 -10.891 26.764 19.448 1.00 26.39 N +ATOM 1079 CA SER A 170 -11.620 28.010 19.273 1.00 29.28 C +ATOM 1080 C SER A 170 -12.530 27.948 18.058 1.00 27.74 C +ATOM 1081 O SER A 170 -13.713 28.290 18.144 1.00 29.84 O +ATOM 1082 CB SER A 170 -10.629 29.163 19.148 1.00 30.55 C +ATOM 1083 OG SER A 170 -11.265 30.280 18.605 1.00 37.66 O +ATOM 1084 N GLY A 171 -11.998 27.504 16.912 1.00 27.22 N +ATOM 1085 CA GLY A 171 -12.840 27.347 15.733 1.00 29.08 C +ATOM 1086 C GLY A 171 -13.972 26.355 15.954 1.00 34.04 C +ATOM 1087 O GLY A 171 -15.109 26.585 15.527 1.00 32.64 O +ATOM 1088 N GLY A 172 -13.677 25.242 16.623 1.00 29.62 N +ATOM 1089 CA GLY A 172 -14.738 24.312 16.987 1.00 35.93 C +ATOM 1090 C GLY A 172 -15.843 24.980 17.784 1.00 35.98 C +ATOM 1091 O GLY A 172 -17.028 24.821 17.484 1.00 34.06 O +ATOM 1092 N LEU A 173 -15.462 25.769 18.791 1.00 31.07 N +ATOM 1093 CA LEU A 173 -16.448 26.467 19.615 1.00 33.96 C +ATOM 1094 C LEU A 173 -17.248 27.477 18.801 1.00 34.50 C +ATOM 1095 O LEU A 173 -18.467 27.606 18.975 1.00 33.51 O +ATOM 1096 CB LEU A 173 -15.745 27.176 20.765 1.00 32.34 C +ATOM 1097 CG LEU A 173 -16.630 28.054 21.648 1.00 41.56 C +ATOM 1098 CD1 LEU A 173 -17.603 27.170 22.446 1.00 40.06 C +ATOM 1099 CD2 LEU A 173 -15.789 28.920 22.574 1.00 43.08 C +ATOM 1100 N LEU A 174 -16.579 28.231 17.931 1.00 32.74 N +ATOM 1101 CA LEU A 174 -17.302 29.203 17.116 1.00 35.86 C +ATOM 1102 C LEU A 174 -18.302 28.509 16.193 1.00 32.80 C +ATOM 1103 O LEU A 174 -19.409 29.014 15.969 1.00 37.63 O +ATOM 1104 CB LEU A 174 -16.316 30.054 16.317 1.00 32.09 C +ATOM 1105 CG LEU A 174 -15.572 31.043 17.233 1.00 34.21 C +ATOM 1106 CD1 LEU A 174 -14.440 31.725 16.501 1.00 33.17 C +ATOM 1107 CD2 LEU A 174 -16.530 32.075 17.805 1.00 35.70 C +ATOM 1108 N ARG A 175 -17.941 27.342 15.663 1.00 27.64 N +ATOM 1109 CA ARG A 175 -18.876 26.647 14.781 1.00 38.99 C +ATOM 1110 C ARG A 175 -20.031 26.042 15.575 1.00 38.55 C +ATOM 1111 O ARG A 175 -21.190 26.144 15.157 1.00 38.86 O +ATOM 1112 CB ARG A 175 -18.138 25.600 13.954 1.00 35.16 C +ATOM 1113 CG ARG A 175 -17.168 26.251 12.968 1.00 40.56 C +ATOM 1114 CD ARG A 175 -16.512 25.272 12.033 1.00 43.11 C +ATOM 1115 NE ARG A 175 -15.980 24.105 12.729 1.00 49.88 N +ATOM 1116 CZ ARG A 175 -14.710 23.966 13.097 1.00 46.75 C +ATOM 1117 NH1 ARG A 175 -13.826 24.921 12.839 1.00 38.26 N1+ +ATOM 1118 NH2 ARG A 175 -14.323 22.862 13.715 1.00 47.19 N +ATOM 1119 N LEU A 176 -19.742 25.457 16.746 1.00 39.23 N +ATOM 1120 CA LEU A 176 -20.805 25.008 17.648 1.00 34.14 C +ATOM 1121 C LEU A 176 -21.825 26.111 17.912 1.00 41.68 C +ATOM 1122 O LEU A 176 -23.036 25.860 17.910 1.00 45.88 O +ATOM 1123 CB LEU A 176 -20.212 24.525 18.974 1.00 35.22 C +ATOM 1124 CG LEU A 176 -19.767 23.063 19.086 1.00 38.45 C +ATOM 1125 CD1 LEU A 176 -19.526 22.713 20.547 1.00 37.97 C +ATOM 1126 CD2 LEU A 176 -20.797 22.125 18.465 1.00 37.22 C +ATOM 1127 N LEU A 177 -21.355 27.342 18.144 1.00 39.24 N +ATOM 1128 CA LEU A 177 -22.248 28.450 18.465 1.00 39.43 C +ATOM 1129 C LEU A 177 -22.918 29.054 17.244 1.00 38.66 C +ATOM 1130 O LEU A 177 -23.720 29.980 17.398 1.00 43.67 O +ATOM 1131 CB LEU A 177 -21.491 29.555 19.205 1.00 40.82 C +ATOM 1132 CG LEU A 177 -20.894 29.204 20.564 1.00 38.71 C +ATOM 1133 CD1 LEU A 177 -19.789 30.190 20.885 1.00 38.59 C +ATOM 1134 CD2 LEU A 177 -21.971 29.248 21.634 1.00 45.80 C +ATOM 1135 N GLY A 178 -22.602 28.575 16.047 1.00 36.68 N +ATOM 1136 CA GLY A 178 -23.165 29.123 14.835 1.00 41.22 C +ATOM 1137 C GLY A 178 -22.511 30.394 14.341 1.00 44.18 C +ATOM 1138 O GLY A 178 -23.066 31.048 13.451 1.00 41.63 O +ATOM 1139 N LEU A 179 -21.346 30.761 14.878 1.00 41.82 N +ATOM 1140 CA LEU A 179 -20.667 32.002 14.512 1.00 40.91 C +ATOM 1141 C LEU A 179 -19.620 31.817 13.423 1.00 44.27 C +ATOM 1142 O LEU A 179 -18.958 32.790 13.042 1.00 43.83 O +ATOM 1143 CB LEU A 179 -20.016 32.627 15.751 1.00 39.85 C +ATOM 1144 CG LEU A 179 -21.026 32.927 16.847 1.00 40.28 C +ATOM 1145 CD1 LEU A 179 -20.353 33.261 18.181 1.00 39.17 C +ATOM 1146 CD2 LEU A 179 -21.932 34.058 16.377 1.00 46.22 C +ATOM 1147 N GLU A 180 -19.436 30.601 12.930 1.00 39.11 N +ATOM 1148 CA GLU A 180 -18.594 30.325 11.780 1.00 40.05 C +ATOM 1149 C GLU A 180 -19.260 29.223 10.995 1.00 48.24 C +ATOM 1150 O GLU A 180 -19.955 28.372 11.580 1.00 47.23 O +ATOM 1151 CB GLU A 180 -17.169 29.911 12.191 1.00 42.54 C +ATOM 1152 CG GLU A 180 -16.407 31.023 12.889 1.00 42.60 C +ATOM 1153 CD GLU A 180 -14.920 30.756 13.027 1.00 41.27 C +ATOM 1154 OE1 GLU A 180 -14.492 29.585 12.958 1.00 40.57 O +ATOM 1155 OE2 GLU A 180 -14.174 31.747 13.212 1.00 58.53 O1- +ATOM 1156 N PRO A 181 -19.077 29.182 9.669 1.00 48.37 N +ATOM 1157 CA PRO A 181 -19.823 28.242 8.821 1.00 51.65 C +ATOM 1158 C PRO A 181 -19.624 26.796 9.248 1.00 56.26 C +ATOM 1159 O PRO A 181 -18.495 26.344 9.468 1.00 48.82 O +ATOM 1160 CB PRO A 181 -19.255 28.493 7.419 1.00 51.75 C +ATOM 1161 CG PRO A 181 -17.946 29.169 7.654 1.00 51.21 C +ATOM 1162 CD PRO A 181 -18.158 30.014 8.871 1.00 47.93 C +ATOM 1163 N ARG A 182 -20.741 26.070 9.331 1.00 54.01 N +ATOM 1164 CA ARG A 182 -20.745 24.746 9.931 1.00 58.41 C +ATOM 1165 C ARG A 182 -19.775 23.817 9.221 1.00 57.66 C +ATOM 1166 O ARG A 182 -19.607 23.869 7.998 1.00 56.97 O +ATOM 1167 CB ARG A 182 -22.156 24.151 9.910 1.00 60.08 C +ATOM 1168 N LEU A 183 -19.112 22.997 10.023 1.00 61.12 N +ATOM 1169 CA LEU A 183 -18.288 21.881 9.592 1.00 64.63 C +ATOM 1170 C LEU A 183 -17.744 21.322 10.892 1.00 57.64 C +ATOM 1171 O LEU A 183 -18.139 21.798 11.964 1.00 49.16 O +ATOM 1172 CB LEU A 183 -17.167 22.300 8.636 1.00 57.81 C +ATOM 1173 CG LEU A 183 -17.281 21.673 7.240 1.00 61.48 C +ATOM 1174 CD1 LEU A 183 -15.974 21.805 6.475 1.00 61.36 C +ATOM 1175 CD2 LEU A 183 -17.722 20.221 7.320 1.00 51.22 C +TER +END diff --git a/img/SINGA.png b/img/SINGA.png new file mode 100644 index 0000000..87bef56 Binary files /dev/null and b/img/SINGA.png differ diff --git a/main.py b/main.py new file mode 100644 index 0000000..0307adb --- /dev/null +++ b/main.py @@ -0,0 +1,22 @@ +import os +import argparse +import warnings + + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument('--pdb_path', type=str, + default='./example/4yhj.pdb') + parser.add_argument('--lig_path', type=str, + default='./example/4yhj_reference_ligand_partial.sdf') + parser.add_argument('--config', type=str, default='./configs/sample_for_pdb.yml') + parser.add_argument('--device', type=str, default='cpu') + parser.add_argument('--outdir', type=str, default='./output') + args = parser.parse_args() + + # Load configs + config = load_config(args.config) + config_name = os.path.basename(args.config)[:os.path.basename(args.config).rfind('.')] + seed_all(config.sample.seed) + diff --git a/model/Het.py b/model/Het.py new file mode 100644 index 0000000..e69de29 diff --git a/model/P2M_embedding.py b/model/P2M_embedding.py new file mode 100644 index 0000000..d9dc141 --- /dev/null +++ b/model/P2M_embedding.py @@ -0,0 +1,39 @@ +import torch +from torch import Tensor +from torch.nn import Module, Linear, Embedding +from torch.nn import functional as F + + +class AtomEmbedding(Module): + def __init__( + self, + in_scalar:int, + in_vector:int, + out_scalar:int, + out_vector:int, + vector_normalizer:float = 20.0, + ) -> None: + super().__init__() + assert in_vector == 1 + self.in_scalar = in_scalar + self.vector_normalizer = vector_normalizer + self.emb_sca = Linear(in_scalar, out_scalar) + self.emb_vec = Linear(in_vector, out_vector) + + def forward(self, scalar_input:Tensor, vector_input:Tensor): + """ + Input: + scalar_input (Tensor): Shape (*, in_scalar) + vector_input (Tensor): Shape (*, 3) + + Output: Tuple(Tensor, Tensor) + sca_emb (Tensor): Shape (scalar_input.shape[0], out_scalar) + vec_emb (Tensor): Shape (scalar_input.shape[0], out_vector) + """ + vector_input = vector_input / self.vector_normalizer + assert vector_input.shape[1:] == (3, ), 'Not support. Only one vector can be input' + sca_emb = self.emb_sca(scalar_input[:, :self.in_scalar]) # b, f -> b, f' + vec_emb = vector_input.unsqueeze(-1) # b, 3 -> b, 3, 1 + vec_emb = self.emb_vec(vec_emb).transpose(1, -1) # b, 1, 3 -> b, f', 3 + + return sca_emb, vec_emb diff --git a/model/common.py b/model/common.py new file mode 100644 index 0000000..b51036a --- /dev/null +++ b/model/common.py @@ -0,0 +1,142 @@ +import numpy as np +from tqdm import tqdm +import math +import operator +from itertools import chain, product +from functools import partial +from typing import Any, Optional, Callable, Tuple, Dict, Sequence, NamedTuple + +import torch +import torch.nn as nn +from torch import Tensor, LongTensor + +import torch_geometric +from torch_geometric.transforms import BaseTransform, Compose +from torch_geometric.data import Data, Dataset +from torch_geometric.loader import DataLoader +from torch_geometric.nn.aggr import SumAggregation +from torch_scatter import scatter + + + +class EquivariantMPLayer(nn.Module): + def __init__( + self, + in_channels: int, + hidden_channels: int, + act: nn.Module, + ) -> None: + super().__init__() + self.act = act + self.residual_proj = nn.Linear(in_channels, hidden_channels, bias=False) + + # Messages will consist of two (source and target) node embeddings and a scalar distance + message_input_size = 2 * in_channels + 1 + + # equation (3) "phi_l" NN + self.message_mlp = nn.Sequential( + nn.Linear(message_input_size, hidden_channels), + act, + ) + # equation (4) "psi_l" NN + self.node_update_mlp = nn.Sequential( + nn.Linear(in_channels + hidden_channels, hidden_channels), + act, + ) + + def node_message_function( + self, + source_node_embed: Tensor, # h_i + target_node_embed: Tensor, # h_j + node_dist: Tensor, # d_ij + ) -> Tensor: + # implements equation (3) + message_repr = torch.cat((source_node_embed, target_node_embed, node_dist), dim=-1) + return self.message_mlp(message_repr) + + def compute_distances(self, node_pos: Tensor, edge_index: LongTensor) -> Tensor: + row, col = edge_index + xi, xj = node_pos[row], node_pos[col] + # relative squared distance + # implements equation (2) ||X_i - X_j||^2 + rsdist = (xi - xj).pow(2).sum(1, keepdim=True) + return rsdist + + def forward( + self, + node_embed: Tensor, + node_pos: Tensor, + edge_index: Tensor, + ) -> Tensor: + row, col = edge_index + dist = self.compute_distances(node_pos, edge_index) + + # compute messages "m_ij" from equation (3) + node_messages = self.node_message_function(node_embed[row], node_embed[col], dist) + + # message sum aggregation in equation (4) + aggr_node_messages = scatter(node_messages, col, dim=0, reduce="sum") + + # compute new node embeddings "h_i^{l+1}" + # (implements rest of equation (4)) + new_node_embed = self.residual_proj(node_embed) + self.node_update_mlp( + torch.cat((node_embed, aggr_node_messages), dim=-1) + ) + + return new_node_embed + + +class EquivariantGNN(nn.Module): + def __init__( + self, + hidden_channels: int, + final_embedding_size: Optional[int] = None, + target_size: int = 1, + num_mp_layers: int = 2, + ) -> None: + super().__init__() + if final_embedding_size is None: + final_embedding_size = hidden_channels + + # non-linear activation func. + # usually configurable, here we just use Relu for simplicity + self.act = nn.ReLU() + + # equation (1) "psi_0" + self.f_initial_embed = nn.Embedding(100, hidden_channels) + + # create stack of message passing layers + self.message_passing_layers = nn.ModuleList() + channels = [hidden_channels] * (num_mp_layers) + [final_embedding_size] + for d_in, d_out in zip(channels[:-1], channels[1:]): + layer = EquivariantMPLayer(d_in, d_out, self.act) + self.message_passing_layers.append(layer) + + # modules required for readout of a graph-level + # representation and graph-level property prediction + self.aggregation = SumAggregation() + self.f_predict = nn.Sequential( + nn.Linear(final_embedding_size, final_embedding_size), + self.act, + nn.Linear(final_embedding_size, target_size), + ) + + def encode(self, data: Data) -> Tensor: + # theory, equation (1) + node_embed = self.f_initial_embed(data.z) + # message passing + # theory, equation (3-4) + for mp_layer in self.message_passing_layers: + # NOTE here we use the complete edge index defined by the transform earlier on + # to implement the sum over $j \neq i$ in equation (4) + node_embed = mp_layer(node_embed, data.pos, data.complete_edge_index) + return node_embed + + def _predict(self, node_embed, batch_index) -> Tensor: + aggr = self.aggregation(node_embed, batch_index) + return self.f_predict(aggr) + + def forward(self, data: Data) -> Tensor: + node_embed = self.encode(data) + pred = self._predict(node_embed, data.batch) + return pred \ No newline at end of file diff --git a/model/embedding.py b/model/embedding.py new file mode 100644 index 0000000..e69de29 diff --git a/model/encoder.py b/model/encoder.py new file mode 100644 index 0000000..de976cc --- /dev/null +++ b/model/encoder.py @@ -0,0 +1,126 @@ +import torch +from torch import Tensor +from torch.nn import Module, ModuleList, LeakyReLU, LayerNorm +from torch_scatter import scatter_sum +from math import pi as PI + +from common import GaussianSmearing, EdgeExpansion +from invariant import GVLinear, VNLeakyReLU, MessageModule + + +class CFTransformerEncoderVN(Module): + def __init__( + self, + hidden_channels:list = [256, 64], + edge_channels:int = 64, + num_edge_types:int = 4, + key_channels:int = 128, + num_heads:int = 4, + num_interactions:int = 6, + k:int = 32, + cutoff:float = 10.0, + ) -> None: + super().__init__() + self.hidden_channels = hidden_channels + self.edge_channels = edge_channels + self.key_channels = key_channels # not use + self.num_heads = num_heads # not use + self.num_interactions = num_interactions + self.k = k + self.cutoff = cutoff + self.interactions = ModuleList() + + for _ in range(num_interactions): + block = AttentionInteractionBlockVN( + hidden_channels=hidden_channels, + edge_channels=edge_channels, + num_edge_types=num_edge_types, + key_channels=key_channels, + num_heads=num_heads, + cutoff = cutoff + ) + self.interactions.append(block) + + @property + def out_sca(self): + return self.hidden_channels[0] + + @property + def out_vec(self): + return self.hidden_channels[1] + + def forward(self, node_attr:Tensor, pos:Tensor, edge_index:Tensor, edge_feature:Tensor) -> Tensor: + edge_vector = pos[edge_index[0]] - pos[edge_index[1]] + h = list(node_attr) + for interaction in self.interactions: + delta_h = interaction(h, edge_index, edge_feature, edge_vector) + h[0] = h[0] + delta_h[0] + h[1] = h[1] + delta_h[1] + return h + + +class AttentionInteractionBlockVN(Module): + def __init__( + self, + hidden_channels:list, + edge_channels:int, + num_edge_types:int, + key_channels:int, + num_heads:int = 1, + cutoff:float = 10.0, + ) -> None: + super().__init__() + self.num_heads = num_heads + + # edge features + self.distance_expansion = GaussianSmearing(stop=cutoff, num_gaussians=edge_channels-num_edge_types) + self.vector_expansion = EdgeExpansion(edge_channels) # Linear(in_features=1, out_features=edge_channels, bias=False) + ## compare encoder and classifier message passing + + # edge weigths and linear for values + self.message_module = MessageModule(hidden_channels[0], + hidden_channels[1], + edge_channels, + edge_channels, + hidden_channels[0], + hidden_channels[1], + cutoff) + + # centroid nodes and finall linear + self.centroid_lin = GVLinear(hidden_channels[0], hidden_channels[1], hidden_channels[0], hidden_channels[1]) + self.act_sca = LeakyReLU() + self.act_vec = VNLeakyReLU(hidden_channels[1]) + self.out_transform = GVLinear(hidden_channels[0], hidden_channels[1], hidden_channels[0], hidden_channels[1]) + self.layernorm_sca = LayerNorm([hidden_channels[0]]) + self.layernorm_vec = LayerNorm([hidden_channels[1], 3]) + + def forward(self, x:Tensor, edge_index:Tensor, edge_feature:Tensor, edge_vector:Tensor) -> Tensor: + """ + Args: + x: Node features: scalar features (N, feat), vector features(N, feat, 3) + edge_index: (2, E). + edge_attr: (E, H) + """ + scalar, vector = x + N = scalar.size(0) + row, col = edge_index # (E,) , (E,) + + # Compute edge features + edge_dist = torch.norm(edge_vector, dim=-1, p=2) + edge_sca_feat = torch.cat([self.distance_expansion(edge_dist), edge_feature], dim=-1) + edge_vec_feat = self.vector_expansion(edge_vector) + + msg_j_sca, msg_j_vec = self.message_module(x, (edge_sca_feat, edge_vec_feat), col, edge_dist, annealing=True) + + # Aggregate messages + aggr_msg_sca = scatter_sum(msg_j_sca, row, dim=0, dim_size=N) #.view(N, -1) # (N, heads*H_per_head) + aggr_msg_vec = scatter_sum(msg_j_vec, row, dim=0, dim_size=N) #.view(N, -1, 3) # (N, heads*H_per_head, 3) + + x_out_sca, x_out_vec = self.centroid_lin(x) + out_sca = x_out_sca + aggr_msg_sca + out_vec = x_out_vec + aggr_msg_vec + out_sca = self.layernorm_sca(out_sca) + out_vec = self.layernorm_vec(out_vec) + out = self.out_transform((self.act_sca(out_sca), self.act_vec(out_vec))) + + return out diff --git a/model/gan.py b/model/gan.py new file mode 100644 index 0000000..7fd6849 --- /dev/null +++ b/model/gan.py @@ -0,0 +1,114 @@ +import torch +torch.manual_seed(1) +import torch.nn as nn +from torch.nn import Linear, Sequential, BatchNorm1d, ReLU, Dropout +from torch import Tensor, LongTensor +import torch.nn.functional as F + +from torch_geometric.nn import global_mean_pool, global_add_pool +from torch_geometric.data import Data +from torch_geometric.utils import to_networkx +from torch_geometric.loader import DataLoader +from torch_geometric.nn import GATv2Conv, GCNConv, GINConv + +import tensorflow as tf +from tensorflow import keras +import spektral + +import numpy as np +from typing import Any, Optional, Callable, Tuple, Dict, Sequence, NamedTuple + + + +class SINGAModel(keras.Model): + def __init__(self, **kwargs): + allowed_kwargs = {'name', 'logging'} + + for kwarg in kwargs.keys(): + assert kwarg in allowed_kwargs, 'Invalid keyword argument: ' + kwarg + + for kwarg in kwargs.keys(): + assert kwarg in allowed_kwargs, 'Invalid keyword argument: ' + kwarg + + name = kwargs.get('name') + + if not name: + name = self.__class__.__name__.lower() + self.name = name + + logging = kwargs.get('logging', False) + self.logging = logging + self.vars = {} + + def _build(self): + raise NotImplementedError + + def build(self): + """ Wraper for _build() """ + with tf.variable_scope(self.name): + self._build() + variables = tf.get_collection(tf.GraphKeys.GLOBAL_VARIABLES, scope=self.name) + self.vars = {var.name: var for var in variables} + + def fit(self): + pass + + def predict(self): + pass + + + + + + +class SINGAModelVAE(SINGAModel): + def __init__(self, placeholders, num_features:int, num_nodes, features_nonzero, **kwargs): + super(SINGAModelVAE, self).__init__(**kwargs) + + self.inputs = placeholders['features'] + self.input_dim = num_features + self.features_nonzero = features_nonzero + self.n_samples = num_nodes + self.adj = placeholders['adj'] + self.dropout = placeholders['dropout'] + self.build() + + def _build(self): + self.hidden1 = GraphConvolutionalSparse() + + + + +if __name__ == '__main__': + + + """ + + # Create the Vanilla GNN model + gat = GAT(data_list[0].num_features, 32, 2) + print("\n") + print(gat) + + # Train + gat.fit(data_list[0], epochs=100) + + # Test + acc = gat.test(data_list[1]) + print(f'GAT test accuracy: {acc*100:.2f}%') + + + + a = GetAdjacencyMatrix(Chem.MolFromSmiles(x_smiles[0])) + x = data_list[0].x + e = data_list[0].edge_attr + graph_0 = Graph(x=np.array(x), a=np.array(a), e=np.array(e), y=np.array(0)) + + a = GetAdjacencyMatrix(Chem.MolFromSmiles(x_smiles[1])) + x = data_list[1].x + e = data_list[1].edge_attr + graph_1 = Graph(x=np.array(x), a=np.array(a), e=np.array(e), y=np.array(0)) + + graph = [[graph_0, None], [graph_1, None]] + + """ + diff --git a/model/invariant.py b/model/invariant.py new file mode 100644 index 0000000..ad988b3 --- /dev/null +++ b/model/invariant.py @@ -0,0 +1,541 @@ +import torch +import torch.nn as nn +import torch.nn.functional as F +from torch.nn import Module, Linear, LeakyReLU +from torch.nn.modules.loss import _WeightedLoss +from torch_geometric.nn import global_mean_pool, knn, knn_graph +from torch_scatter import scatter_mean, scatter_add + +import math +from math import pi as PI +import numpy as np + +EPS = 1e-6 + + +class MessageModule(Module): + def __init__(self, node_sca, node_vec, edge_sca, edge_vec, out_sca, out_vec, cutoff=10.): + super().__init__() + hid_sca, hid_vec = edge_sca, edge_vec + self.cutoff = cutoff + self.node_gvlinear = GVLinear(node_sca, node_vec, out_sca, out_vec) + self.edge_gvp = GVPerceptronVN(edge_sca, edge_vec, hid_sca, hid_vec) + + self.sca_linear = Linear(hid_sca, out_sca) + self.e2n_linear = Linear(hid_sca, out_vec) + self.n2e_linear = Linear(out_sca, out_vec) + self.edge_vnlinear = VNLinear(hid_vec, out_vec) + + self.out_gvlienar = GVLinear(out_sca, out_vec, out_sca, out_vec) + + def forward(self, node_features, edge_features, edge_index_node, dist_ij=None, annealing=False): + node_scalar, node_vector = self.node_gvlinear(node_features) + node_scalar, node_vector = node_scalar[edge_index_node], node_vector[edge_index_node] + edge_scalar, edge_vector = self.edge_gvp(edge_features) + + y_scalar = node_scalar * self.sca_linear(edge_scalar) + y_node_vector = self.e2n_linear(edge_scalar).unsqueeze(-1) * node_vector + y_edge_vector = self.n2e_linear(node_scalar).unsqueeze(-1) * self.edge_vnlinear(edge_vector) + y_vector = y_node_vector + y_edge_vector + + output = self.out_gvlienar((y_scalar, y_vector)) + + if annealing: + C = 0.5 * (torch.cos(dist_ij * PI / self.cutoff) + 1.0) # (A, 1) + C = C * (dist_ij <= self.cutoff) * (dist_ij >= 0.0) + output = [output[0] * C.view(-1, 1), output[1] * C.view(-1, 1, 1)] # (A, 1) + return output + + +class GVPerceptronVN(Module): + def __init__(self, in_scalar, in_vector, out_scalar, out_vector): + super().__init__() + self.gv_linear = GVLinear(in_scalar, in_vector, out_scalar, out_vector) + self.act_sca = LeakyReLU() + self.act_vec = VNLeakyReLU(out_vector) + + def forward(self, x): + sca, vec = self.gv_linear(x) + vec = self.act_vec(vec) + sca = self.act_sca(sca) + return sca, vec + + +class GVLinear(Module): + def __init__(self, in_scalar, in_vector, out_scalar, out_vector): + super().__init__() + dim_hid = max(in_vector, out_vector) + self.lin_vector = VNLinear(in_vector, dim_hid, bias=False) + self.lin_vector2 = VNLinear(dim_hid, out_vector, bias=False) + self.scalar_to_vector_gates = Linear(out_scalar, out_vector) + self.lin_scalar = Linear(in_scalar + dim_hid, out_scalar, bias=False) + + def forward(self, features): + feat_scalar, feat_vector = features + feat_vector_inter = self.lin_vector(feat_vector) # (N_samples, dim_hid, 3) + feat_vector_norm = torch.norm(feat_vector_inter, p=2, dim=-1) # (N_samples, dim_hid) + feat_scalar_cat = torch.cat([feat_vector_norm, feat_scalar], dim=-1) # (N_samples, dim_hid+in_scalar) + + out_scalar = self.lin_scalar(feat_scalar_cat) + out_vector = self.lin_vector2(feat_vector_inter) + + gating = torch.sigmoid(self.scalar_to_vector_gates(out_scalar)).unsqueeze(dim = -1) + out_vector = gating * out_vector + return out_scalar, out_vector + + +class VNLinear(nn.Module): + def __init__(self, in_channels, out_channels, *args, **kwargs): + super(VNLinear, self).__init__() + self.map_to_feat = nn.Linear(in_channels, out_channels, *args, **kwargs) + + def forward(self, x): + ''' + x: point features of shape [B, N_samples, N_feat, 3] + ''' + x_out = self.map_to_feat(x.transpose(-2,-1)).transpose(-2,-1) + return x_out + + +class VNLeakyReLU(nn.Module): + def __init__(self, in_channels, share_nonlinearity=False, negative_slope=0.01): + super(VNLeakyReLU, self).__init__() + if share_nonlinearity == True: + self.map_to_dir = nn.Linear(in_channels, 1, bias=False) + else: + self.map_to_dir = nn.Linear(in_channels, in_channels, bias=False) + self.negative_slope = negative_slope + + def forward(self, x): + ''' + x: point features of shape [B, N_samples, N_feat, 3] + ''' + d = self.map_to_dir(x.transpose(-2,-1)).transpose(-2,-1) # (N_samples, N_feat, 3) + dotprod = (x*d).sum(-1, keepdim=True) # sum over 3-value dimension + mask = (dotprod >= 0).to(x.dtype) + d_norm_sq = (d*d).sum(-1, keepdim=True) # sum over 3-value dimension + x_out = (self.negative_slope * x + + (1-self.negative_slope) * (mask*x + (1-mask)*(x-(dotprod/(d_norm_sq+EPS))*d))) + return x_out + + +def mean_pool(x, dim=-1, keepdim=False): + return x.mean(dim=dim, keepdim=keepdim) + + +def split_tensor_by_batch(x, batch, num_graphs=None): + """ + Args: + x: (N, ...) + batch: (B, ) + Returns: + [(N_1, ), (N_2, ) ..., (N_B, ))] + """ + if num_graphs is None: + num_graphs = batch.max().item() + 1 + x_split = [] + for i in range (num_graphs): + mask = batch == i + x_split.append(x[mask]) + return x_split + + +def concat_tensors_to_batch(x_split): + x = torch.cat(x_split, dim=0) + batch = torch.repeat_interleave( + torch.arange(len(x_split)), + repeats=torch.LongTensor([s.size(0) for s in x_split]) + ).to(device=x.device) + return x, batch + + +def split_tensor_to_segments(x, segsize): + num_segs = math.ceil(x.size(0) / segsize) + segs = [] + for i in range(num_segs): + segs.append(x[i*segsize : (i+1)*segsize]) + return segs + + +def split_tensor_by_lengths(x, lengths): + segs = [] + for l in lengths: + segs.append(x[:l]) + x = x[l:] + return segs + + +def batch_intersection_mask(batch, batch_filter): + batch_filter = batch_filter.unique() + mask = (batch.view(-1, 1) == batch_filter.view(1, -1)).any(dim=1) + return mask + + +def get_batch_edge(ligand_context_bond_index, ligand_context_bond_type): + return ligand_context_bond_index, ligand_context_bond_type + + +class MeanReadout(nn.Module): + """Mean readout operator over graphs with variadic sizes.""" + def forward(self, input, batch, num_graphs): + """ + Perform readout over the graph(s). + Parameters: + data (torch_geometric.data.Data): batched graph + input (Tensor): node representations + Returns: + Tensor: graph representations + """ + output = scatter_mean(input, batch, dim=0, dim_size=num_graphs) + return output + + +class SumReadout(nn.Module): + """Sum readout operator over graphs with variadic sizes.""" + + def forward(self, input, batch, num_graphs): + """ + Perform readout over the graph(s). + Parameters: + data (torch_geometric.data.Data): batched graph + input (Tensor): node representations + Returns: + Tensor: graph representations + """ + output = scatter_add(input, batch, dim=0, dim_size=num_graphs) + return output + + +class MultiLayerPerceptron(nn.Module): + """ + Multi-layer Perceptron. + Note there is no activation or dropout in the last layer. + Parameters: + input_dim (int): input dimension + hidden_dim (list of int): hidden dimensions + activation (str or function, optional): activation function + dropout (float, optional): dropout rate + """ + def __init__(self, input_dim, hidden_dims, activation="relu", dropout=0): + super(MultiLayerPerceptron, self).__init__() + + self.dims = [input_dim] + hidden_dims + if isinstance(activation, str): + self.activation = getattr(F, activation) + else: + self.activation = None + if dropout: + self.dropout = nn.Dropout(dropout) + else: + self.dropout = None + + self.layers = nn.ModuleList() + for i in range(len(self.dims) - 1): + self.layers.append(nn.Linear(self.dims[i], self.dims[i + 1])) + + def forward(self, input): + """""" + x = input + for i, layer in enumerate(self.layers): + x = layer(x) + if i < len(self.layers) - 1: + if self.activation: + x = self.activation(x) + if self.dropout: + x = self.dropout(x) + return x + + +class SmoothCrossEntropyLoss(_WeightedLoss): + def __init__(self, weight=None, reduction='mean', smoothing=0.0): + super().__init__(weight=weight, reduction=reduction) + self.smoothing = smoothing + self.weight = weight + self.reduction = reduction + + @staticmethod + def _smooth_one_hot(targets:torch.Tensor, n_classes:int, smoothing=0.0): + assert 0 <= smoothing < 1 + with torch.no_grad(): + targets = torch.empty(size=(targets.size(0), n_classes), + device=targets.device) \ + .fill_(smoothing /(n_classes-1)) \ + .scatter_(1, targets.data.unsqueeze(1), 1.-smoothing) + return targets + + def forward(self, inputs, targets): + targets = SmoothCrossEntropyLoss._smooth_one_hot(targets, inputs.size(-1), + self.smoothing) + lsm = F.log_softmax(inputs, -1) + + if self.weight is not None: + lsm = lsm * self.weight.unsqueeze(0) + + loss = -(targets * lsm).sum(-1) + + if self.reduction == 'sum': + loss = loss.sum() + elif self.reduction == 'mean': + loss = loss.mean() + + return loss + + +class EdgeExpansion(nn.Module): + def __init__(self, edge_channels): + super().__init__() + self.nn = nn.Linear(in_features=1, out_features=edge_channels, bias=False) + + def forward(self, edge_vector): + edge_vector = edge_vector / (torch.norm(edge_vector, p=2, dim=1, keepdim=True)+1e-7) + expansion = self.nn(edge_vector.unsqueeze(-1)).transpose(1, -1) + return expansion + + +class GaussianSmearing(nn.Module): + def __init__(self, start=0.0, stop=10.0, num_gaussians=50): + super().__init__() + self.stop = stop + offset = torch.linspace(start, stop, num_gaussians) + self.coeff = -0.5 / (offset[1] - offset[0]).item()**2 + self.register_buffer('offset', offset) + + def forward(self, dist): + dist = dist.clamp_max(self.stop) + dist = dist.view(-1, 1) - self.offset.view(1, -1) + return torch.exp(self.coeff * torch.pow(dist, 2)) + + +class GaussianSmearingVN(nn.Module): + def __init__(self, start=0.0, stop=10.0, num_gaussians=64): + super().__init__() + assert num_gaussians % 8 == 0 + num_per_direction = num_gaussians // 8 + delta = (stop - start) / num_per_direction + offset = torch.linspace(start+delta/2, stop-delta/2, num_per_direction) + unit_vector = self.get_unit_vector() + kernel_vectors = unit_vector.unsqueeze(1) * offset.reshape([1, -1, 1]) + self.kernel_vectors = kernel_vectors.reshape([-1, 3]) + self.coeff = -0.5 / delta.item()**2 + self.register_buffer('offset', offset) + + def get_unit_vector(self,): + vec = torch.tensor([-1., 1.]) + vec = torch.stack([a.reshape(-1) for a in torch.meshgrid(vec, vec, vec, indexing=None)], dim=-1) + vec = vec / np.sqrt(3) + return vec + + def forward(self, dist): + dist = dist.view(-1, 1, 3) - self.kernel_vectors.view(1, -1, 3) + return torch.exp(self.coeff * torch.pow(dist, 2)) + + +class ShiftedSoftplus(nn.Module): + def __init__(self): + super().__init__() + + def forward(self, x): + return F.leaky_relu(x) + + +def compose_context(h_protein, h_ligand, pos_protein, pos_ligand, batch_protein, batch_ligand): + batch_ctx = torch.cat([batch_protein, batch_ligand], dim=0) + sort_idx = batch_ctx.argsort() + + is_mol_atom = torch.cat([ + torch.zeros([batch_protein.size(0)], device=batch_protein.device).bool(), + torch.ones([batch_ligand.size(0)], device=batch_ligand.device).bool(), + ], dim=0)[sort_idx] + + batch_ctx = batch_ctx[sort_idx] + h_ctx = torch.cat([h_protein, h_ligand], dim=0)[sort_idx] # (N_protein+N_ligand, H) + pos_ctx = torch.cat([pos_protein, pos_ligand], dim=0)[sort_idx] # (N_protein+N_ligand, 3) + + return h_ctx, pos_ctx, batch_ctx, is_mol_atom + + +def embed_compose(compose_feature, compose_pos, idx_ligand, idx_protein, + ligand_atom_emb, protein_atom_emb, + emb_dim): + + h_ligand = ligand_atom_emb(compose_feature[idx_ligand], compose_pos[idx_ligand]) + h_protein = protein_atom_emb(compose_feature[idx_protein], compose_pos[idx_protein]) + + h_sca = torch.zeros([len(compose_pos), emb_dim[0]],).to(h_ligand[0]) + h_vec = torch.zeros([len(compose_pos), emb_dim[1], 3],).to(h_ligand[1]) + h_sca[idx_ligand], h_sca[idx_protein] = h_ligand[0], h_protein[0] + h_vec[idx_ligand], h_vec[idx_protein] = h_ligand[1], h_protein[1] + return [h_sca, h_vec] + + +def compose_context_vn(h_ligand, h_protein, pos_ligand, pos_protein, batch_ligand, batch_protein): + batch_ctx = torch.cat([batch_ligand, batch_protein], dim=0) + A = batch_ctx[:, None] == torch.arange(batch_protein.max()+1, device=batch_ctx.device) + sort_idx = torch.nonzero(A.T)[:, -1] + batch_ctx = batch_ctx[sort_idx] + + sca_ctx = torch.cat([h_ligand[0], h_protein[0]], dim=0)[sort_idx] # (N_protein+N_ligand, H) + vec_ctx = torch.cat([h_ligand[1], h_protein[1]], dim=0)[sort_idx] # (N_protein+N_ligand, H) + pos_ctx = torch.cat([pos_ligand, pos_protein], dim=0)[sort_idx] # (N_protein+N_ligand, 3) + + is_mol_atom = torch.cat([ + torch.ones([batch_ligand.size(0)], device=batch_ligand.device).bool(), + torch.zeros([batch_protein.size(0)], device=batch_protein.device).bool(), + ], dim=0)[sort_idx] + + return (sca_ctx, vec_ctx), pos_ctx, batch_ctx, is_mol_atom + + +def get_compose_knn_graph( + pos_compose, + knn, + ligand_context_bond_index, + ligand_context_bond_type, + is_mol_atom, + batch_compose + ): + compose_knn_edge_index = knn_graph(pos_compose, knn, flow='target_to_source', batch=batch_compose) + + # init edge features + compose_knn_edge_feature = torch.cat([ + torch.ones([len(compose_knn_edge_index[0]), 1], dtype=torch.float32), + torch.zeros([len(compose_knn_edge_index[0]), 3], dtype=torch.float32), + ], dim=-1).to(pos_compose) + + # get bond index in compose + idx_ligand_ctx_in_compose = torch.nonzero(is_mol_atom).squeeze(-1) + compose_bond_index = idx_ligand_ctx_in_compose[ligand_context_bond_index] + compose_bond_type = ligand_context_bond_type + + # find the bond in all edges + len_compose = len(batch_compose) + id_compose_edge = compose_knn_edge_index[0] * len_compose + compose_knn_edge_index[1] + id_compose_bond = compose_bond_index[0] * len_compose + compose_bond_index[1] + idx_bond = [torch.nonzero(id_compose_edge == id_) for id_ in id_compose_bond] + idx_bond = torch.tensor([a.squeeze() if len(a) >0 else torch.tensor(-1) for a in idx_bond], dtype=torch.long) + compose_knn_edge_feature[idx_bond[idx_bond>=0]] = F.one_hot(compose_bond_type[idx_bond>=0], num_classes=4).to(torch.float32) # 0 (1,2,3)-onehot + + return compose_knn_edge_index, compose_knn_edge_feature + + +def get_query_compose_knn_edge( + pos_query, + pos_compose, + k, + batch_query, + batch_compose, + ): + query_compose_knn_edge_index = knn( + x=pos_compose, + y=pos_query, + k=k, + batch_x=batch_compose, + batch_y=batch_query + ) + return query_compose_knn_edge_index + + +def get_edge_atten_input(edge_index_query, n_query, context_bond_index, context_bond_type): + if (len(edge_index_query) != 0) and (edge_index_query.size(1) > 0): + device = edge_index_query.device + row, col = edge_index_query + acc_num_edges = 0 + index_real_cps_edge_i_list, index_real_cps_edge_j_list = [], [] # index of real-ctx edge (for attention) + for node in torch.arange(n_query): + num_edges = (row == node).sum() + index_edge_i = torch.arange(num_edges, dtype=torch.long, device=device) + acc_num_edges + index_edge_i, index_edge_j = torch.meshgrid(index_edge_i, index_edge_i, indexing=None) + index_edge_i, index_edge_j = index_edge_i.flatten(), index_edge_j.flatten() + index_real_cps_edge_i_list.append(index_edge_i) + index_real_cps_edge_j_list.append(index_edge_j) + acc_num_edges += num_edges + index_real_cps_edge_i = torch.cat(index_real_cps_edge_i_list, dim=0) # add len(real_compose_edge_index) in the dataloader for batch + index_real_cps_edge_j = torch.cat(index_real_cps_edge_j_list, dim=0) + + node_a_cps_tri_edge = col[index_real_cps_edge_i] # the node of tirangle edge for the edge attention (in the compose) + node_b_cps_tri_edge = col[index_real_cps_edge_j] + + if context_bond_index.size(1) > 0: + n_context = 1 + torch.maximum(context_bond_index.flatten().max(), col.max()) # NOTE:for only one batch + adj_mat = torch.zeros([n_context, n_context], dtype=torch.long, device=device) - torch.eye(n_context, dtype=torch.long, device=device) + adj_mat[context_bond_index[0], context_bond_index[1]] = context_bond_type + tri_edge_type = adj_mat[node_a_cps_tri_edge, node_b_cps_tri_edge] + tri_edge_feat = (tri_edge_type.view([-1, 1]) == torch.tensor([[-1, 0, 1, 2, 3]], device=device)).long() + else: + n_context = 1 + col.max() + adj_mat = torch.zeros([n_context, n_context], dtype=torch.long) - torch.eye(n_context, dtype=torch.long) + tri_edge_type = adj_mat[node_a_cps_tri_edge, node_b_cps_tri_edge] + tri_edge_feat = (tri_edge_type.view([-1, 1]) == torch.tensor([[-1, 0, 1, 2, 3]])).long().to(device) + + index_real_cps_edge_for_atten = torch.stack([ + index_real_cps_edge_i, index_real_cps_edge_j # plus len(real_compose_edge_index_0) for dataloader batch + ], dim=0) + tri_edge_index = torch.stack([ + node_a_cps_tri_edge, node_b_cps_tri_edge # plus len(compose_pos) for dataloader batch + ], dim=0) + tri_edge_feat = tri_edge_feat + return index_real_cps_edge_for_atten, tri_edge_index, tri_edge_feat + else: + return [], [], [] + + +def get_complete_graph(batch): + """ + Args: + batch: Batch index. + Returns: + edge_index: (2, N_1 + N_2 + ... + N_{B-1}), where N_i is the number of nodes of the i-th graph. + neighbors: (B, ), number of edges per graph. + """ + natoms = scatter_add(torch.ones_like(batch), index=batch, dim=0) + + natoms_sqr = (natoms ** 2).long() + num_atom_pairs = torch.sum(natoms_sqr) + natoms_expand = torch.repeat_interleave(natoms, natoms_sqr) + + index_offset = torch.cumsum(natoms, dim=0) - natoms + index_offset_expand = torch.repeat_interleave(index_offset, natoms_sqr) + + index_sqr_offset = torch.cumsum(natoms_sqr, dim=0) - natoms_sqr + index_sqr_offset = torch.repeat_interleave(index_sqr_offset, natoms_sqr) + + atom_count_sqr = torch.arange(num_atom_pairs, device=num_atom_pairs.device) - index_sqr_offset + + index1 = (atom_count_sqr // natoms_expand).long() + index_offset_expand + index2 = (atom_count_sqr % natoms_expand).long() + index_offset_expand + edge_index = torch.cat([index1.view(1, -1), index2.view(1, -1)]) + mask = torch.logical_not(index1 == index2) + edge_index = edge_index[:, mask] + + num_edges = natoms_sqr - natoms # Number of edges per graph + + return edge_index, num_edges + + +def compose_context_stable(h_protein, h_ligand, pos_protein, pos_ligand, batch_protein, batch_ligand): + num_graphs = batch_ligand.max().item() + 1 + + batch_ctx = [] + h_ctx = [] + pos_ctx = [] + mask_protein = [] + + for i in range(num_graphs): + mask_p, mask_l = (batch_protein == i), (batch_ligand == i) + batch_p, batch_l = batch_protein[mask_p], batch_ligand[mask_l] + + batch_ctx += [batch_p, batch_l] + h_ctx += [h_protein[mask_p], h_ligand[mask_l]] + pos_ctx += [pos_protein[mask_p], pos_ligand[mask_l]] + mask_protein += [ + torch.ones([batch_p.size(0)], device=batch_p.device, dtype=torch.bool), + torch.zeros([batch_l.size(0)], device=batch_l.device, dtype=torch.bool), + ] + + batch_ctx = torch.cat(batch_ctx, dim=0) + h_ctx = torch.cat(h_ctx, dim=0) + pos_ctx = torch.cat(pos_ctx, dim=0) + mask_protein = torch.cat(mask_protein, dim=0) + + return h_ctx, pos_ctx, batch_ctx, mask_protein + diff --git a/model/trained_egnn.pth b/model/trained_egnn.pth new file mode 100644 index 0000000..1a6c80a Binary files /dev/null and b/model/trained_egnn.pth differ diff --git a/model/vanillaGenerate.py b/model/vanillaGenerate.py new file mode 100644 index 0000000..949f8a6 --- /dev/null +++ b/model/vanillaGenerate.py @@ -0,0 +1,135 @@ +import torch +import torch_geometric.transforms as T +from torch_geometric.data import Data +from torch_geometric.datasets import TUDataset +from torch_geometric.datasets import QM9 +from torch_geometric.loader import DataLoader + +import numpy as np +from helper import * + + +# Parameters +num_graphs = 6400 +num_nodes_per_graph = 10 +num_classes = 2 +batch_size = 128 + + +# Generate random graphs +""" +graphs = [] +for _ in range(num_graphs): + class_label = torch.randint(0, num_classes, (1,)) + num_nodes = num_nodes_per_graph + x = torch.randn(num_nodes, 3) # Node features (3-dimensional) + edge_index = torch.randint(0, num_nodes, (2, num_nodes * 2)) # Random edge indices + edge_attr = torch.randn(num_nodes * 2, 2) # Random edge features (2-dimensional) + + data = Data(x=x, edge_index=edge_index, edge_attr=edge_attr, y=class_label) + graphs.append(data) + + +# Create a DataLoader +loader = DataLoader(graphs, batch_size=batch_size, shuffle=True) + +# Iterate through the DataLoader +for batch in loader: + print("Batch Node Features Shape:", batch.x.shape) + print("Batch Edge Index Shape:", batch.edge_index.shape) + print("Batch Edge Features Shape:", batch.edge_attr.shape) + print("Batch Class Labels:", batch.y) + print("--------------------------") +""" + +# Cora dataset +""" +name_data = 'Cora' +dataset = Planetoid(root='../dataset/' + name_data, name=name_data) +dataset.transform = T.NormalizeFeatures() +""" + +# MUTAG dataset +""" +path = "../dataset/" +name_data = 'MUTAG' +dataset = TUDataset(path, name=name_data).shuffle() + +print(f"Number of classes in {name_data}:", dataset.num_classes) +print(f"Number of node features in {name_data}:", dataset.num_node_features) +""" + +class QM9DataModule: + def __init__( + self, + train_ratio: float = 0.8, + val_ratio: float = 0.1, + test_ratio: float = 0.1, + target_idx: int = 5, + seed: float = 420, + ) -> None: + """Encapsulates everything related to the dataset + + Parameters + ---------- + train_ratio : float, optional + fraction of data used for training, by default 0.8 + val_ratio : float, optional + fraction of data used for validation, by default 0.1 + test_ratio : float, optional + fraction of data used for testing, by default 0.1 + target_idx : int, optional + index of the target (see torch geometric docs), by default 5 (electronic spatial extent) + (https://pytorch-geometric.readthedocs.io/en/latest/modules/datasets.html?highlight=qm9#torch_geometric.datasets.QM9) + seed : float, optional + random seed for data split, by default 420 + """ + assert sum([train_ratio, val_ratio, test_ratio]) == 1 + self.target_idx = target_idx + self.num_examples = len(self.dataset()) + rng = np.random.default_rng(seed) + self.shuffled_index = rng.permutation(self.num_examples) + self.train_split = self.shuffled_index[: int(self.num_examples * train_ratio)] + self.val_split = self.shuffled_index[ + int(self.num_examples * train_ratio) : int( + self.num_examples * (train_ratio + val_ratio) + ) + ] + self.test_split = self.shuffled_index[ + int(self.num_examples * (train_ratio + val_ratio)) : self.num_examples + ] + + def dataset(self, transform=None) -> QM9: + dataset = QM9( + root="../dataset/QM9", + pre_filter=lambda data: num_heavy_atoms(data) < 9, + pre_transform=add_complete_graph_edge_index, + ) + dataset.data.y = dataset.data.y[:, self.target_idx].view(-1, 1) + return dataset + + def loader(self, split, **loader_kwargs) -> DataLoader: + dataset = self.dataset()[split] + return DataLoader(dataset, **loader_kwargs) + + def train_loader(self, **loader_kwargs) -> DataLoader: + return self.loader(self.train_split, shuffle=True, **loader_kwargs) + + def val_loader(self, **loader_kwargs) -> DataLoader: + return self.loader(self.val_split, shuffle=False, **loader_kwargs) + + def test_loader(self, **loader_kwargs) -> DataLoader: + return self.loader(self.test_split, shuffle=False, **loader_kwargs) + + +dataset = QM9( + root="../dataset/QM9", + # Filter out molecules with more than 8 heavy atoms + pre_filter=lambda data: num_heavy_atoms(data) < 9, + # implement point cloud adjacency as a complete graph + pre_transform=add_complete_graph_edge_index, +) + +print(f"Num. examples in QM9 restricted to molecules with at most 8 heavy atoms: {len(dataset)}") + +data_module = QM9DataModule() diff --git a/model/vanillaHelper.py b/model/vanillaHelper.py new file mode 100644 index 0000000..bdd1fb9 --- /dev/null +++ b/model/vanillaHelper.py @@ -0,0 +1,125 @@ +import numpy as np +import math +from itertools import chain, product + +import torch +import torch.nn as nn +from torch import Tensor, LongTensor + +import torch_geometric +from torch_geometric.data import Data + + + +def num_heavy_atoms(qm9_data: Data) -> int: + """Count the number of heavy atoms in a torch geometric + Data object. + + Parameters + ---------- + qm9_data : Data + A pytorch geometric qm9 data object representing a small molecule + where atomic numbers are stored in a + tensor-valued attribute `qm9_data.z` + + Returns + ------- + int + The number of heavy atoms in the molecule. + """ + # every atom with atomic number other than 1 is heavy + return (qm9_data.z != 1).sum() + + +def complete_edge_index(n: int) -> LongTensor: + """ + Constructs a complete edge index. + + NOTE: representing complete graphs + with sparse edge tensors is arguably a bad idea + due to performance reasons, but for this tutorial it'll do. + + Parameters + ---------- + n : int + the number of nodes in the graph. + + Returns + ------- + LongTensor + A PyTorch `edge_index` represents a complete graph with n nodes, + without self-loops. Shape (2, n). + """ + # filter removes self loops + edges = list(filter(lambda e: e[0] != e[1], product(range(n), range(n)))) + return torch.tensor(edges, dtype=torch.long).T + + +def add_complete_graph_edge_index(data: Data) -> Data: + """ + On top of any edge information already there, + add a second edge index that represents + the complete graph corresponding to a given + torch geometric data object + + Parameters + ---------- + data : Data + The torch geometric data object. + + Returns + ------- + Data + The torch geometric `Data` object with a new + attribute `complete_edge_index` as described above. + """ + data.complete_edge_index = complete_edge_index(data.num_nodes) + return data + + +# use rotations along z-axis as demo e(3) transformation +def rotation_matrix_z(theta: float) -> Tensor: + """Generates a rotation matrix and returns + a corresponing tensor. The rotation is about the $z$-axis. + (https://en.wikipedia.org/wiki/Rotation_matrix) + + Parameters + ---------- + theta : float + the angle of rotation. + + Returns + ------- + Tensor + the rotation matrix as float tensor. + """ + return torch.tensor( + [ + [math.cos(theta), -math.sin(theta), 0], + [math.sin(theta), math.cos(theta), 0], + [0, 0, 1], + ] + ) + + +# We will be using mean absolute error +# as a metric for validation and testing +def total_absolute_error(pred: Tensor, target: Tensor, batch_dim: int = 0) -> Tensor: + """Total absolute error, i.e. sums over batch dimension. + + Parameters + ---------- + pred : Tensor + batch of model predictions + target : Tensor + batch of ground truth / target values + batch_dim : int, optional + dimension that indexes batch elements, by default 0 + + Returns + ------- + Tensor + total absolute error + """ + return (pred - target).abs().sum(batch_dim) + \ No newline at end of file diff --git a/model/vanillaModel.py b/model/vanillaModel.py new file mode 100644 index 0000000..0d490f1 --- /dev/null +++ b/model/vanillaModel.py @@ -0,0 +1,180 @@ +import os +import numpy as np +import matplotlib.pyplot as plt +from vanillaGenerate import * + +import torch +os.environ['TORCH'] = torch.__version__ +print(f"Using Torch version: {torch.__version__}") +from torch import Tensor +import torch.nn as nn +import torch.nn.functional as F + +from torch_geometric.data import Data +from torch_geometric.nn import GATConv, MLP, GINConv, global_add_pool +from torch_geometric.nn import Linear +import torch_geometric.transforms as T + + + +class GATLayer(nn.Module): + def __init__( + self, + in_features:int, + out_features:int, + dropout:float, + alpha:float, + concat:bool = True, + ) -> None: + super(GATLayer, self).__init__() + self.dropout = dropout + self.in_features = in_features + self.out_features = out_features + self.alpha = alpha + self.concat = concat + + # Xavier initialization of weights + self.W = nn.Parameter(torch.zeros(size=(in_features, out_features))) + nn.init.xavier_uniform_(self.W.data, gain=1.414) + + self.a = nn.Parameter(torch.zeros(size=(2*out_features, 1))) + nn.init.xavier_uniform_(self.a.data, gain=1.414) + + # LeakyReLU + self.leakyrelu = nn.LeakyReLU(self.alpha) + + + def forward( + self, + input: Tensor, + adj: Tensor, + ) -> Tensor: + h = torch.mm(input, self.W) + N = h.size()[0] + print(N) + + # Attention mechanism + a_input = torch.cat([h.repeat(1, N).view(N*N, -1), h.repeat(N, 1)], dim=1).view(N, -1, 2*self.out_features) + e = self.leakyrelu(torch.matmul(a_input, self.a).squeeze(2)) + + # Masked attention + zero_vec = -9e15 * torch.ones_like(e) + attention = torch.where(adj>0, e, zero_vec) + + attention = F.softmax(attention, dim=1) + attention = F.dropout(attention, self.dropout, training=self.training) + h_prime = torch.matmul(attention, h) + + if self.concat: + return F.elu(h_prime) + else: + h_prime + + +class GAT(nn.Module): + def __init__( + self, + dataset, + hid:int = 8, + in_head:int = 8, + out_head:int = 1, + dropout:float = 0.6, + concat:bool = False, + training:bool = True, + ) -> None: + super(GAT, self).__init__() + self.hid = hid + self.in_head = in_head + self.out_head = out_head + self.dropout = dropout + self.concat = concat + self.num_features = 7, + self.num_classes = 2, + + self.conv1 = GATConv(self.num_features, self.hid, heads=self.in_head, dropout=self.dropout) + self.conv2 = GATConv(self.hid*self.in_head, self.num_classes, concat=self.concat, heads=self.out_head, dropout=self.dropout) + + def forward( + self, + data:Data, + ) -> Tensor: + x, edge_index = data.x, data.edge_index + + x = F.dropout(x, p=0.6, training=self.training) + x = self.conv1(x, edge_index) + x = F.elu(x) + x = F.dropout(x, p=0.6, training=self.training) + x = self.conv2(x, edge_index) + + return F.log_softmax(x, dim=1) + + +class Net(nn.Module): + def __init__( + self, + in_channels:int, + hidden_channels:int, + out_channels:int, + num_layers:int, + dropout:float = 0.5, + ) -> None: + super().__init__() + self.convs = torch.nn.ModuleList() + + for _ in range(num_layers): + mlp = MLP([in_channels, hidden_channels, hidden_channels]) + self.convs.append(GINConv(nn=mlp, train_eps=False)) + in_channels = hidden_channels + + self.mlp = MLP([hidden_channels, hidden_channels, out_channels], + norm=None, dropout=dropout) + + def forward( + self, + x:Tensor, + edge_index:Tensor, + batch:Tensor, + ): + for conv in self.convs: + x = conv(x, edge_index).relu() + x = global_add_pool(x, batch) + return self.mlp(x) + + +class Discriminator(nn.Module): + def __init__( + self, + in_channels:int, + hidden_channels:int, + out_channels:int, + num_layers:int, + dropout:float = 0.5, + ) -> None: + super().__init__() + self.convs = torch.nn.ModuleList() + + for _ in range(num_layers): + mlp = MLP([in_channels, hidden_channels, hidden_channels]) + self.convs.append(GINConv(nn=mlp, train_eps=False)) + in_channels = hidden_channels + + self.mlp = MLP([hidden_channels, hidden_channels, out_channels], + norm=None, dropout=dropout) + self.linear = Linear(out_channels, 1) + self.activation = nn.Sigmoid() + + def forward( + self, + x:Tensor, + edge_index:Tensor, + batch:Tensor, + ): + for conv in self.convs: + x = conv(x, edge_index).relu() + + x = global_add_pool(x, batch) + x = self.mlp(x) + x = self.linear(x) + x = self.activation(x) + + return x.view(-1, 1) diff --git a/model/vanillaTrain.py b/model/vanillaTrain.py new file mode 100644 index 0000000..2abdeeb --- /dev/null +++ b/model/vanillaTrain.py @@ -0,0 +1,312 @@ +import torch +import torch.nn as nn +import torch.nn.functional as F +from torch.optim import Adam +from torch_geometric.loader import DataLoader +from torch_geometric.logging import init_wandb, log + +from typing import Any, Optional, Callable, Tuple, Dict, Sequence, NamedTuple +from tqdm import tqdm + +from common import EquivariantGNN +from vanillaHelper import * +from vanillaModel import GAT, Net, Discriminator +from vanillaGenerate import dataset, data_module, QM9DataModule + + + +EPOCHS = 25 +LR = 2e-4 +WEIGHT_DECAY = 1e-8 +BATCH_SIZE = 32 +DEVICE = torch.device('cuda' if torch.cuda.is_available() else 'cpu') +HIDDEN_CHANNELS = 64 +NUM_LAYERS = 5 + +init_wandb(name='vanilla', + batch_size=BATCH_SIZE, + lr=LR, + epochs=EPOCHS, + hidden_channels=1, + num_layers=1, + device=DEVICE) + +""" +for i in tqdm(range(len(graphs))): + graphs[i].to(DEVICE) + +train_dataset = dataset[len(dataset) // 10:] +train_loader = DataLoader(train_dataset, BATCH_SIZE, shuffle=True) + +test_dataset = dataset[:len(dataset) // 10] +test_loader = DataLoader(test_dataset, BATCH_SIZE) + +#model = GAT(dataset=train_loader).to(DEVICE) +model = Net(in_channels=dataset.num_features, + hidden_channels=HIDDEN_CHANNELS, + out_channels=dataset.num_classes, + num_layers=NUM_LAYERS + ).to(DEVICE) +""" + +model = EquivariantGNN(hidden_channels=HIDDEN_CHANNELS, num_mp_layers=NUM_LAYERS) + +#model = Discriminator(in_channels=dataset.num_features, +# hidden_channels=HIDDEN_CHANNELS, +# out_channels=dataset.num_classes, +# num_layers=NUM_LAYERS +# ).to(DEVICE) + +optimizer = Adam(model.parameters(), lr=LR, weight_decay=WEIGHT_DECAY) +criterion = nn.BCELoss() + + +def train(): + model.train() + total_loss = 0 + + for data in train_loader: + data = data.to(DEVICE) + optimizer.zero_grad() + out = model(data.x, data.edge_index, data.batch) + loss = F.cross_entropy(out, data.y) + loss.backward() + optimizer.step() + total_loss += float(loss) * data.num_graphs + + return total_loss / len(train_loader.dataset) + + +@torch.no_grad() +def test(loader): + model.eval() + total_correct = 0 + + for data in loader: + data = data.to(DEVICE) + pred = model(data.x, data.edge_index, data.batch).argmax(dim=-1) + total_correct += int((pred == data.y).sum()) + + return total_correct / len(loader.dataset) + +""" +for epoch in range(1, EPOCHS+1): + loss = train() + train_acc = test(train_loader) + test_acc = test(test_loader) + log(Epoch=epoch, Loss=loss, Train=train_acc, Test=test_acc) +""" + +def run_epoch( + model: nn.Module, + loader: DataLoader, + criterion: Callable[[Tensor, Tensor], Tensor], + pbar: Optional[Any] = None, + optim: Optional[torch.optim.Optimizer] = None, +): + """Run a single epoch. + + Parameters + ---------- + model : nn.Module + the NN used for regression + loader : DataLoader + an iterable over data batches + criterion : Callable[[Tensor, Tensor], Tensor] + a criterion (loss) that is optimized + pbar : Optional[Any], optional + a tqdm progress bar, by default None + optim : Optional[torch.optim.Optimizer], optional + a optimizer that is optimizing the criterion, by default None + """ + + def step( + data_batch: Data, + ) -> Tuple[float, float]: + """Perform a single train/val step on a data batch. + + Parameters + ---------- + data_batch : Data + + Returns + ------- + Tuple[float, float] + Loss (mean squared error) and validation critierion (absolute error). + """ + pred = model.forward(data_batch) + target = data_batch.y + loss = criterion(pred, target) + if optim is not None: + optim.zero_grad() + loss.backward() + optim.step() + return loss.detach().item(), total_absolute_error(pred.detach(), target.detach()) + + if optim is not None: + model.train() + # This enables pytorch autodiff s.t. we can compute gradients + model.requires_grad_(True) + else: + model.eval() + # disable autodiff: when evaluating we do not need to track gradients + model.requires_grad_(False) + + total_loss = 0 + total_mae = 0 + for data in loader: + loss, mae = step(data) + total_loss += loss * data.num_graphs + total_mae += mae + if pbar is not None: + pbar.update(1) + + return total_loss / len(loader.dataset), total_mae / len(loader.dataset) + + +def train_model( + data_module: QM9DataModule, + model: nn.Module, + num_epochs: int = 30, + lr: float = 3e-4, + batch_size: int = 32, + weight_decay: float = 1e-8, + best_model_path: str = "trained_model.pth", + ) -> Dict[str, Any]: + """Takes data and model as input and runs training, collecting additional validation metrics + while doing so. + + Parameters + ---------- + data_module : QM9DataModule + a data module as defined earlier + model : nn.Module + a gnn model + num_epochs : int, optional + number of epochs to train for, by default 30 + lr : float, optional + "learning rate": optimizer SGD step size, by default 3e-4 + batch_size : int, optional + number of examples used for one training step, by default 32 + weight_decay : float, optional + L2 regularization parameter, by default 1e-8 + best_model_path : Path, optional + path where the model weights with lowest val. error should be stored + , by default DATA.joinpath("trained_model.pth") + + Returns + ------- + Dict[str, Any] + a training result, ie statistics and info about the model + """ + # create data loaders + train_loader = data_module.train_loader(batch_size=batch_size) + val_loader = data_module.val_loader(batch_size=batch_size) + + # setup optimizer and loss + optim = torch.optim.Adam(model.parameters(), lr, weight_decay=1e-8) + loss_fn = nn.MSELoss() + + # keep track of the epoch with the best validation mae + # st we can save the "best" model weights + best_val_mae = float("inf") + + # Statistics that will be plotted later on + # and model info + result = { + "model": model, + "path_to_best_model": best_model_path, + "train_loss": np.full(num_epochs, float("nan")), + "val_loss": np.full(num_epochs, float("nan")), + "train_mae": np.full(num_epochs, float("nan")), + "val_mae": np.full(num_epochs, float("nan")), + } + + # Auxiliary functions for updating and reporting + # Training progress statistics + def update_statistics(i_epoch: int, **kwargs: float): + for key, value in kwargs.items(): + result[key][i_epoch] = value + + def desc(i_epoch: int) -> str: + return " | ".join( + [f"Epoch {i_epoch + 1:3d} / {num_epochs}"] + + [ + f"{key}: {value[i_epoch]:8.2f}" + for key, value in result.items() + if isinstance(value, np.ndarray) + ] + ) + + # main training loop + for i_epoch in range(0, num_epochs): + progress_bar = tqdm(total=len(train_loader) + len(val_loader)) + try: + # tqdm for reporting progress + progress_bar.set_description(desc(i_epoch)) + + # training epoch + train_loss, train_mae = run_epoch(model, train_loader, loss_fn, progress_bar, optim) + # validation epoch + val_loss, val_mae = run_epoch(model, val_loader, loss_fn, progress_bar) + + update_statistics( + i_epoch, + train_loss=train_loss, + val_loss=val_loss, + train_mae=train_mae, + val_mae=val_mae, + ) + + progress_bar.set_description(desc(i_epoch)) + + if val_mae < best_val_mae: + best_val_mae = val_mae + torch.save(model.state_dict(), best_model_path) + finally: + progress_bar.close() + + return result + + +@torch.no_grad() +def test_model(model: nn.Module, data_module: QM9DataModule) -> Tuple[float, Tensor, Tensor]: + """ + Test a model. + + Parameters + ---------- + model : nn.Module + a trained model + data_module : QM9DataModule + a data module as defined earlier + from which we'll get the test data + + Returns + ------- + _Tuple[float, Tensor, Tensor] + Test MAE, and model predictions & targets for further processing + """ + test_mae = 0 + preds, targets = [], [] + loader = data_module.test_loader() + for data in loader: + pred = model(data) + target = data.y + preds.append(pred) + targets.append(target) + test_mae += total_absolute_error(pred, target).item() + + test_mae = test_mae / len(data_module.test_split) + return test_mae, torch.cat(preds, dim=0), torch.cat(targets, dim=0) + + +egnn_train_result = train_model( + data_module=data_module, + model=model, + num_epochs=EPOCHS, + lr=LR, + batch_size=BATCH_SIZE, + weight_decay=WEIGHT_DECAY, + best_model_path="trained_egnn.pth", +) diff --git a/train.py b/train.py new file mode 100644 index 0000000..d63a2f7 --- /dev/null +++ b/train.py @@ -0,0 +1,113 @@ +import torch +import torch_geometric +from torch_geometric.data import HeteroData + +import numpy as np + +from tqdm import tqdm +import os +import pickle +import yaml +import random +import warnings +import argparse +import traceback +import logging + +from utils.misc import load_config + + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument('--config', type=str, + default='./config/train.yml') + parser.add_argument('--data', type=str, + default='./dataset/crossdocked_vina10') + parser.add_argument('--device', type=str, + default='cpu') + parser.add_argument('--logdir', type=str, + default='./logs') + parser.add_argument('--outdir', type=str, + default='./output') + args = parser.parse_args() + + + # Logging + log_dir = get_new_log_dir(args.logdir, prefix=config_name) + ckpt_dir = os.path.join(log_dir, 'checkpoints') + os.makedirs(ckpt_dir, exist_ok=True) + logger = get_logger('train', log_dir) + writer = torch.utils.tensorboard.SummaryWriter(log_dir) + logger.info(args) + logger.info(config) + shutil.copyfile(args.config, os.path.join(log_dir, os.path.basename(args.config))) + shutil.copytree('./models', os.path.join(log_dir, 'models')) + + # Load config + outDirExists = os.path.isfile(args.config) + if not outDirExists: + raise FileNotFoundError("Configuration YML (config.yml) file does not exist or is not specified.") + else: + logger.info("Reading configuration YML file...") + config = load_config(args.config) + seed_all(config.featuriser.seed) + split_dict = torch.load(config.dataset.split) + logger.info(f"Found {len(split_dict['train'])} samples in the Crossdock dataset for training.") + if config.train.use_apex: + from apex import amp + + + print("\n") + outDirExists = os.path.exists(args.outdir) + if not outDirExists: + os.makedirs(args.outdir) + logger.info("Output directory {args.outdir} is created.") + + + + + + # Model + logger.info('Building model...') + if config.model.vn == 'singa': + model = MaskFillModelVN( + config.model, + num_classes = contrastive_sampler.num_elements, + num_bond_types = edge_sampler.num_bond_types, + protein_atom_feature_dim = protein_featurizer.feature_dim, + ligand_atom_feature_dim = ligand_featurizer.feature_dim, + ).to(args.device) + print('Num of parameters is', np.sum([p.numel() for p in model.parameters()])) + + # Optimizer and scheduler + optimizer = get_optimizer(config.train.optimizer, model) + scheduler = get_scheduler(config.train.scheduler, optimizer) + if config.train.use_apex: + model, optimizer = amp.initialize(model, optimizer, opt_level='O1' + + + + + + try: + model.train() + for it in range(1, config.train.max_iters+1): + try: + train(it) + except RuntimeError as e: + logger.error('Runtime Error ' + str(e)) + if it % config.train.val_freq == 0 or it == config.train.max_iters: + validate(it) + ckpt_path = os.path.join(ckpt_dir, '%d.pt' % it) + torch.save({ + 'config': config, + 'model': model.state_dict(), + 'optimizer': optimizer.state_dict(), + 'scheduler': scheduler.state_dict(), + 'iteration': it, + }, ckpt_path) + model.train() + except KeyboardInterrupt: + logger.info('Terminating...') + diff --git a/utils/.Featuriser.py b/utils/.Featuriser.py new file mode 100644 index 0000000..7df0963 --- /dev/null +++ b/utils/.Featuriser.py @@ -0,0 +1,149 @@ +################################################################# +# Main functionality # +# ================== # +# 1. Find RMSD of docked ligand poses from crystal structure # +# 2. Retrieve molecular features of protein and ligand # +# 3. Prepare node and edge features (ODDT) # +# 4. Dump all relevant info to pickle file # +# # +################################################################# + +import rdkit +from rdkit import Chem +from rdkit.Chem.rdmolops import AddHs +import oddt +from oddt.docking.AutodockVina import autodock_vina +import torch + +from tqdm import tqdm +import os, glob +import pickle, yaml +import random +import warnings +import argparse +import traceback +import logging +import itertools + +from misc import * +import PLInteraction +from PLParser import StructureDual, parse_sdf_file +from PLFeature import ComputeSASA, ClassifyAtoms, RetrieveMolecularFeatures + + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument('--config', type=str, + default='./config/config.yml') + parser.add_argument('--outdir', type=str, + default='./dataset/crossdocked_vina10') + args = parser.parse_args() + + # Logging + log_dir = args.outdir + logger = get_logger('feature_extract_log', log_dir) + logger.info(args) + + print("\n") + outDirExists = os.path.exists(args.outdir) + if not outDirExists: + os.makedirs(args.outdir) + logger.info("Output directory {args.outdir} is created.") + + # Load config + outDirExists = os.path.isfile(args.config) + if not outDirExists: + raise FileNotFoundError("Configuration YML (config.yml) file does not exist or is not specified.") + else: + logger.info("Reading configuration YML file...") + config = load_config(args.config) + #seed_all(config.featuriser.seed) + split_dict = torch.load(config.dataset.split) + logger.info(f"Found {len(split_dict['train'])} samples in the Crossdock dataset for training.") + + # Docking ligands with Autodock Vina implemented in ODDT + logger.info("Extracting features...") + for i in tqdm(range(len(split_dict['train']))): + #for i in tqdm(range(1)): + logger.info(" ") + complexDict, skippedComplex = {}, [] + name = str(split_dict['train'][i][0].split(".")[0]) + + outDirExists = os.path.exists(os.path.join(args.outdir, name.split("/")[0])) + if not outDirExists: + os.makedirs(os.path.join(args.outdir, name.split('/')[0])) + logger.info(f"Output directory {name.split('/')[0]} is created.") + + logger.info(f"Now reading {name}...") + proteinDual = StructureDual(os.path.join(config.dataset.path, split_dict['train'][i][0]), isProtein=True) + ligandDual = StructureDual(os.path.join(config.dataset.path, split_dict['train'][i][1]), isProtein=False) + + protein, _protein = proteinDual.parse_to_oddt(), proteinDual.parse_to_rdkit() + ligand, _ligand = ligandDual.parse_to_oddt(), ligandDual.parse_to_rdkit() + ligand_com = parse_sdf_file(os.path.join(config.dataset.path, split_dict['train'][i][1]))['center_of_mass'] + + vina = autodock_vina(protein=protein, + auto_ligand=ligand, + center=tuple(ligand_com), + num_modes=int(config.autodock.num_modes), + executable=config.autodock.executable) + + # Extracting vina score of native structure + vina_score = float(vina.predict_ligand(ligand).data['vina_affinity']) + protein_cc, ligand_cc = PLInteraction.close_contacts(x=protein.atom_dict, + y=ligand.atom_dict, + cutoff=float(config.featuriser.sasa_cutoff)) + protein_cc_idx, ligand_cc_idx = list(np.unique(protein_cc['id'])), list(np.unique(ligand_cc['id'])) + protein_cc_radii, ligand_cc_radii = ClassifyAtoms(config.featuriser.symbol_radius_path, _protein, protein_cc_idx), ClassifyAtoms(config.featuriser.symbol_radius_path, _ligand, ligand_cc_idx) + + + logger.info("Extracting protein node features...") + # Computing SASA + try: + protein_cc_coords = proteinDual.RetrieveCoords(protein_cc_idx) + protein_cc_coords = list(itertools.chain.from_iterable(protein_cc_coords)) + + sasa = ComputeSASA(protein_cc_coords, protein_cc_idx) + protein_feature = RetrieveMolecularFeatures(molList=[_protein], labelList=[[0.0, vina_score, sasa]])[0] + except Exception as e: + logger.error(traceback.format_exc()) + skippedComplex.append(name) + continue + + + logging.info("Extracting ligand node features...") + # Computing SASA + try: + ligand_cc_coords = ligandDual.RetrieveCoords(ligand_cc_idx) + ligand_cc_coords = list(itertools.chain.from_iterable(ligand_cc_coords)) + + sasa = ComputeSASA(ligand_cc_coords, ligand_cc_idx) + ligand_feature = RetrieveMolecularFeatures(molList=[_ligand], labelList=[[0.0, vina_score, sasa]])[0] + except Exception as e: + logger.error(traceback.format_exc()) + skippedComplex.append(name) + continue + else: + logger.info("Retrieving PL interaction (edge) features...") + fp, fl = PLInteraction.fingerprint(protein, ligand) + + logger.info("Dumping features into pickle...") + complexDict['name'] = name + complexDict['vina_score'] = vina_score + complexDict['protein_feature'] = protein_feature + complexDict['ligand_feature'] = ligand_feature + complexDict['interaction_fp'] = fp + complexDict['interaction_fl'] = fl + + # Pickle dump + with open(args.outdir + '/' + name + '.pkl', 'wb') as file: + pickle.dump(complexDict, file) + """ + with open('trail.pkl', 'wb') as file: + pickle.dump(complexDict, file) + """ + + logger.info(f"Skipped {len(skippedComplex)} complexes: {skippedComplex}") + logger.info("Process terminated successfully.\n") + \ No newline at end of file diff --git a/utils/.PLIConfig.py b/utils/.PLIConfig.py new file mode 100644 index 0000000..df0384c --- /dev/null +++ b/utils/.PLIConfig.py @@ -0,0 +1,301 @@ +import math +from math import sin, cos +from scipy.spatial.distance import cdist +import numpy as np + + +""" +Spatial functions included in ODDT +Mainly used by other modules, but can be accessed directly. +""" + +def angle(p1, p2, p3): + """Returns an angle from a series of 3 points (point #2 is centroid). + Angle is returned in degrees. + + Parameters + ---------- + p1,p2,p3 : numpy arrays, shape = [n_points, n_dimensions] + Triplets of points in n-dimensional space, aligned in rows. + + Returns + ------- + angles : numpy array, shape = [n_points] + Series of angles in degrees + """ + v1 = p1 - p2 + v2 = p3 - p2 + return angle_2v(v1, v2) + + +def angle_2v(v1, v2): + """Returns an angle between two vecors.Angle is returned in degrees. + + Parameters + ---------- + v1,v2 : numpy arrays, shape = [n_vectors, n_dimensions] + Pairs of vectors in n-dimensional space, aligned in rows. + + Returns + ------- + angles : numpy array, shape = [n_vectors] + Series of angles in degrees + """ + # better than np.dot(v1, v2), multiple vectors can be applied + dot = (v1 * v2).sum(axis=-1) + norm = np.linalg.norm(v1, axis=-1) * np.linalg.norm(v2, axis=-1) + return np.degrees(np.arccos(np.clip(dot/norm, -1, 1))) + + +def distance(x, y): + """Computes distance between each pair of points from x and y. + + Parameters + ---------- + x : numpy arrays, shape = [n_x, 3] + Array of poinds in 3D + + y : numpy arrays, shape = [n_y, 3] + Array of poinds in 3D + + Returns + ------- + dist_matrix : numpy arrays, shape = [n_x, n_y] + Distance matrix + """ + return cdist(x, y) + + +def close_contacts(x, y, cutoff, x_column='coords', y_column='coords', + cutoff_low=0.): + """Returns pairs of atoms which are within close contac distance cutoff. + The cutoff is semi-inclusive, i.e (cutoff_low, cutoff]. + + Parameters + ---------- + x, y : atom_dict-type numpy array + Atom dictionaries generated by oddt.toolkit.Molecule objects. + + cutoff : float + Cutoff distance for close contacts + + x_column, ycolumn : string, (default='coords') + Column containing coordinates of atoms (or pseudo-atoms, + i.e. ring centroids) + + cutoff_low : float (default=0.) + Lower bound of contacts to find (exclusive). Zero by default. + .. versionadded:: 0.6 + + Returns + ------- + x_, y_ : atom_dict-type numpy array + Aligned pairs of atoms in close contact for further processing. + """ + if len(x[x_column]) > 0 and len(x[x_column]) > 0: + d = distance(x[x_column], y[y_column]) + index = np.argwhere((d > cutoff_low) & (d <= cutoff)) + return x[index[:, 0]], y[index[:, 1]] + else: + return x[[]], y[[]] + + +def _check_angles(angles, hybridizations, tolerance): + """Helper function for checking if interactions are strict""" + angles = np.nan_to_num(angles) # NaN's throw warning on comparisons + ideal_angles = np.take(BASE_ANGLES, hybridizations)[:, np.newaxis] + lower_bound = ideal_angles - tolerance + upper_bound = ideal_angles + tolerance + return ((angles > lower_bound) & (angles < upper_bound)).any(axis=-1) + + +def hbond_acceptor_donor(mol1, mol2, cutoff=3.5, tolerance=30, donor_exact=False): + """Returns pairs of acceptor-donor atoms, which meet H-bond criteria + + Parameters + ---------- + mol1, mol2 : oddt.toolkit.Molecule object + Molecules to compute H-bond acceptor and H-bond donor pairs + + cutoff : float, (default=3.5) + Distance cutoff for A-D pairs + + tolerance : int, (default=30) + Range (+/- tolerance) from perfect direction defined by acceptor/donor hybridization + in which H-bonds are considered as strict. + donor_exact : bool + Use exact protonation states for donors, i.e. require Hs on donor. + By default ODDT implies some tautomeric structures as protonated, + even if there is no H on specific atom. + + Returns + ------- + a, d : atom_dict-type numpy array + Aligned arrays of atoms forming H-bond, firstly acceptors, + secondly donors. + + strict : numpy array, dtype=bool + Boolean array align with atom pairs, informing whether atoms + form 'strict' H-bond (pass all angular cutoffs). If false, + only distance cutoff is met, therefore the bond is 'crude'. + """ + donor_mask = mol2.atom_dict['isdonor'] + if donor_exact: + donor_mask = donor_mask & (mol2.atom_dict['numhs'] > 0) + a, d = close_contacts(mol1.atom_dict[mol1.atom_dict['isacceptor']], + mol2.atom_dict[donor_mask], + cutoff) + # skip empty values + if len(a) > 0 and len(d) > 0: + angle1 = angle(d['coords'][:, np.newaxis, :], + a['coords'][:, np.newaxis, :], + a['neighbors']) + angle2 = angle(a['coords'][:, np.newaxis, :], + d['coords'][:, np.newaxis, :], + d['neighbors']) + strict = (_check_angles(angle1, a['hybridization'], tolerance) & + _check_angles(angle2, d['hybridization'], tolerance)) + return a, d, angle1, angle2, strict + else: + return a, d, np.array([], dtype=bool), np.array([], dtype=bool), np.array([], dtype=bool) + +def halogenbond_acceptor_halogen(mol1, + mol2, + tolerance=30, + cutoff=4): + """Returns pairs of acceptor-halogen atoms, which meet halogen bond criteria + + Parameters + ---------- + mol1, mol2 : oddt.toolkit.Molecule object + Molecules to compute halogen bond acceptor and halogen pairs + + cutoff : float, (default=4) + Distance cutoff for A-H pairs + + tolerance : int, (default=30) + Range (+/- tolerance) from perfect direction defined by atoms hybridization + in which halogen bonds are considered as strict. + + Returns + ------- + a, h : atom_dict-type numpy array + Aligned arrays of atoms forming halogen bond, firstly acceptors, + secondly halogens + + strict : numpy array, dtype=bool + Boolean array align with atom pairs, informing whether atoms + form 'strict' halogen bond (pass all angular cutoffs). If false, + only distance cutoff is met, therefore the bond is 'crude'. + """ + a, h = close_contacts(mol1.atom_dict[mol1.atom_dict['isacceptor']], + mol2.atom_dict[mol2.atom_dict['ishalogen']], + cutoff) + # skip empty values + if len(a) > 0 and len(h) > 0: + angle1 = angle(h['coords'][:, np.newaxis, :], + a['coords'][:, np.newaxis, :], + a['neighbors']) + angle2 = angle(a['coords'][:, np.newaxis, :], + h['coords'][:, np.newaxis, :], + h['neighbors']) + strict = (_check_angles(angle1, a['hybridization'], tolerance) & + _check_angles(angle2, np.ones_like(h['hybridization']), tolerance)) + return a, h, angle1, angle2, strict + else: + return a, h, np.array([], dtype=bool), np.array([], dtype=bool), np.array([], dtype=bool) + + +def salt_bridge_plus_minus(mol1, mol2, cutoff=4, cation_exact=False, anion_exact=False): + """Returns pairs of plus-mins atoms, which meet salt bridge criteria + + Parameters + ---------- + mol1, mol2 : oddt.toolkit.Molecule object + Molecules to compute plus and minus pairs + + cutoff : float, (default=4) + Distance cutoff for A-H pairs + + cation_exact, anion_exact : bool + Requires interacting atoms to have non-zero formal charge. + + Returns + ------- + plus, minus : atom_dict-type numpy array + Aligned arrays of atoms forming salt bridge, firstly plus, secondly minus + + """ + cation_map = mol1.atom_dict['isplus'] + if cation_exact: + cation_map = cation_map & (mol1.atom_dict['formalcharge'] > 0) + anion_map = mol2.atom_dict['isminus'] + if anion_exact: + anion_map = anion_map & (mol2.atom_dict['formalcharge'] < 0) + m1_plus, m2_minus = close_contacts(mol1.atom_dict[cation_map], + mol2.atom_dict[anion_map], + cutoff) + return m1_plus, m2_minus + + +def calculate_atomic_rmsd(reference_mol, target_mol): + reference_atoms = reference_mol.GetAtoms() + target_atoms = target_mol.GetAtoms() + + if len(reference_atoms) != len(target_atoms): + raise ValueError("The number of atoms in the molecules does not match.") + + squared_sum = 0.0 + count = 0 + + for ref_atom, tgt_atom in zip(reference_atoms, target_atoms): + ref_coords = ref_atom.GetPosition() + tgt_coords = tgt_atom.GetPosition() + + squared_sum += (ref_coords.x - tgt_coords.x) ** 2 + squared_sum += (ref_coords.y - tgt_coords.y) ** 2 + squared_sum += (ref_coords.z - tgt_coords.z) ** 2 + count += 3 + + rmsd = (squared_sum / count) ** 0.5 + + return rmsd + + +BASE_ANGLES = np.array((0, 180, 120, 109.5, 90), dtype=float) + +settings = {} +settings['nonpolar'] = {6:1.7, 9:1.47, 17:1.75, 35:1.85, 53:1.98} +settings['hbond_dist_cut'] = 3.5 +settings['hbond_angle_cut'] = 180.0 +settings['hbond_dist_bound'] = 2.5 +settings['hbond_angle_bound'] = 90.0 + +settings['hphob_dist_cut'] = 4.0 +settings['hphob_dist_bound'] = 1.25 + +settings['contact_scale_cut'] = 1.75 +settings['contact_scale_opt'] = 1.25 + +settings['sbridge_dist_cut'] = 5.0 +settings['sbridge_dist_bound'] = 3.25 +settings['saltbridge_resonance'] = True + +settings['pistack_dist_cut'] = 6.5 +settings['pistack_dist_bound'] = 3.8 +settings['pistack_angle_bound'] = 60.0 +settings['pistack_angle_cut'] = 90.0 + +settings['pication_dist_cut'] = 6.5 +settings['pication_dist_bound'] = 4.3 +settings['pication_angle_cut'] = 90.0 +settings['pication_angle_bound'] = 30.0 + +settings['xbond_dist_cut'] = 5.0 +settings['xbond_angle_cut'] = 150.0 +settings['xbond_dist_bound'] = 3.5 +settings['xbond_angle_bound'] = 135.0 + +settings['acceptor_metal_dist_cut'] = 4.0 +settings['pimetal_dist_cut'] = 5.0 + diff --git a/utils/.PLInteraction.py b/utils/.PLInteraction.py new file mode 100644 index 0000000..c5eba67 --- /dev/null +++ b/utils/.PLInteraction.py @@ -0,0 +1,870 @@ +import numpy as np +import pandas as pd +from scipy.spatial.distance import cdist +import oddt +import rdkit +from rdkit import Chem +import math +from math import sin, cos +import yaml + + + +BASE_ANGLES = np.array((0, 180, 120, 109.5, 90), dtype=float) +with open("../config/train.yml", "r") as file: + settings = yaml.safe_load(file) + + + +####################################################################################### +################################### Initialisation #################################### +####################################################################################### + +""" +Spatial functions included in ODDT +Mainly used by other modules, but can be accessed directly. +""" + +def angle(p1, p2, p3): + """Returns an angle from a series of 3 points (point #2 is centroid). + Angle is returned in degrees. + + Parameters + ---------- + p1,p2,p3 : numpy arrays, shape = [n_points, n_dimensions] + Triplets of points in n-dimensional space, aligned in rows. + + Returns + ------- + angles : numpy array, shape = [n_points] + Series of angles in degrees + """ + v1 = p1 - p2 + v2 = p3 - p2 + return angle_2v(v1, v2) + + +def angle_2v(v1, v2): + """Returns an angle between two vecors.Angle is returned in degrees. + + Parameters + ---------- + v1,v2 : numpy arrays, shape = [n_vectors, n_dimensions] + Pairs of vectors in n-dimensional space, aligned in rows. + + Returns + ------- + angles : numpy array, shape = [n_vectors] + Series of angles in degrees + """ + # better than np.dot(v1, v2), multiple vectors can be applied + dot = (v1 * v2).sum(axis=-1) + norm = np.linalg.norm(v1, axis=-1) * np.linalg.norm(v2, axis=-1) + return np.degrees(np.arccos(np.clip(dot/norm, -1, 1))) + + +def distance(x, y): + """Computes distance between each pair of points from x and y. + + Parameters + ---------- + x : numpy arrays, shape = [n_x, 3] + Array of poinds in 3D + + y : numpy arrays, shape = [n_y, 3] + Array of poinds in 3D + + Returns + ------- + dist_matrix : numpy arrays, shape = [n_x, n_y] + Distance matrix + """ + return cdist(x, y) + + +def close_contacts(x, y, cutoff, x_column='coords', y_column='coords', cutoff_low=0.): + """Returns pairs of atoms which are within close contac distance cutoff. + The cutoff is semi-inclusive, i.e (cutoff_low, cutoff]. + + Parameters + ---------- + x, y : atom_dict-type numpy array + Atom dictionaries generated by oddt.toolkit.Molecule objects. + + cutoff : float + Cutoff distance for close contacts + + x_column, ycolumn : string, (default='coords') + Column containing coordinates of atoms (or pseudo-atoms, + i.e. ring centroids) + + cutoff_low : float (default=0.) + Lower bound of contacts to find (exclusive). Zero by default. + .. versionadded:: 0.6 + + Returns + ------- + x_, y_ : atom_dict-type numpy array + Aligned pairs of atoms in close contact for further processing. + """ + if len(x[x_column]) > 0 and len(x[x_column]) > 0: + d = distance(x[x_column], y[y_column]) + index = np.argwhere((d > cutoff_low) & (d <= cutoff)) + return x[index[:, 0]], y[index[:, 1]] + else: + return x[[]], y[[]] + + +def _check_angles(angles, hybridizations, tolerance): + """Helper function for checking if interactions are strict""" + angles = np.nan_to_num(angles) # NaN's throw warning on comparisons + ideal_angles = np.take(BASE_ANGLES, hybridizations)[:, np.newaxis] + lower_bound = ideal_angles - tolerance + upper_bound = ideal_angles + tolerance + return ((angles > lower_bound) & (angles < upper_bound)).any(axis=-1) + + +def hbond_acceptor_donor(mol1, mol2, cutoff=3.5, tolerance=30, donor_exact=False): + """Returns pairs of acceptor-donor atoms, which meet H-bond criteria + + Parameters + ---------- + mol1, mol2 : oddt.toolkit.Molecule object + Molecules to compute H-bond acceptor and H-bond donor pairs + + cutoff : float, (default=3.5) + Distance cutoff for A-D pairs + + tolerance : int, (default=30) + Range (+/- tolerance) from perfect direction defined by acceptor/donor hybridization + in which H-bonds are considered as strict. + donor_exact : bool + Use exact protonation states for donors, i.e. require Hs on donor. + By default ODDT implies some tautomeric structures as protonated, + even if there is no H on specific atom. + + Returns + ------- + a, d : atom_dict-type numpy array + Aligned arrays of atoms forming H-bond, firstly acceptors, + secondly donors. + + strict : numpy array, dtype=bool + Boolean array align with atom pairs, informing whether atoms + form 'strict' H-bond (pass all angular cutoffs). If false, + only distance cutoff is met, therefore the bond is 'crude'. + """ + donor_mask = mol2.atom_dict['isdonor'] + if donor_exact: + donor_mask = donor_mask & (mol2.atom_dict['numhs'] > 0) + a, d = close_contacts(mol1.atom_dict[mol1.atom_dict['isacceptor']], + mol2.atom_dict[donor_mask], + cutoff) + # skip empty values + if len(a) > 0 and len(d) > 0: + angle1 = angle(d['coords'][:, np.newaxis, :], + a['coords'][:, np.newaxis, :], + a['neighbors']) + angle2 = angle(a['coords'][:, np.newaxis, :], + d['coords'][:, np.newaxis, :], + d['neighbors']) + strict = (_check_angles(angle1, a['hybridization'], tolerance) & + _check_angles(angle2, d['hybridization'], tolerance)) + return a, d, angle1, angle2, strict + else: + return a, d, np.array([], dtype=bool), np.array([], dtype=bool), np.array([], dtype=bool) + +def halogenbond_acceptor_halogen(mol1, + mol2, + tolerance=30, + cutoff=4): + """Returns pairs of acceptor-halogen atoms, which meet halogen bond criteria + + Parameters + ---------- + mol1, mol2 : oddt.toolkit.Molecule object + Molecules to compute halogen bond acceptor and halogen pairs + + cutoff : float, (default=4) + Distance cutoff for A-H pairs + + tolerance : int, (default=30) + Range (+/- tolerance) from perfect direction defined by atoms hybridization + in which halogen bonds are considered as strict. + + Returns + ------- + a, h : atom_dict-type numpy array + Aligned arrays of atoms forming halogen bond, firstly acceptors, + secondly halogens + + strict : numpy array, dtype=bool + Boolean array align with atom pairs, informing whether atoms + form 'strict' halogen bond (pass all angular cutoffs). If false, + only distance cutoff is met, therefore the bond is 'crude'. + """ + a, h = close_contacts(mol1.atom_dict[mol1.atom_dict['isacceptor']], + mol2.atom_dict[mol2.atom_dict['ishalogen']], + cutoff) + # skip empty values + if len(a) > 0 and len(h) > 0: + angle1 = angle(h['coords'][:, np.newaxis, :], + a['coords'][:, np.newaxis, :], + a['neighbors']) + angle2 = angle(a['coords'][:, np.newaxis, :], + h['coords'][:, np.newaxis, :], + h['neighbors']) + strict = (_check_angles(angle1, a['hybridization'], tolerance) & + _check_angles(angle2, np.ones_like(h['hybridization']), tolerance)) + return a, h, angle1, angle2, strict + else: + return a, h, np.array([], dtype=bool), np.array([], dtype=bool), np.array([], dtype=bool) + + +def salt_bridge_plus_minus(mol1, mol2, cutoff=4, cation_exact=False, anion_exact=False): + """Returns pairs of plus-mins atoms, which meet salt bridge criteria + + Parameters + ---------- + mol1, mol2 : oddt.toolkit.Molecule object + Molecules to compute plus and minus pairs + + cutoff : float, (default=4) + Distance cutoff for A-H pairs + + cation_exact, anion_exact : bool + Requires interacting atoms to have non-zero formal charge. + + Returns + ------- + plus, minus : atom_dict-type numpy array + Aligned arrays of atoms forming salt bridge, firstly plus, secondly minus + + """ + cation_map = mol1.atom_dict['isplus'] + if cation_exact: + cation_map = cation_map & (mol1.atom_dict['formalcharge'] > 0) + anion_map = mol2.atom_dict['isminus'] + if anion_exact: + anion_map = anion_map & (mol2.atom_dict['formalcharge'] < 0) + m1_plus, m2_minus = close_contacts(mol1.atom_dict[cation_map], + mol2.atom_dict[anion_map], + cutoff) + return m1_plus, m2_minus + + +def calculate_atomic_rmsd(reference_mol, target_mol): + reference_atoms = reference_mol.GetAtoms() + target_atoms = target_mol.GetAtoms() + + if len(reference_atoms) != len(target_atoms): + raise ValueError("The number of atoms in the molecules does not match.") + + squared_sum = 0.0 + count = 0 + + for ref_atom, tgt_atom in zip(reference_atoms, target_atoms): + ref_coords = ref_atom.GetPosition() + tgt_coords = tgt_atom.GetPosition() + + squared_sum += (ref_coords.x - tgt_coords.x) ** 2 + squared_sum += (ref_coords.y - tgt_coords.y) ** 2 + squared_sum += (ref_coords.z - tgt_coords.z) ** 2 + count += 3 + + rmsd = (squared_sum / count) ** 0.5 + + return rmsd + + +####################################################################################### +##################################### Extraction ###################################### +####################################################################################### + +def hbonds_oddt(protein, ligand, fp, fl, _int=True, cutoff=settings['hbond_dist_cut'], tolerance=30, mol1_exact=False, mol2_exact=False): + """ + a1, d2 : protein as acceptor, ligand as donor + """ + a1, d2, angle1, angle2, strict = hbond_acceptor_donor(protein, ligand, cutoff, tolerance, mol2_exact) + """ + angle1 = angle(a1d2[1]['coords'][:, np.newaxis, :], + a1d2[0]['coords'][:, np.newaxis, :], + a1d2[0]['neighbors']) + angle2 = angle(a1d2[0]['coords'][:, np.newaxis, :], + a1d2[1]['coords'][:, np.newaxis, :], + a1d2[1]['neighbors']) + """ + + for i in range(len(a1)): + _dist = math.dist(a1['coords'][i], d2['coords'][i]) + a_charge, d_charge = a1['charge'][i], d2['charge'][i] + a_resname, d_resname = a1['resname'][i], d2['resname'][i] + a_atom, d_atom = a1['atomicnum'][i], d2['atomicnum'][i] + a_is_aromatic, d_is_aromatic = a1['isaromatic'][i], d2['isaromatic'][i] + a_is_acceptor, d_is_acceptor = a1['isacceptor'][i], d2['isacceptor'][i] + a_is_donor, d_is_donor = a1['isdonor'][i], d2['isdonor'][i] + a_neighbors, d_neighbors = a1['neighbors_id'][i], d2['neighbors_id'][i] + a_num_neighbors, d_num_neighbors = np.count_nonzero(a_neighbors), np.count_nonzero(d_neighbors) + + if _int == True: + if a_resname == '': + a_resname = 'LIG' + elif d_resname == '': + d_resname = 'LIG' + + fp.loc[int(a1['id'][i]), 'is_hbond'], fl.loc[int(d2['id'][i]), 'is_hbond'] = True, True + fp.loc[int(a1['id'][i]), 'hbond_partner'], fl.loc[int(d2['id'][i]), 'hbond_partner'] = int(d2['id'][i]), int(a1['id'][i]) + fp.loc[int(a1['id'][i]), 'hbond_dist'], fl.loc[int(d2['id'][i]), 'hbond_dist'] = float(_dist), float(_dist) + fp.loc[int(a1['id'][i]), 'hbond_angle'], fl.loc[int(d2['id'][i]), 'hbond_angle'] = float(angle2[i][0]), float(angle2[i][0]) + fp.loc[int(a1['id'][i]), 'hbond_charge'], fl.loc[int(d2['id'][i]), 'hbond_charge'] = float(a_charge), float(d_charge) + fp.loc[int(a1['id'][i]), 'hbond_num_neighbors'], fl.loc[int(d2['id'][i]), 'hbond_num_neighbors'] = int(a_num_neighbors), int(d_num_neighbors) + fp.loc[int(a1['id'][i]), 'hbond_atomicnum'], fl.loc[int(d2['id'][i]), 'hbond_atomicnum'] = int(a_atom), int(d_atom) + fp.loc[int(a1['id'][i]), 'hbond_resname'], fl.loc[int(d2['id'][i]), 'hbond_resname'] = str(a_resname), str(d_resname) + fp.loc[int(a1['id'][i]), 'hbond_is_aromatic'], fl.loc[int(d2['id'][i]), 'hbond_is_aromatic'] = a_is_aromatic, d_is_aromatic + fp.loc[int(a1['id'][i]), 'hbond_is_acceptor'], fl.loc[int(d2['id'][i]), 'hbond_is_acceptor'] = True, False + fp.loc[int(a1['id'][i]), 'hbond_is_donor'], fl.loc[int(d2['id'][i]), 'hbond_is_donor'] = False, True + + """ + a2, d1 : protein as donor, ligand as acceptor + """ + a2, d1, angle1, angle2, strict = hbond_acceptor_donor(ligand, protein, cutoff, tolerance, mol1_exact) + """ + angle1 = angle(a2d1[1]['coords'][:, np.newaxis, :], + a2d1[0]['coords'][:, np.newaxis, :], + a2d1[0]['neighbors']) + angle2 = angle(a2d1[0]['coords'][:, np.newaxis, :], + a2d1[1]['coords'][:, np.newaxis, :], + a2d1[1]['neighbors']) + """ + + for i in range(len(a2)): + _dist = math.dist(a2['coords'][i], d1['coords'][i]) + a_charge, d_charge = a2['charge'][i], d1['charge'][i] + a_resname, d_resname = a2['resname'][i], d1['resname'][i] + a_atom, d_atom = a2['atomicnum'][i], d1['atomicnum'][i] + a_is_aromatic, d_is_aromatic = a2['isaromatic'][i], d1['isaromatic'][i] + a_is_acceptor, d_is_acceptor = a2['isacceptor'][i], d1['isacceptor'][i] + a_is_donor, d_is_donor = a2['isdonor'][i], d1['isdonor'][i] + a_neighbors, d_neighbors = a2['neighbors_id'][i], d1['neighbors_id'][i] + a_num_neighbors, d_num_neighbors = np.count_nonzero(a_neighbors), np.count_nonzero(d_neighbors) + + if _int == True: + if a_resname == '': + a_resname = 'LIG' + elif d_resname == '': + d_resname = 'LIG' + else: + pass + + fl.loc[int(a2['id'][i]), 'is_hbond'], fp.loc[int(d1['id'][i]), 'is_hbond'] = True, True + fl.loc[int(a2['id'][i]), 'hbond_partner'], fp.loc[int(d1['id'][i]), 'hbond_partner'] = int(d1['id'][i]), int(a2['id'][i]) + fl.loc[int(a2['id'][i]), 'hbond_dist'], fp.loc[int(d1['id'][i]), 'hbond_dist'] = float(_dist), float(_dist) + fl.loc[int(a2['id'][i]), 'hbond_angle'], fp.loc[int(d1['id'][i]), 'hbond_angle'] = float(angle2[i][0]), float(angle2[i][0]) + fl.loc[int(a2['id'][i]), 'hbond_charge'], fp.loc[int(d1['id'][i]), 'hbond_charge'] = float(a_charge), float(d_charge) + fl.loc[int(a2['id'][i]), 'hbond_num_neighbors'], fp.loc[int(d1['id'][i]), 'hbond_num_neighbors'] = int(a_num_neighbors), int(d_num_neighbors) + fl.loc[int(a2['id'][i]), 'hbond_atomicnum'], fp.loc[int(d1['id'][i]), 'hbond_atomicnum'] = int(a_atom), int(d_atom) + fl.loc[int(a2['id'][i]), 'hbond_resname'], fp.loc[int(d1['id'][i]), 'hbond_resname'] = str(a_resname), str(d_resname) + fl.loc[int(a2['id'][i]), 'hbond_is_aromatic'], fp.loc[int(d1['id'][i]), 'hbond_is_aromatic'] = a_is_aromatic, d_is_aromatic + fl.loc[int(a2['id'][i]), 'hbond_is_acceptor'], fp.loc[int(d1['id'][i]), 'hbond_is_acceptor'] = True, False + fl.loc[int(a2['id'][i]), 'hbond_is_donor'], fp.loc[int(d1['id'][i]), 'hbond_is_donor'] = False, True + + return fp, fl + + +def xbonds_oddt(protein, ligand, fp, fl, _int=True, cutoff=settings['xbond_dist_cut'], tolerance=30, mol1_exact=False, mol2_exact=False): + """ + a1, h2 : protein as acceptor, ligand as halogen donor + """ + a1, h2, angle1, angle2, strict = halogenbond_acceptor_halogen(protein, ligand, cutoff, tolerance) + """ + angle1 = angle(a1h2[1]['coords'][:, np.newaxis, :], + a1h2[0]['coords'][:, np.newaxis, :], + a1h2[0]['neighbors']) + angle2 = angle(a1h2[0]['coords'][:, np.newaxis, :], + a1h2[1]['coords'][:, np.newaxis, :], + a1h2[1]['neighbors']) + """ + + for i in range(len(a1)): + _dist = math.dist(a1['coords'][i], h2['coords'][i]) + a_charge, h_charge = a1['charge'][i], h2['charge'][i] + a_resname, h_resname = a1['resname'][i], h2['resname'][i] + a_atom, h_atom = a1['atomicnum'][i], h2['atomicnum'][i] + a_is_aromatic, h_is_aromatic = a1['isaromatic'][i], h2['isaromatic'][i] + a_is_acceptor, h_is_acceptor = a1['isacceptor'][i], h2['isacceptor'][i] + a_is_donor, h_is_donor = a1['isdonor'][i], h2['isdonor'][i] + a_neighbors, h_neighbors = a1['neighbors_id'][i], h2['neighbors_id'][i] + a_num_neighbors, h_num_neighbors = np.count_nonzero(a_neighbors), np.count_nonzero(h_neighbors) + + if _int == True: + if a_resname == '': + a_resname = 'LIG' + elif h_resname == '': + h_resname = 'LIG' + else: + pass + + fp.loc[int(a1['id'][i]), 'is_xbond'], fl.loc[int(h2['id'][i]), 'is_hbond'] = True, True + fp.loc[int(a1['id'][i]), 'xbond_partner'], fl.loc[int(h2['id'][i]), 'xbond_partner'] = int(h2['id'][i]), int(a1['id'][i]) + fp.loc[int(a1['id'][i]), 'xbond_dist'], fl.loc[int(h2['id'][i]), 'xbond_dist'] = float(_dist), float(_dist) + fp.loc[int(a1['id'][i]), 'xbond_angle'], fl.loc[int(h2['id'][i]), 'xbond_angle'] = float(angle2[i][0]), float(angle2[i][0]) + fp.loc[int(a1['id'][i]), 'xbond_charge'], fl.loc[int(h2['id'][i]), 'xbond_charge'] = float(a_charge), float(h_charge) + fp.loc[int(a1['id'][i]), 'xbond_num_neighbors'], fl.loc[int(h2['id'][i]), 'xbond_num_neighbors'] = int(a_num_neighbors), int(h_num_neighbors) + fp.loc[int(a1['id'][i]), 'xbond_atomicnum'], fl.loc[int(h2['id'][i]), 'xbond_atomicnum'] = int(a_atom), int(h_atom) + fp.loc[int(a1['id'][i]), 'xbond_resname'], fl.loc[int(h2['id'][i]), 'xbond_resname'] = str(a_resname), str(h_resname) + fp.loc[int(a1['id'][i]), 'xbond_is_aromatic'], fl.loc[int(h2['id'][i]), 'xbond_is_aromatic'] = a_is_aromatic, h_is_aromatic + fp.loc[int(a1['id'][i]), 'xbond_is_acceptor'], fl.loc[int(h2['id'][i]), 'xbond_is_acceptor'] = True, False + fp.loc[int(a1['id'][i]), 'xbond_is_donor'], fl.loc[int(h2['id'][i]), 'xbond_is_donor'] = False, True + + """ + a2h1 : protein as donor, ligand as halogen acceptor + """ + a2, h1, angle1, angle2, strict = halogenbond_acceptor_halogen(ligand, protein, cutoff, tolerance) + """ + angle1 = angle(a2h1[1]['coords'][:, np.newaxis, :], + a2h1[0]['coords'][:, np.newaxis, :], + a2h1[0]['neighbors']) + angle2 = angle(a2h1[0]['coords'][:, np.newaxis, :], + a2h1[1]['coords'][:, np.newaxis, :], + a2h1[1]['neighbors']) + """ + for i in range(len(a2)): + _dist = math.dist(a2['coords'][i], h1['coords'][i]) + a_charge, h_charge = a2['charge'][i], h1['charge'][i] + a_resname, h_resname = a2['resname'][i], h1['resname'][i] + a_atom, h_atom = a2['atomicnum'][i], h1['atomicnum'][i] + a_is_aromatic, h_is_aromatic = a2['isaromatic'][i], h1['isaromatic'][i] + a_is_acceptor, h_is_acceptor = a2['isacceptor'][i], h1['isacceptor'][i] + a_is_donor, h_is_donor = a2['isdonor'][i], h1['isdonor'][i] + a_neighbors, h_neighbors = a2['neighbors_id'][i], h1['neighbors_id'][i] + a_num_neighbors, h_num_neighbors = np.count_nonzero(a_neighbors), np.count_nonzero(h_neighbors) + + if _int == True: + if a_resname == '': + a_resname = 'LIG' + elif h_resname == '': + h_resname = 'LIG' + else: + pass + + fl.loc[int(a2['id'][i]), 'is_xbond'], fp.loc[int(h1['id'][i]), 'is_xbond'] = True, True + fl.loc[int(a2['id'][i]), 'xbond_partner'], fp.loc[int(h1['id'][i]), 'xbond_partner'] = int(h1['id'][i]), int(a2['id'][i]) + fl.loc[int(a2['id'][i]), 'xbond_dist'], fp.loc[int(h1['id'][i]), 'xbond_dist'] = float(_dist), float(_dist) + fl.loc[int(a2['id'][i]), 'xbond_angle'], fp.loc[int(h1['id'][i]), 'xbond_angle'] = float(angle2[i][0]), float(angle2[i][0]) + fl.loc[int(a2['id'][i]), 'xbond_charge'], fp.loc[int(h1['id'][i]), 'xbond_charge'] = float(a_charge), float(h_charge) + fl.loc[int(a2['id'][i]), 'xbond_num_neighbors'], fp.loc[int(h1['id'][i]), 'xbond_num_neighbors'] = int(a_num_neighbors), int(h_num_neighbors) + fl.loc[int(a2['id'][i]), 'xbond_atomicnum'], fp.loc[int(h1['id'][i]), 'xbond_atomicnum'] = int(a_atom), int(h_atom) + fl.loc[int(a2['id'][i]), 'xbond_resname'], fp.loc[int(h1['id'][i]), 'xbond_resname'] = str(a_resname), str(h_resname) + fl.loc[int(a2['id'][i]), 'xbond_is_aromatic'], fp.loc[int(h1['id'][i]), 'xbond_is_aromatic'] = a_is_aromatic, h_is_aromatic + fl.loc[int(a2['id'][i]), 'xbond_is_acceptor'], fp.loc[int(h1['id'][i]), 'xbond_is_acceptor'] = True, False + fl.loc[int(a2['id'][i]), 'xbond_is_donor'], fp.loc[int(h1['id'][i]), 'xbond_is_donor'] = False, True + + return fp, fl + + +def hphob_oddt(protein, ligand, fp, fl, cutoff=settings['hphob_dist_cut'], _int=True): + h1, h2 = close_contacts(protein.atom_dict[protein.atom_dict['ishydrophobe']], + ligand.atom_dict[ligand.atom_dict['ishydrophobe']], + cutoff) + + for i in range(len(h1)): + _dist = math.dist(h1['coords'][i], h2['coords'][i]) + _charge_h1, _charge_h2 = h1['charge'][i], h2['charge'][i] + _resname_h1, _resname_h2 = h1['resname'][i], h2['resname'][i] + _atom_h1, _atom_h2 = h1['atomicnum'][i], h2['atomicnum'][i] + _neighbors_h1, _neighbors_h2 = h1['neighbors_id'][i], h2['neighbors_id'][i] + _num_neighbors_h1, _num_neighbors_h2 = np.count_nonzero(_neighbors_h1), np.count_nonzero(_neighbors_h2) + _is_aromatic_h1, _is_aromatic_h2 = h1['isaromatic'][i], h2['isaromatic'][i] + + if _int == True: + if _resname_h1 == '': + _resname_h1 = 'LIG' + elif _resname_h2 == '': + _resname_h2 = 'LIG' + + fp.loc[int(h1['id'][i]), 'is_hphob'], fl.loc[int(h2['id'][i]), 'is_hphob'] = True, True + fp.loc[int(h1['id'][i]), 'hphob_partner'], fl.loc[int(h2['id'][i]), 'hphob_partner'] = int(h1['id'][i]), int(h2['id'][i]) + fp.loc[int(h1['id'][i]), 'hphob_dist'], fl.loc[int(h2['id'][i]), 'hphob_dist'] = float(_dist), float(_dist) + fp.loc[int(h1['id'][i]), 'hphob_charge'], fl.loc[int(h2['id'][i]), 'hphob_charge'] = float(_charge_h1), float(_charge_h2) + fp.loc[int(h1['id'][i]), 'hphob_atomicnum'], fl.loc[int(h2['id'][i]), 'hphob_atomicnum'] = int(_atom_h1), int(_atom_h2) + fp.loc[int(h1['id'][i]), 'hphob_resname'], fl.loc[int(h2['id'][i]), 'hphob_resname'] = str(_resname_h1), str(_resname_h2) + fp.loc[int(h1['id'][i]), 'hphob_num_neighbors'], fl.loc[int(h2['id'][i]), 'hphob_num_neighbors'] = int(_num_neighbors_h1), int(_num_neighbors_h2) + fp.loc[int(h1['id'][i]), 'hphob_is_aromatic'], fl.loc[int(h2['id'][i]), 'hphob_is_aromatic'] = _is_aromatic_h1, _is_aromatic_h2 + + return fp, fl + + +def sbridge_oddt(protein, ligand, fp, fl, _int=True, cutoff=settings['sbridge_dist_cut'], mol1_exact=True, mol2_exact=True): + p1, l2 = salt_bridge_plus_minus(protein, ligand, cutoff) + l1, p2 = salt_bridge_plus_minus(ligand, protein, cutoff) + + """ + p1, l2: protein positive, ligand negative + """ + for i in range(len(p1)): + _dist = math.dist(p1['coords'][i], l2['coords'][i]) + c_charge, a_charge = p1['charge'][i], l2['charge'][i] + c_resname, a_resname = p1['resname'][i], l2['resname'][i] + c_atom, a_atom = p1['atomicnum'][i], l2['atomicnum'][i] + c_neighbors, a_neighbors = p1['neighbors_id'][i], l2['neighbors_id'][i] + c_num_neighbors, a_num_neighbors = np.count_nonzero(c_neighbors), np.count_nonzero(a_neighbors) + c_is_aromatic, a_is_aromatic = p1['isaromatic'][i], l2['isaromatic'][i] + + if _int == True: + if a_resname == '': + a_resname = 'LIG' + elif c_resname == '': + c_resname = 'LIG' + else: + pass + + fp.loc[int(p1['id'][i]), 'is_sbridge'], fl.loc[int(l2['id'][i]), 'is_sbridge'] = True, True + fp.loc[int(p1['id'][i]), 'sbridge_partner'], fl.loc[int(l2['id'][i]), 'sbridge_partner'] = int(l2['id'][i]), int(p1['id'][i]) + fp.loc[int(p1['id'][i]), 'sbridge_dist'], fl.loc[int(l2['id'][i]), 'sbridge_dist'] = float(_dist), float(_dist) + fp.loc[int(p1['id'][i]), 'sbridge_charge'], fl.loc[int(l2['id'][i]), 'sbridge_charge'] = float(c_charge), float(a_charge) + fp.loc[int(p1['id'][i]), 'sbridge_atomicnum'], fl.loc[int(l2['id'][i]), 'sbridge_atomicnum'] = int(c_atom), int(a_atom) + fp.loc[int(p1['id'][i]), 'sbridge_resname'], fl.loc[int(l2['id'][i]), 'sbridge_resname'] = str(c_resname), str(a_resname) + fp.loc[int(p1['id'][i]), 'sbridge_num_neighbors'], fl.loc[int(l2['id'][i]), 'sbridge_num_neighbors'] = int(c_num_neighbors), int(a_num_neighbors) + fp.loc[int(p1['id'][i]), 'sbridge_is_aromatic'], fl.loc[int(l2['id'][i]), 'sbridge_is_aromatic'] = c_is_aromatic, a_is_aromatic + fp.loc[int(p1['id'][i]), 'sbridge_is_pos'], fl.loc[int(l2['id'][i]), 'sbridge_is_neg'] = True, False + + """ + l1, p2: ligand positive, protein negative + """ + for i in range(len(l1)): + _dist = math.dist(l1['coords'][i], p2['coords'][i]) + c_charge, a_charge = l1['charge'][i], p2['charge'][i] + c_resname, a_resname = l1['resname'][i], p2['resname'][i] + c_atom, a_atom = l1['atomicnum'][i], p2['atomicnum'][i] + c_neighbors, a_neighbors = l1['neighbors_id'][i], p2['neighbors_id'][i] + c_num_neighbors, a_num_neighbors = np.count_nonzero(c_neighbors), np.count_nonzero(a_neighbors) + c_is_aromatic, a_is_aromatic = l1['isaromatic'][i], p2['isaromatic'][i] + + if _int == True: + if a_resname == '': + a_resname = 'LIG' + elif c_resname == '': + c_resname = 'LIG' + else: + pass + + fp.loc[int(p2['id'][i]), 'is_sbridge'], fl.loc[int(l1['id'][i]), 'is_sbridge'] = True, True + fp.loc[int(p2['id'][i]), 'sbridge_partner'], fl.loc[int(l1['id'][i]), 'sbridge_partner'] = int(l1['id'][i]), int(p2['id'][i]) + fp.loc[int(p2['id'][i]), 'sbridge_dist'], fl.loc[int(l1['id'][i]), 'sbridge_dist'] = float(_dist), float(_dist) + fp.loc[int(p2['id'][i]), 'sbridge_charge'], fl.loc[int(l1['id'][i]), 'sbridge_charge'] = float(a_charge), float(c_charge) + fp.loc[int(p2['id'][i]), 'sbridge_atomicnum'], fl.loc[int(l1['id'][i]), 'sbridge_atomicnum'] = int(a_atom), int(c_atom) + fp.loc[int(p2['id'][i]), 'sbridge_resname'], fl.loc[int(l1['id'][i]), 'sbridge_resname'] = str(a_resname), str(c_resname) + fp.loc[int(p2['id'][i]), 'sbridge_num_neighbors'], fl.loc[int(l1['id'][i]), 'sbridge_num_neighbors'] = int(a_num_neighbors), int(c_num_neighbors) + fp.loc[int(p2['id'][i]), 'sbridge_is_aromatic'], fl.loc[int(l1['id'][i]), 'sbridge_is_aromatic'] = a_is_aromatic, c_is_aromatic + fp.loc[int(p2['id'][i]), 'sbridge_is_pos'], fl.loc[int(l1['id'][i]), 'sbridge_is_neg'] = False, True + + return fp, fl + + +def pistack_oddt(protein, ligand, fp, fl, _int=True, cutoff=settings['pistack_dist_cut'], tolerance=30): + r1, r2 = close_contacts(protein.ring_dict, ligand.ring_dict, cutoff, x_column='centroid', y_column='centroid') + + angle1 = angle_2v(r1['vector'], r2['vector']) + angle2 = angle(r1['vector'] + r1['centroid'], + r1['centroid'], + r2['centroid']) + angle3 = angle(r2['vector'] + r2['centroid'], + r2['centroid'], + r1['centroid']) + + for i in range(len(r1)): + _dist = math.dist(r1['centroid'][i], r2['centroid'][i]) + _resname_r1, _resname_r2 = r1['resname'][i], r2['resname'][i] + _resnum_r1, _resnum_r2 = r1['resnum'][i], r2['resnum'][i] + + if _int == True: + if _resname_r1 == '': + _resname_r1 = 'LIG' + elif _resname_r2 == '': + _resname_r2 = 'LIG' + + _atoms_array_r1 = np.where(protein.atom_dict['resnum'] == _resnum_r1)[0] + _atoms_array_r2 = np.where(ligand.atom_dict['resnum'] == _resnum_r2)[0] + + for j in range(len(_atoms_array_r1)): + idx = int(_atoms_array_r1[j]) + + for k in range(len(_atoms_array_r2)): + idy = int(_atoms_array_r2[k]) + + fp.loc[idx, 'is_pistack'], fl.loc[idy, 'is_pistack'] = True, True + fp.loc[idx, 'pistack_partner'], fl.loc[idy, 'pistack_partner'] = idy, idx + fp.loc[idx, 'pistack_dist'], fl.loc[idy, 'pistack_dist'] = float(_dist), float(_dist) + fp.loc[idx, 'pistack_angle'], fl.loc[idy, 'pistack_angle'] = float(angle1[i]), float(angle1[i]) + fp.loc[idx, 'pistack_resname'], fl.loc[idy, 'pistack_resname'] = str(_resname_r1), str(_resname_r2) + fp.loc[idx, 'pistack_atomicnum'], fl.loc[idy, 'pistack_atomicnum'] = int(protein.atom_dict[idx]['atomicnum']), int(ligand.atom_dict[idy]['atomicnum']) + fp.loc[idx, 'pistack_num_neighbors'], fl.loc[idy, 'pistack_num_neighbors'] = int(np.count_nonzero(protein.atom_dict[idx]['neighbors_id'])), int(np.count_nonzero(ligand.atom_dict[idy]['neighbors_id'])) + + return fp, fl + + +def pication_oddt(protein, ligand, fp, fl, _int=True, cutoff=settings['pication_dist_cut'], tolerance=30, cation_exact=False): + cation_map = ligand.atom_dict['isplus'] + r1, plus2 = close_contacts(protein.ring_dict, ligand.atom_dict[cation_map], cutoff, x_column='centroid') + angle1 = angle_2v(r1['vector'], plus2['coords'] - r1['centroid']) + + for i in range(len(r1)): + _dist = math.dist(r1['centroid'][i], plus2['coords'][i]) + _resname_r1, _resname_plus2 = r1['resname'][i], plus2['resname'][i] + _resnum_r1, _resnum_plus2 = r1['resnum'][i], plus2['resnum'][i] + _atom_plus2 = plus2['atomicnum'][i] + _neighbors_plus2 = plus2['neighbors_id'][i] + _num_neighbors_plus2 = np.count_nonzero(_neighbors_plus2) + + if _int == True: + if _resname_r1 == '': + _resname_r1 = 'LIG' + elif _resname_plus2 == '': + _resname_plus2 = 'LIG' + + + _atoms_array = np.where(protein.atom_dict['resnum'] == _resnum_r1)[0] + for j in range(len(_atoms_array)): + idx = int(_atoms_array[j]) + + fp.loc[idx, 'is_picat'], fl.loc[int(plus2['id'][i]), 'is_picat'] = True, True + fp.loc[idx, 'picat_partner'], fl.loc[int(plus2['id'][i]), 'picat_partner'] = int(plus2['id'][i]), idx + fp.loc[idx, 'picat_dist'], fl.loc[int(plus2['id'][i]), 'picat_dist'] = float(_dist), float(_dist) + fp.loc[idx, 'picat_angle'], fl.loc[int(plus2['id'][i]), 'picat_angle'] = float(angle1[i]), float(angle1[i]) + fp.loc[idx, 'picat_resname'], fl.loc[int(plus2['id'][i]), 'picat_resname'] = str(_resname_r1), str(_resname_plus2) + fp.loc[idx, 'picat_atomicnum'], fl.loc[int(plus2['id'][i]), 'picat_atomicnum'] = int(protein.atom_dict[idx]['atomicnum']), int(_atom_plus2) + fp.loc[idx, 'picat_num_neighbors'], fl.loc[int(plus2['id'][i]), 'picat_num_neighbors'] = int(np.count_nonzero(protein.atom_dict[idx]['neighbors_id'])), int(_num_neighbors_plus2) + fp.loc[idx, 'picat_is_ring'], fl.loc[int(plus2['id'][i]), 'picat_is_ring'] = True, False + fp.loc[idx, 'picat_is_cat'], fl.loc[int(plus2['id'][i]), 'picat_is_cat'] = False, True + + cation_map = protein.atom_dict['isplus'] + r1, plus2 = close_contacts(ligand.ring_dict, protein.atom_dict[cation_map], cutoff, x_column='centroid') + angle1 = angle_2v(r1['vector'], plus2['coords'] - r1['centroid']) + + for i in range(len(r1)): + _dist = math.dist(r1['centroid'][i], plus2['coords'][i]) + _resname_r1, _resname_plus2 = r1['resname'][i], plus2['resname'][i] + _resnum_r1, _resnum_plus2 = r1['resnum'][i], plus2['resnum'][i] + _atom_plus2 = plus2['atomicnum'][i] + _neighbors_plus2 = plus2['neighbors_id'][i] + _num_neighbors_plus2 = np.count_nonzero(_neighbors_plus2) + + if _int == True: + if _resname_r1 == '': + _resname_r1 = 'LIG' + elif _resname_plus2 == '': + _resname_plus2 = 'LIG' + else: + pass + + _atoms_array = np.where(ligand.atom_dict['resnum'] == _resnum_r1)[0] + for j in range(len(_atoms_array)): + idx = int(_atoms_array[j]) + + fl.loc[idx, 'is_picat'], fp.loc[int(plus2['id'][i]), 'is_picat'] = True, True + fl.loc[idx, 'picat_partner'], fp.loc[int(plus2['id'][i]), 'picat_partner'] = int(plus2['id'][i]), idx + fl.loc[idx, 'picat_dist'], fp.loc[int(plus2['id'][i]), 'picat_dist'] = float(_dist), float(_dist) + fl.loc[idx, 'picat_angle'], fp.loc[int(plus2['id'][i]), 'picat_angle'] = float(angle1[i]), float(angle1[i]) + fl.loc[idx, 'picat_resname'], fp.loc[int(plus2['id'][i]), 'picat_resname'] = str(_resname_r1), str(_resname_plus2) + fl.loc[idx, 'picat_atomicnum'], fp.loc[int(plus2['id'][i]), 'picat_atomicnum'] = int(ligand.atom_dict[idx]['atomicnum']), int(_atom_plus2) + fl.loc[idx, 'picat_num_neighbors'], fp.loc[int(plus2['id'][i]), 'picat_num_neighbors'] = int(np.count_nonzero(ligand.atom_dict[idx]['neighbors_id'])), int(_num_neighbors_plus2) + fl.loc[idx, 'picat_is_ring'], fp.loc[int(plus2['id'][i]), 'picat_is_ring'] = True, False + fl.loc[idx, 'picat_is_cat'], fp.loc[int(plus2['id'][i]), 'picat_is_cat'] = False, True + + return fp, fl + + + +def acceptor_metal_oddt(mol1, mol2, fp, fl, _int=True, cutoff=settings['acceptor_metal_dist_cut'], tolerance=30): + """Returns pairs of acceptor-metal atoms, which meet metal coordination criteria + Note: This function is directional (mol1 holds acceptors, mol2 holds metals) + + Parameters + ---------- + mol1, mol2 : oddt.toolkit.Molecule object + Molecules to compute acceptor and metal pairs + + cutoff : float, (default=4) + Distance cutoff for A-M pairs + + tolerance : int, (default=30) + Range (+/- tolerance) from perfect direction defined by atoms hybridization + in metal coordination are considered as strict. + + Returns + ------- + a, d : atom_dict-type numpy array + Aligned arrays of atoms forming metal coordination, + firstly acceptors, secondly metals. + + strict : numpy array, dtype=bool + Boolean array align with atom pairs, informing whether atoms + form 'strict' metal coordination (pass all angular cutoffs). + If false, only distance cutoff is met, therefore the interaction + is 'crude'. + """ + a, m = close_contacts(mol1.atom_dict[mol1.atom_dict['isacceptor']], + mol2.atom_dict[mol2.atom_dict['ismetal']], + cutoff) + # skip empty values + if len(a) > 0 and len(m) > 0: + angle1 = angle(m['coords'][:, np.newaxis, :], + a['coords'][:, np.newaxis, :], + a['neighbors']) + else: + return fp, fl + + if _int == True: + for i in range(len(a)): + _dist = math.dist(a['coords'][i], m['coords'][i]) + _charge_a, _charge_m= a['charge'][i], m['charge'][i] + _resname_a, _resname_m = a['resname'][i], m['resname'][i] + _atom_a, _atom_m = a['atomicnum'][i], m['atomicnum'][i] + _neighbors_a, _neighbors_m = a['neighbors_id'][i], m['neighbors_id'][i] + _num_neighbors_a, _num_neighbors_m = np.count_nonzero(_neighbors_a), np.count_nonzero(_neighbors_m) + _is_aromatic_a, _is_aromatic_m = a['isaromatic'][i], m['isaromatic'][i] + + + fp.loc[int(a['id'][i]), 'is_acmetal'], fl.loc[int(m['id'][i]), 'is_acmetal'] = True, True + fp.loc[int(a['id'][i]), 'acmetal_partner'], fl.loc[int(m['id'][i]), 'acmetal_partner'] = int(m['id'][i]), int(a['id'][i]) + fp.loc[int(a['id'][i]), 'acmetal_dist'], fl.loc[int(m['id'][i]), 'acmetal_dist'] = float(_dist), float(_dist) + fp.loc[int(a['id'][i]), 'acmetal_angle'], fl.loc[int(m['id'][i]), 'acmetal_angle'] = float(angle1[i][0]), float(angle1[i][0]) + fp.loc[int(a['id'][i]), 'acmetal_charge'], fl.loc[int(m['id'][i]), 'acmetal_charge'] = float(_charge_a), float(_charge_m) + fp.loc[int(a['id'][i]), 'acmetal_atomicnum'], fl.loc[int(m['id'][i]), 'acmetal_atomicnum'] = int(_atom_a), int(_atom_m) + fp.loc[int(a['id'][i]), 'acmetal_resname'], fl.loc[int(m['id'][i]), 'acmetal_resname'] = str(_resname_a), 'METAL' + fp.loc[int(a['id'][i]), 'acmetal_num_neighbors'], fl.loc[int(m['id'][i]), 'acmetal_num_neighbors'] = int(_num_neighbors_a), 0 + fp.loc[int(a['id'][i]), 'acmetal_is_aromatic'], fl.loc[int(m['id'][i]), 'acmetal_is_aromatic'] = int(_is_aromatic_a), int(_is_aromatic_m) + + return fp, fl + + + + +def pimetal_oddt(mol1, mol2, fp, fl, _int=True, cutoff=settings['pimetal_dist_cut'], tolerance=30): + """Returns pairs of ring-metal atoms, which meet pi-metal criteria + + Parameters + ---------- + mol1, mol2 : oddt.toolkit.Molecule object + Molecules to compute ring-metal pairs + + cutoff : float, (default=5) + Distance cutoff for Pi-metal pairs + + tolerance : int, (default=30) + Range (+/- tolerance) from perfect direction (perpendicular) + in which pi-metal are considered as strict. + + Returns + ------- + r1 : ring_dict-type numpy array + Aligned rings forming pi-metal + + m : atom_dict-type numpy array + Aligned metals forming pi-metal + + strict_parallel : numpy array, dtype=bool + Boolean array align with ring-metal pairs, informing whether + they form 'strict' pi-metal. If false, only distance cutoff is met, + therefore the interaction is 'crude'. + + """ + r1, m = close_contacts(mol1.ring_dict, + mol2.atom_dict[mol2.atom_dict['ismetal']], + cutoff, + x_column='centroid') + + if len(r1) > 0 and len(m) > 0: + angle1 = angle_2v(r1['vector'], m['coords'] - r1['centroid']) + strict = (angle1 > 180 - tolerance) | (angle1 < tolerance) + else: + return fp, fl + + + if _int == True: + for i in range(len(r1)): + _dist = math.dist(r1['coords'][i], m['coords'][i]) + _charge_m = m['charge'][i] + _resname_r1, _resname_m = r1['resname'][i], m['resname'][i] + _atom_m = m['atomicnum'][i] + + _resnum_r1 = int(r1['resnum'][i]) + if _resname_r1 == '': + _atoms_array = np.where(mol2.atom_dict['resnum'] == _resnum_r1)[0] + else: + _atoms_array = np.where(mol1.atom_dict['resnum'] == _resnum_r1)[0] + + + for j in range(len(_atoms_array)): + idx = int(_atoms_array[j]) + + fp.loc[idx, 'is_pimetal'], fl.loc[m['id'][i], 'is_pimetal'] = True, True + fp.loc[idx, 'pimetal_partner'], fl.loc[m['id'][i], 'pimetal_partner'] = int(m['id'][i]), idx + fp.loc[idx, 'pimetal_dist'], fl.loc[m['id'][i], 'pimetal_dist'] = float(_dist), float(_dist) + fp.loc[idx, 'pimetal_angle'], fl.loc[m['id'][i], 'pimetal_angle'] = float(angle1[i][0]), float(angle1[i][0]) + fp.loc[idx, 'pimetal_charge'], fl.loc[m['id'][i], 'pimetal_charge'] = float(mol1.atom_dict[idx]['charge']), float(_charge_m) + fp.loc[idx, 'pimetal_atomicnum'], fl.loc[m['id'][i], 'pimetal_atomicnum'] = int(mol1.atom_dict[idx]['atomicnum']), int(_atom_m) + fp.loc[idx, 'pimetal_resname'], fl.loc[m['id'][i], 'pimetal_resname'] = str(_resname_r1), 'METAL' + + return fp, fl + + + +####################################################################################### +####################################### Parsing ####################################### +####################################################################################### + +def fingerprint(protein, ligand, _int=True, settings=settings): + """ + Parameters + ---------- + protein, ligand : list, with len(protein) == len(ligand) == 2 + First entry is the Molecule class object based on RDKit. + Second entry is the oddt.toolkit.Molecule object used exclusively to + compute pi_stacking only using ODDT library. + + Returns + ------- + fp : pandas DataFrame, shape = [n rows x 18 columns] + A table which contains all the computed data, e.g., distance, angles, etc. + """ + + max_len, lig_len = len(protein.atom_dict), len(ligand.atom_dict) + + # construct an empty DataFrame for ligand + fl = pd.DataFrame( + columns=["is_hbond", "hbond_partner", "hbond_dist", "hbond_angle", "hbond_charge", "hbond_atomicnum", "hbond_resname", "hbond_num_neighbors", "hbond_is_aromatic", "hbond_is_acceptor", "hbond_is_donor", + "is_xbond", "xbond_partner", "xbond_dist", "xbond_angle", "xbond_charge", "xbond_atomicnum", "xbond_resname", "xbond_num_neighbors", "xbond_is_aromatic", "xbond_is_acceptor", "xbond_is_donor", + "is_hphob", "hphob_partner", "hphob_dist", "hphob_charge", "hphob_atomicnum", "hphob_resname", "hphob_num_neighbors", "hphob_is_aromatic", + "is_sbridge", "sbridge_partner", "sbridge_dist", "sbridge_charge", "sbridge_atomicnum", "sbridge_resname", "sbridge_num_neighbors", "sbridge_is_aromatic", "sbridge_is_pos", "sbridge_is_neg", + "is_pistack", "pistack_partner", "pistack_dist", "pistack_angle", "pistack_resname", "pistack_atomicnum", "pistack_num_neighbors", + "is_picat", "picat_partner", "picat_dist", "picat_angle", "picat_resname", "picat_num_neighbors", "picat_atomicnum", "picat_is_ring", "picat_is_cat", + "is_acmetal", "acmetal_partner", "acmetal_dist", "acmetal_angle", "acmetal_charge", "acmetal_atomicnum", "acmetal_resname", "acmetal_num_neighbors", "acmetal_is_aromatic", + "is_pimetal", "pimetal_partner", "pimetal_dist", "pimetal_angle", "pimetal_charge", "pimetal_atomicnum", "pimetal_resname"], index=range(lig_len)) + fl.fillna(0) + + # construct an empty DataFrame for protein + fp = pd.DataFrame( + columns=["is_hbond", "hbond_partner", "hbond_dist", "hbond_angle", "hbond_charge", "hbond_atomicnum", "hbond_resname", "hbond_num_neighbors", "hbond_is_aromatic", "hbond_is_acceptor", "hbond_is_donor", + "is_xbond", "xbond_partner", "xbond_dist", "xbond_angle", "xbond_charge", "xbond_atomicnum", "xbond_resname", "xbond_num_neighbors", "xbond_is_aromatic", "xbond_is_acceptor", "xbond_is_donor", + "is_hphob", "hphob_partner", "hphob_dist", "hphob_charge", "hphob_atomicnum", "hphob_resname", "hphob_num_neighbors", "hphob_is_aromatic", + "is_sbridge", "sbridge_partner", "sbridge_dist", "sbridge_charge", "sbridge_atomicnum", "sbridge_resname", "sbridge_num_neighbors", "sbridge_is_aromatic", "sbridge_is_pos", "sbridge_is_neg", + "is_pistack", "pistack_partner", "pistack_dist", "pistack_angle", "pistack_resname", "pistack_atomicnum", "pistack_num_neighbors", + "is_picat", "picat_partner", "picat_dist", "picat_angle", "picat_resname", "picat_num_neighbors", "picat_atomicnum", "picat_is_ring", "picat_is_cat", + "is_acmetal", "acmetal_partner", "acmetal_dist", "acmetal_angle", "acmetal_charge", "acmetal_atomicnum", "acmetal_resname", "acmetal_num_neighbors", "acmetal_is_aromatic", + "is_pimetal", "pimetal_partner", "pimetal_dist", "pimetal_angle", "pimetal_charge", "pimetal_atomicnum", "pimetal_resname"], index=range(max_len)) + fp.fillna(0) + + fp, fl = hbonds_oddt(protein, ligand, fp, fl, cutoff=settings['hbond_dist_cut'], _int=True) + fp, fl = hphob_oddt(protein, ligand, fp, fl, cutoff=settings['hphob_dist_cut'], _int=True) + fp, fl = sbridge_oddt(protein, ligand, fp, fl, cutoff=settings['sbridge_dist_cut'], _int=True) + fp, fl = pistack_oddt(protein, ligand, fp, fl, cutoff=settings['pistack_dist_cut'], _int=True) + fp, fl = pication_oddt(protein, ligand, fp, fl, cutoff=settings['pication_dist_cut'], _int=True) + fp, fl = xbonds_oddt(protein, ligand, fp, fl, cutoff=settings['xbond_dist_cut'], _int=True) + fp, fl = acceptor_metal_oddt(protein, ligand, fp, fl, cutoff=settings['acceptor_metal_dist_cut'], _int=True) + fp, fl = pimetal_oddt(protein, ligand, fp, fl, cutoff=settings['pimetal_dist_cut'], _int=True) + + return fp.dropna(axis=0, how="all"), fl.dropna(axis=0, how="all") + + + diff --git a/utils/.ipynb_checkpoints/MakeGraph-checkpoint.ipynb b/utils/.ipynb_checkpoints/MakeGraph-checkpoint.ipynb new file mode 100644 index 0000000..c753002 --- /dev/null +++ b/utils/.ipynb_checkpoints/MakeGraph-checkpoint.ipynb @@ -0,0 +1,1769 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "b516f7bb-9194-4c0b-bcd7-3d0dec646b9a", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/yuyang/anaconda3/envs/SINGA/lib/python3.10/site-packages/torch/cuda/__init__.py:126: UserWarning: CUDA initialization: Unexpected error from cudaGetDeviceCount(). Did you run some cuda functions before calling NumCudaDevices() that might have already set an error? Error 804: forward compatibility was attempted on non supported HW (Triggered internally at /opt/conda/conda-bld/pytorch_1689059489744/work/c10/cuda/CUDAFunctions.cpp:108.)\n", + " return torch._C._cuda_getDeviceCount() > 0\n", + "2023-07-25 06:05:26.255179: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.\n", + "To enable the following instructions: AVX2 AVX512F FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.\n", + "2023-07-25 06:05:29.346444: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT\n" + ] + } + ], + "source": [ + "import torch\n", + "import torch_geometric\n", + "from torch_geometric.data import Data, HeteroData\n", + "from torch_geometric.utils import erdos_renyi_graph, to_networkx, from_networkx\n", + "import networkx as nx\n", + "\n", + "from rdkit import Chem\n", + "from rdkit.Chem import AllChem\n", + "\n", + "import numpy as np\n", + "import pandas as pd\n", + "import matplotlib.pyplot as plt\n", + "\n", + "from keras.layers import Input, Dense\n", + "from keras.regularizers import l2\n", + "from keras.models import Model\n", + "from keras.optimizers import Adam\n", + "from keras.callbacks import EarlyStopping\n", + "\n", + "from sklearn.model_selection import train_test_split\n", + "from sklearn.metrics import confusion_matrix\n", + "\n", + "from spektral.layers import GATConv, GlobalAttentionPool\n", + "from spektral.utils import label_to_one_hot, load_sdf\n", + "#from spektral.utils import nx_to_numpy\n", + "#from spektral.chem import sdf_to_nx" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "76817739-9d47-4a4a-96f1-1f9aedf5c6c6", + "metadata": {}, + "outputs": [], + "source": [ + "import logging\n", + "from sklearn.base import BaseEstimator, TransformerMixin\n", + "logger = logging.getLogger(__name__)\n", + "\n", + "class MoleculeToGraph(BaseEstimator, TransformerMixin):\n", + " def __init__(self, file_format='sdf'):\n", + " \"\"\"Constructor.\n", + "\n", + " valid 'file_format' strings and what the transformer will expect\n", + "\n", + " smi: path to .smi file\n", + " sdf: pat to .sdf file\n", + " \"\"\"\n", + " self.file_format = file_format\n", + "\n", + " def transform(self, data):\n", + " \"\"\"Transform.\"\"\"\n", + " try:\n", + " if self.file_format == 'smi':\n", + " graphs = smi_to_nx(data)\n", + " elif self.file_format == 'sdf':\n", + " graphs = sdf_to_nx(data)\n", + " else:\n", + " raise Exception('file_format must be smi or sdf')\n", + " for graph in graphs:\n", + " yield graph\n", + "\n", + " except Exception as e:\n", + " logger.debug('Failed iteration. Reason: %s' % e)\n", + " logger.debug('Exception', exc_info=True)\n", + "\n", + "\n", + "################\n", + "# import to networkx graphs\n", + "###############\n", + "def load_sdf(file):\n", + " suppl = Chem.SDMolSupplier(file)\n", + " for mol in suppl:\n", + " if mol:\n", + " yield mol\n", + "\n", + "def load_smi(file):\n", + " suppl = Chem.SmilesMolSupplier(file)\n", + " for mol in suppl:\n", + " if mol:\n", + " yield mol\n", + "\n", + "def sdf_to_nx(file):\n", + " # read sdf file\n", + " suppl = load_sdf(file)\n", + " for mol in suppl:\n", + " yield rdkmol_to_nx(mol)\n", + "\n", + "def smi_to_nx(file):\n", + " # read smi file\n", + " suppl = load_smi(file)\n", + " for mol in suppl:\n", + " yield rdkmol_to_nx(mol)\n", + "\n", + "def rdkmol_to_nx(mol):\n", + " # rdkit-mol object to nx.graph\n", + " graph = nx.Graph()\n", + " for e in mol.GetAtoms():\n", + " graph.add_node(e.GetIdx(), label=e.GetSymbol())\n", + " for b in mol.GetBonds():\n", + " graph.add_edge(b.GetBeginAtomIdx(), b.GetEndAtomIdx(), label=str(int(b.GetBondTypeAsDouble())))\n", + " return graph\n", + "\n", + "def smiles_strings_to_nx(smileslist):\n", + " # smiles strings\n", + " for smile in smileslist:\n", + " mol = Chem.MolFromSmiles(smile)\n", + " yield rdkmol_to_nx(mol)\n", + "\n", + "################\n", + "# exporting networkx graphs\n", + "###############\n", + "\n", + "def nx_to_smi(graphs, file):\n", + " # writes smiles strings to a file\n", + " chem = [nx_to_rdkit(graph) for graph in graphs]\n", + " smis = [Chem.MolToSmiles(m) for m in chem]\n", + " with open(file, 'w') as f:\n", + " f.write(\"SMILES\\n\")\n", + " f.write('\\n'.join(smis))\n", + "\n", + "def nx_to_rdkit(graph):\n", + " m = Chem.MolFromSmiles('')\n", + " mw = Chem.RWMol(m)\n", + " atom_index = {}\n", + " for n, d in graph.nodes(data=True):\n", + " atom_index[n] = mw.AddAtom(Chem.Atom(d['label']))\n", + " for a, b, d in graph.edges(data=True):\n", + " start = atom_index[a]\n", + " end = atom_index[b]\n", + " bond_type = d.get(\"label\", '1')\n", + " if bond_type == '1':\n", + " mw.AddBond(start, end, Chem.BondType.SINGLE)\n", + " elif bond_type == '2':\n", + " mw.AddBond(start, end, Chem.BondType.DOUBLE)\n", + " elif bond_type == '3':\n", + " mw.AddBond(start, end, Chem.BondType.TRIPLE)\n", + " # more options:\n", + " # http://www.rdkit.org/Python_Docs/rdkit.Chem.rdchem.BondType-class.html\n", + " else:\n", + " raise Exception('bond type not implemented')\n", + "\n", + " mol = mw.GetMol()\n", + " return mol" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "bf4a9dc4-676e-4b5a-90ae-560e7627332f", + "metadata": {}, + "outputs": [], + "source": [ + "def get_graph_info(mol):\n", + " # Extract atom features and coordinates\n", + " atom_features = []\n", + " coordinates = []\n", + " beginIdx, endIdx = [], []\n", + "\n", + " for i in range(len(mol.GetBonds())):\n", + " beginAtomIdx = mol.GetBondWithIdx(i).GetBeginAtomIdx()\n", + " endAtomIdx = mol.GetBondWithIdx(i).GetEndAtomIdx()\n", + " beginIdx.append(beginAtomIdx)\n", + " endIdx.append(endAtomIdx)\n", + " \n", + " bond_index = np.array([beginIdx, endIdx])\n", + " bond_index = torch.LongTensor(bond_index)\n", + "\n", + " for atom in mol.GetAtoms():\n", + " atom_features.append(atom.GetAtomicNum())\n", + " coordinates.append(list(mol.GetConformer().GetAtomPosition(atom.GetIdx())))\n", + "\n", + " # Create edge index tensor (fully connected graph)\n", + " num_atoms = len(atom_features)\n", + " edge_index = torch.tensor([(i, j) for i in range(num_atoms) for j in range(num_atoms) if i != j], dtype=torch.long).t().contiguous()\n", + " \n", + " # Convert atom features and coordinates to tensors\n", + " x = torch.tensor(atom_features, dtype=torch.float).view(-1, 1)\n", + " pos = torch.tensor(coordinates, dtype=torch.float)\n", + "\n", + " return x, pos, edge_index, bond_index" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "e92b10cc-e968-4579-a8e4-8c5d4f35bc95", + "metadata": {}, + "outputs": [], + "source": [ + "def pdb_to_graph(pdb_ligand_file, pdb_protein_file):\n", + " # Read PDB files\n", + " mol_ligand = Chem.MolFromPDBFile(pdb_ligand_file, removeHs = False, sanitize = False)\n", + " mol_protein = Chem.MolFromPDBFile(pdb_protein_file, removeHs = False, sanitize = False)\n", + "\n", + " # Generate 3D coordinates\n", + " mol_ligand, mol_protein = Chem.AddHs(mol_ligand), Chem.AddHs(mol_protein)\n", + " AllChem.EmbedMolecule(mol_ligand)\n", + " AllChem.EmbedMolecule(mol_protein)\n", + "\n", + " x, pos, edge_index, bond_index = get_graph_info(mol_ligand)\n", + "\n", + " # Create the Data object\n", + " #data = Data(x=x, pos=pos, edge_index=bond_index)\n", + " data = HeteroData()\n", + " data['ligand'].x = x\n", + " data['ligand'].pos = pos\n", + " #data['ligand'].edge_index = bond_index\n", + " data['ligand', 'conc_l', 'ligand'].edge_index = bond_index\n", + "\n", + " x, pos, edge_index, bond_index = get_graph_info(mol_protein)\n", + " data['protein'].x = x\n", + " data['protein'].pos = pos\n", + " #data['protein'].edge_index = bond_index\n", + " data['protein', 'conc_p', 'protein'].edge_index = bond_index\n", + "\n", + " return data" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "fb89aecf-2a89-47e8-bf1b-f391904c50a4", + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "[06:54:10] UFFTYPER: Warning: hybridization set to SP3 for atom 0\n", + "[06:54:10] UFFTYPER: Warning: hybridization set to SP3 for atom 23\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "HeteroData(\n", + " \u001b[1mligand\u001b[0m={\n", + " x=[54, 1],\n", + " pos=[54, 3]\n", + " },\n", + " \u001b[1mprotein\u001b[0m={\n", + " x=[678, 1],\n", + " pos=[678, 3]\n", + " },\n", + " \u001b[1m(ligand, conc_l, ligand)\u001b[0m={ edge_index=[2, 56] },\n", + " \u001b[1m(protein, conc_p, protein)\u001b[0m={ edge_index=[2, 663] }\n", + ")\n" + ] + } + ], + "source": [ + "# Specify the path to the PDB file\n", + "pdb_ligand_file_path = '../../download/v2020-other-PL/9icd/9icd_ligand_dock001.pdb'\n", + "pdb_protein_file_path = '../../download/v2020-other-PL/9icd/9icd_pocket.pdb'\n", + "\n", + "# Convert PDB to graph data\n", + "graph_data = pdb_to_graph(pdb_ligand_file_path, pdb_protein_file_path)\n", + "\n", + "# Print the graph data\n", + "print(graph_data)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "0f5dd701-c091-4b68-9603-fcb41d579fab", + "metadata": {}, + "outputs": [], + "source": [ + "# a = to_networkx(graph_data, to_undirected=True)\n", + "# nx.draw(a)" + ] + }, + { + "cell_type": "markdown", + "id": "b597454b-2994-4787-8175-8c50b7a4d05f", + "metadata": {}, + "source": [ + "## Another approach" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "a94e4c79-9651-4614-be86-b3ae6a193006", + "metadata": {}, + "outputs": [], + "source": [ + "def nx_to_numpy(graph):\n", + " # Get the adjacency matrix from the NetworkX graph\n", + " adj_matrix = nx.adjacency_matrix(graph)\n", + "\n", + " # Convert the adjacency matrix to a dense NumPy array\n", + " adj_array = adj_matrix.toarray()\n", + "\n", + " # Get the node labels from the NetworkX graph\n", + " node_labels = np.array(list(nx.get_node_attributes(graph, 'label').values()))\n", + "\n", + " return adj_array, node_labels" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "b987ef9e-eec0-4c17-b433-8f4cef99d7f2", + "metadata": {}, + "outputs": [], + "source": [ + "sdf_loaded = Chem.SDMolSupplier(\"Trainingset_Delaunay-CHNO5000selected.sdf\", removeHs=False, sanitize=False)\n", + "#sdf_loaded = load_sdf('Trainingset_Delaunay-CHNO5000selected.sdf')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "d6b2031f-e4fd-41bf-a05a-21147669806e", + "metadata": {}, + "outputs": [], + "source": [ + "sdf_nx = rdkmol_to_nx(sdf_loaded[0])\n", + "sdf_adj, sdf_node = nx_to_numpy(sdf_nx)\n", + "\n", + "uniq_node = np.unique([v for x in sdf_node for v in np.unique(x)])\n", + "node = [label_to_one_hot(x, uniq_node) for x in sdf_node]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "0204b306-5b94-4232-abe6-01e806297ca5", + "metadata": {}, + "outputs": [], + "source": [ + "uniq_node" + ] + }, + { + "cell_type": "markdown", + "id": "6fb0918e-03e9-4055-93bf-7c13a5fff35d", + "metadata": {}, + "source": [ + "## Analyse protein-ligand (non-contact) interactions" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "id": "ad508204-9a86-4745-9697-9685c53589c0", + "metadata": {}, + "outputs": [], + "source": [ + "from pathlib import Path\n", + "import time\n", + "import warnings\n", + "warnings.filterwarnings(\"ignore\")\n", + "\n", + "import nglview as nv\n", + "import openbabel\n", + "from matplotlib import colors\n", + "from plip.structure.preparation import PDBComplex\n", + "from plip.exchange.report import BindingSiteReport\n", + "from opencadd.structure.core import Structure" + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "id": "02a92029-db9b-439f-8773-e3a43a666962", + "metadata": {}, + "outputs": [], + "source": [ + "import parmed as pmd\n", + "\n", + "pdb_id = '11gs'\n", + "pdb1 = pmd.load_file(f'../../download/v2020-other-PL/{pdb_id}/{pdb_id}_protein.pdb')\n", + "pdb2 = pmd.load_file(f'../../download/v2020-other-PL/{pdb_id}/{pdb_id}_ligand_dock001.pdb')\n", + "\n", + "combined = pdb1 + pdb2\n", + "combined.save(f'{pdb_id}.pdb')" + ] + }, + { + "cell_type": "code", + "execution_count": 30, + "id": "bfc3aa02-9d2e-48e4-bf8f-fb7bb7b74a6a", + "metadata": {}, + "outputs": [], + "source": [ + "def retrieve_plip_interactions(pdb_file):\n", + " \"\"\"\n", + " Retrieves the interactions from PLIP.\n", + "\n", + " Parameters\n", + " ----------\n", + " pdb_file :\n", + " The PDB file of the complex.\n", + "\n", + " Returns\n", + " -------\n", + " dict :\n", + " A dictionary of the binding sites and the interactions.\n", + " \"\"\"\n", + " protlig = PDBComplex()\n", + " protlig.load_pdb(pdb_file) # load the pdb file\n", + " for ligand in protlig.ligands:\n", + " protlig.characterize_complex(ligand) # find ligands and analyze interactions\n", + " sites = {}\n", + " # loop over binding sites\n", + " for key, site in sorted(protlig.interaction_sets.items()):\n", + " binding_site = BindingSiteReport(site) # collect data about interactions\n", + " # tuples of *_features and *_info will be converted to pandas DataFrame\n", + " keys = (\n", + " \"hydrophobic\",\n", + " \"hbond\",\n", + " \"waterbridge\",\n", + " \"saltbridge\",\n", + " \"pistacking\",\n", + " \"pication\",\n", + " \"halogen\",\n", + " \"metal\",\n", + " )\n", + " # interactions is a dictionary which contains relevant information for each\n", + " # of the possible interactions: hydrophobic, hbond, etc. in the considered\n", + " # binding site. Each interaction contains a list with\n", + " # 1. the features of that interaction, e.g. for hydrophobic:\n", + " # ('RESNR', 'RESTYPE', ..., 'LIGCOO', 'PROTCOO')\n", + " # 2. information for each of these features, e.g. for hydrophobic\n", + " # (residue nb, residue type,..., ligand atom 3D coord., protein atom 3D coord.)\n", + " interactions = {\n", + " k: [getattr(binding_site, k + \"_features\")] + getattr(binding_site, k + \"_info\")\n", + " for k in keys\n", + " }\n", + " sites[key] = interactions\n", + " return sites" + ] + }, + { + "cell_type": "markdown", + "id": "4928886f-dcaf-42ff-9fca-309aadb9079e", + "metadata": {}, + "source": [ + "We create the dictionary for the complex of interest and see how many binding sites are detected:" + ] + }, + { + "cell_type": "code", + "execution_count": 68, + "id": "78a3c530-1081-4bf3-b113-f601c895a22f", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Number of binding sites detected in 11gs.pdb : 1\n", + "with dict_keys(['LIG:Z:591'])\n" + ] + } + ], + "source": [ + "interactions_by_site = retrieve_plip_interactions(f\"{pdb_id}.pdb\")\n", + "print(\n", + " f\"Number of binding sites detected in {pdb_id}.pdb : \"\n", + " f\"{len(interactions_by_site)}\\n\"\n", + " f\"with {interactions_by_site.keys()}\"\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "a45542a9-6632-479a-8a4f-54a6b8152ceb", + "metadata": {}, + "source": [ + "In this case, the first binding site containing ligand 03P will be further investigated." + ] + }, + { + "cell_type": "code", + "execution_count": 69, + "id": "a9ed186b-7891-42fd-a002-918424832891", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "LIG:Z:591\n" + ] + } + ], + "source": [ + "index_of_selected_site = 0\n", + "selected_site = list(interactions_by_site.keys())[index_of_selected_site]\n", + "print(selected_site)" + ] + }, + { + "cell_type": "markdown", + "id": "525baad8-c720-4029-ab2a-fbd756be308b", + "metadata": {}, + "source": [ + "We can construct a ```pandas.DataFrame``` for a binding site and particular interaction type." + ] + }, + { + "cell_type": "code", + "execution_count": 70, + "id": "2507f14f-67a9-41e5-b731-0e46ac310833", + "metadata": {}, + "outputs": [], + "source": [ + "def create_df_from_binding_site(selected_site_interactions, interaction_type=\"hbond\"):\n", + " \"\"\"\n", + " Creates a data frame from a binding site and interaction type.\n", + "\n", + " Parameters\n", + " ----------\n", + " selected_site_interactions : dict\n", + " Precaluclated interactions from PLIP for the selected site\n", + " interaction_type : str\n", + " The interaction type of interest (default set to hydrogen bond).\n", + "\n", + " Returns\n", + " -------\n", + " pd.DataFrame :\n", + " DataFrame with information retrieved from PLIP.\n", + " \"\"\"\n", + "\n", + " # check if interaction type is valid:\n", + " valid_types = [\n", + " \"hydrophobic\",\n", + " \"hbond\",\n", + " \"waterbridge\",\n", + " \"saltbridge\",\n", + " \"pistacking\",\n", + " \"pication\",\n", + " \"halogen\",\n", + " \"metal\",\n", + " ]\n", + "\n", + " if interaction_type not in valid_types:\n", + " print(\"!!! Wrong interaction type specified. Hbond is chosen by default!!!\\n\")\n", + " interaction_type = \"hbond\"\n", + "\n", + " df = pd.DataFrame.from_records(\n", + " # data is stored AFTER the column names\n", + " selected_site_interactions[interaction_type][1:],\n", + " # column names are always the first element\n", + " columns=selected_site_interactions[interaction_type][0],\n", + " )\n", + " \n", + " return df" + ] + }, + { + "cell_type": "markdown", + "id": "59ae0de0-2ea8-4c49-ab31-6d12f4a71d5d", + "metadata": {}, + "source": [ + "In the next cell, we show the hydrophobic interactions from the selected binding site." + ] + }, + { + "cell_type": "code", + "execution_count": 71, + "id": "d47fa786-ab74-4855-97ba-c840a6d3d463", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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RESNRRESTYPERESCHAINRESNR_LIGRESTYPE_LIGRESCHAIN_LIGDISTLIGCARBONIDXPROTCARBONIDXLIGCOOPROTCOO
07PHEA591LIGZ3.856740112(6.689, 1.326, 30.431)(10.072, 2.163, 32.063)
19VALA591LIGZ3.546741149(8.517, 1.116, 28.027)(11.207, -1.184, 28.013)
2103ILEA591LIGZ3.5767341627(10.154, 3.047, 23.083)(11.308, 4.406, 19.99)
3107TYRA591LIGZ3.8467341696(10.154, 3.047, 23.083)(6.599, 1.683, 22.625)
4107TYRA591LIGZ3.7867271694(6.907, 3.074, 26.738)(4.842, 1.213, 24.182)
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" + ], + "text/plain": [ + " RESNR RESTYPE RESCHAIN RESNR_LIG RESTYPE_LIG RESCHAIN_LIG DIST \\\n", + "0 7 PHE A 591 LIG Z 3.85 \n", + "1 9 VAL A 591 LIG Z 3.54 \n", + "2 103 ILE A 591 LIG Z 3.57 \n", + "3 107 TYR A 591 LIG Z 3.84 \n", + "4 107 TYR A 591 LIG Z 3.78 \n", + "\n", + " LIGCARBONIDX PROTCARBONIDX LIGCOO \\\n", + "0 6740 112 (6.689, 1.326, 30.431) \n", + "1 6741 149 (8.517, 1.116, 28.027) \n", + "2 6734 1627 (10.154, 3.047, 23.083) \n", + "3 6734 1696 (10.154, 3.047, 23.083) \n", + "4 6727 1694 (6.907, 3.074, 26.738) \n", + "\n", + " PROTCOO \n", + "0 (10.072, 2.163, 32.063) \n", + "1 (11.207, -1.184, 28.013) \n", + "2 (11.308, 4.406, 19.99) \n", + "3 (6.599, 1.683, 22.625) \n", + "4 (4.842, 1.213, 24.182) " + ] + }, + "execution_count": 71, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "create_df_from_binding_site(interactions_by_site[selected_site], interaction_type=\"hydrophobic\")" + ] + }, + { + "cell_type": "markdown", + "id": "9cc7cdf9-01a2-4e76-9993-7522f46dcc11", + "metadata": {}, + "source": [ + "If hydrogen interactions are of interest, the table can be generated as follow:" + ] + }, + { + "cell_type": "code", + "execution_count": 72, + "id": "b98e5369-7f4e-45f6-b0e6-d7457da426bf", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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RESNRRESTYPERESCHAINRESNR_LIGRESTYPE_LIGRESCHAIN_LIGSIDECHAINDIST_H-ADIST_D-ADON_ANGLEPROTISDONDONORIDXDONORTYPEACCEPTORIDXACCEPTORTYPELIGCOOPROTCOO
051LEUA591LIGZFalse1.722.67150.45True789Nam6715O2(10.585, 7.113, 30.729)(12.883, 8.479, 30.778)
137TRPA591LIGZTrue3.644.04105.47True591Nar6718Nam(9.046, 8.58, 29.984)(6.904, 8.136, 33.385)
250GLNA591LIGZTrue3.183.78117.41True786Nam6718Nam(9.046, 8.58, 29.984)(8.896, 10.638, 26.82)
350GLNA591LIGZFalse3.133.48108.29False6721O2777O2(10.614, 10.885, 31.207)(14.041, 10.31, 31.406)
451LEUA591LIGZFalse1.642.62168.35False6712Nam794O2(11.05, 7.321, 27.713)(13.511, 7.308, 28.618)
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" + ], + "text/plain": [ + " RESNR RESTYPE RESCHAIN RESNR_LIG RESTYPE_LIG RESCHAIN_LIG SIDECHAIN \\\n", + "0 51 LEU A 591 LIG Z False \n", + "1 37 TRP A 591 LIG Z True \n", + "2 50 GLN A 591 LIG Z True \n", + "3 50 GLN A 591 LIG Z False \n", + "4 51 LEU A 591 LIG Z False \n", + "\n", + " DIST_H-A DIST_D-A DON_ANGLE PROTISDON DONORIDX DONORTYPE ACCEPTORIDX \\\n", + "0 1.72 2.67 150.45 True 789 Nam 6715 \n", + "1 3.64 4.04 105.47 True 591 Nar 6718 \n", + "2 3.18 3.78 117.41 True 786 Nam 6718 \n", + "3 3.13 3.48 108.29 False 6721 O2 777 \n", + "4 1.64 2.62 168.35 False 6712 Nam 794 \n", + "\n", + " ACCEPTORTYPE LIGCOO PROTCOO \n", + "0 O2 (10.585, 7.113, 30.729) (12.883, 8.479, 30.778) \n", + "1 Nam (9.046, 8.58, 29.984) (6.904, 8.136, 33.385) \n", + "2 Nam (9.046, 8.58, 29.984) (8.896, 10.638, 26.82) \n", + "3 O2 (10.614, 10.885, 31.207) (14.041, 10.31, 31.406) \n", + "4 O2 (11.05, 7.321, 27.713) (13.511, 7.308, 28.618) " + ] + }, + "execution_count": 72, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "create_df_from_binding_site(interactions_by_site[selected_site], interaction_type=\"hbond\")" + ] + }, + { + "cell_type": "code", + "execution_count": 73, + "id": "b425d5a5-54e1-4698-9316-854813497872", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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RESNRRESTYPERESCHAINRESNR_LIGRESTYPE_LIGRESCHAIN_LIGDIST_A-WDIST_D-WDON_ANGLEWATER_ANGLEPROTISDONDONOR_IDXDONORTYPEACCEPTOR_IDXACCEPTORTYPEWATER_IDXLIGCOOPROTCOOWATERCOO
012ARGA591LIGZ3.683.12160.48121.20True199Ng+6703N36607(13.421, 9.166, 22.647)(13.664, 6.134, 22.049)(10.628, 6.786, 22.377)
112ARGA591LIGZ3.613.12160.4872.60True199Ng+6706O.co26607(10.633, 10.38, 22.738)(13.664, 6.134, 22.049)(10.628, 6.786, 22.377)
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" + ], + "text/plain": [ + " RESNR RESTYPE RESCHAIN RESNR_LIG RESTYPE_LIG RESCHAIN_LIG DIST_A-W \\\n", + "0 12 ARG A 591 LIG Z 3.68 \n", + "1 12 ARG A 591 LIG Z 3.61 \n", + "\n", + " DIST_D-W DON_ANGLE WATER_ANGLE PROTISDON DONOR_IDX DONORTYPE \\\n", + "0 3.12 160.48 121.20 True 199 Ng+ \n", + "1 3.12 160.48 72.60 True 199 Ng+ \n", + "\n", + " ACCEPTOR_IDX ACCEPTORTYPE WATER_IDX LIGCOO \\\n", + "0 6703 N3 6607 (13.421, 9.166, 22.647) \n", + "1 6706 O.co2 6607 (10.633, 10.38, 22.738) \n", + "\n", + " PROTCOO WATERCOO \n", + "0 (13.664, 6.134, 22.049) (10.628, 6.786, 22.377) \n", + "1 (13.664, 6.134, 22.049) (10.628, 6.786, 22.377) " + ] + }, + "execution_count": 73, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "create_df_from_binding_site(interactions_by_site[selected_site], interaction_type=\"waterbridge\")" + ] + }, + { + "cell_type": "code", + "execution_count": 74, + "id": "26c0f465-3573-48ad-98a1-f8cb8c29ba86", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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RESNRRESTYPERESCHAINPROT_IDX_LISTRESNR_LIGRESTYPE_LIGRESCHAIN_LIGDISTPROTISPOSLIG_GROUPLIG_IDX_LISTLIGCOOPROTCOO
012ARGA199,202,205591LIGZ5.00TrueCarboxylate6706,6707(10.472999999999999, 9.370000000000001, 22.333)(14.368333333333332, 6.532, 20.98966666666667)
143LYSA689591LIGZ3.18TrueCarboxylate6722,6721(9.575, 11.23, 31.326999999999998)(6.949, 12.901, 31.966)
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" + ], + "text/plain": [ + " RESNR RESTYPE RESCHAIN PROT_IDX_LIST RESNR_LIG RESTYPE_LIG RESCHAIN_LIG \\\n", + "0 12 ARG A 199,202,205 591 LIG Z \n", + "1 43 LYS A 689 591 LIG Z \n", + "\n", + " DIST PROTISPOS LIG_GROUP LIG_IDX_LIST \\\n", + "0 5.00 True Carboxylate 6706,6707 \n", + "1 3.18 True Carboxylate 6722,6721 \n", + "\n", + " LIGCOO \\\n", + "0 (10.472999999999999, 9.370000000000001, 22.333) \n", + "1 (9.575, 11.23, 31.326999999999998) \n", + "\n", + " PROTCOO \n", + "0 (14.368333333333332, 6.532, 20.98966666666667) \n", + "1 (6.949, 12.901, 31.966) " + ] + }, + "execution_count": 74, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "create_df_from_binding_site(interactions_by_site[selected_site], interaction_type=\"saltbridge\")" + ] + }, + { + "cell_type": "code", + "execution_count": 75, + "id": "adf47b37-5e3c-44cf-92b1-ac06c2c74963", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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RESNRRESTYPERESCHAINRESNR_LIGRESTYPE_LIGRESCHAIN_LIGPROT_IDX_LISTCENTDISTANGLEOFFSETTYPELIG_IDX_LISTLIGCOOPROTCOO
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" + ], + "text/plain": [ + "Empty DataFrame\n", + "Columns: [RESNR, RESTYPE, RESCHAIN, RESNR_LIG, RESTYPE_LIG, RESCHAIN_LIG, PROT_IDX_LIST, CENTDIST, ANGLE, OFFSET, TYPE, LIG_IDX_LIST, LIGCOO, PROTCOO]\n", + "Index: []" + ] + }, + "execution_count": 75, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "create_df_from_binding_site(interactions_by_site[selected_site], interaction_type=\"pistacking\")" + ] + }, + { + "cell_type": "code", + "execution_count": 76, + "id": "31c4b0d0-b7c8-4998-a466-9081689e949c", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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RESNRRESTYPERESCHAINPROT_IDX_LISTRESNR_LIGRESTYPE_LIGRESCHAIN_LIGDISTOFFSETPROTCHARGEDLIG_GROUPLIG_IDX_LISTLIGCOOPROTCOO
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" + ], + "text/plain": [ + "Empty DataFrame\n", + "Columns: [RESNR, RESTYPE, RESCHAIN, PROT_IDX_LIST, RESNR_LIG, RESTYPE_LIG, RESCHAIN_LIG, DIST, OFFSET, PROTCHARGED, LIG_GROUP, LIG_IDX_LIST, LIGCOO, PROTCOO]\n", + "Index: []" + ] + }, + "execution_count": 76, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "create_df_from_binding_site(interactions_by_site[selected_site], interaction_type=\"pication\")" + ] + }, + { + "cell_type": "code", + "execution_count": 77, + "id": "a3ce6a88-bebf-49f4-9eed-379e1e9c9061", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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RESNRRESTYPERESCHAINRESNR_LIGRESTYPE_LIGRESCHAIN_LIGSIDECHAINDISTDON_ANGLEACC_ANGLEDON_IDXDONORTYPEACC_IDXACCEPTORTYPELIGCOOPROTCOO
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" + ], + "text/plain": [ + "Empty DataFrame\n", + "Columns: [RESNR, RESTYPE, RESCHAIN, RESNR_LIG, RESTYPE_LIG, RESCHAIN_LIG, SIDECHAIN, DIST, DON_ANGLE, ACC_ANGLE, DON_IDX, DONORTYPE, ACC_IDX, ACCEPTORTYPE, LIGCOO, PROTCOO]\n", + "Index: []" + ] + }, + "execution_count": 77, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "create_df_from_binding_site(interactions_by_site[selected_site], interaction_type=\"halogen\")" + ] + }, + { + "cell_type": "code", + "execution_count": 78, + "id": "84bc5fb8-9582-48f3-86cf-584222936be3", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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RESNRRESTYPERESCHAINRESNR_LIGRESTYPE_LIGRESCHAIN_LIGMETAL_IDXMETAL_TYPETARGET_IDXTARGET_TYPECOORDINATIONDISTLOCATIONRMSGEOMETRYCOMPLEXNUMMETALCOOTARGETCOO
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" + ], + "text/plain": [ + "Empty DataFrame\n", + "Columns: [RESNR, RESTYPE, RESCHAIN, RESNR_LIG, RESTYPE_LIG, RESCHAIN_LIG, METAL_IDX, METAL_TYPE, TARGET_IDX, TARGET_TYPE, COORDINATION, DIST, LOCATION, RMS, GEOMETRY, COMPLEXNUM, METALCOO, TARGETCOO]\n", + "Index: []" + ] + }, + "execution_count": 78, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "create_df_from_binding_site(interactions_by_site[selected_site], interaction_type=\"metal\")" + ] + }, + { + "cell_type": "markdown", + "id": "ab063574-6b7c-4f35-98db-873419586cb7", + "metadata": {}, + "source": [ + "Now, let’s try to represent those interactions in the NGL viewer. We can draw cylinders between the interaction points (```LIGCOO``` and ```PROTCOO``` in the ```pandas.DataFrame```) and colour-code them as shown in ```colour_map```, which uses RGB tuples." + ] + }, + { + "cell_type": "code", + "execution_count": 79, + "id": "9c8d89aa-e439-4657-8468-e60460fd9c5a", + "metadata": {}, + "outputs": [], + "source": [ + "color_map = {\n", + " \"hydrophobic\": [0.90, 0.10, 0.29],\n", + " \"hbond\": [0.26, 0.83, 0.96],\n", + " \"waterbridge\": [1.00, 0.88, 0.10],\n", + " \"saltbridge\": [0.67, 1.00, 0.76],\n", + " \"pistacking\": [0.75, 0.94, 0.27],\n", + " \"pication\": [0.27, 0.60, 0.56],\n", + " \"halogen\": [0.94, 0.20, 0.90],\n", + " \"metal\": [0.90, 0.75, 1.00],\n", + "}" + ] + }, + { + "cell_type": "markdown", + "id": "a31e36c3-e852-4651-bbd5-d4265d17b817", + "metadata": {}, + "source": [ + "Define a helper function to show the interactions." + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "id": "f84af5d0-4cc4-4976-9345-9410358320d9", + "metadata": {}, + "outputs": [], + "source": [ + "def show_interactions_3d(\n", + " pdb_id, selected_site_interactions, highlight_interaction_colors=color_map\n", + "):\n", + " \"\"\"\n", + " 3D visualization of protein-ligand interactions.\n", + "\n", + " Parameters\n", + " ----------\n", + " pdb_id : str\n", + " The pdb ID of interest.\n", + " selected_site_interactions : dict\n", + " Precaluclated interactions from PLIP for the selected site\n", + " highlight_interaction_colors : dict\n", + " The colors used to highlight the different interaction types.\n", + "\n", + " Returns\n", + " -------\n", + " NGL viewer with explicit interactions given by PLIP.\n", + " \"\"\"\n", + "\n", + " # Create NGLviewer\n", + " viewer = nv.NGLWidget(height=\"600px\", default=True, gui=True)\n", + " # Add protein\n", + " prot_component = viewer.add_pdbid(pdb_id)\n", + " # Add the ligands\n", + " viewer.add_representation(repr_type=\"ball+stick\", selection=\"hetero and not water\")\n", + "\n", + " interacting_residues = []\n", + " for interaction_type, interaction_list in selected_site_interactions.items():\n", + " color = highlight_interaction_colors[interaction_type]\n", + " if len(interaction_list) == 1:\n", + " continue\n", + " df_interactions = pd.DataFrame.from_records(\n", + " interaction_list[1:], columns=interaction_list[0]\n", + " )\n", + " for _, interaction in df_interactions.iterrows():\n", + " name = interaction_type\n", + " # add cylinder between ligand and protein coordinate\n", + " viewer.shape.add_cylinder(\n", + " interaction[\"LIGCOO\"],\n", + " interaction[\"PROTCOO\"],\n", + " color,\n", + " [0.1],\n", + " name,\n", + " )\n", + " interacting_residues.append(interaction[\"RESNR\"])\n", + " \n", + " # Display interacting residues\n", + " res_sele = \" or \".join([f\"({r} and not _H)\" for r in interacting_residues])\n", + " res_sele_nc = \" or \".join([f\"({r} and ((_O) or (_N) or (_S)))\" for r in interacting_residues])\n", + " prot_component.add_ball_and_stick(sele=res_sele, colorScheme=\"chainindex\", aspectRatio=1.5)\n", + " prot_component.add_ball_and_stick(sele=res_sele_nc, colorScheme=\"element\", aspectRatio=1.5)\n", + " \n", + " # Center on ligand\n", + " viewer.center(\"ligand\")\n", + " \n", + " return viewer" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "id": "be094efb-670d-4128-8c93-53ab8ef04bef", + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": "", + "text/plain": [ + "" + ] + }, + "execution_count": 28, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "viewer_3d = show_interactions_3d('combine', interactions_by_site[selected_site])\n", + "viewer_3d.render_image(trim=True, factor=2, transparent=True);\n", + "viewer_3d._display_image()" + ] + }, + { + "cell_type": "code", + "execution_count": 80, + "id": "4028863a-2988-4618-8dc1-44104d43436b", + "metadata": {}, + "outputs": [], + "source": [ + "all_intr_types = (\"hydrophobic\",\n", + " \"hbond\",\n", + " \"waterbridge\",\n", + " \"saltbridge\",\n", + " \"pistacking\",\n", + " \"pication\",\n", + " \"halogen\",\n", + " \"metal\")\n", + "\n", + "allPLInteractions = pd.DataFrame()\n", + "for intr_type in all_intr_types:\n", + " _df = create_df_from_binding_site(interactions_by_site[selected_site], interaction_type=intr_type)\n", + " allPLInteractions = pd.concat([allPLInteractions, _df], ignore_index=True)" + ] + }, + { + "cell_type": "code", + "execution_count": 81, + "id": "846f4bcf-99a2-49a2-8fe5-44111d2229bd", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " RESNR RESTYPE RESCHAIN RESNR_LIG RESTYPE_LIG RESCHAIN_LIG DIST \\\n", + "0 7 PHE A 591 LIG Z 3.85 \n", + "1 9 VAL A 591 LIG Z 3.54 \n", + "2 103 ILE A 591 LIG Z 3.57 \n", + "3 107 TYR A 591 LIG Z 3.84 \n", + "4 107 TYR A 591 LIG Z 3.78 \n", + "\n", + " LIGCARBONIDX PROTCARBONIDX LIGCOO ... METAL_TYPE \\\n", + "0 6740.0 112.0 (6.689, 1.326, 30.431) ... NaN \n", + "1 6741.0 149.0 (8.517, 1.116, 28.027) ... NaN \n", + "2 6734.0 1627.0 (10.154, 3.047, 23.083) ... NaN \n", + "3 6734.0 1696.0 (10.154, 3.047, 23.083) ... NaN \n", + "4 6727.0 1694.0 (6.907, 3.074, 26.738) ... NaN \n", + "\n", + " TARGET_IDX TARGET_TYPE COORDINATION LOCATION RMS GEOMETRY COMPLEXNUM \\\n", + "0 NaN NaN NaN NaN NaN NaN NaN \n", + "1 NaN NaN NaN NaN NaN NaN NaN \n", + "2 NaN NaN NaN NaN NaN NaN NaN \n", + "3 NaN NaN NaN NaN NaN NaN NaN \n", + "4 NaN NaN NaN NaN NaN NaN NaN \n", + "\n", + " METALCOO TARGETCOO \n", + "0 NaN NaN \n", + "1 NaN NaN \n", + "2 NaN NaN \n", + "3 NaN NaN \n", + "4 NaN NaN \n", + "\n", + "[5 rows x 50 columns]\n" + ] + } + ], + "source": [ + "print(allPLInteractions.head(5))" + ] + }, + { + "cell_type": "code", + "execution_count": 82, + "id": "17cd14e5-0d15-46f0-9298-e89f3036f201", + "metadata": {}, + "outputs": [], + "source": [ + "allPLInteractions.to_csv(\"allPLI.csv\")" + ] + }, + { + "cell_type": "code", + "execution_count": 83, + "id": "1b6a91e5-a7d9-4a39-8fd4-5977bfd6dcf4", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "plip.structure.preparation.PDBComplex" + ] + }, + "execution_count": 83, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "protlig = PDBComplex()\n", + "protlig.load_pdb(\"11gs.pdb\") # load the pdb file\n", + "type(protlig)" + ] + }, + { + "cell_type": "code", + "execution_count": 84, + "id": "c1df9636-428c-4fcb-848f-213c2da164ca", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "(30.676, 3.06, 38.855)" + ] + }, + "execution_count": 84, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "list(protlig.atoms.values())[0].coords" + ] + }, + { + "cell_type": "code", + "execution_count": 85, + "id": "bbe8377f-f110-414d-aef7-40947b17c475", + "metadata": {}, + "outputs": [], + "source": [ + "import openbabel as ob\n", + "\n", + "def find_atom_by_coordinates(molecule, target_coordinates):\n", + " for atom in list(molecule.atoms.values()):\n", + " atom_coordinates = atom.coords\n", + "\n", + " # Compare the coordinates\n", + " if round(atom_coordinates[0], 3) == round(target_coordinates[0], 3) and \\\n", + " round(atom_coordinates[1], 3) == round(target_coordinates[1], 3) and \\\n", + " round(atom_coordinates[2], 3) == round(target_coordinates[2], 3):\n", + " return atom\n", + "\n", + " # If no match found\n", + " return None" + ] + }, + { + "cell_type": "code", + "execution_count": 86, + "id": "f61d77aa-c1cc-4f95-b3d7-75f48dbb6a6e", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Atom Found:\n", + "Atom Type: C3\n", + "Atom Index: 6739\n", + "Atom Coordinates: (8.517, 1.116, 28.027)\n" + ] + } + ], + "source": [ + "# Find the atom with the target coordinates\n", + "target_coords = (8.517, 1.116, 28.027)\n", + "target_atom = find_atom_by_coordinates(protlig, target_coordinates=list(target_coords))\n", + "\n", + "# Print the atom information\n", + "if target_atom is not None:\n", + " print('Atom Found:')\n", + " print('Atom Type:', target_atom.type)\n", + " print('Atom Index:', target_atom.idx)\n", + " print('Atom Coordinates:', target_atom.coords)\n", + "else:\n", + " print('Atom Not Found.')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "9d602053-98d9-46a4-8aca-7a3a438c6500", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "markdown", + "id": "364a16e5-c9d0-45c4-8f56-73415fa74107", + "metadata": {}, + "source": [ + "## Import node and edge features" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "958acf4d-86e9-408d-8296-4e40e574a30f", + "metadata": {}, + "outputs": [], + "source": [ + "import pickle\n", + "\n", + "with open(\"../features/PLComplex.pkl\", 'rb') as file:\n", + " totalDict = pickle.load(file)\n", + "\n", + "repGraph = totalDict['repDict']['9icd_1']\n" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.12" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/utils/.ipynb_checkpoints/centreofmass-checkpoint.ipynb b/utils/.ipynb_checkpoints/centreofmass-checkpoint.ipynb new file mode 100644 index 0000000..a9958c6 --- /dev/null +++ b/utils/.ipynb_checkpoints/centreofmass-checkpoint.ipynb @@ -0,0 +1,343 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "381df901-7128-4795-b408-74517df1a070", + "metadata": {}, + "source": [ + "# Finding Centre of Mass of Ligands for Docking using LeDock" + ] + }, + { + "cell_type": "code", + "execution_count": 32, + "id": "97999055-4041-4cc9-8b86-74359cb0e2f0", + "metadata": {}, + "outputs": [], + "source": [ + "from rdkit import Chem\n", + "from rdkit.Geometry import Point3D\n", + "\n", + "import pandas as pd\n", + "import numpy as np\n", + "import os, glob" + ] + }, + { + "cell_type": "code", + "execution_count": 67, + "id": "3cb83472-fbab-4e4a-9825-7be9dd7c99a4", + "metadata": {}, + "outputs": [], + "source": [ + "def calculate_centre_of_mass(sdf_file):\n", + " # Read the .sdf file\n", + " mol = Chem.SDMolSupplier(sdf_file, removeHs = False, sanitize = False)[0]\n", + " # Assuming there is only one molecule in the file\n", + "\n", + " # Calculate the center of mass\n", + " centre_of_mass = np.array([0.0, 0.0, 0.0])\n", + " total_mass = 0.0\n", + " \n", + " for atom in mol.GetAtoms():\n", + " _atom_mass = atom.GetMass()\n", + " _atom_coords = mol.GetConformer().GetAtomPosition(atom.GetIdx())\n", + " atom_mass = np.array([_atom_mass, _atom_mass, _atom_mass])\n", + " atom_coords = np.array([_atom_coords[0], _atom_coords[1], _atom_coords[2]])\n", + " centre_of_mass += atom_mass * atom_coords\n", + " total_mass += _atom_mass\n", + " \n", + " centre_of_mass /= np.array([total_mass, total_mass, total_mass])\n", + "\n", + " return centre_of_mass" + ] + }, + { + "cell_type": "markdown", + "id": "4115db8d-f6b5-4621-ad5b-673adfe85e55", + "metadata": {}, + "source": [ + "Assume that you have stored the PDBbind database at the directory as mentioned." + ] + }, + { + "cell_type": "code", + "execution_count": 60, + "id": "3a8c1720-9b2f-4380-b1f7-3f8e8e562006", + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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goEDVvRDyBMUoYVt5Odavx6pVuH+f9douLi4ANmzYIBKJWC9OSNvQTj1hlUwGf3988w10dRESgh9+gIEBi+Xz8/P9/PxycnKsrKwiIiJCQ0Np+lGicjQaJawqKoKDA3r1Qo8emDgRly6xW97W1nbHjh0eHh4lJSXz5893cnLauXOnVCpldyuEvBaKUcIqPh9icetrsbj1Ocus8vPzu3LlSmJioqura35+flhY2Jgxo2pqkljfECGviGKUsMrCArW1SEvDtWtITcXQoWhsZH0jHA5n6tSpWVlZK1euNDY2Tk+/umjRO6dOudXXp7K+LUJeio6NEraJxThyBCIR3nkHu3cjJgZXrsDOjvXtJCcnBwQEiMVi+b9hdXV8+SXGjvXs1Wubjo4n65sj5HloNErYpqGBmTPh7AxfX6SkoKIC8+ezvhF5hjY1NYWFhZ05cyYg4F2G4Xp6chsbr2ZnD75zx7229tiDB/8qLFwkk9E5faJcNBolyvH551i5Eg4OePQINTU4fBjvvcdW7cTExKCgIIlEsmTJkk2bNsnfLC0tlEg2V1bulMmEXK62vv7b9vY/cLlabG2UkOehGCXK0dyMQYNw+zYmTRLdv7/awmL1L7/o6ekpXjg+Pn7WrFktLS3Lli374osvnlnKMOLKyt0Aw+fbV1RsMzCYbGrK/liYkKfRTj1RDj4fO3Yweno/NzaO1NbedPr06tWrFa/6448/yjN0+fLlf81QAByOhqnpAlPThQYGEx0dk5ua7gmFVxTfLiEvQDFKlMbH59N//OPdkyd5Ghrq6upff/31jRs3FKn33XffyTN0zZo10dHRL165vPybigqBWHyXz7dWZKOEvBTFKFGipVFRpqamly5d8vb25nK5SUlJbb5UfteuXXPmzJHJZFFRUZGRkS9d38TkfV3dEfb2h9TVKUaJctGxUaJc27dvX7BgAZ/Pl0qlUqlUV1d3yJAhfn5+fn5+gwYN4nJf6Q+5QCD44IMPGIaJiYlZvHixsnsm5LVQjJLnKi8vr6ury8rKGjt2rLa2dhsqZGRkBAQE3L9/38DAYMSIEdnZ2Tk5OY+XmpiY+Pr6jho1atSoUa6urs8rsn379oULFwKIjY0NDw9vQxuEKBdDyN9JTk62tLQcPHgwAC0trUmTJgkEgrKyslevcODAAR0dHQADBw7MycmRv/nw4cP4+Pi5c+fa29s//e/QzMwsMDAwNjb22rVrTxf58ssvAXA4nK+//prNr0cIeyhGybOqq6tDQkLk6da/f39PT08OhyP/VV1d3c/Pb9u2bUVFRS+o0NTU9HjYGBwcLBQK/3a1nJycXbt2BQUFWVpaPh2pNjY2ISEh+/btW7FiBQAul7tnzx7lfFdCWEAxSv4kJSXFxsZGPgKNjo6WSqUMw2zevNnf39/Hx4fP5z8Ou759+0ZGRt66deuZCgUFBV5eXgA0NTUFAsErbjc3N1cgEAQHB1tbPzkjZGBgwOVy4+LiWP6ShLCKYpS0amxsXL58ufycz5AhQ7Kzsx8vGjhw4ONx4vjx4/38/J6+kN7BwSE8PPzs2bMymSw5OblHjx4AevXqdfny5Ta0IZPJMjIyYmNjhw8fzuPx7O3t2fuKhCgFxShhGIa5ePGis7OzfLc9MjKypaXl6aW//vprWFiYhYXF04cyx44d6+fnJw9NORMTE3kKT548ubq6WsGWxGKxqakpgCtXrihYihClohglzNGjR+VPiBs4cGBGRsbzVpNKpefOnVu6dGnv3r0fR6e+vv7o0aPnzJnj6OiooaHB5/NnzpwpPxSguCVLlgCYM2cOK9UIURKKUcLs3btXTU0tKCiourr6yJEjr/KRrKys6Ohob29v+dmn3NxcmUwWEREBoHfv3k1NTaw0lp2dzeFwdHV1a2trWSlIiDJQjBJm7dq1AAYMGODi4sLhcC5cuPDqn83Ly9u7d6/8tUQi6devH4CNGzey1ZuPjw+AVz9VRUj7o8vvCUQiUd++fR88eDBx4sTk5GQ3N7erV6++4v1Fzzh58uTo0aP19PSys7OtrKwU7+37778PDg728PC4evWq4tUIUQa6p560XtsE4MqVKz179rxx48aBAwfaVuqtt97y9/evr6//9NNPWektMDDQxMTk2rVrl9h+Oh4hbKEYJQAwffp0Hx+fioqK/v37A1i+fHldXV3bSsXExGhqasbFxV2+fFnxxjQ0NEJCQtzd3adMmRIXF6d4QUJYRzFKWsXGxvJ4vN9++83d3b2srOylM9E9j4ODw+LFixmGWbBggUwmU7yxTZs22dvbV1RUzJ49e+LEibm5uYrXJIRNqj44SzqQ0NBQAD4+Plwul8/n37t3r211hEJhr169AOzfv5+VxqRS6f79+01MTABoampGRkaKRCJWKhOiOIpR8kRZWZmBgQGA0aNHA3jvvffaXEp+dNXc3JzFa5Wqqqrmzp0rv8Sqd+/ex44dY6syIYqgnXryhJmZ2cqVKwEUFBRYWFi4u7szbb2QIyAgYMSIEWVlZZ9//jlb7fXo0UMgEJw+ffrNN9/Mzc2dMGHC5MmTCwoK2KpPSBupOsdJxyIWi+V3hcbExLStglQqFQgEvXr1SklJkR8cSElJYbdJiUQSGxsrv69fW1s7MjJS/rR6QlSCYpQ86+jRowD09PTi4uIaGhpe67MZGRmenp7yv9AfffSRvr5+z549uVyun59ffHy8RCJhsc/i4uLg4GD5tvr06fPbb7+xWJyQV0cxSp4lEAi4XK58ujxNTc1XnLC5ubk5OjpaQ0MDgIWFxejRo+UHMXv27Kml1fqw+J49e65du7a4uJjFblNTU11cXABwOJzg4ODXmliaEFZQjJKniERL586VR9L48ePlz6GTJ6C6uvqYMWN27NhRUlLy18/duHHjjTfeAMDlcidOnCifM1R+Sl0sFtfU1AgEgjfffFNeSj44TUpKkslkrHQtFoujo6M1NTUBGBoaxsbGPjNDFSFKRTFK/lBczHh5Vbq59TAwSExMlL9XUVGxf//+SZMmPZ6wmcvluru7R0ZG3r179/FHMzIy+Hy+nZ3dmDFj5Kt5e3vfuXPn6fIymSw1NTUwMFBdXR0AX4fvleUVUxZTJalipf379++//fbbAMzNzWtqalipSciroBglDMMwzLVrjKUlAzD29tWZmX9d/ujRo/j4+ODgYF1d3cfnJ+UT4MufnhQREWFsbCw/5/N42vy/VVJSEhUVNSl2Eq4D16GZrhmSF3Kx4SIr3yMhIeHw4cOslCLkFdHUJN2YSIQtW1Bejn798Pbb8PSEoyMSEmBm9oIPCYXCY8eO/fTTT8nJyY9vGDUzMysvLwcwYcKEb7/9Vn5c9cVkkJ2sP7mzcueRmiNSRgrAVdM1zCQs1CRUl/skqYslxTzwLNQtnl+JEBWjGO3GlixBQACGDkVsLCws4O4Oe3uoqb3ip1taWi5dupSQkBAfH6+hoVFYWBgVFdWGGUnymvMEFYK9VXvLW8oB6PP0D9gdOFl/UsJI6qX1XjpeNnybKQZTXrcsIe2GLr/vxvLyMHQoAAQFIS0NTk6vnqEA1NTUhg8fvmXLlqKiIg8PD5lMJr/k6HW7sOfbR1tHF/YrjLeP99PzE8qEYpnYiGe0zWbbfrv9pmqmr1uQkHZGMdqNMQzkU4fU1uKpR9S9Lh6PJxAIzMzM0tLS9u3b17YifA4/0CgwxSkl7408ESNy1XQFwAGnzV0R0m4oRrul/Hzk5mLaNKxcibNnsWYN/vlPReoZGxtv3rwZwOLFi4uLixUpZcO36c3vndWUpUgRQtoTHRvtfm7dwrhx4PNx/jyqq3H3LgYPBhsz1b/zzjtJSUkBAQEJCQkKllpStKSJaRLJRMN0h1mrW4/XH694e4QoCcVoN3PpEiZNQlUVfH3x888wMGCxdmFhofsw975b+i56a5G/oT+LlQnpyChGu5OkJMyYAZEI/v7497/xxz2aLBI8FMx7OM9K3ep239sGPDYzmpAOi46Ndhu7d+O99yASYf58JCYqI0MBzLGcM1x3eImk5OPij5VRn5AOiGK0W9i4cePcuDhIpVi+HNu3g8dT0oa44O7utVuTq7mrcldqfaqStkJIh0I79V2cTCYLDw/ftm0bj8e7uHev5x8zyylV1MOo1Q9XO2k4/e76uxZXKcNeQjoOitGurLm5OSQk5NChQxoaGnFxcdOmTWuf7UoYiXu2e64497jjcR9dn/bZKCGqQjHaZTU0NEydOvXEiROGhoZHjx718WnXOMsUZWpxtWqltT/V/NSL38uAa2CrYTtEZ0h79kBI+6Bjo13WqlWrTpw4YWVldfr06XbOUAD9tPpxwV1fun6Z+TIXTZdSaalIJmrnHghpHxSjXdOlS5d+/PFHZ2fn8+fP9+/fXyU9nKw/Odt4tgHPwEfXR4/b9ptNCengKEa7pps3b5aVlQ0dOtTOzk5VPahx1JplzaraOiHt5jVm9CGdSEZGBgBVjUPlxuuP/2f+P/to9imVlIoZsQo7IUSpKEa7JnmMDhgwQIU9mKubC3oJjtUdM+IZDdcZbqJmosJmCFEeOlPfBTEMY2hoWFdXV1ZWZvbCqewJIYqjY6NdUF5eXl1dnaWlJWUoIe2AYrQL6gh79IR0H3RstFO5cQNHjsDUFHPnvmBukd9//x2qPr9ESPdBMdp55ORg0ybs2oU7dxAWBj8/bNgAY2P5T7Kj4211dWNjYxMTk7S0NNBolJD2QjHaeZw4gX/9Czo68PCAUIgHD5Cd/XjhqUGDNqWnP706jUYJaR8Uo52HujokktbX8kfRubtDWxsaGuDzedra4y0sJBKJSCTKzMxsbm7m8/kqbJaQ7oNitPOYNAkLFsDREbdvw8YG9+7h+vXHC3+zsLheWip/bWRk1NTUNGrUqJSUlL59+6qoXUK6C7putFPJz0dyMiws4O+PggIUFKCqCpWVqKhYXVubX1paVVVVWVlpbm4uEolSUlKMjIyOHz/u5eWl6r4J6cooRrumpqamadOm/fLLL/r6+peOH3cdNkzVHRHSZVGMdllSqTQ0NNQqK+vz3FwcPIhx41TdESFdE8VoVyaTyZj/+z/e9u3g8/HDDwgIUHVHhHRBdBdTV8blcnnffIOlS9HcjBkzsGePqjsipAui0Wj3EBWF1athYICcHJjQTEuEsIlitNv45hv07w9LS8TEQFMTxsYIDcWhQ1i8GACWL8fGjapukZBOia4b7TYWLgSAgAB89x309bF1K44fR3Fx69K8PBW2RkinRjHazUil0NcHgBEjcOAAzpzBRx8BQFOTavsipPOiGO1mpFIwDDgcFBTA3By+vti0CQDa6xH2hHQ9dKa+m5k9G/PmYetW/PADpkxRdTeEdAV0iqn7qa9HZSVsbcEwEApb9/Grq2FkpOrOCOmUKEYJIUQhtFNPCCEKoRglhBCFUIwSQohCKEYJIUQhFKOEEKKQ/wfyIhKlFdU9aQAAAth6VFh0cmRraXRQS0wgcmRraXQgMjAyMi4wMy4yAAB4nHWRe0jTURTH7+9ubnPzsencs22/abZVgtgIEdGdE0QESQ+HSIiM/hjLLDLMf0S0xPpDREjIopdkmr0koocNUUmTBGOFlYimwTLNBmqCGkh09zBJ7cLhex/nfM7jznY9GidsRZPQ4phZwlbFicmxwB0nEBEn2wg4EbEGVCgJKZUQd/CeCzlQuqb/OopDjpT7H2k1UE74gK7z3whcywzrQOHzRg0GsMx/N5uWIFjXy2rzm/UWLmEVoAjWzoVFxmYZwRGOEirkqcBKRRFELCKRYl4ssVJpJImWEqmMyGJ5WZSVxsqJXEEU8bwizkpjoolO6aYqpVOZwCeYiTmRJG610sQkXq1yU43aqdfwGq2banVOg57ot1gpbyAGIzGaiCqZqLcRPoYoOZFSpdZodepxLvSvASMWef4JjKtOQa3QgzU/jmOTzoTX+3rRu1SOdY0x6GvpRWV7FVYWiXA5dxBF587j7b1SvDnrwaEcB0qH47Ekqw8r7AfxbIOUqZdZBhqOEnROerG6JwVbrxG02d7g8wUbXlTNg8s1gofqTCx2FJZzRzFzIoHF+qG6ZxK3F5hZrhUo9PgZJ4mdH0Bt8Rh2GNNxoOwyRNEhnHxHMPXzNGQ8/Yb5GX4oVy7CQNkcvh0cA4dPwdhzaEnrYTwVNmiWcLjZD78/GDFNMoPy/JdAd6aCr+ULYzdDZ6kM/Ie/s7evwHph/Ilg/s5SG9w5/QmFeTOwcq8ELGlefHKjG4R5FyBL+h7b+u9Cg6YY6hpH0FTD4cmpWui69RqPdPyEoZxWeHymG+tfaTFLWgme/b2MH8jvgMqiDhz9tQuTRWbY43zBZr2D1d0E+tR+lDysggPpV+3t+6bZ7Mugrb82+/78PPuLRrhyKq7b4VvAQF0V9mfZLtcS461AQf0le+bEFO4u1LA+JbBo/YiqP7xW6h7mQVJaAAADoHpUWHRNT0wgcmRraXQgMjAyMi4wMy4yAAB4nH1Wy24dNwzd+yv0AxVEUi8uuojtIC2KXAON221RoEAQIOim/X+UDz1Gs6h9YczVHFGHh4eUAb7+88f3b1///Puvp6A/v77+8u3fsH7o9UnW0/98mDn8Timlp89BH8Lzx08/P8LL+4fnufLy9tvj/Usg1k/S3xP74f3t81yB8AiQY0ssIQOk2DrqE1LEYk8S76dPP8LcgOFFN1R9lwJHztnwOeYGhp9IUmSJLXdd7pEBJ7LUA5nDW4AaUy+OzMkiYYklnzGLIwnIkTVPtlTbgax6uiRR2XliTuP0QulANkVi5DJj1nk6p5NnVyTE0kZGCXEi+3k6K08Rk9tAUh/IhOVAQtIKgPAzaBN6LmiL0G5QkPNF8Wan1mhnGjLDSRTQkEOTFoktN+yxAZ9IcqZD+xZ7d6YcC5/aQ9b0U8RkwUqkUsb5xbXb0BK+aFI5G0L95UpJ6dqNapX8RaACfj62Nqh212wjtVCSixu0Raus2EzIlxtSC1WjvdfaA/SJrLf0tVDiPC80x+wVFWS/VRSTIFXJMnyPbeiEJZ9ILZP4nj3l2GhmlPqpKKLELBGS6ygF5xET6ll6JMsdsDqSYJa+3/TEbMhZxthTHsr3dItZXE+02lFsHkk82vlUCatlxB4zR+A+YsKtl7AZEvOIWTtPM99jao1EEh4OoTanQ0unmZBN+eIOFbm8qaTnmW4TJ5ntq4sj732LThy4Ib2VupuN5kCRmGlMvYVEb3roQ/rivYYyMfAGJW+Q2kaDjF7XnNqZE2mVsgCMFqycWCbFWSXSKlHso8OkP2g4dIi8kVV0kqOyCf1Dkjk1zZz7aRJqAl3eSNLJeSD5Np5IyvQ9LJsJU29pcTP30/dy2QhU5oYbSuzsqYhNaj6jfny8HreQ30vPb4/XfS+BXDWXWwdkouO+WvQt7fsDZKnsS0LehbxvApAZX/e4Bxnkbc900Bnc9+RGWePLeAYdvHCdwqCzEBY5wIFZ/EAJ6vI6VTagrSzSMiNBpx8sKvpFpxwsMvpFpxleRxvqH9gMWTESbCWMqoh0Im75QFfouqKcZRkXZzRRRbkdx3TNYsHLyEB1JC3OqJx1ZWUqB2fdiitTafVsW3dk5SzLuCJbFRWz4pBxlqKvs0g5W7xLx6HFWWqQcSaBXRrIdtHKnYyzfLafVGcRgHZk9YVkQTsye2RYnNXFV8/q9/l/mDw//QceOtjitbm7EAAAAdR6VFh0U01JTEVTIHJka2l0IDIwMjIuMDMuMgAAeJxNkj2OWzEMhK+S0sYqhPgnkhC2ek0qu0gZpHK7R9jDZ6hNgDR61mdyOCR1Xdft+onjcd3en/cLv349fujb7/u5P78+j+v/24tfr9ft+Y+9btcH2PXx7fPGTJxrCDnjFCqRXZQRQ0lZhyhNb7QYpNKHGBnz5kkrdDhNOSxCN8TMfOAyZcgijdVxMjtOHXFB7gq1ChkLZZoYr84Ui4G/1ZpxeDOPHIkKUHMUj1aLimaazVB8M1y7gi147LgJPSVZNQqqbQ412WgJQNkhFtwoZo3WTOlOBZ2yU1hXLZYT6FBbNNF5ks1TwY2b9XxQ1U6urkBfONGEFgaXFFxtuFODMmG4yIs33DsDCaaMsNTcyIGFIHhWZHjuRW2fOQ9YBTDnAjJMAygxja7k3ZNEa4tba1dvQOO4j6mIcjhwYgwORku5E0Wxz4jV/WTV7vkmErmyV8cKItZBK+us5ARFQZdCj/OZDMQTi8XGqj3w8m1YCw/+KlhYlW+lxIrwFPBkYB7CWyinAalbo5JODKvxfWLvp0fLBass/T6V20RGE5wtj6cGE5W2/473KMJ8TscuHC3Cl3qjZX7//AMBg6jr3yx7ZQAAAABJRU5ErkJggg==", + "text/plain": [ + "" + ] + }, + "execution_count": 60, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "mol2_file_path = '../../download/v2020-other-PL/11gs/11gs_ligand.sdf'\n", + "mol = Chem.SDMolSupplier(mol2_file_path)[0]\n", + "mol" + ] + }, + { + "cell_type": "code", + "execution_count": 61, + "id": "3c8f3f17-3c2f-4fdb-8ea1-d18e490ca750", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Centre of Mass: 9.217, 5.222, 27.027\n" + ] + } + ], + "source": [ + "com = calculate_centre_of_mass(mol2_file_path)\n", + "print(f\"Centre of Mass: {com[0]:.3f}, {com[1]:.3f}, {com[2]:.3f}\")" + ] + }, + { + "cell_type": "code", + "execution_count": 62, + "id": "69148dab-9b3c-4f6b-b879-3fee0c672d83", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[ 9.21687027 5.22203154 27.02683079]\n" + ] + } + ], + "source": [ + "centre_of_mass = np.array([0.0, 0.0, 0.0])\n", + "total_mass = 0.0\n", + "for atom in mol.GetAtoms():\n", + " _atom_mass = atom.GetMass()\n", + " _atom_coords = mol.GetConformer().GetAtomPosition(atom.GetIdx())\n", + " atom_mass = np.array([_atom_mass, _atom_mass, _atom_mass])\n", + " atom_coords = np.array([_atom_coords[0], _atom_coords[1], _atom_coords[2]])\n", + " centre_of_mass += atom_mass * atom_coords\n", + " total_mass += _atom_mass\n", + "centre_of_mass /= np.array([total_mass, total_mass, total_mass])\n", + "print(centre_of_mass)" + ] + }, + { + "cell_type": "markdown", + "id": "eaef74b2-3302-4004-b157-72fbda10a934", + "metadata": {}, + "source": [ + "Now, we performed calculation on all compounds." + ] + }, + { + "cell_type": "code", + "execution_count": 63, + "id": "33ecf5dd-980f-42a4-91b0-3aa607bc68ec", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "There are 14129 files in General Set and 5318 files in the Refined Set.\n" + ] + } + ], + "source": [ + "filePathtoGeneralSet = glob.glob(os.path.join('../../download/v2020-other-PL', \"*\"))\n", + "filePathtoRefinedSet = glob.glob(os.path.join('../../download/refined-set', \"*\"))\n", + "print(f\"There are {len(filePathtoGeneralSet)} files in General Set and {len(filePathtoRefinedSet)} files in the Refined Set.\")" + ] + }, + { + "cell_type": "markdown", + "id": "e7c97e8e-d4cd-42c4-a75b-d4569452c66c", + "metadata": {}, + "source": [ + "For general set," + ] + }, + { + "cell_type": "code", + "execution_count": 70, + "id": "d2509b7c-25d1-49d3-bfd1-2a3cee65e6af", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "[03:44:12] \n", + "\n", + "****\n", + "Post-condition Violation\n", + "Element 'Du' not found\n", + "Violation occurred on line 93 in file /home/conda/feedstock_root/build_artifacts/rdkit_1651075169244/work/Code/GraphMol/PeriodicTable.h\n", + "Failed Expression: anum > -1\n", + "****\n", + "\n", + "[03:44:12] ERROR: Element 'Du' not found\n", + "[03:44:12] ERROR: moving to the beginning of the next molecule\n", + "[03:44:16] \n", + "\n", + "****\n", + "Post-condition Violation\n", + "Element 'Du' not found\n", + "Violation occurred on line 93 in file /home/conda/feedstock_root/build_artifacts/rdkit_1651075169244/work/Code/GraphMol/PeriodicTable.h\n", + "Failed Expression: anum > -1\n", + "****\n", + "\n", + "[03:44:16] ERROR: Element 'Du' not found\n", + "[03:44:16] ERROR: moving to the beginning of the next molecule\n", + "[03:44:18] \n", + "\n", + "****\n", + "Post-condition Violation\n", + "Element 'Du' not found\n", + "Violation occurred on line 93 in file /home/conda/feedstock_root/build_artifacts/rdkit_1651075169244/work/Code/GraphMol/PeriodicTable.h\n", + "Failed Expression: anum > -1\n", + "****\n", + "\n", + "[03:44:18] ERROR: Element 'Du' not found\n", + "[03:44:18] ERROR: moving to the beginning of the next molecule\n", + "[03:44:27] \n", + "\n", + "****\n", + "Post-condition Violation\n", + "Element 'Du' not found\n", + "Violation occurred on line 93 in file /home/conda/feedstock_root/build_artifacts/rdkit_1651075169244/work/Code/GraphMol/PeriodicTable.h\n", + "Failed Expression: anum > -1\n", + "****\n", + "\n", + "[03:44:27] ERROR: Element 'Du' not found\n", + "[03:44:27] ERROR: moving to the beginning of the next molecule\n", + "[03:44:39] \n", + "\n", + "****\n", + "Post-condition Violation\n", + "Element 'Du' not found\n", + "Violation occurred on line 93 in file /home/conda/feedstock_root/build_artifacts/rdkit_1651075169244/work/Code/GraphMol/PeriodicTable.h\n", + "Failed Expression: anum > -1\n", + "****\n", + "\n", + "[03:44:39] ERROR: Element 'Du' not found\n", + "[03:44:39] ERROR: moving to the beginning of the next molecule\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Excluded molecules: ['2foy', '3bho', '2fov', '3qlb', '2fou']\n" + ] + } + ], + "source": [ + "id, coords_x, coords_y, coords_z, exclusion_list = list(), list(), list(), list(), list()\n", + "for i in range(len(filePathtoGeneralSet)):\n", + " _id = str(filePathtoGeneralSet[i].split(\"/\")[-1])\n", + " if _id in ['index', 'readme']: continue\n", + " try:\n", + " com = calculate_centre_of_mass(filePathtoGeneralSet[i] + \"/\" + _id + \"_ligand.sdf\")\n", + " except AttributeError:\n", + " exclusion_list.append(_id)\n", + " continue\n", + " id.append(_id)\n", + " coords_x.append(round(com[0], 3))\n", + " coords_y.append(round(com[1], 3))\n", + " coords_z.append(round(com[2], 3))\n", + "comGeneralSet = {'pdb_id': id, 'com_x': coords_x, 'com_y': coords_y, 'com_z': coords_z}\n", + "df = pd.DataFrame(comGeneralSet)\n", + "with open('general-set-com.txt', 'a') as file:\n", + " df_string = df.to_string(header=False, index=False)\n", + " file.write(df_string)\n", + "\n", + "print(f\"Excluded molecules: {exclusion_list}\")" + ] + }, + { + "cell_type": "markdown", + "id": "f2a5d5ce-1299-4672-9223-e9043e130a77", + "metadata": {}, + "source": [ + "For refined set," + ] + }, + { + "cell_type": "code", + "execution_count": 72, + "id": "b43c6a48-b33c-4ffb-9d5a-4109b0b8b850", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Excluded molecules: []\n" + ] + } + ], + "source": [ + "id, coords_x, coords_y, coords_z, exclusion_list = list(), list(), list(), list(), list()\n", + "for i in range(len(filePathtoRefinedSet)):\n", + " _id = str(filePathtoRefinedSet[i].split(\"/\")[-1])\n", + " if _id in ['index', 'readme']: continue\n", + " try:\n", + " com = calculate_centre_of_mass(filePathtoRefinedSet[i] + \"/\" + _id + \"_ligand.sdf\")\n", + " except AttributeError:\n", + " exclusion_list.append(_id)\n", + " continue\n", + " id.append(_id)\n", + " coords_x.append(round(com[0], 3))\n", + " coords_y.append(round(com[1], 3))\n", + " coords_z.append(round(com[2], 3))\n", + "comRefinedSet = {'pdb_id': id, 'com_x': coords_x, 'com_y': coords_y, 'com_z': coords_z}\n", + "df = pd.DataFrame(comRefinedSet)\n", + "with open('refined-set-com.txt', 'a') as file:\n", + " df_string = df.to_string(header=False, index=False)\n", + " file.write(df_string)\n", + "\n", + "print(f\"Excluded molecules: {exclusion_list}\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "d97e1536-aa70-4b09-ba4d-a43582f065f6", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.12" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/utils/.prepare_data.py b/utils/.prepare_data.py new file mode 100644 index 0000000..ee299c9 --- /dev/null +++ b/utils/.prepare_data.py @@ -0,0 +1,264 @@ +# Main functionality +# ================== +# 1. Find RMSD of docked ligand poses from crystal structure +# 2. Retrieve molecular features of protein and ligand +# 3. Prepare node and edge features (ODDT) +# 4. Dump all relevant info to pickle file +# +# Note: Compatible with LeDock generated (and corrected) poses only + +import rdkit +from rdkit import Chem +from rdkit.Chem import rdMolAlign +import prolif as plf + +from spyrmsd import io, rmsd +from spyrmsd.molecule import Molecule +from spyrmsd.rmsd import rmsdwrapper + +from tqdm import tqdm +import os, sys, glob +import pickle, yaml +import warnings +import argparse +import traceback +import logging + +from Mol2Graph import * +import PLInteraction + + + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument('--ref_path', type=str, + default='../download/v2020-other-PL') + parser.add_argument('--dok_path', type=str, + default='./dataset/general') + parser.add_argument('--mesh_path', type=str, + default='./dataset/general_mesh') + parser.add_argument('--config', type=str, + default='./config/config.yaml') + parser.add_argument('--outdir', type=str, + default='./features') + args = parser.parse_args() + + if args.ref_path.split("/")[-1] not in ['v2020-other-PL', 'refined-set']: + raise FileNotFoundError("Sorry, option for `--ref_path` not supported / does not exist.") + if args.dok_path.split("/")[-1] not in ['general', 'refined']: + raise FileNotFoundError("Sorry, option for `--dok_path` not supported / does not exist.") + if args.mesh_path.split("/")[-1] not in ['general_mesh', 'refined_mesh']: + raise FileNotFoundError("Sorry, option for `--mesh_path` not supported / does not exist.") + + print("\n") + outDirisExist = os.path.exists(args.outdir) + if not outDirisExist: + # Create a new directory because it does not exist + os.makedirs(args.outdir) + print("The outdir directory is created!") + + outDirisExist = os.path.isfile(args.config) + if not outDirisExist: + warnings.warn("Configuration YAML file does not exist or is not specified. Assumed all complexes are utilised.") + meshNotExist = list() + else: + with open(args.config, 'rb') as file: + ymlDict = yaml.safe_load(file) + meshNotExist = ymlDict['pymeshSkippedComplex'] + print("Reading configuration YAML file...") + print(f"Skipped {len(meshNotExist)} complexes for PyMesh file does not exist.") + + + """ + Part 2: Fix LeDock output docked files + maybe carry out using the bash script modifyDOK.sh (?) + + """ + + + + + """ + Part 3: Find docked poses' RMSD from crystal structure using spyrmsd. + This RMSD value will be out value `y`. + """ + allAvailableComplex = os.listdir(args.ref_path) + print(f"Found {len(allAvailableComplex)-2} in {args.ref_path.split('/')[-1]} for RMSD calculation.") + + #allAvailableComplex = ['9icd', '4kqo', '5qj2'] + allAvailableComplex = ['9icd'] + skippedComplex, rmsdDict = [], {} + print("\nProcessing complexes RMSD...") + + for i in tqdm(range(len(allAvailableComplex))): + if (str(allAvailableComplex[i]) in ['index', 'readme']) or (str(allAvailableComplex[i]) in meshNotExist): continue + + refMol = Chem.SDMolSupplier(args.ref_path + "/" + \ + str(allAvailableComplex[i]) + "/" + \ + str(allAvailableComplex[i]) + "_ligand.sdf") + refMol = Molecule.from_rdkit(refMol[0]) + refMol.strip() # remove hydrogen atoms + + #allDokPoses = glob.glob(args.dok_path + "/" + str(allAvailableComplex[i]) + "*_dock*.pdb") + allDokPoses = glob.glob(args.ref_path + "/" + \ + str(allAvailableComplex[i]) + "/" + \ + str(allAvailableComplex[i]) + "*_dock*.pdb") + + if len(allDokPoses) == 0: skippedComplex.append(allAvailableComplex[i]) + else: + for j in range(len(allDokPoses)): + dokMol = Chem.rdmolfiles.MolFromPDBFile(allDokPoses[j], removeHs=True) + dokMol = Molecule.from_rdkit(dokMol) + dokMol.strip() # remove hydrogen atoms + + RMSD = rmsdwrapper(refMol, dokMol)[0] + print(f'Complex {allAvailableComplex[i]} docked poses {j+1}: RMSD = {round(RMSD, 3)}') + + rmsdDict[str(allAvailableComplex[i]) + "_" + str(j+1)] = round(RMSD, 3) + + + """ + Part 4: Retrieve molecular features + """ + + ligRMSDList, repDict, ligDict = [], {}, {} + print("\nRetrieving molecular features...") + + for i in tqdm(range(len(allAvailableComplex))): + if (allAvailableComplex[i] in ['readme', 'index'] + skippedComplex) or (str(allAvailableComplex[i]) in meshNotExist): continue + repFile = args.ref_path + "/" + \ + str(allAvailableComplex[i]) + "/" + \ + str(allAvailableComplex[i]) + "_pocket.pdb" + repDict[str(allAvailableComplex[i])] = RetrieveMolecularFeatures([repFile], [0.0], removeHs=False)[0] + + #allDokPoses = glob.glob(args.dok_path + "/" + str(allAvailableComplex[i]) + "*_dock*.pdb") + allDokPoses = glob.glob(args.ref_path + "/" + \ + str(allAvailableComplex[i]) + "/" + \ + str(allAvailableComplex[i]) + "*_dock*.pdb") + + for j in range(len(allDokPoses)): + ligFile = allDokPoses[j] + ligRMSD = rmsdDict[str(allAvailableComplex[i]) + "_" + str(j+1)] + ligDict[str(allAvailableComplex[i]) + "_" + str(j+1)] = RetrieveMolecularFeatures([ligFile], [ligRMSD], removeHs=False)[0] + + + + """ + Part 5(A): Prepare node and edge features: + Protein-ligand interactions as recognised by PLIP. + (?) oddt or plip or prolif though ... + + iaDict = {} + totalIA = ["Hydrophobic", "HBAcceptor", "HBDonor" , "XBAcceptor" , "XBDonor", + "Cationic" , "Anionic" , "CationPi" , "PiCation" , "FaceToFace", + "EdgeToFace" , "PiStacking", "MetalDonor", "MetalAcceptor", "VdWContact"] + print("\nPreparing node and edge features") + + for i in tqdm(range(len(allAvailableComplex))): + if (allAvailableComplex[i] in ['readme', 'index'] + skippedComplex) or (str(allAvailableComplex[i]) in meshNotExist): continue + else: + mol = Chem.MolFromPDBFile(args.ref_path + "/" + \ + str(allAvailableComplex[i]) + "/" + \ + str(allAvailableComplex[i]) + "_pocket.pdb", removeHs=False) + prot = plf.Molecule(mol) + + allDokPoses = glob.glob(args.dok_path + "/" + str(allAvailableComplex[i]) + "*_dock*.pdb") + allDokPoses = glob.glob(args.ref_path + "/" + \ + str(allAvailableComplex[i]) + "/" + \ + str(allAvailableComplex[i]) + "*_dock*.pdb") + + for j in range(len(allDokPoses)): + mol = Chem.MolFromPDBFile(allDokPoses[j], removeHs=False) + lig = plf.Molecule(mol) + + fp = plf.Fingerprint() + fp.run_from_iterable([lig], prot) + df = fp.to_dataframe() + occ = df.mean() + occ = occ.reset_index() + + ### map each color to an integer + mapping = {} + for x in range(len(totalIA)): + mapping[totalIA[x]] = x + + one_hot_encode = [] + + for someIA in np.array(occ['interaction']).tolist(): + arr = list(np.zeros(len(totalIA), dtype = int)) + arr[mapping[someIA]] = 1 + one_hot_encode.append(arr) + + occ['OneHotInteraction'] = one_hot_encode + occ[['ResidueID', 'ResidueNum', 'dot', 'ChainID']] = occ['protein'].str.extract(r'(\D{3})(\d+)(\.)(\D)') + occ.drop(['dot', 'ligand'], axis=1, inplace=True) + + iaDict[str(allAvailableComplex[i]) + "_" + str(j+1)] = occ + """ + + + + """ + Part 5(B): Prepare edge features for PL Interactions + using ODDT package. Export data to iaDict + """ + print("\nRetrieving PL interaction (edge) features...") + + iaDict = {} + for i in tqdm(range(len(allAvailableComplex))): + if (allAvailableComplex[i] in ['readme', 'index'] + skippedComplex) or (str(allAvailableComplex[i]) in meshNotExist): continue + repFile = args.ref_path + "/" + \ + str(allAvailableComplex[i]) + "/" + \ + str(allAvailableComplex[i]) + "_protein.pdb" + allDokPoses = glob.glob(args.ref_path + "/" + \ + str(allAvailableComplex[i]) + "/" + \ + str(allAvailableComplex[i]) + "*_dock*.pdb") + for j in range(len(allDokPoses)): + ligFile = allDokPoses[j] + protein, ligand, max_len, lig_len = PLInteraction.read_prolig(repFile, ligFile) + fp, fl = PLInteraction.fingerprint(protein, ligand, max_len, lig_len) + iaDict[str(allAvailableComplex[i]) + "_" + str(j+1)] = [fp, fl] + + + """ + Part 6: Processing PyMesh data for proteins + """ + print("\nRetrieving protein mesh files...") + + meshDict = {} + for i in tqdm(range(len(allAvailableComplex))): + if (allAvailableComplex[i] in ['readme', 'index'] + skippedComplex) or (str(allAvailableComplex[i]) in meshNotExist): continue + with open(args.mesh_path + "/" + str(allAvailableComplex[i]) + "_protein.ply", 'r') as file: + meshDict[str(allAvailableComplex[i])] = yaml.safe_load(file) + + + """ + Part 7: Conclusion + """ + print("\nSaving pickle and shutting down processes...\n") + + allDict = {} + allDict['rmsdDict'] = rmsdDict + allDict['repDict'] = repDict + allDict['ligDict'] = ligDict + allDict['iaDict'] = iaDict + allDict['meshDict'] = meshDict + ymlDict['processSkippedComplex'] = skippedComplex + + # Pickle dump + file = open(args.outdir + '/PLComplex.pkl', 'wb') + pickle.dump(allDict, file) + file.close() + + with open(args.config, 'r') as file: + _ymlDict = yaml.safe_load(file) + _ymlDict.update(ymlDict) + + with open(args.config, 'w') as file: + yaml.safe_dump(_ymlDict, file) + + print(f"Skipped complexes: {skippedComplex}") + print("Process terminated successfully.\n") + + \ No newline at end of file diff --git a/utils/CentreOfMass.ipynb b/utils/CentreOfMass.ipynb new file mode 100644 index 0000000..a9958c6 --- /dev/null +++ b/utils/CentreOfMass.ipynb @@ -0,0 +1,343 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "381df901-7128-4795-b408-74517df1a070", + "metadata": {}, + "source": [ + "# Finding Centre of Mass of Ligands for Docking using LeDock" + ] + }, + { + "cell_type": "code", + "execution_count": 32, + "id": "97999055-4041-4cc9-8b86-74359cb0e2f0", + "metadata": {}, + "outputs": [], + "source": [ + "from rdkit import Chem\n", + "from rdkit.Geometry import Point3D\n", + "\n", + "import pandas as pd\n", + "import numpy as np\n", + "import os, glob" + ] + }, + { + "cell_type": "code", + "execution_count": 67, + "id": "3cb83472-fbab-4e4a-9825-7be9dd7c99a4", + "metadata": {}, + "outputs": [], + "source": [ + "def calculate_centre_of_mass(sdf_file):\n", + " # Read the .sdf file\n", + " mol = Chem.SDMolSupplier(sdf_file, removeHs = False, sanitize = False)[0]\n", + " # Assuming there is only one molecule in the file\n", + "\n", + " # Calculate the center of mass\n", + " centre_of_mass = np.array([0.0, 0.0, 0.0])\n", + " total_mass = 0.0\n", + " \n", + " for atom in mol.GetAtoms():\n", + " _atom_mass = atom.GetMass()\n", + " _atom_coords = mol.GetConformer().GetAtomPosition(atom.GetIdx())\n", + " atom_mass = np.array([_atom_mass, _atom_mass, _atom_mass])\n", + " atom_coords = np.array([_atom_coords[0], _atom_coords[1], _atom_coords[2]])\n", + " centre_of_mass += atom_mass * atom_coords\n", + " total_mass += _atom_mass\n", + " \n", + " centre_of_mass /= np.array([total_mass, total_mass, total_mass])\n", + "\n", + " return centre_of_mass" + ] + }, + { + "cell_type": "markdown", + "id": "4115db8d-f6b5-4621-ad5b-673adfe85e55", + "metadata": {}, + "source": [ + "Assume that you have stored the PDBbind database at the directory as mentioned." + ] + }, + { + "cell_type": "code", + "execution_count": 60, + "id": "3a8c1720-9b2f-4380-b1f7-3f8e8e562006", + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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goEDVvRDyBMUoYVt5Odavx6pVuH+f9douLi4ANmzYIBKJWC9OSNvQTj1hlUwGf3988w10dRESgh9+gIEBi+Xz8/P9/PxycnKsrKwiIiJCQ0Np+lGicjQaJawqKoKDA3r1Qo8emDgRly6xW97W1nbHjh0eHh4lJSXz5893cnLauXOnVCpldyuEvBaKUcIqPh9icetrsbj1Ocus8vPzu3LlSmJioqura35+flhY2Jgxo2pqkljfECGviGKUsMrCArW1SEvDtWtITcXQoWhsZH0jHA5n6tSpWVlZK1euNDY2Tk+/umjRO6dOudXXp7K+LUJeio6NEraJxThyBCIR3nkHu3cjJgZXrsDOjvXtJCcnBwQEiMVi+b9hdXV8+SXGjvXs1Wubjo4n65sj5HloNErYpqGBmTPh7AxfX6SkoKIC8+ezvhF5hjY1NYWFhZ05cyYg4F2G4Xp6chsbr2ZnD75zx7229tiDB/8qLFwkk9E5faJcNBolyvH551i5Eg4OePQINTU4fBjvvcdW7cTExKCgIIlEsmTJkk2bNsnfLC0tlEg2V1bulMmEXK62vv7b9vY/cLlabG2UkOehGCXK0dyMQYNw+zYmTRLdv7/awmL1L7/o6ekpXjg+Pn7WrFktLS3Lli374osvnlnKMOLKyt0Aw+fbV1RsMzCYbGrK/liYkKfRTj1RDj4fO3Yweno/NzaO1NbedPr06tWrFa/6448/yjN0+fLlf81QAByOhqnpAlPThQYGEx0dk5ua7gmFVxTfLiEvQDFKlMbH59N//OPdkyd5Ghrq6upff/31jRs3FKn33XffyTN0zZo10dHRL165vPybigqBWHyXz7dWZKOEvBTFKFGipVFRpqamly5d8vb25nK5SUlJbb5UfteuXXPmzJHJZFFRUZGRkS9d38TkfV3dEfb2h9TVKUaJctGxUaJc27dvX7BgAZ/Pl0qlUqlUV1d3yJAhfn5+fn5+gwYN4nJf6Q+5QCD44IMPGIaJiYlZvHixsnsm5LVQjJLnKi8vr6ury8rKGjt2rLa2dhsqZGRkBAQE3L9/38DAYMSIEdnZ2Tk5OY+XmpiY+Pr6jho1atSoUa6urs8rsn379oULFwKIjY0NDw9vQxuEKBdDyN9JTk62tLQcPHgwAC0trUmTJgkEgrKyslevcODAAR0dHQADBw7MycmRv/nw4cP4+Pi5c+fa29s//e/QzMwsMDAwNjb22rVrTxf58ssvAXA4nK+//prNr0cIeyhGybOqq6tDQkLk6da/f39PT08OhyP/VV1d3c/Pb9u2bUVFRS+o0NTU9HjYGBwcLBQK/3a1nJycXbt2BQUFWVpaPh2pNjY2ISEh+/btW7FiBQAul7tnzx7lfFdCWEAxSv4kJSXFxsZGPgKNjo6WSqUMw2zevNnf39/Hx4fP5z8Ou759+0ZGRt66deuZCgUFBV5eXgA0NTUFAsErbjc3N1cgEAQHB1tbPzkjZGBgwOVy4+LiWP6ShLCKYpS0amxsXL58ufycz5AhQ7Kzsx8vGjhw4ONx4vjx4/38/J6+kN7BwSE8PPzs2bMymSw5OblHjx4AevXqdfny5Ta0IZPJMjIyYmNjhw8fzuPx7O3t2fuKhCgFxShhGIa5ePGis7OzfLc9MjKypaXl6aW//vprWFiYhYXF04cyx44d6+fnJw9NORMTE3kKT548ubq6WsGWxGKxqakpgCtXrihYihClohglzNGjR+VPiBs4cGBGRsbzVpNKpefOnVu6dGnv3r0fR6e+vv7o0aPnzJnj6OiooaHB5/NnzpwpPxSguCVLlgCYM2cOK9UIURKKUcLs3btXTU0tKCiourr6yJEjr/KRrKys6Ohob29v+dmn3NxcmUwWEREBoHfv3k1NTaw0lp2dzeFwdHV1a2trWSlIiDJQjBJm7dq1AAYMGODi4sLhcC5cuPDqn83Ly9u7d6/8tUQi6devH4CNGzey1ZuPjw+AVz9VRUj7o8vvCUQiUd++fR88eDBx4sTk5GQ3N7erV6++4v1Fzzh58uTo0aP19PSys7OtrKwU7+37778PDg728PC4evWq4tUIUQa6p560XtsE4MqVKz179rxx48aBAwfaVuqtt97y9/evr6//9NNPWektMDDQxMTk2rVrl9h+Oh4hbKEYJQAwffp0Hx+fioqK/v37A1i+fHldXV3bSsXExGhqasbFxV2+fFnxxjQ0NEJCQtzd3adMmRIXF6d4QUJYRzFKWsXGxvJ4vN9++83d3b2srOylM9E9j4ODw+LFixmGWbBggUwmU7yxTZs22dvbV1RUzJ49e+LEibm5uYrXJIRNqj44SzqQ0NBQAD4+Plwul8/n37t3r211hEJhr169AOzfv5+VxqRS6f79+01MTABoampGRkaKRCJWKhOiOIpR8kRZWZmBgQGA0aNHA3jvvffaXEp+dNXc3JzFa5Wqqqrmzp0rv8Sqd+/ex44dY6syIYqgnXryhJmZ2cqVKwEUFBRYWFi4u7szbb2QIyAgYMSIEWVlZZ9//jlb7fXo0UMgEJw+ffrNN9/Mzc2dMGHC5MmTCwoK2KpPSBupOsdJxyIWi+V3hcbExLStglQqFQgEvXr1SklJkR8cSElJYbdJiUQSGxsrv69fW1s7MjJS/rR6QlSCYpQ86+jRowD09PTi4uIaGhpe67MZGRmenp7yv9AfffSRvr5+z549uVyun59ffHy8RCJhsc/i4uLg4GD5tvr06fPbb7+xWJyQV0cxSp4lEAi4XK58ujxNTc1XnLC5ubk5OjpaQ0MDgIWFxejRo+UHMXv27Kml1fqw+J49e65du7a4uJjFblNTU11cXABwOJzg4ODXmliaEFZQjJKniERL586VR9L48ePlz6GTJ6C6uvqYMWN27NhRUlLy18/duHHjjTfeAMDlcidOnCifM1R+Sl0sFtfU1AgEgjfffFNeSj44TUpKkslkrHQtFoujo6M1NTUBGBoaxsbGPjNDFSFKRTFK/lBczHh5Vbq59TAwSExMlL9XUVGxf//+SZMmPZ6wmcvluru7R0ZG3r179/FHMzIy+Hy+nZ3dmDFj5Kt5e3vfuXPn6fIymSw1NTUwMFBdXR0AX4fvleUVUxZTJalipf379++//fbbAMzNzWtqalipSciroBglDMMwzLVrjKUlAzD29tWZmX9d/ujRo/j4+ODgYF1d3cfnJ+UT4MufnhQREWFsbCw/5/N42vy/VVJSEhUVNSl2Eq4D16GZrhmSF3Kx4SIr3yMhIeHw4cOslCLkFdHUJN2YSIQtW1Bejn798Pbb8PSEoyMSEmBm9oIPCYXCY8eO/fTTT8nJyY9vGDUzMysvLwcwYcKEb7/9Vn5c9cVkkJ2sP7mzcueRmiNSRgrAVdM1zCQs1CRUl/skqYslxTzwLNQtnl+JEBWjGO3GlixBQACGDkVsLCws4O4Oe3uoqb3ip1taWi5dupSQkBAfH6+hoVFYWBgVFdWGGUnymvMEFYK9VXvLW8oB6PP0D9gdOFl/UsJI6qX1XjpeNnybKQZTXrcsIe2GLr/vxvLyMHQoAAQFIS0NTk6vnqEA1NTUhg8fvmXLlqKiIg8PD5lMJr/k6HW7sOfbR1tHF/YrjLeP99PzE8qEYpnYiGe0zWbbfrv9pmqmr1uQkHZGMdqNMQzkU4fU1uKpR9S9Lh6PJxAIzMzM0tLS9u3b17YifA4/0CgwxSkl7408ESNy1XQFwAGnzV0R0m4oRrul/Hzk5mLaNKxcibNnsWYN/vlPReoZGxtv3rwZwOLFi4uLixUpZcO36c3vndWUpUgRQtoTHRvtfm7dwrhx4PNx/jyqq3H3LgYPBhsz1b/zzjtJSUkBAQEJCQkKllpStKSJaRLJRMN0h1mrW4/XH694e4QoCcVoN3PpEiZNQlUVfH3x888wMGCxdmFhofsw975b+i56a5G/oT+LlQnpyChGu5OkJMyYAZEI/v7497/xxz2aLBI8FMx7OM9K3ep239sGPDYzmpAOi46Ndhu7d+O99yASYf58JCYqI0MBzLGcM1x3eImk5OPij5VRn5AOiGK0W9i4cePcuDhIpVi+HNu3g8dT0oa44O7utVuTq7mrcldqfaqStkJIh0I79V2cTCYLDw/ftm0bj8e7uHev5x8zyylV1MOo1Q9XO2k4/e76uxZXKcNeQjoOitGurLm5OSQk5NChQxoaGnFxcdOmTWuf7UoYiXu2e64497jjcR9dn/bZKCGqQjHaZTU0NEydOvXEiROGhoZHjx718WnXOMsUZWpxtWqltT/V/NSL38uAa2CrYTtEZ0h79kBI+6Bjo13WqlWrTpw4YWVldfr06XbOUAD9tPpxwV1fun6Z+TIXTZdSaalIJmrnHghpHxSjXdOlS5d+/PFHZ2fn8+fP9+/fXyU9nKw/Odt4tgHPwEfXR4/b9ptNCengKEa7pps3b5aVlQ0dOtTOzk5VPahx1JplzaraOiHt5jVm9CGdSEZGBgBVjUPlxuuP/2f+P/to9imVlIoZsQo7IUSpKEa7JnmMDhgwQIU9mKubC3oJjtUdM+IZDdcZbqJmosJmCFEeOlPfBTEMY2hoWFdXV1ZWZvbCqewJIYqjY6NdUF5eXl1dnaWlJWUoIe2AYrQL6gh79IR0H3RstFO5cQNHjsDUFHPnvmBukd9//x2qPr9ESPdBMdp55ORg0ybs2oU7dxAWBj8/bNgAY2P5T7Kj4211dWNjYxMTk7S0NNBolJD2QjHaeZw4gX/9Czo68PCAUIgHD5Cd/XjhqUGDNqWnP706jUYJaR8Uo52HujokktbX8kfRubtDWxsaGuDzedra4y0sJBKJSCTKzMxsbm7m8/kqbJaQ7oNitPOYNAkLFsDREbdvw8YG9+7h+vXHC3+zsLheWip/bWRk1NTUNGrUqJSUlL59+6qoXUK6C7putFPJz0dyMiws4O+PggIUFKCqCpWVqKhYXVubX1paVVVVWVlpbm4uEolSUlKMjIyOHz/u5eWl6r4J6cooRrumpqamadOm/fLLL/r6+peOH3cdNkzVHRHSZVGMdllSqTQ0NNQqK+vz3FwcPIhx41TdESFdE8VoVyaTyZj/+z/e9u3g8/HDDwgIUHVHhHRBdBdTV8blcnnffIOlS9HcjBkzsGePqjsipAui0Wj3EBWF1athYICcHJjQTEuEsIlitNv45hv07w9LS8TEQFMTxsYIDcWhQ1i8GACWL8fGjapukZBOia4b7TYWLgSAgAB89x309bF1K44fR3Fx69K8PBW2RkinRjHazUil0NcHgBEjcOAAzpzBRx8BQFOTavsipPOiGO1mpFIwDDgcFBTA3By+vti0CQDa6xH2hHQ9dKa+m5k9G/PmYetW/PADpkxRdTeEdAV0iqn7qa9HZSVsbcEwEApb9/Grq2FkpOrOCOmUKEYJIUQhtFNPCCEKoRglhBCFUIwSQohCKEYJIUQhFKOEEKKQ/wfyIhKlFdU9aQAAAth6VFh0cmRraXRQS0wgcmRraXQgMjAyMi4wMy4yAAB4nHWRe0jTURTH7+9ubnPzsencs22/abZVgtgIEdGdE0QESQ+HSIiM/hjLLDLMf0S0xPpDREjIopdkmr0koocNUUmTBGOFlYimwTLNBmqCGkh09zBJ7cLhex/nfM7jznY9GidsRZPQ4phZwlbFicmxwB0nEBEn2wg4EbEGVCgJKZUQd/CeCzlQuqb/OopDjpT7H2k1UE74gK7z3whcywzrQOHzRg0GsMx/N5uWIFjXy2rzm/UWLmEVoAjWzoVFxmYZwRGOEirkqcBKRRFELCKRYl4ssVJpJImWEqmMyGJ5WZSVxsqJXEEU8bwizkpjoolO6aYqpVOZwCeYiTmRJG610sQkXq1yU43aqdfwGq2banVOg57ot1gpbyAGIzGaiCqZqLcRPoYoOZFSpdZodepxLvSvASMWef4JjKtOQa3QgzU/jmOTzoTX+3rRu1SOdY0x6GvpRWV7FVYWiXA5dxBF587j7b1SvDnrwaEcB0qH47Ekqw8r7AfxbIOUqZdZBhqOEnROerG6JwVbrxG02d7g8wUbXlTNg8s1gofqTCx2FJZzRzFzIoHF+qG6ZxK3F5hZrhUo9PgZJ4mdH0Bt8Rh2GNNxoOwyRNEhnHxHMPXzNGQ8/Yb5GX4oVy7CQNkcvh0cA4dPwdhzaEnrYTwVNmiWcLjZD78/GDFNMoPy/JdAd6aCr+ULYzdDZ6kM/Ie/s7evwHph/Ilg/s5SG9w5/QmFeTOwcq8ELGlefHKjG4R5FyBL+h7b+u9Cg6YY6hpH0FTD4cmpWui69RqPdPyEoZxWeHymG+tfaTFLWgme/b2MH8jvgMqiDhz9tQuTRWbY43zBZr2D1d0E+tR+lDysggPpV+3t+6bZ7Mugrb82+/78PPuLRrhyKq7b4VvAQF0V9mfZLtcS461AQf0le+bEFO4u1LA+JbBo/YiqP7xW6h7mQVJaAAADoHpUWHRNT0wgcmRraXQgMjAyMi4wMy4yAAB4nH1Wy24dNwzd+yv0AxVEUi8uuojtIC2KXAON221RoEAQIOim/X+UDz1Gs6h9YczVHFGHh4eUAb7+88f3b1///Puvp6A/v77+8u3fsH7o9UnW0/98mDn8Timlp89BH8Lzx08/P8LL+4fnufLy9tvj/Usg1k/S3xP74f3t81yB8AiQY0ssIQOk2DrqE1LEYk8S76dPP8LcgOFFN1R9lwJHztnwOeYGhp9IUmSJLXdd7pEBJ7LUA5nDW4AaUy+OzMkiYYklnzGLIwnIkTVPtlTbgax6uiRR2XliTuP0QulANkVi5DJj1nk6p5NnVyTE0kZGCXEi+3k6K08Rk9tAUh/IhOVAQtIKgPAzaBN6LmiL0G5QkPNF8Wan1mhnGjLDSRTQkEOTFoktN+yxAZ9IcqZD+xZ7d6YcC5/aQ9b0U8RkwUqkUsb5xbXb0BK+aFI5G0L95UpJ6dqNapX8RaACfj62Nqh212wjtVCSixu0Raus2EzIlxtSC1WjvdfaA/SJrLf0tVDiPC80x+wVFWS/VRSTIFXJMnyPbeiEJZ9ILZP4nj3l2GhmlPqpKKLELBGS6ygF5xET6ll6JMsdsDqSYJa+3/TEbMhZxthTHsr3dItZXE+02lFsHkk82vlUCatlxB4zR+A+YsKtl7AZEvOIWTtPM99jao1EEh4OoTanQ0unmZBN+eIOFbm8qaTnmW4TJ5ntq4sj732LThy4Ib2VupuN5kCRmGlMvYVEb3roQ/rivYYyMfAGJW+Q2kaDjF7XnNqZE2mVsgCMFqycWCbFWSXSKlHso8OkP2g4dIi8kVV0kqOyCf1Dkjk1zZz7aRJqAl3eSNLJeSD5Np5IyvQ9LJsJU29pcTP30/dy2QhU5oYbSuzsqYhNaj6jfny8HreQ30vPb4/XfS+BXDWXWwdkouO+WvQt7fsDZKnsS0LehbxvApAZX/e4Bxnkbc900Bnc9+RGWePLeAYdvHCdwqCzEBY5wIFZ/EAJ6vI6VTagrSzSMiNBpx8sKvpFpxwsMvpFpxleRxvqH9gMWTESbCWMqoh0Im75QFfouqKcZRkXZzRRRbkdx3TNYsHLyEB1JC3OqJx1ZWUqB2fdiitTafVsW3dk5SzLuCJbFRWz4pBxlqKvs0g5W7xLx6HFWWqQcSaBXRrIdtHKnYyzfLafVGcRgHZk9YVkQTsye2RYnNXFV8/q9/l/mDw//QceOtjitbm7EAAAAdR6VFh0U01JTEVTIHJka2l0IDIwMjIuMDMuMgAAeJxNkj2OWzEMhK+S0sYqhPgnkhC2ek0qu0gZpHK7R9jDZ6hNgDR61mdyOCR1Xdft+onjcd3en/cLv349fujb7/u5P78+j+v/24tfr9ft+Y+9btcH2PXx7fPGTJxrCDnjFCqRXZQRQ0lZhyhNb7QYpNKHGBnz5kkrdDhNOSxCN8TMfOAyZcgijdVxMjtOHXFB7gq1ChkLZZoYr84Ui4G/1ZpxeDOPHIkKUHMUj1aLimaazVB8M1y7gi147LgJPSVZNQqqbQ412WgJQNkhFtwoZo3WTOlOBZ2yU1hXLZYT6FBbNNF5ks1TwY2b9XxQ1U6urkBfONGEFgaXFFxtuFODMmG4yIs33DsDCaaMsNTcyIGFIHhWZHjuRW2fOQ9YBTDnAjJMAygxja7k3ZNEa4tba1dvQOO4j6mIcjhwYgwORku5E0Wxz4jV/WTV7vkmErmyV8cKItZBK+us5ARFQZdCj/OZDMQTi8XGqj3w8m1YCw/+KlhYlW+lxIrwFPBkYB7CWyinAalbo5JODKvxfWLvp0fLBass/T6V20RGE5wtj6cGE5W2/473KMJ8TscuHC3Cl3qjZX7//AMBg6jr3yx7ZQAAAABJRU5ErkJggg==", + "text/plain": [ + "" + ] + }, + "execution_count": 60, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "mol2_file_path = '../../download/v2020-other-PL/11gs/11gs_ligand.sdf'\n", + "mol = Chem.SDMolSupplier(mol2_file_path)[0]\n", + "mol" + ] + }, + { + "cell_type": "code", + "execution_count": 61, + "id": "3c8f3f17-3c2f-4fdb-8ea1-d18e490ca750", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Centre of Mass: 9.217, 5.222, 27.027\n" + ] + } + ], + "source": [ + "com = calculate_centre_of_mass(mol2_file_path)\n", + "print(f\"Centre of Mass: {com[0]:.3f}, {com[1]:.3f}, {com[2]:.3f}\")" + ] + }, + { + "cell_type": "code", + "execution_count": 62, + "id": "69148dab-9b3c-4f6b-b879-3fee0c672d83", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[ 9.21687027 5.22203154 27.02683079]\n" + ] + } + ], + "source": [ + "centre_of_mass = np.array([0.0, 0.0, 0.0])\n", + "total_mass = 0.0\n", + "for atom in mol.GetAtoms():\n", + " _atom_mass = atom.GetMass()\n", + " _atom_coords = mol.GetConformer().GetAtomPosition(atom.GetIdx())\n", + " atom_mass = np.array([_atom_mass, _atom_mass, _atom_mass])\n", + " atom_coords = np.array([_atom_coords[0], _atom_coords[1], _atom_coords[2]])\n", + " centre_of_mass += atom_mass * atom_coords\n", + " total_mass += _atom_mass\n", + "centre_of_mass /= np.array([total_mass, total_mass, total_mass])\n", + "print(centre_of_mass)" + ] + }, + { + "cell_type": "markdown", + "id": "eaef74b2-3302-4004-b157-72fbda10a934", + "metadata": {}, + "source": [ + "Now, we performed calculation on all compounds." + ] + }, + { + "cell_type": "code", + "execution_count": 63, + "id": "33ecf5dd-980f-42a4-91b0-3aa607bc68ec", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "There are 14129 files in General Set and 5318 files in the Refined Set.\n" + ] + } + ], + "source": [ + "filePathtoGeneralSet = glob.glob(os.path.join('../../download/v2020-other-PL', \"*\"))\n", + "filePathtoRefinedSet = glob.glob(os.path.join('../../download/refined-set', \"*\"))\n", + "print(f\"There are {len(filePathtoGeneralSet)} files in General Set and {len(filePathtoRefinedSet)} files in the Refined Set.\")" + ] + }, + { + "cell_type": "markdown", + "id": "e7c97e8e-d4cd-42c4-a75b-d4569452c66c", + "metadata": {}, + "source": [ + "For general set," + ] + }, + { + "cell_type": "code", + "execution_count": 70, + "id": "d2509b7c-25d1-49d3-bfd1-2a3cee65e6af", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "[03:44:12] \n", + "\n", + "****\n", + "Post-condition Violation\n", + "Element 'Du' not found\n", + "Violation occurred on line 93 in file /home/conda/feedstock_root/build_artifacts/rdkit_1651075169244/work/Code/GraphMol/PeriodicTable.h\n", + "Failed Expression: anum > -1\n", + "****\n", + "\n", + "[03:44:12] ERROR: Element 'Du' not found\n", + "[03:44:12] ERROR: moving to the beginning of the next molecule\n", + "[03:44:16] \n", + "\n", + "****\n", + "Post-condition Violation\n", + "Element 'Du' not found\n", + "Violation occurred on line 93 in file /home/conda/feedstock_root/build_artifacts/rdkit_1651075169244/work/Code/GraphMol/PeriodicTable.h\n", + "Failed Expression: anum > -1\n", + "****\n", + "\n", + "[03:44:16] ERROR: Element 'Du' not found\n", + "[03:44:16] ERROR: moving to the beginning of the next molecule\n", + "[03:44:18] \n", + "\n", + "****\n", + "Post-condition Violation\n", + "Element 'Du' not found\n", + "Violation occurred on line 93 in file /home/conda/feedstock_root/build_artifacts/rdkit_1651075169244/work/Code/GraphMol/PeriodicTable.h\n", + "Failed Expression: anum > -1\n", + "****\n", + "\n", + "[03:44:18] ERROR: Element 'Du' not found\n", + "[03:44:18] ERROR: moving to the beginning of the next molecule\n", + "[03:44:27] \n", + "\n", + "****\n", + "Post-condition Violation\n", + "Element 'Du' not found\n", + "Violation occurred on line 93 in file /home/conda/feedstock_root/build_artifacts/rdkit_1651075169244/work/Code/GraphMol/PeriodicTable.h\n", + "Failed Expression: anum > -1\n", + "****\n", + "\n", + "[03:44:27] ERROR: Element 'Du' not found\n", + "[03:44:27] ERROR: moving to the beginning of the next molecule\n", + "[03:44:39] \n", + "\n", + "****\n", + "Post-condition Violation\n", + "Element 'Du' not found\n", + "Violation occurred on line 93 in file /home/conda/feedstock_root/build_artifacts/rdkit_1651075169244/work/Code/GraphMol/PeriodicTable.h\n", + "Failed Expression: anum > -1\n", + "****\n", + "\n", + "[03:44:39] ERROR: Element 'Du' not found\n", + "[03:44:39] ERROR: moving to the beginning of the next molecule\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Excluded molecules: ['2foy', '3bho', '2fov', '3qlb', '2fou']\n" + ] + } + ], + "source": [ + "id, coords_x, coords_y, coords_z, exclusion_list = list(), list(), list(), list(), list()\n", + "for i in range(len(filePathtoGeneralSet)):\n", + " _id = str(filePathtoGeneralSet[i].split(\"/\")[-1])\n", + " if _id in ['index', 'readme']: continue\n", + " try:\n", + " com = calculate_centre_of_mass(filePathtoGeneralSet[i] + \"/\" + _id + \"_ligand.sdf\")\n", + " except AttributeError:\n", + " exclusion_list.append(_id)\n", + " continue\n", + " id.append(_id)\n", + " coords_x.append(round(com[0], 3))\n", + " coords_y.append(round(com[1], 3))\n", + " coords_z.append(round(com[2], 3))\n", + "comGeneralSet = {'pdb_id': id, 'com_x': coords_x, 'com_y': coords_y, 'com_z': coords_z}\n", + "df = pd.DataFrame(comGeneralSet)\n", + "with open('general-set-com.txt', 'a') as file:\n", + " df_string = df.to_string(header=False, index=False)\n", + " file.write(df_string)\n", + "\n", + "print(f\"Excluded molecules: {exclusion_list}\")" + ] + }, + { + "cell_type": "markdown", + "id": "f2a5d5ce-1299-4672-9223-e9043e130a77", + "metadata": {}, + "source": [ + "For refined set," + ] + }, + { + "cell_type": "code", + "execution_count": 72, + "id": "b43c6a48-b33c-4ffb-9d5a-4109b0b8b850", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Excluded molecules: []\n" + ] + } + ], + "source": [ + "id, coords_x, coords_y, coords_z, exclusion_list = list(), list(), list(), list(), list()\n", + "for i in range(len(filePathtoRefinedSet)):\n", + " _id = str(filePathtoRefinedSet[i].split(\"/\")[-1])\n", + " if _id in ['index', 'readme']: continue\n", + " try:\n", + " com = calculate_centre_of_mass(filePathtoRefinedSet[i] + \"/\" + _id + \"_ligand.sdf\")\n", + " except AttributeError:\n", + " exclusion_list.append(_id)\n", + " continue\n", + " id.append(_id)\n", + " coords_x.append(round(com[0], 3))\n", + " coords_y.append(round(com[1], 3))\n", + " coords_z.append(round(com[2], 3))\n", + "comRefinedSet = {'pdb_id': id, 'com_x': coords_x, 'com_y': coords_y, 'com_z': coords_z}\n", + "df = pd.DataFrame(comRefinedSet)\n", + "with open('refined-set-com.txt', 'a') as file:\n", + " df_string = df.to_string(header=False, index=False)\n", + " file.write(df_string)\n", + "\n", + "print(f\"Excluded molecules: {exclusion_list}\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "d97e1536-aa70-4b09-ba4d-a43582f065f6", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.12" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/utils/Data.py b/utils/Data.py new file mode 100644 index 0000000..32a5f12 --- /dev/null +++ b/utils/Data.py @@ -0,0 +1,189 @@ +import os.path as osp +import re +import multiprocessing as mp +from typing import List, Tuple, Union, Dict +from dataclasses import dataclass, field + +import numpy as np +import pandas as pd +from biopandas.pdb import PandasPdb +import torch +import torch_geometric as pyg +import pytorch_lightning as pl + +import oddt.interactions as interactions +from oddt.spatial import distance +from oddt.toolkits.ob import Molecule, readfile +from openbabel import openbabel + + + +def atom_type_one_hot(atomic_num:int) -> List[int]: + """ + 43 + 1 atom types considered: + ['C', 'N', 'O', 'S', 'F', 'Si', 'P', 'Cl', 'Br', 'Mg', + 'Na', 'Ca', 'Fe', 'As', 'Al', 'I', 'B', 'V', 'K', 'Tl', + 'Be', 'Sb', 'Sn', 'Ag', 'Pd', 'Co', 'Se', 'Ti', 'Zn', 'Li', + 'Ge', 'Cu', 'Au', 'Ni', 'Cd', 'In', 'Mn', 'Zr', 'Cr', 'Pt', + 'Hg', 'Pb', 'Ga', 'Unknown'] + + Args: + atomic_num (int): Atom's atomic number + + Output: + List[int]: One-hot vector + + """ + one_hot = 43 * [0] + used_atom_num = [ 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, + 14, 15, 16, 17, 19, 20, 22, 23, 24, 25, + 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, + 40, 46, 47, 48, 49, 50, 51, 53, 78, 79, + 80, 81, 82] + d_atom_num = {3:0, 4:1, 5:2, 6:3, 7:4, 8:5, 9:6, 11:7, 12:8, 13:9, + 14:10, 15:11, 16:12, 17:13, 19:14, 20:15, 22:16, 23:17, 24:18, 25:19, + 26:20, 27:21, 28:22, 29:23, 30:24, 31:25, 32:26, 33:27, 34:28, 35:29, + 40:30, 46:31, 47:32, 48:33, 49:34, 50:35, 51:36, 53:37, 78:38, 79:39, + 80:40, 81:41, 82:42} + idx = 43 + if atomic_num in used_atom_num: + idx = d_atom_num[atomic_num] + one_hot[idx] = 1 + + return one_hot + + +def atom_hybridisation_one_hot(hybridisation:int) -> List[int]: + """ + Hybridisation considered: + [other, sp, sp2, sp3, sq.planer, trig, bipy, octahedral] + + Args: + hybridisation (int): Hybridisation + + Output: + List[int]: One-hot vector + + """ + one_hot_hybridisation = 7 * [0] + if hybridisation not in [1, 2, 3, 4, 5, 6]: + hybridisation = 0 + one_hot_hybridisation[hybridisation] = 1 + + return one_hot_hybridisation + + +def atom_degree_one_hot(degree:int) -> List[int]: + """ + Hetero/heavy degree considered: + [0, 1, 2, 3, 4, 5, 6+] + + Args: + degree (int): Hetero/heavy degree + + Output: + List[int]: One-hot vector + """ + oh_degree = 7 * [0] + if degree > 6: + oh_degree[6] = 1 + else: + oh_degree[degree] = 1 + + return oh_degree + + +def get_bond_properties(bond:openbabel.OBBond) -> List: + """ + Bond properties considered: + - Bond length + - Is in an aromatic ring + - Is in a ring + - Is single bond + - Is double bond + - Is triple bond + + Args: + bond (openbabel.OBBond): openbabel bond + + Output: + List: A list of bond properties + """ + order = bond.GetBondOrder() + length = bond.GetLength() + aromatic = bond.IsAromatic() + ring = bond.IsInRing() + + return [length, aromatic, ring, order==1, order==2, order==3] + + +def get_molecular_properties(mol:Molecule) -> Tuple[List, List, List]: + """ + Compute all atomic and molecular properties of a molecule + + Args: + pybel_mol (Molecule): An ODDT Molecule object + + Output: + Tuple[List, List, List]: (Atoms' properties, edge index, edge attributes) + """ + oh_atom_type = np.array(list(map(atom_type_one_hot, mol.atom_dict['atomicnum'].tolist()))) + oh_hybridisation = np.array(list(map(atom_hybridisation_one_hot, mol.atom_dict['hybridization'].tolist()))) + partial_charge = mol.atom_dict['charge'].reshape(-1, 1) + hydrophobic = mol.atom_dict['ishydrophobe'].reshape(-1, 1) + isaromatic = mol.atom_dict['isaromatic'].reshape(-1, 1) + isacceptor = mol.atom_dict['isacceptor'].reshape(-1, 1) + isdonor = mol.atom_dict['isdonor'].reshape(-1, 1) + isdonorh = mol.atom_dict['isdonor'].reshape(-1, 1) + isminus = mol.atom_dict['isminus'].reshape(-1, 1) + isplus = mol.atom_dict['isplus'].reshape(-1, 1) + + atom_properties_list = np.concatenate((oh_atom_type, oh_hybridisation, partial_charge, hydrophobic, isaromatic, isacceptor, isdonor, isdonorh, isminus, isplus), axis=1).tolist() + + edge_index, edge_attr = [[], []], [] + + for bond in mol.bonds: + ob_bond = bond.OBBond + begin_id = ob_bond.GetBeginAtom().GetIdx() - 1 + end_id = ob_bond.GetEndAtom().GetIdx() - 1 + edge_index[0] += [begin_id, end_id] + edge_index[1] += [end_id, begin_id] + edge_attr += [get_bond_properties(ob_bond), + get_bond_properties(ob_bond)] + + return (atom_properties_list, edge_index, edge_attr) + +""" +@dataclass +class CrossdockedDataSet(pyg.data.InMemoryDataset): + # Torch Geometric Dataset + root:str + stage:str + atomic_distance_cutoff:float + + def __post_init__(self): + self.df = pd.read_csv() + super().__init__(self.root) + self.data, self.slices = torch.load(self.processed_paths[0]) + + +@dataclass +class CrossdockedDataModule(pl.LightningDataModule): + # PyTorch Lightning Data Module + root: str # path to data directory + atomic_distance_cutoff: float # cutoff for interatomic distance + batch_size:int = field(default=1) # batch size + num_workers:int = field(default=1) # number of workers + persistent_workers:bool = field(default=True) # use persistant workers in dataloader + + def __post_init__(self): + super().__init__() + + def prepare_data(self): + pass + + def setup(self, stage=''): + self.dt_train = CrossdockedDataSet() + self.dt_val = CrossdockedDataset() +""" + diff --git a/utils/Featuriser.py b/utils/Featuriser.py new file mode 100644 index 0000000..2f5afa9 --- /dev/null +++ b/utils/Featuriser.py @@ -0,0 +1,141 @@ +import os +import re +import multiprocessing as mp +from typing import Tuple, Dict, Union, List +from dataclasses import dataclass, field + +from oddt.toolkits.ob import Molecule +import biopandas.pdb as bpdb +import torch +import torch_geometric as pyg + +try: + from Data import get_molecular_properties + from PLIneraction import get_bonds_protein_ligand +except: + from .utils.Data import get_molecular_properties + from .utils.PLIneraction import get_bonds_protein_ligand + + +def featurise(protein:Molecule, + ligand:Molecule, + list_atom_name:list, + cutoff:float, + ) -> Tuple: + """ + Featurize a protein and a ligand to a set of nodes and edges + + Args: + protein (ob.Molecule): + ligand (ob.Molecule): + cutoff (float): + + Output: + Tuple: Nodes and edges + """ + + assert ligand is not None, 'Error when loading ligand file' + assert protein is not None, 'Error when loading protein file' + assert list_atom_name is not None, 'Missing a list of atom names' + + with stderr_redirected(to='obabel.err'): + (protein_atom_properties_list, + protein_edge_index, protein_edge_attr) = get_molecule_properties(protein) + (ligand_atom_properties_list, + ligand_edge_index, ligand_edge_attr) = get_molecule_properties(ligand) + + (p_atm_to_l_edge_index, l_to_p_atm_edge_index, p_atm_to_l_edge_attr, + l_to_p_atm_edge_attr) = get_bonds_protein_ligand(protein, ligand, + cutoff=cutoff, + list_atom_name=list_atom_name) + + return (protein_atom_properties_list, # protein_atoms.x + ligand_atom_properties_list, # ligand_atoms.x + + protein_edge_index, # protein_atoms <-> protein_atoms + ligand_edge_index, # ligand_atoms <-> ligand_atoms + l_to_p_atm_edge_index, # ligand_atoms -> protein_atom + p_atm_to_l_edge_index, # protein_atoms -> ligand_atoms + + protein_edge_attr, # protein_atoms <-> protein_atoms + ligand_edge_attr, # ligand_atoms <-> ligand_atoms + l_to_p_atm_edge_attr, # ligand_atoms -> protein_atoms + p_atm_to_l_edge_attr # protein_atoms -> ligand_atoms + ) + + +def create_pyg_graph(protein:Molecule, + ligand:Molecule, + list_atom_name: list, + score:float = 0.0, + rmsd:float = 0.0, + protein_sasa:float = None, + ligand_sasa:float = None, + name:str = None, + cutoff:float = 4.0, + ) -> pyg.data.HeteroData: + """ + Create a torch_geometric HeteroGraph of a protein-ligand complex + + Args: + protein (Molecule): + ligand (Molecule): + list_atom_name (list): + cutoff (float): The maximal distance between two atoms to connect them with an edge. Defaults to 4.0. + + score (float, optional): Affinity target. Defaults to None. + rmsd (float, optional): Used for docking power. Defaults to 0.0. + name (str, optional): PDB ID for casf output. Defaults to None. + protein_sasa (float, optional): + ligand_sasa (float, optional): + + Output: + data (pyg.data.HeteroData): Containing several sets of nodes, and different sets of + edges that can link nodes of the same set or of different sets + """ + (protein_atm_x, + ligand_atm_x, + + protein_atm_to_protein_atm_edge_index, + ligand_atm_to_ligand_atm_edge_index, + ligand_atm_to_protein_atm_edge_index, + protein_atm_to_ligand_atm_edge_index, + + protein_atm_to_protein_atm_edge_attr, + ligand_atm_to_ligand_atm_edge_attr, + ligand_atm_to_protein_atm_edge_attr, + protein_atm_to_ligand_atm_edge_attr + ) = featurize(protein, ligand, cutoff=cutoff, list_atom_name=list_atom_name) + + data = pyg.data.HeteroData() + + data['protein_atoms'].x = torch.tensor(protein_atm_x) + data['ligand_atoms'].x = torch.tensor(ligand_atm_x) + + data['protein_atoms', 'linked_to', 'protein_atoms'].edge_index = torch.tensor( + protein_atm_to_protein_atm_edge_index) + data['ligand_atoms', 'linked_to', 'ligand_atoms'].edge_index = torch.tensor( + ligand_atm_to_ligand_atm_edge_index) + data['ligand_atoms', 'interact_with', 'protein_atoms'].edge_index = torch.tensor( + ligand_atm_to_protein_atm_edge_index) + data['protein_atoms', 'interact_with', 'ligand_atoms'].edge_index = torch.tensor( + protein_atm_to_ligand_atm_edge_index) + + data['protein_atoms', 'linked_to', 'protein_atoms'].edge_attr = torch.tensor( + protein_atm_to_protein_atm_edge_attr).float() + data['ligand_atoms', 'linked_to', 'ligand_atoms'].edge_attr = torch.tensor( + ligand_atm_to_ligand_atm_edge_attr).float() + data['ligand_atoms', 'interact_with', 'protein_atoms'].edge_attr = torch.tensor( + ligand_atm_to_protein_atm_edge_attr).float() + data['protein_atoms', 'interact_with', 'ligand_atoms'].edge_attr = torch.tensor( + protein_atm_to_ligand_atm_edge_attr).float() + + data.name = name + data.rmsd = rmsd + data.y = score + data.protein_sasa = protein_sasa + data.ligand_sasa = ligand_sasa + + return data + + \ No newline at end of file diff --git a/utils/MakeGraph.ipynb b/utils/MakeGraph.ipynb new file mode 100644 index 0000000..c753002 --- /dev/null +++ b/utils/MakeGraph.ipynb @@ -0,0 +1,1769 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "b516f7bb-9194-4c0b-bcd7-3d0dec646b9a", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/yuyang/anaconda3/envs/SINGA/lib/python3.10/site-packages/torch/cuda/__init__.py:126: UserWarning: CUDA initialization: Unexpected error from cudaGetDeviceCount(). Did you run some cuda functions before calling NumCudaDevices() that might have already set an error? Error 804: forward compatibility was attempted on non supported HW (Triggered internally at /opt/conda/conda-bld/pytorch_1689059489744/work/c10/cuda/CUDAFunctions.cpp:108.)\n", + " return torch._C._cuda_getDeviceCount() > 0\n", + "2023-07-25 06:05:26.255179: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.\n", + "To enable the following instructions: AVX2 AVX512F FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.\n", + "2023-07-25 06:05:29.346444: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT\n" + ] + } + ], + "source": [ + "import torch\n", + "import torch_geometric\n", + "from torch_geometric.data import Data, HeteroData\n", + "from torch_geometric.utils import erdos_renyi_graph, to_networkx, from_networkx\n", + "import networkx as nx\n", + "\n", + "from rdkit import Chem\n", + "from rdkit.Chem import AllChem\n", + "\n", + "import numpy as np\n", + "import pandas as pd\n", + "import matplotlib.pyplot as plt\n", + "\n", + "from keras.layers import Input, Dense\n", + "from keras.regularizers import l2\n", + "from keras.models import Model\n", + "from keras.optimizers import Adam\n", + "from keras.callbacks import EarlyStopping\n", + "\n", + "from sklearn.model_selection import train_test_split\n", + "from sklearn.metrics import confusion_matrix\n", + "\n", + "from spektral.layers import GATConv, GlobalAttentionPool\n", + "from spektral.utils import label_to_one_hot, load_sdf\n", + "#from spektral.utils import nx_to_numpy\n", + "#from spektral.chem import sdf_to_nx" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "76817739-9d47-4a4a-96f1-1f9aedf5c6c6", + "metadata": {}, + "outputs": [], + "source": [ + "import logging\n", + "from sklearn.base import BaseEstimator, TransformerMixin\n", + "logger = logging.getLogger(__name__)\n", + "\n", + "class MoleculeToGraph(BaseEstimator, TransformerMixin):\n", + " def __init__(self, file_format='sdf'):\n", + " \"\"\"Constructor.\n", + "\n", + " valid 'file_format' strings and what the transformer will expect\n", + "\n", + " smi: path to .smi file\n", + " sdf: pat to .sdf file\n", + " \"\"\"\n", + " self.file_format = file_format\n", + "\n", + " def transform(self, data):\n", + " \"\"\"Transform.\"\"\"\n", + " try:\n", + " if self.file_format == 'smi':\n", + " graphs = smi_to_nx(data)\n", + " elif self.file_format == 'sdf':\n", + " graphs = sdf_to_nx(data)\n", + " else:\n", + " raise Exception('file_format must be smi or sdf')\n", + " for graph in graphs:\n", + " yield graph\n", + "\n", + " except Exception as e:\n", + " logger.debug('Failed iteration. Reason: %s' % e)\n", + " logger.debug('Exception', exc_info=True)\n", + "\n", + "\n", + "################\n", + "# import to networkx graphs\n", + "###############\n", + "def load_sdf(file):\n", + " suppl = Chem.SDMolSupplier(file)\n", + " for mol in suppl:\n", + " if mol:\n", + " yield mol\n", + "\n", + "def load_smi(file):\n", + " suppl = Chem.SmilesMolSupplier(file)\n", + " for mol in suppl:\n", + " if mol:\n", + " yield mol\n", + "\n", + "def sdf_to_nx(file):\n", + " # read sdf file\n", + " suppl = load_sdf(file)\n", + " for mol in suppl:\n", + " yield rdkmol_to_nx(mol)\n", + "\n", + "def smi_to_nx(file):\n", + " # read smi file\n", + " suppl = load_smi(file)\n", + " for mol in suppl:\n", + " yield rdkmol_to_nx(mol)\n", + "\n", + "def rdkmol_to_nx(mol):\n", + " # rdkit-mol object to nx.graph\n", + " graph = nx.Graph()\n", + " for e in mol.GetAtoms():\n", + " graph.add_node(e.GetIdx(), label=e.GetSymbol())\n", + " for b in mol.GetBonds():\n", + " graph.add_edge(b.GetBeginAtomIdx(), b.GetEndAtomIdx(), label=str(int(b.GetBondTypeAsDouble())))\n", + " return graph\n", + "\n", + "def smiles_strings_to_nx(smileslist):\n", + " # smiles strings\n", + " for smile in smileslist:\n", + " mol = Chem.MolFromSmiles(smile)\n", + " yield rdkmol_to_nx(mol)\n", + "\n", + "################\n", + "# exporting networkx graphs\n", + "###############\n", + "\n", + "def nx_to_smi(graphs, file):\n", + " # writes smiles strings to a file\n", + " chem = [nx_to_rdkit(graph) for graph in graphs]\n", + " smis = [Chem.MolToSmiles(m) for m in chem]\n", + " with open(file, 'w') as f:\n", + " f.write(\"SMILES\\n\")\n", + " f.write('\\n'.join(smis))\n", + "\n", + "def nx_to_rdkit(graph):\n", + " m = Chem.MolFromSmiles('')\n", + " mw = Chem.RWMol(m)\n", + " atom_index = {}\n", + " for n, d in graph.nodes(data=True):\n", + " atom_index[n] = mw.AddAtom(Chem.Atom(d['label']))\n", + " for a, b, d in graph.edges(data=True):\n", + " start = atom_index[a]\n", + " end = atom_index[b]\n", + " bond_type = d.get(\"label\", '1')\n", + " if bond_type == '1':\n", + " mw.AddBond(start, end, Chem.BondType.SINGLE)\n", + " elif bond_type == '2':\n", + " mw.AddBond(start, end, Chem.BondType.DOUBLE)\n", + " elif bond_type == '3':\n", + " mw.AddBond(start, end, Chem.BondType.TRIPLE)\n", + " # more options:\n", + " # http://www.rdkit.org/Python_Docs/rdkit.Chem.rdchem.BondType-class.html\n", + " else:\n", + " raise Exception('bond type not implemented')\n", + "\n", + " mol = mw.GetMol()\n", + " return mol" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "bf4a9dc4-676e-4b5a-90ae-560e7627332f", + "metadata": {}, + "outputs": [], + "source": [ + "def get_graph_info(mol):\n", + " # Extract atom features and coordinates\n", + " atom_features = []\n", + " coordinates = []\n", + " beginIdx, endIdx = [], []\n", + "\n", + " for i in range(len(mol.GetBonds())):\n", + " beginAtomIdx = mol.GetBondWithIdx(i).GetBeginAtomIdx()\n", + " endAtomIdx = mol.GetBondWithIdx(i).GetEndAtomIdx()\n", + " beginIdx.append(beginAtomIdx)\n", + " endIdx.append(endAtomIdx)\n", + " \n", + " bond_index = np.array([beginIdx, endIdx])\n", + " bond_index = torch.LongTensor(bond_index)\n", + "\n", + " for atom in mol.GetAtoms():\n", + " atom_features.append(atom.GetAtomicNum())\n", + " coordinates.append(list(mol.GetConformer().GetAtomPosition(atom.GetIdx())))\n", + "\n", + " # Create edge index tensor (fully connected graph)\n", + " num_atoms = len(atom_features)\n", + " edge_index = torch.tensor([(i, j) for i in range(num_atoms) for j in range(num_atoms) if i != j], dtype=torch.long).t().contiguous()\n", + " \n", + " # Convert atom features and coordinates to tensors\n", + " x = torch.tensor(atom_features, dtype=torch.float).view(-1, 1)\n", + " pos = torch.tensor(coordinates, dtype=torch.float)\n", + "\n", + " return x, pos, edge_index, bond_index" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "e92b10cc-e968-4579-a8e4-8c5d4f35bc95", + "metadata": {}, + "outputs": [], + "source": [ + "def pdb_to_graph(pdb_ligand_file, pdb_protein_file):\n", + " # Read PDB files\n", + " mol_ligand = Chem.MolFromPDBFile(pdb_ligand_file, removeHs = False, sanitize = False)\n", + " mol_protein = Chem.MolFromPDBFile(pdb_protein_file, removeHs = False, sanitize = False)\n", + "\n", + " # Generate 3D coordinates\n", + " mol_ligand, mol_protein = Chem.AddHs(mol_ligand), Chem.AddHs(mol_protein)\n", + " AllChem.EmbedMolecule(mol_ligand)\n", + " AllChem.EmbedMolecule(mol_protein)\n", + "\n", + " x, pos, edge_index, bond_index = get_graph_info(mol_ligand)\n", + "\n", + " # Create the Data object\n", + " #data = Data(x=x, pos=pos, edge_index=bond_index)\n", + " data = HeteroData()\n", + " data['ligand'].x = x\n", + " data['ligand'].pos = pos\n", + " #data['ligand'].edge_index = bond_index\n", + " data['ligand', 'conc_l', 'ligand'].edge_index = bond_index\n", + "\n", + " x, pos, edge_index, bond_index = get_graph_info(mol_protein)\n", + " data['protein'].x = x\n", + " data['protein'].pos = pos\n", + " #data['protein'].edge_index = bond_index\n", + " data['protein', 'conc_p', 'protein'].edge_index = bond_index\n", + "\n", + " return data" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "fb89aecf-2a89-47e8-bf1b-f391904c50a4", + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "[06:54:10] UFFTYPER: Warning: hybridization set to SP3 for atom 0\n", + "[06:54:10] UFFTYPER: Warning: hybridization set to SP3 for atom 23\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "HeteroData(\n", + " \u001b[1mligand\u001b[0m={\n", + " x=[54, 1],\n", + " pos=[54, 3]\n", + " },\n", + " \u001b[1mprotein\u001b[0m={\n", + " x=[678, 1],\n", + " pos=[678, 3]\n", + " },\n", + " \u001b[1m(ligand, conc_l, ligand)\u001b[0m={ edge_index=[2, 56] },\n", + " \u001b[1m(protein, conc_p, protein)\u001b[0m={ edge_index=[2, 663] }\n", + ")\n" + ] + } + ], + "source": [ + "# Specify the path to the PDB file\n", + "pdb_ligand_file_path = '../../download/v2020-other-PL/9icd/9icd_ligand_dock001.pdb'\n", + "pdb_protein_file_path = '../../download/v2020-other-PL/9icd/9icd_pocket.pdb'\n", + "\n", + "# Convert PDB to graph data\n", + "graph_data = pdb_to_graph(pdb_ligand_file_path, pdb_protein_file_path)\n", + "\n", + "# Print the graph data\n", + "print(graph_data)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "0f5dd701-c091-4b68-9603-fcb41d579fab", + "metadata": {}, + "outputs": [], + "source": [ + "# a = to_networkx(graph_data, to_undirected=True)\n", + "# nx.draw(a)" + ] + }, + { + "cell_type": "markdown", + "id": "b597454b-2994-4787-8175-8c50b7a4d05f", + "metadata": {}, + "source": [ + "## Another approach" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "a94e4c79-9651-4614-be86-b3ae6a193006", + "metadata": {}, + "outputs": [], + "source": [ + "def nx_to_numpy(graph):\n", + " # Get the adjacency matrix from the NetworkX graph\n", + " adj_matrix = nx.adjacency_matrix(graph)\n", + "\n", + " # Convert the adjacency matrix to a dense NumPy array\n", + " adj_array = adj_matrix.toarray()\n", + "\n", + " # Get the node labels from the NetworkX graph\n", + " node_labels = np.array(list(nx.get_node_attributes(graph, 'label').values()))\n", + "\n", + " return adj_array, node_labels" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "b987ef9e-eec0-4c17-b433-8f4cef99d7f2", + "metadata": {}, + "outputs": [], + "source": [ + "sdf_loaded = Chem.SDMolSupplier(\"Trainingset_Delaunay-CHNO5000selected.sdf\", removeHs=False, sanitize=False)\n", + "#sdf_loaded = load_sdf('Trainingset_Delaunay-CHNO5000selected.sdf')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "d6b2031f-e4fd-41bf-a05a-21147669806e", + "metadata": {}, + "outputs": [], + "source": [ + "sdf_nx = rdkmol_to_nx(sdf_loaded[0])\n", + "sdf_adj, sdf_node = nx_to_numpy(sdf_nx)\n", + "\n", + "uniq_node = np.unique([v for x in sdf_node for v in np.unique(x)])\n", + "node = [label_to_one_hot(x, uniq_node) for x in sdf_node]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "0204b306-5b94-4232-abe6-01e806297ca5", + "metadata": {}, + "outputs": [], + "source": [ + "uniq_node" + ] + }, + { + "cell_type": "markdown", + "id": "6fb0918e-03e9-4055-93bf-7c13a5fff35d", + "metadata": {}, + "source": [ + "## Analyse protein-ligand (non-contact) interactions" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "id": "ad508204-9a86-4745-9697-9685c53589c0", + "metadata": {}, + "outputs": [], + "source": [ + "from pathlib import Path\n", + "import time\n", + "import warnings\n", + "warnings.filterwarnings(\"ignore\")\n", + "\n", + "import nglview as nv\n", + "import openbabel\n", + "from matplotlib import colors\n", + "from plip.structure.preparation import PDBComplex\n", + "from plip.exchange.report import BindingSiteReport\n", + "from opencadd.structure.core import Structure" + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "id": "02a92029-db9b-439f-8773-e3a43a666962", + "metadata": {}, + "outputs": [], + "source": [ + "import parmed as pmd\n", + "\n", + "pdb_id = '11gs'\n", + "pdb1 = pmd.load_file(f'../../download/v2020-other-PL/{pdb_id}/{pdb_id}_protein.pdb')\n", + "pdb2 = pmd.load_file(f'../../download/v2020-other-PL/{pdb_id}/{pdb_id}_ligand_dock001.pdb')\n", + "\n", + "combined = pdb1 + pdb2\n", + "combined.save(f'{pdb_id}.pdb')" + ] + }, + { + "cell_type": "code", + "execution_count": 30, + "id": "bfc3aa02-9d2e-48e4-bf8f-fb7bb7b74a6a", + "metadata": {}, + "outputs": [], + "source": [ + "def retrieve_plip_interactions(pdb_file):\n", + " \"\"\"\n", + " Retrieves the interactions from PLIP.\n", + "\n", + " Parameters\n", + " ----------\n", + " pdb_file :\n", + " The PDB file of the complex.\n", + "\n", + " Returns\n", + " -------\n", + " dict :\n", + " A dictionary of the binding sites and the interactions.\n", + " \"\"\"\n", + " protlig = PDBComplex()\n", + " protlig.load_pdb(pdb_file) # load the pdb file\n", + " for ligand in protlig.ligands:\n", + " protlig.characterize_complex(ligand) # find ligands and analyze interactions\n", + " sites = {}\n", + " # loop over binding sites\n", + " for key, site in sorted(protlig.interaction_sets.items()):\n", + " binding_site = BindingSiteReport(site) # collect data about interactions\n", + " # tuples of *_features and *_info will be converted to pandas DataFrame\n", + " keys = (\n", + " \"hydrophobic\",\n", + " \"hbond\",\n", + " \"waterbridge\",\n", + " \"saltbridge\",\n", + " \"pistacking\",\n", + " \"pication\",\n", + " \"halogen\",\n", + " \"metal\",\n", + " )\n", + " # interactions is a dictionary which contains relevant information for each\n", + " # of the possible interactions: hydrophobic, hbond, etc. in the considered\n", + " # binding site. Each interaction contains a list with\n", + " # 1. the features of that interaction, e.g. for hydrophobic:\n", + " # ('RESNR', 'RESTYPE', ..., 'LIGCOO', 'PROTCOO')\n", + " # 2. information for each of these features, e.g. for hydrophobic\n", + " # (residue nb, residue type,..., ligand atom 3D coord., protein atom 3D coord.)\n", + " interactions = {\n", + " k: [getattr(binding_site, k + \"_features\")] + getattr(binding_site, k + \"_info\")\n", + " for k in keys\n", + " }\n", + " sites[key] = interactions\n", + " return sites" + ] + }, + { + "cell_type": "markdown", + "id": "4928886f-dcaf-42ff-9fca-309aadb9079e", + "metadata": {}, + "source": [ + "We create the dictionary for the complex of interest and see how many binding sites are detected:" + ] + }, + { + "cell_type": "code", + "execution_count": 68, + "id": "78a3c530-1081-4bf3-b113-f601c895a22f", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Number of binding sites detected in 11gs.pdb : 1\n", + "with dict_keys(['LIG:Z:591'])\n" + ] + } + ], + "source": [ + "interactions_by_site = retrieve_plip_interactions(f\"{pdb_id}.pdb\")\n", + "print(\n", + " f\"Number of binding sites detected in {pdb_id}.pdb : \"\n", + " f\"{len(interactions_by_site)}\\n\"\n", + " f\"with {interactions_by_site.keys()}\"\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "a45542a9-6632-479a-8a4f-54a6b8152ceb", + "metadata": {}, + "source": [ + "In this case, the first binding site containing ligand 03P will be further investigated." + ] + }, + { + "cell_type": "code", + "execution_count": 69, + "id": "a9ed186b-7891-42fd-a002-918424832891", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "LIG:Z:591\n" + ] + } + ], + "source": [ + "index_of_selected_site = 0\n", + "selected_site = list(interactions_by_site.keys())[index_of_selected_site]\n", + "print(selected_site)" + ] + }, + { + "cell_type": "markdown", + "id": "525baad8-c720-4029-ab2a-fbd756be308b", + "metadata": {}, + "source": [ + "We can construct a ```pandas.DataFrame``` for a binding site and particular interaction type." + ] + }, + { + "cell_type": "code", + "execution_count": 70, + "id": "2507f14f-67a9-41e5-b731-0e46ac310833", + "metadata": {}, + "outputs": [], + "source": [ + "def create_df_from_binding_site(selected_site_interactions, interaction_type=\"hbond\"):\n", + " \"\"\"\n", + " Creates a data frame from a binding site and interaction type.\n", + "\n", + " Parameters\n", + " ----------\n", + " selected_site_interactions : dict\n", + " Precaluclated interactions from PLIP for the selected site\n", + " interaction_type : str\n", + " The interaction type of interest (default set to hydrogen bond).\n", + "\n", + " Returns\n", + " -------\n", + " pd.DataFrame :\n", + " DataFrame with information retrieved from PLIP.\n", + " \"\"\"\n", + "\n", + " # check if interaction type is valid:\n", + " valid_types = [\n", + " \"hydrophobic\",\n", + " \"hbond\",\n", + " \"waterbridge\",\n", + " \"saltbridge\",\n", + " \"pistacking\",\n", + " \"pication\",\n", + " \"halogen\",\n", + " \"metal\",\n", + " ]\n", + "\n", + " if interaction_type not in valid_types:\n", + " print(\"!!! Wrong interaction type specified. Hbond is chosen by default!!!\\n\")\n", + " interaction_type = \"hbond\"\n", + "\n", + " df = pd.DataFrame.from_records(\n", + " # data is stored AFTER the column names\n", + " selected_site_interactions[interaction_type][1:],\n", + " # column names are always the first element\n", + " columns=selected_site_interactions[interaction_type][0],\n", + " )\n", + " \n", + " return df" + ] + }, + { + "cell_type": "markdown", + "id": "59ae0de0-2ea8-4c49-ab31-6d12f4a71d5d", + "metadata": {}, + "source": [ + "In the next cell, we show the hydrophobic interactions from the selected binding site." + ] + }, + { + "cell_type": "code", + "execution_count": 71, + "id": "d47fa786-ab74-4855-97ba-c840a6d3d463", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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RESNRRESTYPERESCHAINRESNR_LIGRESTYPE_LIGRESCHAIN_LIGDISTLIGCARBONIDXPROTCARBONIDXLIGCOOPROTCOO
07PHEA591LIGZ3.856740112(6.689, 1.326, 30.431)(10.072, 2.163, 32.063)
19VALA591LIGZ3.546741149(8.517, 1.116, 28.027)(11.207, -1.184, 28.013)
2103ILEA591LIGZ3.5767341627(10.154, 3.047, 23.083)(11.308, 4.406, 19.99)
3107TYRA591LIGZ3.8467341696(10.154, 3.047, 23.083)(6.599, 1.683, 22.625)
4107TYRA591LIGZ3.7867271694(6.907, 3.074, 26.738)(4.842, 1.213, 24.182)
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" + ], + "text/plain": [ + " RESNR RESTYPE RESCHAIN RESNR_LIG RESTYPE_LIG RESCHAIN_LIG DIST \\\n", + "0 7 PHE A 591 LIG Z 3.85 \n", + "1 9 VAL A 591 LIG Z 3.54 \n", + "2 103 ILE A 591 LIG Z 3.57 \n", + "3 107 TYR A 591 LIG Z 3.84 \n", + "4 107 TYR A 591 LIG Z 3.78 \n", + "\n", + " LIGCARBONIDX PROTCARBONIDX LIGCOO \\\n", + "0 6740 112 (6.689, 1.326, 30.431) \n", + "1 6741 149 (8.517, 1.116, 28.027) \n", + "2 6734 1627 (10.154, 3.047, 23.083) \n", + "3 6734 1696 (10.154, 3.047, 23.083) \n", + "4 6727 1694 (6.907, 3.074, 26.738) \n", + "\n", + " PROTCOO \n", + "0 (10.072, 2.163, 32.063) \n", + "1 (11.207, -1.184, 28.013) \n", + "2 (11.308, 4.406, 19.99) \n", + "3 (6.599, 1.683, 22.625) \n", + "4 (4.842, 1.213, 24.182) " + ] + }, + "execution_count": 71, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "create_df_from_binding_site(interactions_by_site[selected_site], interaction_type=\"hydrophobic\")" + ] + }, + { + "cell_type": "markdown", + "id": "9cc7cdf9-01a2-4e76-9993-7522f46dcc11", + "metadata": {}, + "source": [ + "If hydrogen interactions are of interest, the table can be generated as follow:" + ] + }, + { + "cell_type": "code", + "execution_count": 72, + "id": "b98e5369-7f4e-45f6-b0e6-d7457da426bf", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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RESNRRESTYPERESCHAINRESNR_LIGRESTYPE_LIGRESCHAIN_LIGSIDECHAINDIST_H-ADIST_D-ADON_ANGLEPROTISDONDONORIDXDONORTYPEACCEPTORIDXACCEPTORTYPELIGCOOPROTCOO
051LEUA591LIGZFalse1.722.67150.45True789Nam6715O2(10.585, 7.113, 30.729)(12.883, 8.479, 30.778)
137TRPA591LIGZTrue3.644.04105.47True591Nar6718Nam(9.046, 8.58, 29.984)(6.904, 8.136, 33.385)
250GLNA591LIGZTrue3.183.78117.41True786Nam6718Nam(9.046, 8.58, 29.984)(8.896, 10.638, 26.82)
350GLNA591LIGZFalse3.133.48108.29False6721O2777O2(10.614, 10.885, 31.207)(14.041, 10.31, 31.406)
451LEUA591LIGZFalse1.642.62168.35False6712Nam794O2(11.05, 7.321, 27.713)(13.511, 7.308, 28.618)
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" + ], + "text/plain": [ + " RESNR RESTYPE RESCHAIN RESNR_LIG RESTYPE_LIG RESCHAIN_LIG SIDECHAIN \\\n", + "0 51 LEU A 591 LIG Z False \n", + "1 37 TRP A 591 LIG Z True \n", + "2 50 GLN A 591 LIG Z True \n", + "3 50 GLN A 591 LIG Z False \n", + "4 51 LEU A 591 LIG Z False \n", + "\n", + " DIST_H-A DIST_D-A DON_ANGLE PROTISDON DONORIDX DONORTYPE ACCEPTORIDX \\\n", + "0 1.72 2.67 150.45 True 789 Nam 6715 \n", + "1 3.64 4.04 105.47 True 591 Nar 6718 \n", + "2 3.18 3.78 117.41 True 786 Nam 6718 \n", + "3 3.13 3.48 108.29 False 6721 O2 777 \n", + "4 1.64 2.62 168.35 False 6712 Nam 794 \n", + "\n", + " ACCEPTORTYPE LIGCOO PROTCOO \n", + "0 O2 (10.585, 7.113, 30.729) (12.883, 8.479, 30.778) \n", + "1 Nam (9.046, 8.58, 29.984) (6.904, 8.136, 33.385) \n", + "2 Nam (9.046, 8.58, 29.984) (8.896, 10.638, 26.82) \n", + "3 O2 (10.614, 10.885, 31.207) (14.041, 10.31, 31.406) \n", + "4 O2 (11.05, 7.321, 27.713) (13.511, 7.308, 28.618) " + ] + }, + "execution_count": 72, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "create_df_from_binding_site(interactions_by_site[selected_site], interaction_type=\"hbond\")" + ] + }, + { + "cell_type": "code", + "execution_count": 73, + "id": "b425d5a5-54e1-4698-9316-854813497872", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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RESNRRESTYPERESCHAINRESNR_LIGRESTYPE_LIGRESCHAIN_LIGDIST_A-WDIST_D-WDON_ANGLEWATER_ANGLEPROTISDONDONOR_IDXDONORTYPEACCEPTOR_IDXACCEPTORTYPEWATER_IDXLIGCOOPROTCOOWATERCOO
012ARGA591LIGZ3.683.12160.48121.20True199Ng+6703N36607(13.421, 9.166, 22.647)(13.664, 6.134, 22.049)(10.628, 6.786, 22.377)
112ARGA591LIGZ3.613.12160.4872.60True199Ng+6706O.co26607(10.633, 10.38, 22.738)(13.664, 6.134, 22.049)(10.628, 6.786, 22.377)
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RESNRRESTYPERESCHAINPROT_IDX_LISTRESNR_LIGRESTYPE_LIGRESCHAIN_LIGDISTPROTISPOSLIG_GROUPLIG_IDX_LISTLIGCOOPROTCOO
012ARGA199,202,205591LIGZ5.00TrueCarboxylate6706,6707(10.472999999999999, 9.370000000000001, 22.333)(14.368333333333332, 6.532, 20.98966666666667)
143LYSA689591LIGZ3.18TrueCarboxylate6722,6721(9.575, 11.23, 31.326999999999998)(6.949, 12.901, 31.966)
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" + ], + "text/plain": [ + " RESNR RESTYPE RESCHAIN PROT_IDX_LIST RESNR_LIG RESTYPE_LIG RESCHAIN_LIG \\\n", + "0 12 ARG A 199,202,205 591 LIG Z \n", + "1 43 LYS A 689 591 LIG Z \n", + "\n", + " DIST PROTISPOS LIG_GROUP LIG_IDX_LIST \\\n", + "0 5.00 True Carboxylate 6706,6707 \n", + "1 3.18 True Carboxylate 6722,6721 \n", + "\n", + " LIGCOO \\\n", + "0 (10.472999999999999, 9.370000000000001, 22.333) \n", + "1 (9.575, 11.23, 31.326999999999998) \n", + "\n", + " PROTCOO \n", + "0 (14.368333333333332, 6.532, 20.98966666666667) \n", + "1 (6.949, 12.901, 31.966) " + ] + }, + "execution_count": 74, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "create_df_from_binding_site(interactions_by_site[selected_site], interaction_type=\"saltbridge\")" + ] + }, + { + "cell_type": "code", + "execution_count": 75, + "id": "adf47b37-5e3c-44cf-92b1-ac06c2c74963", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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RESNRRESTYPERESCHAINRESNR_LIGRESTYPE_LIGRESCHAIN_LIGPROT_IDX_LISTCENTDISTANGLEOFFSETTYPELIG_IDX_LISTLIGCOOPROTCOO
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" + ], + "text/plain": [ + "Empty DataFrame\n", + "Columns: [RESNR, RESTYPE, RESCHAIN, RESNR_LIG, RESTYPE_LIG, RESCHAIN_LIG, PROT_IDX_LIST, CENTDIST, ANGLE, OFFSET, TYPE, LIG_IDX_LIST, LIGCOO, PROTCOO]\n", + "Index: []" + ] + }, + "execution_count": 75, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "create_df_from_binding_site(interactions_by_site[selected_site], interaction_type=\"pistacking\")" + ] + }, + { + "cell_type": "code", + "execution_count": 76, + "id": "31c4b0d0-b7c8-4998-a466-9081689e949c", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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RESNRRESTYPERESCHAINPROT_IDX_LISTRESNR_LIGRESTYPE_LIGRESCHAIN_LIGDISTOFFSETPROTCHARGEDLIG_GROUPLIG_IDX_LISTLIGCOOPROTCOO
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" + ], + "text/plain": [ + "Empty DataFrame\n", + "Columns: [RESNR, RESTYPE, RESCHAIN, PROT_IDX_LIST, RESNR_LIG, RESTYPE_LIG, RESCHAIN_LIG, DIST, OFFSET, PROTCHARGED, LIG_GROUP, LIG_IDX_LIST, LIGCOO, PROTCOO]\n", + "Index: []" + ] + }, + "execution_count": 76, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "create_df_from_binding_site(interactions_by_site[selected_site], interaction_type=\"pication\")" + ] + }, + { + "cell_type": "code", + "execution_count": 77, + "id": "a3ce6a88-bebf-49f4-9eed-379e1e9c9061", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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RESNRRESTYPERESCHAINRESNR_LIGRESTYPE_LIGRESCHAIN_LIGSIDECHAINDISTDON_ANGLEACC_ANGLEDON_IDXDONORTYPEACC_IDXACCEPTORTYPELIGCOOPROTCOO
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" + ], + "text/plain": [ + "Empty DataFrame\n", + "Columns: [RESNR, RESTYPE, RESCHAIN, RESNR_LIG, RESTYPE_LIG, RESCHAIN_LIG, SIDECHAIN, DIST, DON_ANGLE, ACC_ANGLE, DON_IDX, DONORTYPE, ACC_IDX, ACCEPTORTYPE, LIGCOO, PROTCOO]\n", + "Index: []" + ] + }, + "execution_count": 77, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "create_df_from_binding_site(interactions_by_site[selected_site], interaction_type=\"halogen\")" + ] + }, + { + "cell_type": "code", + "execution_count": 78, + "id": "84bc5fb8-9582-48f3-86cf-584222936be3", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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RESNRRESTYPERESCHAINRESNR_LIGRESTYPE_LIGRESCHAIN_LIGMETAL_IDXMETAL_TYPETARGET_IDXTARGET_TYPECOORDINATIONDISTLOCATIONRMSGEOMETRYCOMPLEXNUMMETALCOOTARGETCOO
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" + ], + "text/plain": [ + "Empty DataFrame\n", + "Columns: [RESNR, RESTYPE, RESCHAIN, RESNR_LIG, RESTYPE_LIG, RESCHAIN_LIG, METAL_IDX, METAL_TYPE, TARGET_IDX, TARGET_TYPE, COORDINATION, DIST, LOCATION, RMS, GEOMETRY, COMPLEXNUM, METALCOO, TARGETCOO]\n", + "Index: []" + ] + }, + "execution_count": 78, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "create_df_from_binding_site(interactions_by_site[selected_site], interaction_type=\"metal\")" + ] + }, + { + "cell_type": "markdown", + "id": "ab063574-6b7c-4f35-98db-873419586cb7", + "metadata": {}, + "source": [ + "Now, let’s try to represent those interactions in the NGL viewer. We can draw cylinders between the interaction points (```LIGCOO``` and ```PROTCOO``` in the ```pandas.DataFrame```) and colour-code them as shown in ```colour_map```, which uses RGB tuples." + ] + }, + { + "cell_type": "code", + "execution_count": 79, + "id": "9c8d89aa-e439-4657-8468-e60460fd9c5a", + "metadata": {}, + "outputs": [], + "source": [ + "color_map = {\n", + " \"hydrophobic\": [0.90, 0.10, 0.29],\n", + " \"hbond\": [0.26, 0.83, 0.96],\n", + " \"waterbridge\": [1.00, 0.88, 0.10],\n", + " \"saltbridge\": [0.67, 1.00, 0.76],\n", + " \"pistacking\": [0.75, 0.94, 0.27],\n", + " \"pication\": [0.27, 0.60, 0.56],\n", + " \"halogen\": [0.94, 0.20, 0.90],\n", + " \"metal\": [0.90, 0.75, 1.00],\n", + "}" + ] + }, + { + "cell_type": "markdown", + "id": "a31e36c3-e852-4651-bbd5-d4265d17b817", + "metadata": {}, + "source": [ + "Define a helper function to show the interactions." + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "id": "f84af5d0-4cc4-4976-9345-9410358320d9", + "metadata": {}, + "outputs": [], + "source": [ + "def show_interactions_3d(\n", + " pdb_id, selected_site_interactions, highlight_interaction_colors=color_map\n", + "):\n", + " \"\"\"\n", + " 3D visualization of protein-ligand interactions.\n", + "\n", + " Parameters\n", + " ----------\n", + " pdb_id : str\n", + " The pdb ID of interest.\n", + " selected_site_interactions : dict\n", + " Precaluclated interactions from PLIP for the selected site\n", + " highlight_interaction_colors : dict\n", + " The colors used to highlight the different interaction types.\n", + "\n", + " Returns\n", + " -------\n", + " NGL viewer with explicit interactions given by PLIP.\n", + " \"\"\"\n", + "\n", + " # Create NGLviewer\n", + " viewer = nv.NGLWidget(height=\"600px\", default=True, gui=True)\n", + " # Add protein\n", + " prot_component = viewer.add_pdbid(pdb_id)\n", + " # Add the ligands\n", + " viewer.add_representation(repr_type=\"ball+stick\", selection=\"hetero and not water\")\n", + "\n", + " interacting_residues = []\n", + " for interaction_type, interaction_list in selected_site_interactions.items():\n", + " color = highlight_interaction_colors[interaction_type]\n", + " if len(interaction_list) == 1:\n", + " continue\n", + " df_interactions = pd.DataFrame.from_records(\n", + " interaction_list[1:], columns=interaction_list[0]\n", + " )\n", + " for _, interaction in df_interactions.iterrows():\n", + " name = interaction_type\n", + " # add cylinder between ligand and protein coordinate\n", + " viewer.shape.add_cylinder(\n", + " interaction[\"LIGCOO\"],\n", + " interaction[\"PROTCOO\"],\n", + " color,\n", + " [0.1],\n", + " name,\n", + " )\n", + " interacting_residues.append(interaction[\"RESNR\"])\n", + " \n", + " # Display interacting residues\n", + " res_sele = \" or \".join([f\"({r} and not _H)\" for r in interacting_residues])\n", + " res_sele_nc = \" or \".join([f\"({r} and ((_O) or (_N) or (_S)))\" for r in interacting_residues])\n", + " prot_component.add_ball_and_stick(sele=res_sele, colorScheme=\"chainindex\", aspectRatio=1.5)\n", + " prot_component.add_ball_and_stick(sele=res_sele_nc, colorScheme=\"element\", aspectRatio=1.5)\n", + " \n", + " # Center on ligand\n", + " viewer.center(\"ligand\")\n", + " \n", + " return viewer" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "id": "be094efb-670d-4128-8c93-53ab8ef04bef", + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": "", + "text/plain": [ + "" + ] + }, + "execution_count": 28, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "viewer_3d = show_interactions_3d('combine', interactions_by_site[selected_site])\n", + "viewer_3d.render_image(trim=True, factor=2, transparent=True);\n", + "viewer_3d._display_image()" + ] + }, + { + "cell_type": "code", + "execution_count": 80, + "id": "4028863a-2988-4618-8dc1-44104d43436b", + "metadata": {}, + "outputs": [], + "source": [ + "all_intr_types = (\"hydrophobic\",\n", + " \"hbond\",\n", + " \"waterbridge\",\n", + " \"saltbridge\",\n", + " \"pistacking\",\n", + " \"pication\",\n", + " \"halogen\",\n", + " \"metal\")\n", + "\n", + "allPLInteractions = pd.DataFrame()\n", + "for intr_type in all_intr_types:\n", + " _df = create_df_from_binding_site(interactions_by_site[selected_site], interaction_type=intr_type)\n", + " allPLInteractions = pd.concat([allPLInteractions, _df], ignore_index=True)" + ] + }, + { + "cell_type": "code", + "execution_count": 81, + "id": "846f4bcf-99a2-49a2-8fe5-44111d2229bd", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " RESNR RESTYPE RESCHAIN RESNR_LIG RESTYPE_LIG RESCHAIN_LIG DIST \\\n", + "0 7 PHE A 591 LIG Z 3.85 \n", + "1 9 VAL A 591 LIG Z 3.54 \n", + "2 103 ILE A 591 LIG Z 3.57 \n", + "3 107 TYR A 591 LIG Z 3.84 \n", + "4 107 TYR A 591 LIG Z 3.78 \n", + "\n", + " LIGCARBONIDX PROTCARBONIDX LIGCOO ... METAL_TYPE \\\n", + "0 6740.0 112.0 (6.689, 1.326, 30.431) ... NaN \n", + "1 6741.0 149.0 (8.517, 1.116, 28.027) ... NaN \n", + "2 6734.0 1627.0 (10.154, 3.047, 23.083) ... NaN \n", + "3 6734.0 1696.0 (10.154, 3.047, 23.083) ... NaN \n", + "4 6727.0 1694.0 (6.907, 3.074, 26.738) ... NaN \n", + "\n", + " TARGET_IDX TARGET_TYPE COORDINATION LOCATION RMS GEOMETRY COMPLEXNUM \\\n", + "0 NaN NaN NaN NaN NaN NaN NaN \n", + "1 NaN NaN NaN NaN NaN NaN NaN \n", + "2 NaN NaN NaN NaN NaN NaN NaN \n", + "3 NaN NaN NaN NaN NaN NaN NaN \n", + "4 NaN NaN NaN NaN NaN NaN NaN \n", + "\n", + " METALCOO TARGETCOO \n", + "0 NaN NaN \n", + "1 NaN NaN \n", + "2 NaN NaN \n", + "3 NaN NaN \n", + "4 NaN NaN \n", + "\n", + "[5 rows x 50 columns]\n" + ] + } + ], + "source": [ + "print(allPLInteractions.head(5))" + ] + }, + { + "cell_type": "code", + "execution_count": 82, + "id": "17cd14e5-0d15-46f0-9298-e89f3036f201", + "metadata": {}, + "outputs": [], + "source": [ + "allPLInteractions.to_csv(\"allPLI.csv\")" + ] + }, + { + "cell_type": "code", + "execution_count": 83, + "id": "1b6a91e5-a7d9-4a39-8fd4-5977bfd6dcf4", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "plip.structure.preparation.PDBComplex" + ] + }, + "execution_count": 83, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "protlig = PDBComplex()\n", + "protlig.load_pdb(\"11gs.pdb\") # load the pdb file\n", + "type(protlig)" + ] + }, + { + "cell_type": "code", + "execution_count": 84, + "id": "c1df9636-428c-4fcb-848f-213c2da164ca", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "(30.676, 3.06, 38.855)" + ] + }, + "execution_count": 84, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "list(protlig.atoms.values())[0].coords" + ] + }, + { + "cell_type": "code", + "execution_count": 85, + "id": "bbe8377f-f110-414d-aef7-40947b17c475", + "metadata": {}, + "outputs": [], + "source": [ + "import openbabel as ob\n", + "\n", + "def find_atom_by_coordinates(molecule, target_coordinates):\n", + " for atom in list(molecule.atoms.values()):\n", + " atom_coordinates = atom.coords\n", + "\n", + " # Compare the coordinates\n", + " if round(atom_coordinates[0], 3) == round(target_coordinates[0], 3) and \\\n", + " round(atom_coordinates[1], 3) == round(target_coordinates[1], 3) and \\\n", + " round(atom_coordinates[2], 3) == round(target_coordinates[2], 3):\n", + " return atom\n", + "\n", + " # If no match found\n", + " return None" + ] + }, + { + "cell_type": "code", + "execution_count": 86, + "id": "f61d77aa-c1cc-4f95-b3d7-75f48dbb6a6e", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Atom Found:\n", + "Atom Type: C3\n", + "Atom Index: 6739\n", + "Atom Coordinates: (8.517, 1.116, 28.027)\n" + ] + } + ], + "source": [ + "# Find the atom with the target coordinates\n", + "target_coords = (8.517, 1.116, 28.027)\n", + "target_atom = find_atom_by_coordinates(protlig, target_coordinates=list(target_coords))\n", + "\n", + "# Print the atom information\n", + "if target_atom is not None:\n", + " print('Atom Found:')\n", + " print('Atom Type:', target_atom.type)\n", + " print('Atom Index:', target_atom.idx)\n", + " print('Atom Coordinates:', target_atom.coords)\n", + "else:\n", + " print('Atom Not Found.')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "9d602053-98d9-46a4-8aca-7a3a438c6500", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "markdown", + "id": "364a16e5-c9d0-45c4-8f56-73415fa74107", + "metadata": {}, + "source": [ + "## Import node and edge features" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "958acf4d-86e9-408d-8296-4e40e574a30f", + "metadata": {}, + "outputs": [], + "source": [ + "import pickle\n", + "\n", + "with open(\"../features/PLComplex.pkl\", 'rb') as file:\n", + " totalDict = pickle.load(file)\n", + "\n", + "repGraph = totalDict['repDict']['9icd_1']\n" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.12" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/utils/MakeGraph.py b/utils/MakeGraph.py new file mode 100644 index 0000000..a7c7e71 --- /dev/null +++ b/utils/MakeGraph.py @@ -0,0 +1,152 @@ +################################################################# +# Main functionality # +# ================== # +# 1. Find RMSD of docked ligand poses from crystal structure # +# 2. Retrieve molecular features of protein and ligand # +# 3. Prepare node and edge features (ODDT) # +# 4. Dump all relevant info to pickle file # +# # +################################################################# + +import rdkit +from rdkit import Chem +from rdkit.Chem.rdmolops import AddHs +import oddt +from oddt.docking.AutodockVina import autodock_vina +import torch + +import os, glob +import pickle, yaml +import random +import warnings +import argparse +import traceback +import logging +import itertools +from tqdm import tqdm + +try: + from misc import * + from Featuriser import create_pyg_graph + from PLParser import StructureDual, parse_sdf_file + from PLFeature import ComputeSASA, ClassifyAtoms + from PLIExtension import close_contacts +except: + from .utils.misc import * + from .utils.Featuriser import create_pyg_graph + from .utils.PLParser import StructureDual, parse_sdf_file + from .utils.PLFeature import ComputeSASA, ClassifyAtoms + from .utils.PLIExtension import close_contacts + + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument('--config', type=str, + default='./config/config.yml') + parser.add_argument('--outdir', type=str, + default='./dataset/crossdocked_vina10') + args = parser.parse_args() + + # Logging + log_dir = args.outdir + logger = get_logger('feature_extract_log', log_dir) + logger.info(args) + + print("\n") + outDirExists = os.path.exists(args.outdir) + if not outDirExists: + os.makedirs(args.outdir) + logger.info("Output directory {args.outdir} is created.") + + # Load config + outDirExists = os.path.isfile(args.config) + if not outDirExists: + raise FileNotFoundError("Configuration YML (config.yml) file does not exist or is not specified.") + else: + logger.info("Reading configuration YML file...") + config = load_config(args.config) + #seed_all(config.featuriser.seed) + split_dict = torch.load(config.dataset.split) + logger.info(f"Found {len(split_dict['train'])} samples in the Crossdock dataset for training.") + + # Docking ligands with Autodock Vina implemented in ODDT + logger.info("Extracting features...") + #for i in tqdm(range(len(split_dict['train']))): + for i in tqdm(range(2)): + logger.info(" ") + complexDict, skippedComplex = {}, [] + name = str(split_dict['train'][i][0].split(".")[0]) + + outDirExists = os.path.exists(os.path.join(args.outdir, name.split("/")[0])) + if not outDirExists: + os.makedirs(os.path.join(args.outdir, name.split('/')[0])) + logger.info(f"Output directory {name.split('/')[0]} is created.") + + logger.info(f"Now reading {name}...") + proteinDual = StructureDual(os.path.join(config.dataset.path, split_dict['train'][i][0]), isProtein=True) + ligandDual = StructureDual(os.path.join(config.dataset.path, split_dict['train'][i][1]), isProtein=False) + + protein, _protein = proteinDual.parse_to_oddt(), proteinDual.parse_to_rdkit() + ligand, _ligand = ligandDual.parse_to_oddt(), ligandDual.parse_to_rdkit() + ligand_com = parse_sdf_file(os.path.join(config.dataset.path, split_dict['train'][i][1]))['center_of_mass'] + + vina = autodock_vina(protein=protein, + auto_ligand=ligand, + center=tuple(ligand_com), + num_modes=int(config.autodock.num_modes), + executable=config.autodock.executable) + + # Extracting vina score of native structure + vina_score = float(vina.predict_ligand(ligand).data['vina_affinity']) + protein_cc, ligand_cc = close_contacts(x=protein.atom_dict, + y=ligand.atom_dict, + cutoff=float(config.featuriser.sasa_cutoff)) + protein_cc_idx, ligand_cc_idx = list(np.unique(protein_cc['id'])), list(np.unique(ligand_cc['id'])) + protein_cc_radii, ligand_cc_radii = ClassifyAtoms(config.featuriser.symbol_radius_path, _protein, protein_cc_idx), ClassifyAtoms(config.featuriser.symbol_radius_path, _ligand, ligand_cc_idx) + + + logger.info("Extracting protein and ligand node features...") + # Computing SASA + try: + protein_cc_coords = proteinDual.RetrieveCoords(protein_cc_idx) + protein_cc_coords = list(itertools.chain.from_iterable(protein_cc_coords)) + protein_sasa = ComputeSASA(protein_cc_coords, protein_cc_idx) + + ligand_cc_coords = ligandDual.RetrieveCoords(ligand_cc_idx) + ligand_cc_coords = list(itertools.chain.from_iterable(ligand_cc_coords)) + ligand_sasa = ComputeSASA(ligand_cc_coords, ligand_cc_idx) + except Exception as e: + logger.error(traceback.format_exc()) + skippedComplex.append(name) + + logger.info("Creating protein-ligand heterogenous grapg...") + list_atom_name = proteinDual.RetrieveAtomNames() + + if (protein_sasa is not None) and (ligand_sasa is not None): + g = create_pyg_graph(protein=protein, + ligand=ligand, + cutoff=args.featuriser.interaction_cutoff, + list_atom_name=list_atom_name, + name=name, + score=vina_score, + rmsd=0.0, + protein_sasa=protein_sasa, + ligand_sasa=ligand_sasa, + ) + else: + g = create_pyg_graph(protein=protein, + ligand=ligand, + cutoff=args.featuriser.interaction_cutoff, + list_atom_name=list_atom_name, + name=name, + score=vina_score, + rmsd=0.0) + + logger.info("Saving graph...") + #torch.save(g, args.outdir + '/' + name + '.pt') + torch.save(g, "example/" + name + ".pt") + + logger.info(f"Skipped {len(skippedComplex)} complexes: {skippedComplex}") + logger.info("Process terminated successfully.\n") + \ No newline at end of file diff --git a/utils/PLFeature.py b/utils/PLFeature.py new file mode 100644 index 0000000..8870ac6 --- /dev/null +++ b/utils/PLFeature.py @@ -0,0 +1,215 @@ +from typing import Optional +import os +os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3' +import json + +import freesasa +import numpy as np +import networkx as nc + +from rdkit import Chem +from rdkit.Chem import rdFreeSASA +from rdkit.Chem.rdmolops import GetAdjacencyMatrix + +import tensorflow as tf +from tensorflow import keras +import torch +from torch_geometric.data import Data +from torch_geometric.utils import to_networkx + + + + +def accuracy(y_pred, y_true): + """Calculate accuracy.""" + return torch.sum(y_pred==y_true)/len(y_true) + + +def one_hot_encoding(x, permitted_list): + if x not in permitted_list: + x = permitted_list[-1] + + binary_encoding = [int(boolean_value) for boolean_value in list(map(lambda s: x==s, permitted_list))] + + return binary_encoding + + +def get_atom_features(atom, use_chirality=True, hydrogens_implicit=True): + permitted_list_of_atoms = ['C', 'N', 'O', 'S', 'F', 'Si', 'P', 'Cl', 'Br', 'Mg', + 'Na', 'Ca', 'Fe', 'As', 'Al', 'I', 'B', 'V', 'K', 'Tl', + 'Yb', 'Sb', 'Sn', 'Ag', 'Pd', 'Co', 'Se', 'Ti', 'Zn', 'Li', + 'Ge', 'Cu', 'Au', 'Ni', 'Cd', 'In', 'Mn', 'Zr', 'Cr', 'Pt', + 'Hg', 'Pb', 'Unknown'] + + if hydrogens_implicit == False: + permitted_list_of_atoms = ['H'] + permitted_list_of_atoms + + atom_type_enc = one_hot_encoding(str(atom.GetSymbol()), permitted_list_of_atoms) + n_heavy_neighbors_enc = one_hot_encoding(int(atom.GetDegree()), + [0, 1, 2, 3, 4, "MoreThanFour"]) + formal_charge_enc = one_hot_encoding(int(atom.GetFormalCharge()), + [-3, -2, -1, 0, 1, 2, 3, "Extreme"]) + hybridization_type_enc = one_hot_encoding(str(atom.GetHybridization()), + ['S', 'SP', 'SP2', 'SP3', 'SP3D', 'SP3D2', 'OTHER']) + is_in_a_ring_enc = [int(atom.IsInRing())] + is_aromatic_enc = [int(atom.GetIsAromatic())] + atomic_mass_scaled = [float((atom.GetMass()-10.812)/116.092)] + vdw_radius_scaled = [float((Chem.GetPeriodicTable().GetRvdw(atom.GetAtomicNum())-1.5)/0.6)] + covalent_radius_scaled = [float((Chem.GetPeriodicTable().GetRcovalent(atom.GetAtomicNum())-0.64)/0.76)] + + atom_feature_vector = atom_type_enc + \ + n_heavy_neighbors_enc + \ + formal_charge_enc + \ + hybridization_type_enc + \ + is_in_a_ring_enc + \ + is_aromatic_enc + \ + atomic_mass_scaled + \ + vdw_radius_scaled + \ + covalent_radius_scaled + + if use_chirality == True: + chirality_type_enc = one_hot_encoding(str(atom.GetChiralTag()), + ["CHI_UNSPECIFIED", + "CHI_TETRAHEDRAL_CW", + "CHI_TETRAHEDRAL_CCW", + "CHI_OTHER"]) + atom_feature_vector += chirality_type_enc + + if hydrogens_implicit == True: + n_hydrogens_enc = one_hot_encoding(int(atom.GetTotalNumHs()), [0, 1, 2, 3, 4, "MoreThanFour"]) + atom_feature_vector += n_hydrogens_enc + + return np.array(atom_feature_vector) + + +def get_bond_features(bond, use_stereochemistry=True): + permitted_list_of_bond_types = [Chem.rdchem.BondType.SINGLE, + Chem.rdchem.BondType.DOUBLE, + Chem.rdchem.BondType.TRIPLE, + Chem.rdchem.BondType.AROMATIC] + + bond_type_enc = one_hot_encoding(bond.GetBondType(), permitted_list_of_bond_types) + bond_is_conj_enc = [int(bond.GetIsConjugated())] + bond_is_in_ring_enc = [int(bond.IsInRing())] + bond_feature_vector = bond_type_enc + bond_is_conj_enc + bond_is_in_ring_enc + + if use_stereochemistry == True: + stereo_type_enc = one_hot_encoding(str(bond.GetStereo()), ["STEREOZ", "STEREOE", "STEREOANY", "STEREONONE"]) + bond_feature_vector += stereo_type_enc + + return np.array(bond_feature_vector) + + +def RetrieveMolecularFeatures(molList:list, labelList:list): + """ + Inputs: + + molList = [smiles_1, smiles_2, ....] ... a list of mol files + labelList = [y_1, y_2, ...] ... a list of numerial labels for the SMILES strings + (such as associated pKi values) + + Outputs: + + data_list = [G_1, G_2, ...] ... + a list of torch_geometric.data.Data objects which represent labeled molecular graphs + that can readily be used for machine learning + """ + + data_list = [] + + for (mol, y_val) in zip(molList, labelList): + # get feature dimen sions + try: + n_nodes = mol.GetNumAtoms() + n_edges = 2 * mol.GetNumBonds() + unrelated_smiles = "O=O" + unrelated_mol = Chem.MolFromSmiles(unrelated_smiles) + n_node_features = len(get_atom_features(unrelated_mol.GetAtomWithIdx(0))) + n_edge_features = len(get_bond_features(unrelated_mol.GetBondBetweenAtoms(0, 1))) + except AttributeError: + print("Extraction of molecular features failed!") + continue + + # construct node feature matrix X of shape (n_nodes, n_node_features) + X = np.zeros((n_nodes, n_node_features)) + pos = list() + + for idx, atom in enumerate(mol.GetAtoms()): + X[atom.GetIdx(), :] = get_atom_features(atom) + coords = mol.GetConformer().GetAtomPosition(idx) + pos.append([coords.x, coords.y, coords.z]) + + X = torch.tensor(X, dtype = torch.float) + pos = torch.tensor(np.array(pos), dtype = torch.float) + + # construct edge index array E of shape (2, n_edges) + (rows, cols) = np.nonzero(GetAdjacencyMatrix(mol)) + torch_rows = torch.from_numpy(rows.astype(np.int64)).to(torch.long) + torch_cols = torch.from_numpy(cols.astype(np.int64)).to(torch.long) + E = torch.stack([torch_rows, torch_cols], dim=0) + + # construct edge feature array EF of shape (n_edges, n_edge_features) + EF = np.zeros((n_edges, n_edge_features)) + + for (k, (i, j)) in enumerate(zip(rows, cols)): + EF[k] = get_bond_features(mol.GetBondBetweenAtoms(int(i), int(j))) + + EF = torch.tensor(EF, dtype=torch.float) + + # construct label tensor + y_tensor = torch.tensor(np.array([y_val]), dtype=torch.float) + + # construct Pytorch Geometric data object and append to data list + data_list.append(Data(x=X, edge_index=E, edge_attr=EF, y=y_tensor, pos=pos)) + + return data_list + + +def ClassifyAtoms(path, mol, cc_index, polar_atoms=[7, 8, 15, 16]): + #Taken from https://github.com/mittinatten/freesasa/blob/master/src/classifier.c + with open(path, 'r') as file: + symbol_radius = json.load(file) + """ + symbol_radius = {"H": 1.10, "C": 1.70, "N": 1.55, "O": 1.52, "P": 1.80, "S": 1.80, "SE": 1.90, "ZN": 1.39, \ + "F": 1.47, "CL": 1.75, "BR": 1.83, "I": 1.98, \ + "LI": 1.81, "BE": 1.53, "B": 1.92, \ + "NA": 2.27, "MG": 1.74, "AL": 1.84, "SI": 2.10, \ + "K": 2.75, "CA": 2.31, "GA": 1.87, "GE": 2.11, "AS": 1.85, \ + "RB": 3.03, "SR": 2.49, "IN": 1.93, "SN": 2.17, "SB": 2.06, "TE": 2.06} + """ + + radii = [] + for i, atom in enumerate(mol.GetAtoms()): + if i not in cc_index: + continue + atom.SetProp("SASAClassName", "Apolar") # mark everything as apolar to start + if atom.GetAtomicNum() in polar_atoms: #identify polar atoms and change their marking + atom.SetProp("SASAClassName", "Polar") # mark as polar + elif atom.GetAtomicNum() == 1: + if atom.GetBonds()[0].GetOtherAtom(atom).GetAtomicNum() in polar_atoms: + atom.SetProp("SASAClassName", "Polar") # mark as polar + radii.append(symbol_radius[atom.GetSymbol().upper()]) + + return radii + + +def ComputeSASA(coords:list, Rvdw:list): + assert len(coords) == 3*len(Rvdw) + sa = freesasa.calcCoord(coords, Rvdw) + + return sa.totalArea() + + +""" +def compute_sasa(mol): + mol = Chem.AddHs(mol) + + # Get Van der Waals radii (angstrom) + ptable = Chem.GetPeriodicTable() + radii = [ptable.GetRvdw(atom.GetAtomicNum()) for atom in mol.GetAtoms()] + + # Compute solvent accessible surface area + sa = rdFreeSASA.CalcSASA(mol, radii, confIdx=-1) + + return sa +""" \ No newline at end of file diff --git a/utils/PLIExtension.py b/utils/PLIExtension.py new file mode 100644 index 0000000..74d1cad --- /dev/null +++ b/utils/PLIExtension.py @@ -0,0 +1,367 @@ +import numpy as np +import pandas as pd +from scipy.spatial.distance import cdist +import oddt +import rdkit +from rdkit import Chem +import math +from math import sin, cos +import yaml + + + +BASE_ANGLES = np.array((0, 180, 120, 109.5, 90), dtype=float) + +####################################################################################### +################################### Initialisation #################################### +####################################################################################### + +""" +Spatial functions included in ODDT +Mainly used by other modules, but can be accessed directly. +""" + +def angle(p1, p2, p3): + """Returns an angle from a series of 3 points (point #2 is centroid). + Angle is returned in degrees. + + Parameters + ---------- + p1,p2,p3 : numpy arrays, shape = [n_points, n_dimensions] + Triplets of points in n-dimensional space, aligned in rows. + + Returns + ------- + angles : numpy array, shape = [n_points] + Series of angles in degrees + """ + v1 = p1 - p2 + v2 = p3 - p2 + return angle_2v(v1, v2) + + +def angle_2v(v1, v2): + """Returns an angle between two vecors.Angle is returned in degrees. + + Parameters + ---------- + v1,v2 : numpy arrays, shape = [n_vectors, n_dimensions] + Pairs of vectors in n-dimensional space, aligned in rows. + + Returns + ------- + angles : numpy array, shape = [n_vectors] + Series of angles in degrees + """ + # better than np.dot(v1, v2), multiple vectors can be applied + dot = (v1 * v2).sum(axis=-1) + norm = np.linalg.norm(v1, axis=-1) * np.linalg.norm(v2, axis=-1) + return np.degrees(np.arccos(np.clip(dot/norm, -1, 1))) + + +def distance(x, y): + """Computes distance between each pair of points from x and y. + + Parameters + ---------- + x : numpy arrays, shape = [n_x, 3] + Array of poinds in 3D + + y : numpy arrays, shape = [n_y, 3] + Array of poinds in 3D + + Returns + ------- + dist_matrix : numpy arrays, shape = [n_x, n_y] + Distance matrix + """ + return cdist(x, y) + + +def close_contacts(x, y, cutoff, x_column='coords', y_column='coords', cutoff_low=0.): + """Returns pairs of atoms which are within close contac distance cutoff. + The cutoff is semi-inclusive, i.e (cutoff_low, cutoff]. + + Parameters + ---------- + x, y : atom_dict-type numpy array + Atom dictionaries generated by oddt.toolkit.Molecule objects. + + cutoff : float + Cutoff distance for close contacts + + x_column, ycolumn : string, (default='coords') + Column containing coordinates of atoms (or pseudo-atoms, + i.e. ring centroids) + + cutoff_low : float (default=0.) + Lower bound of contacts to find (exclusive). Zero by default. + .. versionadded:: 0.6 + + Returns + ------- + x_, y_ : atom_dict-type numpy array + Aligned pairs of atoms in close contact for further processing. + """ + if len(x[x_column]) > 0 and len(x[x_column]) > 0: + d = distance(x[x_column], y[y_column]) + index = np.argwhere((d > cutoff_low) & (d <= cutoff)) + return x[index[:, 0]], y[index[:, 1]] + else: + return x[[]], y[[]] + + +def _check_angles(angles, hybridizations, tolerance): + """Helper function for checking if interactions are strict""" + angles = np.nan_to_num(angles) # NaN's throw warning on comparisons + ideal_angles = np.take(BASE_ANGLES, hybridizations)[:, np.newaxis] + lower_bound = ideal_angles - tolerance + upper_bound = ideal_angles + tolerance + return ((angles > lower_bound) & (angles < upper_bound)).any(axis=-1) + + +def hbond_acceptor_donor(mol1, mol2, cutoff, tolerance=30, donor_exact=False): + """Returns pairs of acceptor-donor atoms, which meet H-bond criteria + + Parameters + ---------- + mol1, mol2 : oddt.toolkit.Molecule object + Molecules to compute H-bond acceptor and H-bond donor pairs + + cutoff : float, (default=3.5) + Distance cutoff for A-D pairs + + tolerance : int, (default=30) + Range (+/- tolerance) from perfect direction defined by acceptor/donor hybridization + in which H-bonds are considered as strict. + donor_exact : bool + Use exact protonation states for donors, i.e. require Hs on donor. + By default ODDT implies some tautomeric structures as protonated, + even if there is no H on specific atom. + + Returns + ------- + a, d : atom_dict-type numpy array + Aligned arrays of atoms forming H-bond, firstly acceptors, + secondly donors. + + strict : numpy array, dtype=bool + Boolean array align with atom pairs, informing whether atoms + form 'strict' H-bond (pass all angular cutoffs). If false, + only distance cutoff is met, therefore the bond is 'crude'. + """ + donor_mask = mol2.atom_dict['isdonor'] + if donor_exact: + donor_mask = donor_mask & (mol2.atom_dict['numhs'] > 0) + a, d = close_contacts(mol1.atom_dict[mol1.atom_dict['isacceptor']], + mol2.atom_dict[donor_mask], + cutoff) + # skip empty values + if len(a) > 0 and len(d) > 0: + angle1 = angle(d['coords'][:, np.newaxis, :], + a['coords'][:, np.newaxis, :], + a['neighbors']) + angle2 = angle(a['coords'][:, np.newaxis, :], + d['coords'][:, np.newaxis, :], + d['neighbors']) + strict = (_check_angles(angle1, a['hybridization'], tolerance) & + _check_angles(angle2, d['hybridization'], tolerance)) + return a, d, angle1, angle2, strict + else: + return a, d, np.array([], dtype=bool), np.array([], dtype=bool), np.array([], dtype=bool) + +def halogenbond_acceptor_halogen(mol1, + mol2, + cutoff, + tolerance=30): + """Returns pairs of acceptor-halogen atoms, which meet halogen bond criteria + + Parameters + ---------- + mol1, mol2 : oddt.toolkit.Molecule object + Molecules to compute halogen bond acceptor and halogen pairs + + cutoff : float, (default=4) + Distance cutoff for A-H pairs + + tolerance : int, (default=30) + Range (+/- tolerance) from perfect direction defined by atoms hybridization + in which halogen bonds are considered as strict. + + Returns + ------- + a, h : atom_dict-type numpy array + Aligned arrays of atoms forming halogen bond, firstly acceptors, + secondly halogens + + strict : numpy array, dtype=bool + Boolean array align with atom pairs, informing whether atoms + form 'strict' halogen bond (pass all angular cutoffs). If false, + only distance cutoff is met, therefore the bond is 'crude'. + """ + a, h = close_contacts(mol1.atom_dict[mol1.atom_dict['isacceptor']], + mol2.atom_dict[mol2.atom_dict['ishalogen']], + cutoff) + # skip empty values + if len(a) > 0 and len(h) > 0: + angle1 = angle(h['coords'][:, np.newaxis, :], + a['coords'][:, np.newaxis, :], + a['neighbors']) + angle2 = angle(a['coords'][:, np.newaxis, :], + h['coords'][:, np.newaxis, :], + h['neighbors']) + strict = (_check_angles(angle1, a['hybridization'], tolerance) & + _check_angles(angle2, np.ones_like(h['hybridization']), tolerance)) + return a, h, angle1, angle2, strict + else: + return a, h, np.array([], dtype=bool), np.array([], dtype=bool), np.array([], dtype=bool) + + +def salt_bridge_plus_minus(mol1, mol2, cutoff, cation_exact=False, anion_exact=False): + """Returns pairs of plus-mins atoms, which meet salt bridge criteria + + Parameters + ---------- + mol1, mol2 : oddt.toolkit.Molecule object + Molecules to compute plus and minus pairs + + cutoff : float, (default=4) + Distance cutoff for A-H pairs + + cation_exact, anion_exact : bool + Requires interacting atoms to have non-zero formal charge. + + Returns + ------- + plus, minus : atom_dict-type numpy array + Aligned arrays of atoms forming salt bridge, firstly plus, secondly minus + + """ + cation_map = mol1.atom_dict['isplus'] + if cation_exact: + cation_map = cation_map & (mol1.atom_dict['formalcharge'] > 0) + anion_map = mol2.atom_dict['isminus'] + if anion_exact: + anion_map = anion_map & (mol2.atom_dict['formalcharge'] < 0) + m1_plus, m2_minus = close_contacts(mol1.atom_dict[cation_map], + mol2.atom_dict[anion_map], + cutoff) + return m1_plus, m2_minus + + + +####################################################################################### +##################################### Extraction ###################################### +####################################################################################### + +def hbond_oddt(protein, ligand, cutoff, tolerance=30, mol1_exact=False, mol2_exact=False): + """ + a1, d2 : protein as acceptor, ligand as donor + + angle1 = angle(a1d2[1]['coords'][:, np.newaxis, :], + a1d2[0]['coords'][:, np.newaxis, :], + a1d2[0]['neighbors']) + angle2 = angle(a1d2[0]['coords'][:, np.newaxis, :], + a1d2[1]['coords'][:, np.newaxis, :], + a1d2[1]['neighbors']) + + Interest: angle*[i][0] + """ + a1, d2, _, angle1, _ = hbond_acceptor_donor(protein, ligand, cutoff, tolerance, mol2_exact) + + """ + a2, d1 : protein as donor, ligand as acceptor + + angle1 = angle(a2d1[1]['coords'][:, np.newaxis, :], + a2d1[0]['coords'][:, np.newaxis, :], + a2d1[0]['neighbors']) + angle2 = angle(a2d1[0]['coords'][:, np.newaxis, :], + a2d1[1]['coords'][:, np.newaxis, :], + a2d1[1]['neighbors']) + """ + a2, d1, _, angle2, _ = hbond_acceptor_donor(ligand, protein, cutoff, tolerance, mol1_exact) + + return np.concatenate((a1, d1)), np.concatenate((d2, a2)), np.concatenate((angle1, angle2)) + + +def xbond_oddt(protein, ligand, cutoff, tolerance=30, mol1_exact=False, mol2_exact=False): + """ + a1, h2 : protein as acceptor, ligand as halogen donor + + angle1 = angle(a1h2[1]['coords'][:, np.newaxis, :], + a1h2[0]['coords'][:, np.newaxis, :], + a1h2[0]['neighbors']) + angle2 = angle(a1h2[0]['coords'][:, np.newaxis, :], + a1h2[1]['coords'][:, np.newaxis, :], + a1h2[1]['neighbors']) + """ + a1, h2, _, angle1, _ = halogenbond_acceptor_halogen(protein, ligand, cutoff, tolerance) + + """ + a2h1 : protein as donor, ligand as halogen acceptor + + angle1 = angle(a2h1[1]['coords'][:, np.newaxis, :], + a2h1[0]['coords'][:, np.newaxis, :], + a2h1[0]['neighbors']) + angle2 = angle(a2h1[0]['coords'][:, np.newaxis, :], + a2h1[1]['coords'][:, np.newaxis, :], + a2h1[1]['neighbors']) + """ + a2, h1, _, angle2, _ = halogenbond_acceptor_halogen(ligand, protein, cutoff, tolerance) + + return np.concatenate((a1, h1)), np.concatenate((h2, a2)), np.concatenate((angle1, angle2)) + + +def hphob_oddt(protein, ligand, cutoff): + h1, h2 = close_contacts(protein.atom_dict[protein.atom_dict['ishydrophobe']], + ligand.atom_dict[ligand.atom_dict['ishydrophobe']], + cutoff) + + return h1, h2 + + +def sbridge_oddt(protein, ligand, cutoff, mol1_exact=False, mol2_exact=False): + """p1, l2: protein positive, ligand negative""" + protein_plus, ligand_minus = salt_bridge_plus_minus(protein, ligand, cutoff) + + """l1, p2: ligand positive, protein negative""" + ligand_plus, protein_minus = salt_bridge_plus_minus(ligand, protein, cutoff) + + return np.concatenate((protein_plus, protein_minus)), np.concatenate((ligand_minus, ligand_plus)) + + +def pistack_oddt(protein, ligand, cutoff, tolerance=30): + """Interested: angle1[i]""" + r1, r2 = close_contacts(protein.ring_dict, ligand.ring_dict, cutoff, x_column='centroid', y_column='centroid') + + if len(r1) > 0 and len(r2) > 0: + angle1 = angle_2v(r1['vector'], r2['vector']) + angle2 = angle(r1['vector'] + r1['centroid'], + r1['centroid'], + r2['centroid']) + angle3 = angle(r2['vector'] + r2['centroid'], + r2['centroid'], + r1['centroid']) + return r1, r2, angle1, angle2 + + else: + return r1, r2, np.array([], dtype=bool), np.array([], dtype=bool) + + +def pication_oddt(protein, ligand, cutoff, tolerance=30, cation_exact=False): + """Interested: angle1[i]""" + cation_map = ligand.atom_dict['isplus'] + if cation_exact: + cation_map = cation_map & (ligand.atom_dict['formalcharge'] > 0) + + r1, plus2 = close_contacts(protein.ring_dict, + ligand.atom_dict[cation_map], + cutoff, + x_column='centroid') + + if len(r1) > 0 and len(plus2) > 0: + angle1 = angle_2v(r1['vector'], plus2['coords'] - r1['centroid']) + return r1, plus2, angle1 + else: + return r1, plus2, np.array([], dtype=bool) + diff --git a/utils/PLInteraction.py b/utils/PLInteraction.py new file mode 100644 index 0000000..e4d8927 --- /dev/null +++ b/utils/PLInteraction.py @@ -0,0 +1,239 @@ +import numpy as np +from oddt.toolkits.ob import Molecule +from oddt.spatial import distance +from typing import List, Tuple + +try: + import .PLIExtension as interactions +except: + import .utils.PLIExtension as interactions + + + +def extract_atom_id_from_oddt_interractions(mol1_atoms_array, mol2_atoms_array) -> dict: + dico = {} + for mol1_atom, mol2_atom in zip(mol1_atoms_array, mol2_atoms_array): + mol1_atom_id = int(mol1_atom[0]) + mol2_atom_id = int(mol2_atom[0]) + if mol1_atom_id not in dico.keys(): + dico[mol1_atom_id] = [] + dico[mol1_atom_id] += [mol2_atom_id] + return dico + + +def extract_residu_id_from_oddt_interractions(protein_residus_array): + list_residu = [] + if protein_residus_array.shape[0] != 0: + for np_row in np.nditer(protein_residus_array): + list_residu.append(np_row.tolist()[2]) + return list_residu + + +def atom_pair_in_dico(dico:dict, mol1_atom_id:str, mol2_atom_id:str): + if mol1_atom_id in dico.keys(): + return mol2_atom_id in dico[mol1_atom_id] + else: + return False + + +def is_pi(res_name:str, atom_name:str) -> bool: + if res_name == 'HIS': + if (atom_name == 'CG' or atom_name == 'CD2' or atom_name == 'NE2' + or atom_name == 'CE1' or atom_name == 'ND1'): + return True + else: + return False + elif res_name == 'PHE': + if (atom_name == 'CG' or atom_name == 'CD2' or atom_name == 'CE2' + or atom_name == 'CZ' or atom_name == 'CE1' + or atom_name == 'CD1'): + return True + else: + return False + elif res_name == 'TYR': + if (atom_name == 'CG' or atom_name == 'CD1' or atom_name == 'CE1' + or atom_name == 'CE2' or atom_name == 'CD2' + or atom_name == 'CZ'): + return True + else: + return False + elif res_name == 'TRP': + if (atom_name == 'CG' or atom_name == 'CD1' or atom_name == 'NE1' + or atom_name == 'CE2' or atom_name == 'CD2' + or atom_name == 'CE3' or atom_name == 'CZ2' + or atom_name == 'CZ3' or atom_name == 'CH2'): + return True + else: + return False + else: + return False + + +def close_contact_to_dict(protein_close_contacts: np.ndarray, + ligand_close_contacts: np.ndarray) -> dict: + dict_close_contacts = {} + for protein_atom, ligand_atom in zip(protein_close_contacts, ligand_close_contacts): + protein_atom_id = int(protein_atom[0]) + ligand_atom_id = int(ligand_atom[0]) + if ligand_atom_id not in dict_close_contacts.keys(): + dict_close_contacts[ligand_atom_id] = [] + dict_close_contacts[ligand_atom_id] += [[protein_atom_id, protein_atom, ligand_atom]] + + return dict_close_contacts + + +def remove_dupl_angles(protein_array: np.ndarray, + ligand_array: np.ndarray, + angles_array:np.ndarray): + """ + It was found that ODDT contains bugs where duplicated pairs of interaction are observed. + Hence, we have to remove duplicated angles when this situation is observed + + Args: + protein_array (np.ndarray): Array of protein atoms found in interaction + ligand_array (np.ndarray): + angle_array (np.ndarray): + + Output: + angle_array (np.ndarray): Clean array of angles + """ + to_be_removed = [] + assert protein_array.shape[0] == ligand_array.shape[0] + + for i in range(protein_array.shape[0]-1): + if (protein_array[i][0], ligand_array[i][0]) == (protein_array[i+1][0], ligand_array[i+1][0]): + to_be_removed.append(i+1) + angles_array = np.delete(angles_array, to_be_removed, 0) + + return angles_array + + +def get_bonds_protein_ligand(protein:Molecule, + ligand:Molecule, + cutoff:float, + list_atom_name:List[str]): + """ + Returns the bond between the protein and the ligand regarding the cutoff. + All ligand must have at least one edge with an protein's atom. + + Args: + protein (Molecule): protein + ligand (Molecule): ligand + cutoff (float): The maximal distance between two atoms to connect them with an edge. + list_atom_name (List[str]): List of PDB atom name, use for pi interactions + + Output: + Tuple(List, List, List, List):Protein to Ligand Edge Index, + Ligand to Protein Edge Index, + Protein to Ligand Edge Attr, + Ligand to Protein Edge Attr + """ + close_contact_protein, close_contact_ligand = interactions.close_contacts(protein.atom_dict, ligand.atom_dict, cutoff=cutoff) + + hbond_protein, hbond_ligand, hbond_angles = interactions.hbond_oddt(protein, ligand, cutoff=cutoff) + dico_hbond = extract_atom_id_from_oddt_interractions(hbond_protein, hbond_ligand) + + xbond_protein, xbond_ligand, xbond_angles = interactions.xbond_oddt(protein, ligand, cutoff=cutoff) + dico_xbond = extract_atom_id_from_oddt_interractions(xbond_protein, xbond_ligand) + + hphob_protein, hphob_ligand = interactions.hphob_oddt(protein, ligand, cutoff=cutoff) + dico_hphob = extract_atom_id_from_oddt_interractions(hphob_protein, hphob_ligand) + + sbridge_protein, sbridge_ligand = interactions.sbridge_oddt(protein, ligand, cutoff=cutoff) + dico_sbridge = extract_atom_id_from_oddt_interractions(sbridge_protein, sbridge_ligand) + + # pi_stacking + pistack_protein_residue, pistack_ligand, pistack_angles, _ = interactions.pistack_oddt(protein, ligand, cutoff=cutoff) + list_residus_pistack = extract_residu_id_from_oddt_interractions(pistack_protein_residue) + + # pi_cation + pication_protein_residue, pication_ligand, pication_angles = interactions.pication_oddt(protein, ligand, cutoff=cutoff) + list_residus_pication = extract_residu_id_from_oddt_interractions(pication_protein_residue) + + protein_atom_to_res_dict = {} + for np_row in np.nditer(protein.atom_dict): + protein_atom_to_res_dict[np_row.tolist()[0]] = np_row.tolist()[9] + + p_to_l_edge_index = [[], []] + p_to_l_edge_attr = [] + l_to_p_edge_index = [[], []] + l_to_p_edge_attr = [] + dict_close_contacts = close_contact_to_dict(close_contact_protein, close_contact_ligand) + dists = distance(protein.atom_dict['coords'], ligand.atom_dict['coords']) + + if len(hbond_angles) != 0: + hbond_angles = remove_dupl_angles(hbond_protein, hbond_ligand, hbond_angles) + if len(xbond_angles) != 0: + xbond_angles = remove_dupl_angles(xbond_protein, xbond_ligand, xbond_angles) + if len(pistack_angles) != 0: + pistack_angles = remove_dupl_angles(pistack_protein, pistack_ligand, pistack_angles) + if len(pication_angles) != 0: + pication_angles = remove_dupl_angles(pication_protein, pication_ligand, pication_angles) + + i, j, k, l = 0, 0, 0, 0 + for ligand_atom_id in range(len(ligand.atoms)): + if ligand_atom_id in dict_close_contacts.keys(): + for close_contact in dict_close_contacts[ligand_atom_id]: + protein_atom_id = close_contact[1][0] + protein_atom = close_contact[1] + ligand_atom = close_contact[2] + dist = distance([protein_atom[1]], [ligand_atom[1]])[0][0] + protein_atom_res = protein_atom_to_res_dict[protein_atom_id] + protein_atom_name = list_atom_name[protein_atom_id] + res_name = protein_atom[11] + + atom_is_pi = is_pi(res_name, protein_atom_name) + + is_hbond = atom_pair_in_dico(dico_hbond, protein_atom_id, ligand_atom_id) + is_xbond = atom_pair_in_dico(dico_xbond, protein_atom_id, ligand_atom_id) + is_hphob = atom_pair_in_dico(dico_hphob, protein_atom_id, ligand_atom_id) + is_sbridge = atom_pair_in_dico(dico_sbridge, protein_atom_id, ligand_atom_id) + is_pistack = protein_atom_res in list_residus_pistack and atom_is_pi + is_pication = protein_atom_res in list_residus_pication and atom_is_pi + + p_to_l_edge_index[0] += [int(protein_atom_id)] + p_to_l_edge_index[1] += [int(ligand_atom_id)] + l_to_p_edge_index[0] += [int(ligand_atom_id)] + l_to_p_edge_index[1] += [int(protein_atom_id)] + + if is_hbond: + angle_hbond = hbond_angles[i][0] + i += 1 + else: + angle_hbond = 0.0 + + if is_xbond: + angle_xbond = xbond_angles[j][0] + j += 1 + else: + angle_xbond = 0.0 + + if is_pistack: + angle_pistack = pistack_angles[k] + k += 1 + else: + angle_pistack = 0.0 + + if is_pication: + angle_pication = pication_angles[l] + l += 1 + else: + angle_pication = 0.0 + + p_to_l_edge_attr += [[dist, angle_hbond, angle_xbond, angle_pistack, angle_pication, + is_hbond, is_xbond, is_hphob, is_sbridge, + is_pistack, is_pication]] + l_to_p_edge_attr += [[dist, angle_hbond, angle_xbond, angle_pistack, angle_pication, + is_hbond, is_xbond, is_hphob, is_sbridge, + is_pistack, is_pication]] + else: + closer_protein_atom_id = np.argmin(dists[:, ligand_atom_id]) + dist = dists[closer_protein_atom_id, ligand_atom_id] + p_to_l_edge_index[0] += [int(closer_protein_atom_id)] + p_to_l_edge_index[1] += [int(ligand_atom_id)] + l_to_p_edge_index[0] += [int(ligand_atom_id)] + l_to_p_edge_index[1] += [int(closer_protein_atom_id)] + p_to_l_edge_attr += [[dist, 0.0, 0.0, 0.0, 0.0, False, False, False, False, False, False]] + l_to_p_edge_attr += [[dist, 0.0, 0.0, 0.0, 0.0, False, False, False, False, False, False]] + + return p_to_l_edge_index, l_to_p_edge_index, p_to_l_edge_attr, l_to_p_edge_attr diff --git a/utils/PLParser.py b/utils/PLParser.py new file mode 100644 index 0000000..08ae65d --- /dev/null +++ b/utils/PLParser.py @@ -0,0 +1,363 @@ +################################################################################### +# Disclaimer: # +# This Python script is extracted from Pocket2Mol project, which is accessible at # +# https://github.com/pengxingang/Pocket2Mol/blob/main/utils/protein_ligand.py # +################################################################################### + +import os +from typing import List +import numpy as np +from rdkit import Chem +from rdkit import RDConfig +from rdkit.Chem.rdchem import BondType +from rdkit.Chem.rdmolops import AddHs +from rdkit.Chem import ChemicalFeatures +import oddt +import biopandas.pdb as bpdb + +ATOM_FAMILIES = ['Acceptor', 'Donor', 'Aromatic', 'Hydrophobe', 'LumpedHydrophobe', 'NegIonizable', 'PosIonizable', 'ZnBinder'] +ATOM_FAMILIES_ID = {s: i for i, s in enumerate(ATOM_FAMILIES)} +BOND_TYPES = {t: i for i, t in enumerate(BondType.names.values())} +BOND_NAMES = {i: t for i, t in enumerate(BondType.names.keys())} + + +class PDBProtein(object): + AA_NAME_SYM = { + 'ALA': 'A', 'CYS': 'C', 'ASP': 'D', 'GLU': 'E', 'PHE': 'F', 'GLY': 'G', 'HIS': 'H', + 'ILE': 'I', 'LYS': 'K', 'LEU': 'L', 'MET': 'M', 'ASN': 'N', 'PRO': 'P', 'GLN': 'Q', + 'ARG': 'R', 'SER': 'S', 'THR': 'T', 'VAL': 'V', 'TRP': 'W', 'TYR': 'Y', + } + + AA_NAME_NUMBER = { + k: i for i, (k, _) in enumerate(AA_NAME_SYM.items()) + } + + BACKBONE_NAMES = ["CA", "C", "N", "O"] + + def __init__(self, data, mode='auto'): + super().__init__() + if (data[-4:].lower() == '.pdb' and mode == 'auto') or mode == 'path': + with open(data, 'r') as f: + self.block = f.read() + else: + self.block = data + + self.ptable = Chem.GetPeriodicTable() + + # Molecule properties + self.title = None + # Atom properties + self.atoms = [] + self.element = [] + self.atomic_weight = [] + self.pos = [] + self.atom_name = [] + self.is_backbone = [] + self.atom_to_aa_type = [] + # Residue properties + self.residues = [] + self.amino_acid = [] + self.center_of_mass = [] + self.pos_CA = [] + self.pos_C = [] + self.pos_N = [] + self.pos_O = [] + self._parse() + + def _enum_formatted_atom_lines(self): + for line in self.block.splitlines(): + if line[0:6].strip() == 'ATOM': + element_symb = line[76:78].strip().capitalize() + if len(element_symb) == 0: + element_symb = line[13:14] + yield { + 'line': line, + 'type': 'ATOM', + 'atom_id': int(line[6:11]), + 'atom_name': line[12:16].strip(), + 'res_name': line[17:20].strip(), + 'chain': line[21:22].strip(), + 'res_id': int(line[22:26]), + 'res_insert_id': line[26:27].strip(), + 'x': float(line[30:38]), + 'y': float(line[38:46]), + 'z': float(line[46:54]), + 'occupancy': float(line[54:60]), + 'segment': line[72:76].strip(), + 'element_symb': element_symb, + 'charge': line[78:80].strip(), + } + elif line[0:6].strip() == 'HEADER': + yield { + 'type': 'HEADER', + 'value': line[10:].strip() + } + elif line[0:6].strip() == 'ENDMDL': + break # Some PDBs have more than 1 model. + + def _parse(self): + # Process atoms + residues_tmp = {} + for atom in self._enum_formatted_atom_lines(): + if atom['type'] == 'HEADER': + self.title = atom['value'].lower() + continue + self.atoms.append(atom) + atomic_number = self.ptable.GetAtomicNumber(atom['element_symb']) + next_ptr = len(self.element) + self.element.append(atomic_number) + self.atomic_weight.append(self.ptable.GetAtomicWeight(atomic_number)) + self.pos.append(np.array([atom['x'], atom['y'], atom['z']], dtype=np.float32)) + self.atom_name.append(atom['atom_name']) + self.is_backbone.append(atom['atom_name'] in self.BACKBONE_NAMES) + self.atom_to_aa_type.append(self.AA_NAME_NUMBER[atom['res_name']]) + + chain_res_id = '%s_%s_%d_%s' % (atom['chain'], atom['segment'], atom['res_id'], atom['res_insert_id']) + if chain_res_id not in residues_tmp: + residues_tmp[chain_res_id] = { + 'name': atom['res_name'], + 'atoms': [next_ptr], + 'chain': atom['chain'], + 'segment': atom['segment'], + } + else: + assert residues_tmp[chain_res_id]['name'] == atom['res_name'] + assert residues_tmp[chain_res_id]['chain'] == atom['chain'] + residues_tmp[chain_res_id]['atoms'].append(next_ptr) + + # Process residues + self.residues = [r for _, r in residues_tmp.items()] + for residue in self.residues: + sum_pos = np.zeros([3], dtype=np.float32) + sum_mass = 0.0 + for atom_idx in residue['atoms']: + sum_pos += self.pos[atom_idx] * self.atomic_weight[atom_idx] + sum_mass += self.atomic_weight[atom_idx] + if self.atom_name[atom_idx] in self.BACKBONE_NAMES: + residue['pos_%s' % self.atom_name[atom_idx]] = self.pos[atom_idx] + residue['center_of_mass'] = sum_pos / sum_mass + + # Process backbone atoms of residues + for residue in self.residues: + self.amino_acid.append(self.AA_NAME_NUMBER[residue['name']]) + self.center_of_mass.append(residue['center_of_mass']) + for name in self.BACKBONE_NAMES: + pos_key = 'pos_%s' % name # pos_CA, pos_C, pos_N, pos_O + if pos_key in residue: + getattr(self, pos_key).append(residue[pos_key]) + else: + getattr(self, pos_key).append(residue['center_of_mass']) + + def to_dict_atom(self): + return { + 'element': np.array(self.element, dtype=np.longlong), + 'molecule_name': self.title, + 'pos': np.array(self.pos, dtype=np.float32), + 'is_backbone': np.array(self.is_backbone, dtype=np.bool), + 'atom_name': self.atom_name, + 'atom_to_aa_type': np.array(self.atom_to_aa_type, dtype=np.longlong) + } + + def to_dict_residue(self): + return { + 'amino_acid': np.array(self.amino_acid, dtype=np.longlong), + 'center_of_mass': np.array(self.center_of_mass, dtype=np.float32), + 'pos_CA': np.array(self.pos_CA, dtype=np.float32), + 'pos_C': np.array(self.pos_C, dtype=np.float32), + 'pos_N': np.array(self.pos_N, dtype=np.float32), + 'pos_O': np.array(self.pos_O, dtype=np.float32), + } + + def query_residues_radius(self, center, radius, criterion='center_of_mass'): + center = np.array(center).reshape(3) + selected = [] + for residue in self.residues: + distance = np.linalg.norm(residue[criterion] - center, ord=2) + print(residue[criterion], distance) + if distance < radius: + selected.append(residue) + + return selected + + def query_residues_ligand(self, ligand, radius, criterion='center_of_mass'): + selected = [] + sel_idx = set() + # The time-complexity is O(mn). + for center in ligand['pos']: + for i, residue in enumerate(self.residues): + distance = np.linalg.norm(residue[criterion] - center, ord=2) + if distance < radius and i not in sel_idx: + selected.append(residue) + sel_idx.add(i) + + return selected + + def residues_to_pdb_block(self, residues, name='POCKET'): + block = "HEADER %s\n" % name + block += "COMPND %s\n" % name + for residue in residues: + for atom_idx in residue['atoms']: + block += self.atoms[atom_idx]['line'] + "\n" + block += "END\n" + + return block + + +def parse_pdbbind_index_file(path): + pdb_id = [] + with open(path, 'r') as f: + lines = f.readlines() + + for line in lines: + if line.startswith('#'): continue + pdb_id.append(line.split()[0]) + + return pdb_id + + +def parse_sdf_file(path): + fdefName = os.path.join(RDConfig.RDDataDir,'BaseFeatures.fdef') + factory = ChemicalFeatures.BuildFeatureFactory(fdefName) + rdmol = next(iter(Chem.SDMolSupplier(path, removeHs=False))) + rd_num_atoms = rdmol.GetNumAtoms() + feat_mat = np.zeros([rd_num_atoms, len(ATOM_FAMILIES)], dtype=np.longlong) + + for feat in factory.GetFeaturesForMol(rdmol): + feat_mat[feat.GetAtomIds(), ATOM_FAMILIES_ID[feat.GetFamily()]] = 1 + + with open(path, 'r') as f: + sdf = f.read() + + sdf = sdf.splitlines() + num_atoms, num_bonds = map(int, [sdf[3][0:3], sdf[3][3:6]]) + assert num_atoms == rd_num_atoms + + ptable = Chem.GetPeriodicTable() + element, pos = [], [] + accum_pos = np.array([0.0, 0.0, 0.0], dtype=np.float32) + accum_mass = 0.0 + + for atom_line in map(lambda x:x.split(), sdf[4:4+num_atoms]): + x, y, z = map(float, atom_line[:3]) + symb = atom_line[3] + atomic_number = ptable.GetAtomicNumber(symb.capitalize()) + element.append(atomic_number) + pos.append([x, y, z]) + + atomic_weight = ptable.GetAtomicWeight(atomic_number) + accum_pos += np.array([x, y, z]) * atomic_weight + accum_mass += atomic_weight + + center_of_mass = np.array(accum_pos / accum_mass, dtype=np.float32) + + element = np.array(element, dtype=np.int64) + pos = np.array(pos, dtype=np.float32) + + BOND_TYPES = {t: i for i, t in enumerate(BondType.names.values())} + bond_type_map = { + 1: BOND_TYPES[BondType.SINGLE], + 2: BOND_TYPES[BondType.DOUBLE], + 3: BOND_TYPES[BondType.TRIPLE], + 4: BOND_TYPES[BondType.AROMATIC], + } + + row, col, edge_type = [], [], [] + for bond_line in sdf[4+num_atoms:4+num_atoms+num_bonds]: + start, end = int(bond_line[0:3])-1, int(bond_line[3:6])-1 + row += [start, end] + col += [end, start] + edge_type += 2 * [bond_type_map[int(bond_line[6:9])]] + + edge_index = np.array([row, col], dtype=np.longlong) + edge_type = np.array(edge_type, dtype=np.longlong) + + perm = (edge_index[0] * num_atoms + edge_index[1]).argsort() + edge_index = edge_index[:, perm] + edge_type = edge_type[perm] + + data = { + 'element': element, + 'pos': pos, + 'bond_index': edge_index, + 'bond_type': edge_type, + 'center_of_mass': center_of_mass, + 'atom_feature': feat_mat, + } + + return data + + +class StructureDual(object): + """A helper class that prepares dual format (RDKit rdChem.Mol and ODDT Ob.Molecule) of a given structure""" + + def __init__(self, path:str, isProtein:bool=False, addHs:bool=True, removeHs:bool=False, sanitise:bool=False): + super().__init__() + if sanitise is False and removeHs is True: + raise ArgumentError("Not allowed to remove Hs while sanitisation is false!") + if path is None: + raise ArgumentError("Path to structure not given!") + if addHs == removeHs: + raise ArgumentError("Adding and removing hydrogens conflict") + + self.addHs = addHs + self.removeHs = removeHs + self.sanitise = sanitiseRet + self.path = path + self.isProtein = isProtein + self.ppdb = bpdb.PandasPdb() + + if not isProtein: + self.fileType = str(path.split(".")[-1]) + else: + self.fileType = 'pdb' + + def parse_to_rdkit(self): + if self.isProtein: + protein = Chem.rdmolfiles.MolFromPDBFile(self.path, self.removeHs, self.sanitise) + if self.addHs: + protein = AddHs(protein, addCoords=True) + return protein + else: + if self.fileType == 'sdf': + ligand = Chem.SDMolSupplier(self.path)[0] + elif self.fileType == 'mol2': + ligand = Chem.rdmolfiles.MolFromMol2File(self.path, self.removeHs, self.sanitise) + + if self.addHs: + ligand = AddHs(ligand, addCoords=True) + return ligand + + def parse_to_oddt(self) -> Molecule: + if self.isProtein: + protein = next(oddt.toolkit.readfile('pdb', self.path)) + protein.protein = True + if self.removeHs: + protein.removeh() + return protein + else: + ligand = next(oddt.toolkit.readfile(self.fileType, self.path)) + if self.removeHs: + ligand.removeh() + return ligand + + def RetrieveCoords(self, consideredIdx=None) -> List: + molecule = self.parse_to_rdkit() + pos = [] + + if consideredIdx is None: + consideredIdx = [i for i in range(molecule.GetNumAtoms())] + + for idx, atom in enumerate(molecule.GetAtoms()): + if idx not in consideredIdx: + continue + else: + coords = molecule.GetConformer().GetAtomPosition(idx) + pos.append([coords.x, coords.y, coords.z]) + return pos + + def RetreiveAtomNames(self) -> List: + self.ppdb.read_pdb(self.path) + atom_df = self.ppdb.df['ATOM'][self.ppdb.df['ATOM']['element_symbol'] != 'H'] + list_atom_name = atom_df['atom_name'].tolist() + return list_atom_name + \ No newline at end of file diff --git a/utils/ledock/LeDock b/utils/ledock/LeDock new file mode 100755 index 0000000..f19cc21 Binary files /dev/null and b/utils/ledock/LeDock differ diff --git a/utils/ledock/LePro b/utils/ledock/LePro new file mode 100755 index 0000000..7ffb43d Binary files /dev/null and b/utils/ledock/LePro differ diff --git a/utils/ledock/centreofmass.sh b/utils/ledock/centreofmass.sh new file mode 100644 index 0000000..a8a4acc --- /dev/null +++ b/utils/ledock/centreofmass.sh @@ -0,0 +1,130 @@ +#!/bin/bash + +# This bash script is used to generate ligand docking poses for +# ligands in PDBbind v2020 general and refined set. Please make +# sure that the centre of mass of each ligand in these sets has +# been calculated via centreofmass.ipynb. The outputs should be +# in .txt format with space delimiter. + +# By default, we set the number of docking poses generated to be +# 10 for each complex and the RMSD=1.0. You may wish to redefine +# any parameter in LeDock's INPUT file. Also, we assume that you +# have the same directory structure as mentioned on our GitHub's +# repository. + +# USAGE: nohup bash ./centreofmass.sh -r 2.0 -n 20 -s 10 & +# ARGUMENTS: +# -r: RMSD for clustering as in LeDock's requirement; +# -n: Number of binding poses needed; +# -s: Spacing/dimension of the binding pocket. +# Check LeDock's documentation for more info. +# As the process takes a long time, we recommend running in bg. + + +LEDOCK=./LeDock +GENERAL_FILE="./general-set-com.txt" +REFINED_FILE="./refined-set-com.txt" + +# Parse command-line arguments using getopts +while getopts "r:n:s:" flag; do + case $flag in + r) + rmsd="$OPTARG" + ;; + n) + num="$OPTARG" + ;; + s) + spacing="$OPTARG" + ;; + *) + echo "Usage: $0 -r -n -s" + exit 1 + ;; + esac +done + +# Check if both rmsd and num were provided +if [[ -z $rmsd ]] || [[ -z $num ]] || [[ -z $spacing ]]; then + echo "ALL -r and -n and -s flags are required." + echo "Usage: $0 -r -n -s " + exit 1 +fi + +# Use the provided values +echo "The value of rmsd is: $rmsd" +echo "The value of num is: $num" +echo "The value of spacing is: $spacing" +echo "=================================" + +# Count how many complexes available for docking, including the last line +num_lines=$( wc -l < ${GENERAL_FILE} ) +num_lines=$(( num_lines + 1 )) + + +# Perform docking +for (( i=1; i<= ${num_lines}; i++ )) +do + # Make a copy of the template files + cp ./input ./input.txt + cp ./ligands.list ./ligands.list.txt + + line=$( tail -n+${i} ${GENERAL_FILE} | head -1 ) + + # Replace the keywords in LeDock's INPUT file + # Read the file line by line + read var1 var2 var3 var4 <<< "$line" + # var1: PDB ID + # var2: COM x coordinate + # var3: COM y coordinate + # var4: COM z coordinate + echo "Processing ${var1}" + + # Check if the element is present in the nohup.out file + if grep -q "${var1}" "newfile.txt"; then + # Element found in the file, so skip the current loop iteration + continue + fi + + MINX=$(awk "BEGIN {print $var2 - $spacing / 2}") + MAXX=$(awk "BEGIN {print $var2 + $spacing / 2}") + MINY=$(awk "BEGIN {print $var3 - $spacing / 2}") + MAXY=$(awk "BEGIN {print $var3 + $spacing / 2}") + MINZ=$(awk "BEGIN {print $var4 - $spacing / 2}") + MAXZ=$(awk "BEGIN {print $var4 + $spacing / 2}") + LIG_FILE="../../download/v2020-other-PL/$var1/${var1}_ligand.mol2" + REP_FILE="../../download/v2020-other-PL/$var1/${var1}_pocket.pdb" + + # Run LePro to clean protein pdb file + ./LePro ../../download/v2020-other-PL/${var1}/${var1}_protein.pdb + + # Process the variables as needed + # Replacing keywords in the template files `input` and `ligands.list` + sed -i "s/MIN_X/$MINX/g" input.txt + sed -i "s/MAX_X/$MAXX/g" input.txt + sed -i "s/MIN_Y/$MINY/g" input.txt + sed -i "s/MAX_Y/$MAXY/g" input.txt + sed -i "s/MIN_Z/$MINZ/g" input.txt + sed -i "s/MAX_Z/$MAXZ/g" input.txt + + sed -i "s/rmsd/$rmsd/g" input.txt + sed -i "s/NUM/$num/g" input.txt + + sed -i "s|receptor_file|pro.pdb|g" input.txt + sed -i "s|ligand_file|${LIG_FILE}|g" ligands.list.txt + + # Run LeDock + $LEDOCK input.txt + OUTPUT_DOK="../../download/v2020-other-PL/${var1}/${var1}_ligand.dok" + $LEDOCK -spli ${OUTPUT_DOK} +done + +# Remove redundant intermediary files no longer used +rm ./dock.in +rm ./pro.pdb +rm ./input.txt +rm ./ligands.list.txt + +echo " " +echo "Process exited successfully." +echo " " diff --git a/utils/ledock/general-set-com.txt b/utils/ledock/general-set-com.txt new file mode 100644 index 0000000..fad57a3 --- /dev/null +++ b/utils/ledock/general-set-com.txt @@ -0,0 +1,14122 @@ +9icd 95.843 70.966 -3.957 +4kqo -1.897 7.316 23.259 +5qj2 -20.465 14.187 34.335 +4a1w -42.866 -15.182 24.902 +5k0s 28.201 6.647 11.499 +6f7t -13.099 -9.444 -77.875 +1a50 49.562 27.352 12.943 +2f6z 39.975 10.873 14.809 +5vlr 38.537 13.874 32.729 +2wev 2.619 48.525 1.931 +4de7 14.926 -12.953 22.958 +2fj0 32.126 49.500 70.070 +5etx -20.646 -19.906 -0.030 +4mvw -41.913 14.754 10.428 +5aep 32.561 13.541 -4.095 +4deh 19.701 11.396 58.078 +4mwx -26.080 -62.750 -17.149 +5tg2 60.871 -54.569 19.193 +2clv 20.455 52.504 9.860 +5jmp 1.314 13.117 18.987 +5th2 -8.093 4.166 -28.434 +6hoi -5.642 -5.671 -5.114 +2cji 8.424 6.033 22.070 +5eok 6.635 -30.471 -0.768 +4hgc 18.406 -7.093 14.912 +4r5x 14.697 9.896 12.994 +3n87 45.529 7.690 24.709 +3bh3 4.340 -32.875 -14.065 +2wez 30.102 1.564 34.461 +6g93 8.443 8.574 43.865 +2c6g 15.606 45.925 41.127 +4cik -7.021 -0.295 17.228 +2qo1 37.452 37.113 51.397 +4ele 20.567 -29.737 -2.404 +1cea 35.072 2.928 -30.863 +4wbg 18.783 -8.688 20.707 +4z7h 34.840 -14.685 10.397 +5yto 71.281 76.366 -11.395 +4o3b 9.079 106.201 24.772 +5j59 -42.081 14.901 10.715 +6ugo -25.816 2.808 15.733 +6r9s -0.148 15.145 22.431 +5a3n 82.732 63.608 13.526 +6ety 17.991 45.641 42.503 +3irx -49.963 -29.699 -39.048 +4izy -13.081 6.025 -21.364 +3ds3 35.282 -7.075 16.094 +3s8x -3.631 4.986 14.613 +6g0v -21.561 10.212 -2.236 +5aqf -24.795 -16.039 31.986 +5jzs -21.169 -16.535 -31.746 +3fuh 24.962 86.601 -2.065 +4yjn 0.856 -21.025 -31.286 +3ttj 21.869 8.638 31.787 +4c4j 0.797 17.856 45.730 +6esa 3.957 -33.688 23.200 +4b95 -5.946 33.413 2.073 +5owf 19.816 57.239 47.322 +5flp -4.277 3.908 14.834 +4oya 17.294 25.190 -2.941 +6myn 42.355 19.199 -2.434 +3tu9 4.196 -31.063 50.222 +5dp6 -25.348 13.457 -19.071 +1rdn 3.033 46.285 1.022 +4zj8 -7.075 0.032 -53.952 +5z1t -10.860 7.754 -3.059 +4z7q 54.313 111.985 73.160 +6eee 175.646 17.042 83.656 +1vj9 30.689 10.417 29.515 +6fzp -2.982 -11.176 12.400 +2q8s 18.223 63.989 13.212 +3vhu 19.059 13.952 1.420 +2o1v 18.498 20.168 52.506 +4o12 15.970 7.000 1.245 +6f96 62.028 28.543 63.311 +3i97 -4.160 -8.634 -14.559 +5w4s 6.365 -14.437 0.898 +2ydm 13.144 -7.739 -21.595 +6e7s -11.061 -62.682 162.600 +1qpe 23.211 37.232 84.470 +5oyd -3.178 129.555 27.975 +5yjb 5.635 -53.035 -35.864 +5qac -13.052 -21.814 26.870 +1qiw 23.154 49.575 23.351 +3k5c 29.823 5.829 14.695 +5eva 7.466 -10.333 5.941 +3uf9 -13.545 18.481 -22.210 +4qlv 10.175 -136.853 16.959 +2rc9 12.585 0.960 7.832 +1o42 19.540 22.448 21.966 +3cfs 10.519 -14.958 34.336 +5w6t -30.649 -59.686 -26.225 +4afe 1.686 -9.464 11.151 +3jwq -8.646 -28.835 44.452 +4fri 69.806 49.602 7.697 +6hx1 -5.949 -9.792 28.048 +4x11 19.115 -23.329 11.803 +1qvt -64.000 -46.626 4.724 +3dga 27.482 4.984 59.458 +4otg -14.104 9.573 -14.511 +5lxb 36.577 -27.588 54.840 +4qtn 49.529 66.845 42.517 +3ess 1.004 4.953 -11.277 +1wdq 1.359 30.167 22.402 +6b1h 10.412 -0.786 -1.590 +1cbr 4.607 6.694 -8.172 +3jzb 27.346 38.991 31.085 +2xfi 30.710 2.375 34.909 +5csx 18.069 -75.214 90.132 +1ro7 22.777 -2.504 13.455 +4anm 23.205 7.417 18.132 +6fzu -16.785 0.158 23.973 +3u4o 25.043 44.488 45.068 +6udx -14.716 7.944 -19.240 +4mvy -42.774 -14.632 -10.433 +5b1s 1.819 -55.420 -17.536 +5f01 -18.883 41.324 6.031 +5uw5 81.301 4.391 162.315 +2viy 30.704 2.223 34.733 +2y2k -9.392 8.951 7.795 +6chm 10.471 162.703 33.747 +3pvu 39.313 -7.812 53.158 +3nnx 5.858 -37.727 -23.440 +2rl5 61.814 48.039 17.056 +2h5i -4.596 74.595 22.306 +1lhg 16.937 -14.010 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35.684 +5akg 13.842 10.284 25.187 +5ldk 105.651 34.902 53.459 +5nwk -16.368 -15.792 -1.655 +1gzv 43.573 33.283 49.565 +5wf6 -7.585 -9.476 55.787 +6cms 39.965 11.725 240.044 +4urw 44.911 39.352 78.630 +6byz 108.040 -50.678 39.869 +3l8x -2.815 -4.308 -19.773 +5wys -14.641 34.977 -0.684 +6bd1 -6.720 -6.819 23.551 +4l7n 21.140 -3.533 12.184 +5u4x 8.358 25.886 21.812 +4zki 17.449 -17.095 1.091 +6oyt -4.322 -17.257 24.493 +3bh9 -37.193 -34.987 10.287 +4jaz 16.606 23.131 8.166 +6gjb 12.202 10.219 43.262 +1ahy -9.927 54.843 24.441 +5hfb 39.257 54.759 22.658 +3pax 40.960 22.810 21.576 +1il4 0.913 1.131 7.090 +5wkh 31.019 -0.127 16.619 +4v04 86.982 0.743 18.360 +6s9b -51.510 21.789 -0.228 +4eg6 -43.098 -14.462 -9.697 +5lcf -32.205 91.944 18.908 +1dpu -4.953 -0.186 -18.505 +3b95 -22.555 -3.679 12.001 +3zst -12.722 91.771 20.554 +5cyv 98.169 150.956 82.661 +5q1f 12.755 23.064 3.329 +4pda 51.396 -19.637 -7.199 +4v25 43.570 -48.787 -10.824 +5ykp 12.679 4.563 20.969 +6hou -22.512 14.486 -14.269 +4btb 72.651 57.041 56.660 +5afm 28.686 7.950 -29.772 +6q7h -3.028 35.178 -8.050 +1yci 20.276 25.578 30.264 +6k9u 11.144 18.904 13.849 +5jyp 5.315 -5.312 78.502 +5sve 9.840 -17.155 29.896 +1g50 104.980 14.774 23.481 +5q0y 13.834 23.581 3.808 +5jv2 4.708 73.718 27.698 +3ufl 31.951 37.115 0.158 +2cnh 16.016 19.931 78.332 +3wp0 30.953 -35.679 11.065 +3vp2 5.362 -9.467 -0.671 +1dtq 1.449 -37.310 21.170 +3oev 11.961 -136.690 19.796 +2aei 31.468 7.781 9.428 +2z7h 30.632 47.505 7.098 +3bun 57.707 -40.652 -8.664 +4q06 -3.942 2.317 13.503 +1ijr 62.770 25.438 34.127 +4tvj 18.853 -1.491 17.608 +4pnq 24.585 48.489 -0.617 +1oit 11.205 -9.429 10.284 +2wpb 3.691 -9.744 31.607 +4do3 22.797 48.875 7.688 +3lnj 6.758 -44.135 4.170 +2z5o 27.999 -33.882 -35.469 +4z1q -17.295 -60.583 137.987 +4er4 35.906 -8.769 -1.090 +4aq3 -22.632 6.256 -10.165 +6fzx 23.817 62.923 26.483 +6ayn 24.732 35.541 30.697 +1kkq 76.285 28.105 23.880 +5q11 -11.318 41.198 -4.594 +6bmr 14.001 42.140 29.222 +2l6e -7.961 4.266 2.570 +6dki -20.434 6.097 -19.555 +5fsb -24.861 -0.795 54.923 +2cll 49.533 26.096 13.641 +5j7j 3.620 -5.599 -0.825 +6bto 10.699 13.291 -6.988 +6qhb -22.981 0.740 -21.034 +4a9r -9.513 49.664 9.602 \ No newline at end of file diff --git a/utils/ledock/input b/utils/ledock/input new file mode 100644 index 0000000..8706809 --- /dev/null +++ b/utils/ledock/input @@ -0,0 +1,16 @@ +Receptor +receptor_file + +RMSD +rmsd + +Binding pocket +MIN_X MAX_X +MIN_Y MAX_Y +MIN_Z MAX_Z + +Number of binding poses +NUM + +Ligands list +ligands.list.txt diff --git a/utils/ledock/ligands.list b/utils/ledock/ligands.list new file mode 100644 index 0000000..ad6a100 --- /dev/null +++ b/utils/ledock/ligands.list @@ -0,0 +1 @@ +ligand_file diff --git a/utils/ledock/modifyDOK.sh b/utils/ledock/modifyDOK.sh new file mode 100644 index 0000000..623c534 --- /dev/null +++ b/utils/ledock/modifyDOK.sh @@ -0,0 +1,29 @@ +#!/bin/bash + +# Create the 'new' directory if it doesn't exist +mkdir -p ../dataset/general + +# Find all .pdb files in the 'v2020' directory and its subdirectories, +# whose filenames contain the string '_ligand_dock', and copy them to the 'new' directory +find ../../download/v2020-other-PL/ -type f -name "*_ligand_dock*.pdb" -exec cp {} ../dataset/general \; + + + +# Specify the directory path +directory="../dataset/general" + +# Loop through each file in the directory +for file in "$directory"/*; do + # Check if the file is a regular file (not a directory) + if [ -f "$file" ]; then + # Process the file as needed + echo "$file" + + # Replace the string in the file + sed -i 's/ CL\([^ ]*\) / CL\1 /g' "$file" + + # Add your custom logic here + fi +done + + diff --git a/utils/ledock/newfile.txt b/utils/ledock/newfile.txt new file mode 100644 index 0000000..e5f98f7 --- /dev/null +++ b/utils/ledock/newfile.txt @@ -0,0 +1,12609 @@ +The value of rmsd is: 2.0 +The value of num is: 20 +The value of spacing is: 10 +================================= +9icd +4kqo +5qj2 +4a1w +5k0s +6f7t +1a50 +2f6z +5vlr +2wev +4de7 +2fj0 +5etx +4mvw +5aep +4deh +4mwx +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +5tg2 +2clv +5jmp +5th2 +6hoi +2cji +5eok +4hgc +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4r5x +3n87 +3bh3 +2wez +6g93 +2c6g +4cik +2qo1 +4ele +1cea +4wbg +4z7h +5yto +4o3b +5j59 +6ugo +6r9s +5a3n +6ety +3irx +4izy +3ds3 +3s8x +6g0v +5aqf +5jzs +3fuh +4yjn +3ttj +4c4j +6esa +4b95 +5owf +5flp +4oya +6myn +3tu9 +5dp6 +1rdn +4zj8 +5z1t +4z7q +6eee +1vj9 +6fzp +2q8s +3vhu +2o1v +4o12 +6f96 +3i97 +5w4s +2ydm +6e7s +1qpe +5oyd +5yjb +5qac +1qiw +3k5c +5eva +3uf9 +4qlv +2rc9 +1o42 +3cfs +5w6t +4afe +3jwq +4fri +6hx1 +4x11 +1qvt +3dga +4otg +5lxb +4qtn +3ess +1wdq +6b1h +1cbr +3jzb +2xfi +5csx +1ro7 +4anm +6fzu +3u4o +6udx +4mvy +5b1s +5f01 +5uw5 +2viy +2y2k +Waring: Missing or wrong elements: B +6chm +3pvu +3nnx +2rl5 +2h5i +1lhg +Waring: Missing or wrong elements: B +4fbe +1g3b +6ccs +4jfd +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4e3k +Waring: Missing or wrong elements: B +1pi5 +Waring: Missing or wrong elements: B +4jib +6ccn +6ebw +4jt9 +1g9a +3ole +3u6j +5aly +6cd9 +5ul1 +4zg9 +2qt5 +3oqf +1t3t +2x6k +5a5z +6b16 +2sfp +6gvi +5wej +6t6a +6lpr +Waring: Missing or wrong elements: B +1h00 +6hgy +4dj7 +3bu6 +1a7c +3kqc +5q1h +4iur +5h22 +6oi9 +2er0 +1o3c +3ccb +2rny +6i77 +5c4s +3tvx +3rxd +5etn +5ahj +3iok +4py2 +4al4 +3rpy +3bel +4j3e +1bgo +1gx0 +5csd +5tbj +5f4l +3p3h +6npe +3udk +4qw6 +4z8a +5aom +5etk +4kww +3r6g +4rss +4uix +3vd7 +5v3x +4msu +6nss +4wyz +6gg3 +5gg4 +1w1d +2g97 +6n0q +5ij7 +4dfw +3s7f +3if7 +5opr +5jqb +3nam +4o71 +1epq +5hey +3io7 +6g84 +2c69 +3avj +4w57 +4zmf +5o48 +4ty9 +3pqz +3cqw +1apb +3mxy +4dei +2b17 +4pxm +4qkx +1h1d +5bvk +5mi5 +6qs1 +3emg +6ode +2xel +4g2y +4gk4 +2jnw +2l84 +5eoc +5vqt +5eec +Waring: Missing or wrong elements: B +6esj +3u3z +1t48 +2qcm +2wxv +1vyw +2j9a +4jzb +3way +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +Waring: Missing or wrong elements: B +5jn9 +4z9l +5j5x +6s55 +4ucs +4p4j +2wxh +5gr9 +5u62 +1oyn +4gvm +1v0p +4u79 +1nhg +6dcg +3eos +4wv6 +2pj2 +6fu4 +1u2y +4awf +3ft4 +3lm1 +2lsr +5akh +6bh8 +4tmr +6agk +3arb +4cd1 +5l2w +4wz4 +Waring: Missing or wrong elements: B +1tnk +5nai +1jvp +4an9 +5qaz +3g2i +4o3t +3unz +2ym6 +4hxz +2aez +2oz2 +4lbp +5jao +5d75 +3dpo +2gfs +2c90 +4prp +4u6x +2ksb +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +6n8y +5uit +3mwe +4x3s +4hkk +3mt8 +6n48 +4qp7 +1w70 +6hop +3dxg +1yyr +3vgc +Waring: Missing or wrong elements: B +5k0i +2m0o +5moc +3v0p +1o9k +3f9y +5gty +5ddd +2ao6 +5ygd +2x7o +4ayy +2hd6 +4zyv +6ovc +2fwy +5lch +2v5a +2c6c +3i0s +2ycm +6asu +4f9g +4ec0 +5h1e +4j52 +6dyo +1dis +2uw3 +3lik +5aip +2wic +5ou3 +5odu +6hkz +4h1j +6e6v +2f5t +4a4h +4qmn +5trf +4pax +3o23 +5ylt +4zh3 +6b8u +2b55 +4jfi +2r6f +3d7h +4aro +3fqa +3g2n +3krj +5zop +1zaf +2b8l +3ud9 +4mxa +3hhu +3mke +Waring: Missing or wrong elements: B +5edq +4a9m +4l0t +4rqi +4qvm +Waring: Missing or wrong elements: B +3qel +3e81 +1d5j +4bw3 +4bjb +5qau +3pxq +4mro +2w10 +5c91 +4yzn +4mue +3fup +1nfs +1mv0 +6m9l +5hor +2mps +3sfc +5j7s +4cfm +5idn +5aad +1iep +1hqg +4lkg +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +6cck +4lng +3ivq +2fai +6ajx +5dtt +4hby +6cz4 +4ach +5joh +1oe7 +1a7t +4j70 +4ok5 +4k6z +5nu1 +2pu0 +1kll +2i4p +6qyo +5dp8 +3ieo +4pyq +4ufy +3rx5 +5xmp +5wap +5cu2 +4qmz +3hy5 +1nlp +1s9t +5bwb +3ebb +1mau +3cst +Waring: Missing or wrong elements: R +2yga +1osv +4i5p +2zit +1yt7 +5qai +5a7y +6q30 +Waring: Missing or wrong elements: B +4fut +5il1 +3qx8 +6o6f +6i0c +2glm +5dlv +4lwu +4jmg +2ovz +3v0l +5gn9 +4jlm +1swp +5ar7 +5jna +3hu1 +5kbh +5t90 +1i9m +3gol +5em6 +3wde +5yzc +5xxf +2ddf +5gjf +2e95 +1b9v +6ckl +3sc1 +1o3p +1kqb +6eqa +5lm6 +3wf7 +3zo2 +1wbo +4qnu +6gl3 +3usn +3dei +1ouy +5ezx +6ful +1nu8 +4ezq +4umu +6m8c +8gpb +5j75 +4a51 +5v37 +5d1s +2xnp +2aow +4eky +1nhv +4i5m +1it6 +2i3z +6j0k +5eq0 +6nt2 +1fvt +5tv1 +4oew +5dht +4xuz +Waring: Missing or wrong elements: B +4xue +6ee2 +5ei8 +1bqn +6oxw +4wx4 +3g6g +4aig +3tz2 +5nmf +5nvz +4z0f +6g6w +6ooz +4qxr +5ml4 +2wmu +4mm8 +4xt9 +3qup +4yl0 +1w31 +4pp7 +3zrl +4kxl +4fqo +6e6w +1sm3 +3ips +2o1c +5i13 +5drq +6i74 +1awf +2mlm +6e8x +1x81 +5hpm +5wqd +4yzc +4mdr +5e7r +3fmq +3hzy +1s50 +5f27 +5fqc +Waring: Missing or wrong elements: B +4d0x +3u7n +5km1 +6c2y +5z1r +3zos +4klv +1xnx +3sw2 +3zy5 +3ftq +2w73 +4mk9 +4eqc +6ggv +3e8n +4ph4 +2xey +1a07 +2zju +1nq0 +3vrw +6h4a +3avm +4p0a +6evm +4pl4 +3l5f +5bvf +2gmx +2ybk +4uyh +3l8s +4bfd +5jnl +4x9v +6rqk +4hmh +4nhx +6cdm +3m2w +3st6 +3o96 +5hzn +4y67 +5q18 +3iqv +5gvl +5a82 +6fh6 +4ebw +1o2x +3fhe +4e3i +Waring: Missing or wrong elements: B +6mlh +3zhf +2xfj +2j4q +2j7x +6c5j +4fea +2vtq +2iu0 +6mu1 +4igq +6hs4 +5vjp +5eeq +3rk5 +6cee +6mo7 +5ual +4aa0 +2ay8 +3lk0 +4bbe +3c3r +2c6k +4res +5dp4 +6kzc +3u4w +5mw2 +5jf8 +3wig +5svy +5lj2 +2lbm +5zhj +2x6i +5ods +2yjq +6dzy +4whq +4d1c +3avh +1szm +6ob0 +4hai +4o45 +2rjr +6iqg +1di8 +4a4x +5enm +5tg5 +Waring: Missing or wrong elements: B +4y24 +3ds4 +5q13 +3bv2 +1fwe +4mrh +3eg6 +5myn +3f9w +1i5h +4uct +6czd +4jiz +6s8a +3e2m +3ook +2bkz +4w9g +2vr4 +2e2b +5m56 +5lrj +2wo9 +6un3 +4m3e +3dz4 +3tkh +5aic +4n7h +4qw4 +4zqt +4kod +5mys +2g9r +1gi6 +3r5m +5bvo +4bdd +5o5f +4os4 +4pd5 +3g08 +5ul6 +4gvu +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +1t7f +3lok +6pyu +4r0i +1o5p +5kqd +4uzh +4ie6 +2z5s +3u8m +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +6os6 +4z8d +2p4i +3c7q +4qmp +4p4b +5tyk +Waring: Missing or wrong elements: B +5nhz +6ary +4iqu +6ht8 +1w84 +2v6n +6gj5 +5v8o +2wuu +2pqj +4j74 +3d7d +3tww +1nxy +Waring: Missing or wrong elements: B +4qw0 +Waring: Missing or wrong elements: B +3vw6 +3rjc +4e5f +3znc +2a4z +2rfy +2za3 +2gg7 +2aq9 +3s3q +4ql8 +1rwx +2c6e +4tyl +1w12 +4i60 +Waring: Missing or wrong elements: R +4mg9 +4joh +1aqi +5qas +6b1w +2z7i +3m94 +4rcf +4uxh +2lty +5j7p +1xhm +2am1 +1h36 +5wo4 +5e0l +3mxf +1kz8 +4mq2 +5tzf +5q1a +5l01 +1akv +6b2p +3zm5 +3nlb +2yoh +6iyw +2xhs +5zwf +5tw5 +5f1z +4mbp +4c6x +5ema +5c4o +6hdn +3sbi +5kbg +4zsj +6g85 +6imr +4zfi +3bea +4bsq +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4rvk +4bcc +6o21 +5db1 +4wup +4x21 +3nw9 +6b3e +4i6h +6cen +4kzl +4qsk +2br8 +3krx +3w2r +4bea +4ask +5wjj +4l7c +1xb7 +4ngt +5l8t +5ye7 +5o0s +3ipe +5xpm +5f3g +3rwf +2xah +5h8b +4eh9 +3ard +4el9 +4b7z +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2ycr +3wqm +3ivi +3g0f +5dhh +6f0y +6gcr +3rak +1dxp +3gxl +4or0 +2fkf +3iqj +6akw +3ifo +5d1n +4ysi +4p90 +3fts +3n5u +4av0 +4o2f +4h4b +5tt7 +2h6q +3h2a +4c1f +3pp1 +5ajz +3tjd +3lvp +3u4u +5drt +1ftk +3zp9 +3avk +1kat +4c1d +6ayh +5uig +5boy +3w2s +5ee7 +6c6o +2liq +4j3d +2ayp +3mrt +5tha +4l7r +6ckx +3h0j +1gqs +2xrw +4wz6 +4xct +2qu2 +4lj3 +3deh +3kr1 +2wtc +1g6g +4r5v +5foo +5icx +4u5u +1pxl +3qw6 +3p3u +3n4l +3asl +2oi3 +5svi +3ck7 +2lsk +4m5l +5d9k +3zjv +Waring: Missing or wrong elements: B +5u94 +6bbs +3wyl +5y7h +2w1e +6hah +6dug +2brc +2jql +5xpo +4jln +6qto +1p01 +Waring: Missing or wrong elements: B +3hqz +4m6p +4na8 +4tv3 +2am9 +4mg6 +6f5l +5dl1 +3drp +5mim +4gy5 +5tpb +6d6t +3i0r +1wbg +3atm +1akt +5mwd +5l8o +4hxs +1hv5 +1h08 +4ogn +4p0w +5hcx +4wki +4obp +3mtw +3lhs +6rpg +4xm8 +4an0 +2r7g +6gbw +4yuz +3pz4 +3q6s +1mxo +Waring: Missing or wrong elements: B +1mqg +1vjd +6hoy +5w8h +2brh +4qy8 +4ge6 +1wc6 +4dh6 +1nlt +3e9b +Waring: Missing or wrong elements: B +4pgb +5ug8 +3bmy +3ri1 +2vi5 +5zk3 +5eps +4nat +5khh +3s1g +5a3h +4n99 +5lrk +1pbk +2qa8 +3cf1 +5fah +6ahs +6idz +3jq7 +3lq5 +3iu8 +2bz8 +4a9i +1p4r +4irx +5kxc +3biz +1n1v +4c4g +6mq3 +1mpa +2rkn +6b0y +3pa5 +5nyz +1eoj +5t8j +3ddb +4exz +3nba +3owk +4ksp +2rnx +6h14 +2yjw +4r6t +3gc7 +1uu7 +2poq +3rdv +3v6s +6qc0 +4alv +5mmp +4h5e +4lxb +2opy +5mnc +3bti +4jjm +3duy +2ww0 +4g0k +2c1b +5k5e +4bo3 +3hhm +5oci +3drs +4h3q +3t8w +1sm2 +2oz6 +4igr +3o6t +5mft +4jv6 +6gev +5m57 +1w8l +2qoa +4j0z +4o10 +5ew9 +6o4x +5y7w +1k9q +1ms0 +6mju +3bhx +1syo +5e5g +2vd4 +1l0a +6an1 +1prm +4ajw +1ggd +6rml +2zlf +3rtx +2bxt +5qcn +2g71 +5gjd +3bg8 +1k1p +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4o55 +4wyy +Waring: Missing or wrong elements: B +5uzj +4ec4 +6dgx +2zas +5lzh +5j79 +3nii +1m5c +6os5 +2osc +4i0z +3fmz +5hkm +3jpv +5wic +3ig6 +2xzq +2y4a +Waring: Missing or wrong elements: B +3nsq +6fob +3eq9 +5xfj +5unj +6n19 +3oay +6mzw +4ktu +4em7 +5kqf +1n7j +4pd7 +6qaf +Waring: Missing or wrong elements: B +4eyr +2c6m +5g1c +3pr0 +3a3y +5hfj +4oz2 +2xkf +6f3i +2xpa +2y07 +5ezg +3f3a +1czl +3sz9 +4qw3 +Waring: Missing or wrong elements: B +3e8u +3ii5 +3eq8 +5jas +5kjk +5zwh +3msl +1m13 +1aw1 +4nk9 +3avg +4rrq +2gh6 +2y5k +6fkp +5qin +6mo1 +6qmt +6grp +5wi1 +4dgm +2nmb +5h5r +5h4j +6dtx +6hmt +6b5o +6hp9 +5jnc +2nnv +5v3h +5orr +5tca +6dlx +3of8 +5jid +6d1x +1xxe +5tpg +6ke0 +5lgn +3ik3 +1qwe +2cvd +4y2b +3l9l +6i0k +5yy6 +5ci7 +1wbt +1tfz +1o6i +1vrt +2y4s +4tjy +5d4a +3dej +1k06 +5v49 +2qve +5j9l +5edr +5x4p +2qcg +3ffu +4jr3 +3g5d +1ihy +Waring: Missing or wrong elements: R +Waring: Missing or wrong elements: R +Waring: Missing or wrong elements: R +Waring: Missing or wrong elements: R +Waring: Missing or wrong elements: R +Waring: Missing or wrong elements: R +Waring: Missing or wrong elements: R +Waring: Missing or wrong elements: R +Waring: Missing or wrong elements: R +Waring: Missing or wrong elements: R +4j09 +4l2x +1r2b +3uii +4jff +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +1a4h +2p2i +2zv9 +6mjw +5t27 +2ow6 +1wun +6qfh +4zh4 +5al3 +1dfo +4wet +6hgv +6eeh +3ua9 +6mmq +4umn +5jc1 +4cku +6h4q +5tdb +5j31 +4qjr +4bcg +6hb5 +1dbb +4wcu +6bqh +4n3r +6ibl +4yyl +5ea7 +5u2e +6e3o +3dya +2zof +3jzr +5m3a +2kaw +3orn +1dwc +4udb +3h59 +3fc8 +3fw3 +6jid +3wv2 +5ukk +3lf0 +2o4p +1s4d +2xl2 +3vva +5m53 +2ohk +6bke +6e3p +4rt1 +4hvd +2wcx +4rxh +1lv8 +3oq5 +2qcd +5mkj +1ulg +5lt9 +6s9d +1lhw +4b12 +4nxq +4npv +1ms7 +6mnp +5jsm +2wva +6h4z +1sts +6qmr +5znl +4d8s +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +5oax +3bla +3p9h +3kba +5tzy +4ere +4lv4 +4msg +2y4m +1c4y +4k66 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +6agp +6acb +3kid +4jt8 +2w06 +5uv1 +3kb3 +1wdr +5yic +4drn +3snc +3cwe +5fnq +4lke +4rz1 +2hfp +3wv1 +3sd5 +6dgt +4uxl +3hxc +4mm9 +1a8i +5goe +2w6q +5ug9 +4wpf +6g9j +1vjb +1bug +5mtv +5oxm +4y62 +1a09 +6qtm +4mfe +4ejf +1e02 +3puk +3rxk +1iwq +1t46 +4yqh +3cd8 +4iax +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4p0v +2of4 +3u7k +2lto +5dhj +4o28 +1z5m +2lha +2x7s +5jmx +3unn +5uis +2yj2 +5ioy +5k4i +5j5t +5e0a +1njj +5enj +5l87 +3r9o +2ghg +6do1 +1h27 +4oem +2w6m +2on3 +3t1n +6cgp +2vnf +6chq +4yz9 +5nzo +6apv +5djp +5ale +5if4 +1xh8 +3wzk +6g3c +4jhz +1qxz +6c91 +4r3c +3ful +5nrf +6csf +6f29 +3tsz +3h03 +1gvk +4jaj +5lm4 +3coh +1yi3 +1err +5teh +4jik +1bkj +4j5d +4j04 +3jqb +4kc2 +6er4 +1hgi +1y0x +2xb9 +3ho9 +3kad +5yp6 +1ouk +4x6p +5v9t +2ogz +3i7g +2rcu +6q2y +Waring: Missing or wrong elements: B +2f89 +1gi9 +5mk1 +4jjf +4kin +1ktt +5q1i +2p83 +5am1 +3pb3 +1mnc +4gye +4yad +3buw +5dd0 +6hhg +5vdw +4os6 +3k27 +2vpp +2ycq +4nga +4m3g +4lkm +1v2q +3mct +1e00 +5cwa +5tzx +6rni +5vdo +5ktu +1s9v +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +6b5m +2ynd +5w0f +4ijq +2yns +1gca +5ocj +2x2i +4g0a +6s9w +3mo5 +5u8a +3h0y +5hh4 +5csz +6dhc +3rpr +2bq6 +4jzd +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +6nad +3e7a +6jjn +4hld +6g01 +3lxl +6e0q +4ytf +3cjf +3uo5 +1ykr +5jr6 +6fsd +6bqg +5lo6 +3g8e +3h5s +4l4l +6cbh +1avp +4b05 +1s17 +6eum +2p99 +5fh6 +2mji +6cq4 +5cxz +3oap +6o1g +6jut +6f8x +4wbo +4mwr +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +5id1 +5ekg +4mao +4d2t +5v5n +6n5f +4zsg +5u8f +3dhk +3kc0 +5t78 +6bix +3tjh +3g0g +4zs0 +5av0 +2yog +2pe0 +1cze +1uk1 +4kmu +5yg4 +3n23 +4um3 +3s7l +4cts +2qmj +4rsp +6en4 +3v2w +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4i73 +6dn6 +5jeo +5l2t +4q1c +1xxh +4wh7 +6rz6 +4waf +4xbo +6e8m +2kp8 +2obf +6en6 +1gja +1m51 +5xvq +4bae +3sov +3fnm +6d1l +4ju6 +2y9g +5wj6 +1d8e +4cki +2y6o +4x1q +2qaf +6dd1 +6isd +4pct +6ee4 +5fwr +3nil +3cx9 +4u7v +5czb +6h4u +3rsr +4zyx +3ce3 +6ntb +6i0b +5za1 +4xy9 +4aw8 +4u6r +3eio +4odq +4yt7 +1rdt +3zt4 +1fq6 +6e4c +6nwc +4fxf +1ek2 +2vle +4b11 +3rk7 +4mi6 +5ea6 +1jwt +3gjq +4ea3 +1ce5 +2yj8 +3ejt +5w5s +3g2v +5moq +3t3e +4gly +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +3k3h +3uxm +5afx +5iay +6r8i +3ud5 +1q4w +1ai6 +4bo7 +4l34 +2ybs +3elj +1b6p +2j3q +2rvn +4w4y +5yjo +6dgo +5td2 +5y6k +3ksl +3fbr +3ujb +1n4m +5y9l +2vfz +2wyi +3g3d +4u2y +4uxq +2xvn +2hiz +1c7f +6i8b +5fbo +2uvm +5qtu +5wa6 +3nzu +1t29 +4mot +3rtp +3l1s +3udp +5dx3 +2r05 +4qr5 +4eon +3ggw +3qtq +2nnq +5ngb +4y8d +4x8s +4ga3 +2hha +6hm4 +3pkd +1fe3 +6hq4 +4p5e +4rn6 +3hik +5wf7 +3vdc +2q2y +1q1y +1w1y +5fbn +3e9h +6ffs +4l7u +1dwd +5wh6 +6n5c +5qb0 +4rxz +6ewe +3dab +6cmj +4c7t +5ksu +6ej4 +5ai5 +3fgc +1xfv +3lhg +4z16 +3fjz +1unh +3c6t +3udm +5dkr +2wcg +3ha6 +5mgx +6ipk +3bxz +3dpe +3ti3 +1q6p +1bio +5z4o +4uiy +6hk6 +3ztc +2vd1 +1rlq +2gz8 +3ijz +4bdb +2ath +4f9v +5zoo +4hy9 +4cfw +4qfs +830c +2z50 +4wpn +5q0p +6f7i +3fqk +5x5o +2xk9 +2co0 +4fcm +2r1w +3g0d +1i9q +5xkm +5l3j +1nu1 +6m95 +5fl0 +2fm2 +1cr6 +5w6o +2alv +3qts +1d3q +3qem +6chh +4zij +4qsw +6p5w +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +2f4j +3sni +1rri +1css +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +centreofmass.sh: line 112: 2019000 Segmentation fault (core dumped) $LEDOCK input.txt +3eys +6j81 +3nm6 +5nkn +4yoj +2wj2 +4xjt +1mqh +2ank +4z2i +1a0t +5clm +3n51 +1vcj +5eko +6r0s +3rwe +4x7o +6ciy +2x52 +3h2f +1fo3 +6mck +5ofu +3fcf +5tzw +4puz +4wf4 +3ftw +3lj3 +4djh +2f01 +6q9l +5ewh +2w6n +5kmh +3dcr +6ipi +2bgn +3lkz +5ap7 +5uex +3cm7 +2xk4 +3pxz +4y2p +5exx +2er9 +4mp2 +6hkx +4dzw +4o5b +3i02 +1o5b +6r4v +2xp6 +6ocw +1ung +3bwf +3rde +4pyx +5jzn +3ps6 +1i32 +4tki +3r0i +3v8s +4akn +3o9l +5t1t +1lt5 +4oho +4a9u +4p4f +4rn0 +1q6t +1wdy +2g0h +2p8s +5ifu +3nww +3oj8 +1tu6 +1y8p +1epp +4na4 +4yk5 +3fqh +2xxn +2l1r +4a4f +5alv +1z6j +3ws9 +3nyn +4rll +6czi +5hdu +5mhq +3ogp +4q1e +3vqs +6ce2 +4ui3 +5e2w +4efu +5x9h +4xek +4y6m +5hyr +1o4m +6h3k +4bhf +4kot +1heg +2r3l +5djv +5web +4gng +6i5p +4xqa +3v5g +4y2j +6cyd +2qhm +5ir1 +5w6r +4alu +4qn9 +1yhm +3qtz +5hv0 +5hjd +2wqp +3h9f +3bls +Waring: Missing or wrong elements: B +4y7r +5tw3 +5wqa +1veb +1uym +5ehg +2fl6 +5h0h +3wiy +3ncz +4ci2 +6fcl +5tg7 +Waring: Missing or wrong elements: B +5w6u +3hxe +1ox9 +6a6w +3u4r +6peg +2azb +3iux +3m6q +6qaa +2yg2 +4ui8 +4ryl +4e96 +2yiq +4ozl +5u51 +4tzn +1uh1 +6duf +3kec +6pno +5uox +6egw +6nd3 +6enm +2zlg +2jj3 +3ur0 +5n8w +6gbx +2ybt +3ara +3a29 +1h25 +6qmu +4r5y +5ttf +4l0s +2h6k +3eml +1xoq +5go2 +5k6s +1c4v +2y4k +6e7v +6msa +3h5u +5q0v +2zyb +5hn0 +3cf9 +3m89 +1rhm +1sz0 +3g2u +4l31 +2wbb +6b5r +3qo2 +4au8 +5vt4 +5y21 +6mm5 +3zxv +1u9x +6hvs +6n17 +4tky +3ndm +2r5q +5esq +4fny +5ylv +5hl9 +3ovx +5q0i +2bts +2vr0 +3zsw +4mny +4ozo +4r5n +4uvy +2yc3 +4nh9 +4ca4 +4l7h +1gni +1ilq +1tsl +1j19 +4dai +3fl8 +6hvu +1xnz +2h5e +4nw2 +3fnu +1at6 +4ow0 +6pyr +4okp +3tll +5y7j +1o4o +6mrg +4eny +1iyl +6arv +6apw +3rwi +3ihz +2bv4 +5i7u +5n9t +3th0 +3p23 +6r8q +2bvx +3kc3 +5x4q +1bji +5ftq +4fod +4ptc +3jqa +4eej +1d04 +4rrn +2brn +6cfd +6rsa +Waring: Missing or wrong elements: V +5wre +6ugq +6ffi +4ayv +1y6b +1qxw +4uiz +1tok +3nf7 +3p78 +3l0n +3l79 +4uu5 +1eou +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +4ehg +5xvf +5vii +4qmx +2cn8 +1i8h +3kpu +5iu2 +1kl3 +3ad8 +4wht +2byi +5ff6 +4c70 +6eqm +5f29 +6oyz +4hxw +2ay1 +3dm6 +2i0g +3rw9 +1bl6 +2fyv +6i75 +1caq +6am8 +5f90 +5fwg +6mo9 +4dkt +3v2x +5qav +5vgo +3rx8 +2xke +3rhx +1tmb +4qqi +3gjt +5elv +6qqt +5o1e +2vx1 +1azg +6h7b +4kz8 +4ayw +3cs8 +6e86 +3vw7 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +6uyz +2g63 +3lq4 +6nji +5a3w +1gfz +1my3 +3k5f +6ek3 +4zsl +2vtt +4gmc +3lzv +5hkb +1bux +3ob0 +4ie0 +2g9q +6iji +3fzs +1c3e +5w7j +4ia0 +4j77 +2ivu +5zma +4h4d +5kzq +2ggx +4ypf +6mey +3oot +6h7d +3efs +3fc1 +2wib +5dxh +2nyr +5uqv +1i3z +1y19 +5lto +5x4n +6erv +1w2k +3ggj +4pri +4m6q +2m3z +3hii +6cjh +5cxh +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +2ou7 +1pxj +3c49 +6mxb +4bgx +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +3kai +2y1d +3au6 +4awm +4iu4 +Waring: Missing or wrong elements: B +3o1d +4tuh +3ppj +4rj4 +5o8t +5v1b +5nwd +6gzh +5lxc +1oko +6cvx +2wi6 +2xzg +4nuf +5tq6 +4qls +3ml4 +6uhu +Waring: Missing or wrong elements: B +5za2 +6cmr +5axi +6afc +5ayf +5ew3 +5wlg +1zz2 +4yk6 +6poq +3fvg +1ybo +6c9q +3i06 +3wi2 +4jbl +5t4f +3jvk +2ajb +6fdq +4qw5 +5e8z +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +6oot +3h8c +3qak +4m7c +6rvl +Waring: Missing or wrong elements: B +1lqf +5cuu +4jkt +4wvu +6n5h +4awk +2q1l +6fa3 +4rkx +3zlx +5ntq +3r04 +4mr4 +4f7l +5n3w +4jog +1mto +2jb5 +5ix1 +2mow +5dde +1rdl +3cr5 +3rpv +4o78 +5nvy +2h9m +5yib +3g2s +4jfe +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +6fr2 +4yef +1c9d +3wqh +5o1c +3luo +4d1a +2hqu +5lh4 +4nmx +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +3rjm +3g58 +2e5y +4lh6 +4wri +4qp9 +4psh +5owa +4mbj +2v7d +3ms2 +2qzl +3tjc +1uom +4bcw +4anv +4uv9 +6te6 +2n0u +4uib +4q3q +Waring: Missing or wrong elements: B +5ypp +5vwi +1ok7 +5lax +4k1e +4q2k +4orx +4ckj +4zx6 +5fv7 +4qpa +3nkx +3ttz +4fk7 +6evq +1f1j +4ylu +1ukh +5a14 +4jfj +4qfg +4uhg +4hev +2xcs +3waw +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +3t2p +3qw8 +5khx +3sqq +6g0w +4gtq +4qp6 +2r3o +5aac +3kfn +6g4y +3s3v +1xh3 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4tya +1tsm +5jic +4o7c +3chq +4kox +3n45 +5yji +3h2c +4kon +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +1g7p +2x9f +2hh5 +3c14 +5n16 +4lkf +6oa3 +1v1k +5wik +1jr1 +3zpq +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2xo8 +6beh +6bky +6ijl +6ft4 +4aac +6cex +5auy +2w2u +2xu5 +1o49 +5tys +4pvt +1uef +6gzy +5acb +2hm1 +1d4t +5jah +4qz1 +3gcv +5j5d +4o3a +2a3b +4cqg +6hmp +3ama +1b39 +4yfi +1nnu +4gs9 +2qhc +4as9 +5zqq +5wbq +4r17 +6axp +1sw1 +4glw +4qmq +1v0o +3i3d +2xae +6oio +4whr +5a5p +4qmm +4zro +2in6 +4e1e +2f6j +4qr4 +6bhd +5ku6 +6oz6 +3h1z +5iy4 +4kij +3wff +3dx0 +4fc0 +5ap5 +4lkh +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2cfg +Waring: Missing or wrong elements: R +4j0t +2xm8 +3qyy +2a8h +4p7s +5agr +Waring: Missing or wrong elements: B +5a54 +4qzx +3hmm +2qky +3o8g +2fsv +4kcg +5kew +4mi3 +4mvn +1xp1 +2fv5 +3m11 +2o5k +5u5h +5m44 +4qz7 +4g19 +5t2l +5vfc +6gw1 +4xbd +6a9o +4lnf +1g5f +3b9g +6dya +3s4q +5zdf +3m58 +2onb +3f2a +5al1 +1j7z +3kwb +3t2v +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4ajn +6ntj +5d6y +4ym2 +4m0z +4mf0 +5ntt +5l44 +4x0u +4azt +6aa4 +4qmy +2vj7 +3tvw +4nyi +1toj +6inm +2cv3 +1nlj +1rwq +1yon +3ztd +1wcc +1uy7 +2jdt +6n9h +2v87 +4nie +4r1v +5aqq +3nzs +5w5o +5fxr +4ppb +6ncp +5c7e +6n9p +6izq +4wmc +2nn8 +4lxa +5mwg +5l3f +2lh8 +5kap +4aze +5le1 +3g6m +4l4m +2w7y +1q4k +1fd7 +5hv1 +4j0a +1my2 +1a85 +2o22 +3blr +5zt1 +1u9e +5dp5 +2ltx +5trg +6f6r +5kau +3esj +6ny4 +2v22 +6dl9 +5ejl +3fyk +5l3e +2ov4 +6qfg +2ay4 +4fpk +4eh5 +4p74 +5eyd +5xp7 +5tq7 +4a7c +5wlv +2op9 +5c87 +4yax +1y2c +6cd5 +3sap +5tcc +4y5s +5q0d +5brn +5jiq +4g2f +1p6e +1mn9 +6bmi +2z78 +4hwt +2w0s +1unl +4qvv +Waring: Missing or wrong elements: B +3thd +5z1d +1lev +5ei2 +6q9s +6saf +6c5t +1ida +5dtm +4eqj +4bnu +3eyh +4rab +6kla +4g31 +2bkt +6tel +5mfs +1uy8 +3emh +5fom +Waring: Missing or wrong elements: B +5cf5 +5m6h +1tvr +4p7e +3rjw +3ava +4ixv +Waring: Missing or wrong elements: B +4d1b +3ddq +4u6y +5wac +Waring: Missing or wrong elements: B +4ft2 +5u7o +5ylj +4tsx +2jal +5mxq +3f3u +4qw1 +Waring: Missing or wrong elements: B +5ujv +1ysi +5n7v +6bg5 +5ai6 +4abi +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +6cw4 +2f14 +2aay +5v1d +2rfn +6me5 +1zfp +5aeh +5itd +4f7j +4lkd +5qb2 +3zs0 +4o5g +2wyn +4af3 +3lpg +4qag +3mt7 +6dqb +5lyy +1jh1 +4qvq +Waring: Missing or wrong elements: B +5x33 +4m5m +5ta6 +3puj +6bod +6h0b +4z2h +5e2v +3wsy +4nmq +4w55 +1d7x +4g2w +6ajg +2xbj +1i72 +2e98 +5yfz +3kr0 +1soj +1jj9 +2rox +2w68 +4fzc +5v24 +5izc +5xxk +1oiy +3l0e +5gub +5fpu +5hdz +6cho +5a3u +3frz +4hw7 +3d1f +2ony +2bed +4dpt +2uym +1eix +1mx1 +5f20 +4k5m +3o0u +6d4w +3k5g +1nl6 +2h5j +4j8r +4f4p +3zxh +1bm2 +6f8u +4ci3 +3hiv +3wzu +2vww +3fkv +Waring: Missing or wrong elements: B +4k5z +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +1fgi +3l7d +1gfw +4o7b +5vfj +4cy1 +1p2g +4j81 +3odl +5ka3 +4jg8 +1ya4 +5bq0 +2kbs +4ea1 +4xkc +Waring: Missing or wrong elements: M +3ans +2y55 +Waring: Missing or wrong elements: B +3okh +2hmw +6mvx +3q96 +6g9a +3kah +6hle +5nib +4qoc +5aqp +6fx1 +2xgo +4lyn +5aph +4rrs +2c4v +6oim +3ehn +1b2i +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2vtd +5xmv +2jdn +2x7c +6om4 +3w2p +4lnb +5vlh +1xp6 +3iaf +2vto +5hvu +4unn +2ynn +1qwu +3qiy +3avl +4ps7 +5jy0 +3t4p +1o2s +1jwm +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +3u18 +5m4k +5d6p +1lhv +2oc4 +1xn0 +2cma +6b1y +1o4g +2y6s +6bcy +3av9 +6miy +5zcu +2wmw +5alz +1r5n +5i25 +2xml +4aza +4yh4 +3b8r +1c8l +2fdd +3vtb +3rqw +2j9h +5up3 +3lrh +3kac +5ar5 +5usy +4ran +4lwi +2ay2 +6g8l +4emv +4e3l +Waring: Missing or wrong elements: B +6r12 +5jbi +2pre +2zgm +6suo +6irt +1r4w +6oos +3nuy +3iej +3o95 +6esn +3gs7 +2upj +4q1d +3arf +1db5 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2woa +5euk +1aht +4e90 +5om9 +3ig1 +3k83 +1abf +6ap6 +5ye8 +2ym3 +2am2 +3t6j +4jxv +4gjd +5t2y +3fv7 +6hys +2f2c +3kcf +5agj +Waring: Missing or wrong elements: B +1o46 +6imo +4b8o +3kqm +3peq +4jda +6db4 +6fam +1gpy +4zpf +5fqv +6au5 +4dfb +1br5 +6b30 +1lfo +4y87 +1c5z +4nrb +2w6c +6dq6 +5m4f +6a06 +6iil +6ajj +4n98 +4qyh +5yc8 +1gbq +3che +4qk4 +4imq +6fi4 +2aeb +Waring: Missing or wrong elements: B +1h3h +5m7t +6b1c +4obv +3fr5 +4ojq +4yh3 +5eay +4azf +5tqe +6bhh +3arv +3vjt +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +1jil +2ylo +4fgz +1t69 +4exh +2qo8 +5ngr +3b28 +5u7l +2ke1 +4j24 +3qj0 +6ijh +3ixk +3lpr +Waring: Missing or wrong elements: B +2e9n +5cuq +5mw3 +4n9e +5h15 +4r92 +5g1p +5t54 +4bdg +4rao +4c72 +4pl6 +4l0i +3q92 +2vqj +4p00 +5a69 +4jhq +6h8c +1d6s +5ywx +6ccu +4elb +2w1d +2bjm +4eqf +4h71 +4z88 +5n1p +4qok +1ga9 +Waring: Missing or wrong elements: B +5tbn +4ekg +5kez +5lxd +6u7p +Waring: Missing or wrong elements: B +3eql +5v19 +5n8j +1way +6hu0 +5cil +5knu +3azb +5qae +9abp +5aqj +1icj +2q9y +4zsa +3zlo +4odl +3q2g +2zz6 +1ctr +2itp +6nnr +4dhr +5eth +4f64 +5wxf +6b7e +5lpr +Waring: Missing or wrong elements: B +5bvn +6qae +3t4v +5wdw +3k9x +4y4g +5uiu +5vtb +1vj6 +6ghp +3ds9 +4ylk +3efr +2zp0 +2qlq +6e9w +4jwr +2wd7 +4olc +6eo9 +6dhu +3ocb +2jqk +3l7b +5ni5 +3snb +4b81 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4j7i +5yvx +5ogl +3fpd +3kfa +5ttv +3qu0 +6bil +6e99 +1qku +3t07 +2rib +6nze +4ztq +2o63 +5j32 +3ob1 +6mo5 +4j5p +3ay0 +1bnm +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +5xs8 +3kdu +6nrf +3wcf +6bfe +3bm8 +3vw0 +3r8z +1bqo +5fum +4y2x +3s1h +3ask +5lhg +5dcz +2is0 +2g24 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4u0c +1wkm +4b2d +4ijh +2uw4 +5qab +5vsc +5ur1 +5ho8 +2z3h +6hvw +6szj +3hp5 +1w83 +5o7i +3wf6 +6bfp +3e7o +4zsq +4d52 +1eve +4bxu +4r8y +2ql7 +3zju +Waring: Missing or wrong elements: B +5u66 +5jjr +4civ +3ft3 +6f2n +3db6 +1u9w +2nnp +5trh +4ucv +1tqf +5bqh +5dtj +6afk +1gt3 +3hxf +2wot +4pz5 +3qcx +3fxv +4jit +2f9b +3pdq +6slg +6iae +3dsu +5w38 +4i12 +4hmk +5hn9 +3fu6 +3pn3 +5a83 +3tlh +4gby +5yov +3rxl +2y1g +2xp4 +2wap +6gcx +3ch9 +3poa +4zs3 +1vsn +5cr7 +5xqx +1hef +4ah9 +1h0w +5q1c +2qe5 +4i4f +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4zz3 +3uwo +3t8s +4z2g +1shc +3ogq +5qaa +2g9v +6bnl +5mgl +5alc +3r2b +2hny +4fmo +5typ +Waring: Missing or wrong elements: B +5n4s +2ax6 +2xiy +3q3t +4qrc +3d14 +6quw +5fxq +2p2h +5ks7 +6bee +3buo +6p12 +4gk3 +6c3l +4xg6 +1wtg +4bgg +4hnp +3ump +6n5g +1idb +4wsy +1p7m +2p94 +4i9c +4m4q +3q8d +3mg7 +5l13 +3ftu +1d8m +1hkk +4mnv +4r5g +3tcy +6e2n +5hbh +4mlt +6ufo +5orl +5try +2g8r +2v13 +3kqp +2fwz +6dqa +4gw8 +2wp1 +3muf +4ppa +1t4e +1w1p +6f5u +5bpp +1v0n +5mb1 +4qz3 +3bhb +6n3n +5thj +3mp1 +3o9h +5xw6 +1vjc +4iho +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +1idg +5k4l +4zwy +4x6x +2aux +5ak3 +3ow6 +5jjm +3hxi +2k1q +5km5 +1tlo +5ngs +5ly1 +4yas +4qir +4gja +1me3 +2kzu +5h5q +4giu +4raq +5tza +1eef +5mo2 +5faq +1t1s +2ydf +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +1leg +6q6o +4rce +4z5w +1efi +1rq2 +2wxg +2jkr +6fut +2wu7 +1af2 +4jg0 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +5bqs +3nok +2e9d +4o7e +6gg5 +3f8w +5ef8 +5ue4 +5c83 +6sfj +3koo +2ggb +2k2r +2bdy +4pry +4n1b +3hg1 +3ekn +4cdr +4li5 +5iw0 +3hec +6d8e +3tfv +3oob +4jv7 +4iuu +4ob0 +Waring: Missing or wrong elements: B +5iz8 +2lp8 +5di1 +1gj5 +4j0v +5c7n +3olg +3qo3 +2mg5 +2w92 +3rvg +2xup +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4ezl +5d9l +1zfk +5lyh +4jq7 +3lgp +5abp +5eou +4hco +1kf6 +4jc1 +4dhp +3f3w +4dcx +4b00 +4btu +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2rjp +4jin +4wf2 +3fcb +2yac +6qzr +4d2v +2ofu +4ux4 +1onh +3bc5 +3atl +1jws +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4mm5 +4bo6 +3krd +2fci +1m6p +3zim +6q7w +3ew2 +3qc9 +4qxq +3qce +1a08 +6oxz +6nzm +4bh4 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2zdz +3mo8 +5c1y +6alc +4qjp +2yiu +4nzn +1avd +4jrg +3rin +3ddu +6hmx +5ggz +5jm4 +2n7b +2hr6 +3rzi +1r5g +4clz +4b82 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +3ion +5zk8 +5eta +4b4g +5mqy +5mlo +3s3m +5mxk +6e13 +3q72 +5wbp +3hxb +6b41 +3q32 +1urw +5z1c +5ek9 +4ie4 +6f94 +1fj4 +6naf +4k6w +1bjr +6cse +5xaf +2vj9 +4az0 +2e9a +4pgh +6cyb +4ehm +4b0j +2xng +4qp1 +3uvm +4v05 +5tq8 +4xcb +2h2d +5jap +6oxs +4x3r +2bge +4fxy +6fff +6ffg +5lgt +3bl2 +4mha +3l16 +1w4l +2q7m +2ate +5dah +5y6d +6mdc +2i7c +4u90 +6qho +2k7l +6af9 +2ckm +6c4g +1mem +5gvk +5j9k +2l1b +2bqw +4amw +6g1v +4y2s +4ngq +4y6s +5unh +6d49 +3v5j +2hwg +5nu3 +3srb +1sje +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +5oje +6ibz +6g02 +4b9h +1aq1 +6p10 +5laz +5n9l +2pv3 +4uia +4mi9 +5t36 +5xmu +5j19 +2rol +4q9s +2fxr +6m7i +6m7h +3ezr +3at1 +3hp2 +1yc5 +5he1 +1xuo +6fzg +3ej1 +2r3c +2yer +2oc7 +2w3i +2hog +1x7a +3l7c +2zvj +3h0e +4cpq +2e7l +3mbl +1so2 +3li2 +3d67 +4z7o +5vfn +3wch +4zy6 +6cw8 +4ynd +4o43 +2y1n +6e3n +4kbi +Waring: Missing or wrong elements: B +1kwr +4y63 +4ds1 +1me4 +4mcb +4bjx +1jii +2w6p +2xy9 +6qfu +3sud +2gek +6qzb +1jrs +2wwj +2r4b +3rz9 +3gw5 +2i0y +1gjb +5f2f +6mny +6aff +5jal +6njh +3wtk +5eb2 +4zjr +4joj +4p72 +6r0x +3d2t +6h13 +5lma +5ezh +4f8h +1no9 +4twc +5l7f +6pz4 +3wqw +2xgm +5yqw +2esm +1al8 +5lss +2wzy +3v5q +3sna +5jga +3iaw +2ym8 +4e49 +4b4m +4ivs +1s5q +3qfv +5ti4 +4qzw +1a61 +3r0t +3btj +6n3f +4jnc +5owc +5mty +4pd9 +4wn1 +2bz5 +3tc5 +6d3x +5eue +3rbm +2ggd +4hkn +3sw9 +2gc8 +2wik +5myg +5iua +5lws +1urc +6uvv +6r8r +3in4 +6afr +3wc7 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2fjm +1d1p +5iee +2e9o +3qaq +4hbv +5yie +5g3m +5tku +3g2w +1joj +5m6f +3nk8 +4tz8 +2z6w +4o62 +1r6g +1pzo +5d7e +5u7k +6ohu +3u6a +6efk +6q96 +6p1d +1at5 +5ewd +5dpw +5dj5 +4zam +4usw +5f41 +2zga +5wkf +2qyn +1s64 +5w2q +2g83 +5d2a +1vot +1nax +2zbk +1j80 +5na0 +1dzm +1ong +1eei +4y2u +1g3c +6pvs +4pul +2phb +4hhy +4eok +5l4e +2xhx +4o6e +6nk1 +1nzq +4e5h +4whl +3g72 +1oiq +5igl +6r7j +5ml6 +2v10 +4w54 +6hvh +3fa3 +2be2 +3zyb +4zt7 +3k39 +6om2 +1ao0 +6cvd +5yhl +2ydv +1r78 +1gj8 +2k4i +3itc +5eiw +5c0k +1o4h +4fvq +1vru +2l7u +5q0m +2vhq +3te5 +4cjn +1qf5 +4iuv +3l8v +6fod +5zbz +3a4o +2o64 +6bh1 +2aqb +3mo2 +3n8n +5ele +5uey +1gt4 +2y7p +5lz2 +5a5o +5wpb +3rsb +6hgz +5n1x +1nmk +2uuo +5l2m +4klb +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +5auz +6g0q +6npp +4x6y +2er6 +5znp +4whh +3drr +5drc +5ntw +1b9t +3vzd +1akr +5t92 +3tzd +5lt6 +5h5o +4zcw +1mpl +8abp +3a1s +1nox +3h2m +5c2e +3r9n +4r02 +2pix +3mxs +Waring: Missing or wrong elements: B +4txe +5mwa +5tkt +6p7q +5cgj +2ohq +5em5 +4bt9 +5lp1 +2imd +1j4q +4utr +6dub +6gub +3fc2 +6g9b +6avi +4c38 +1cyn +4h38 +2g8n +6r4s +4qz5 +3vqu +1lor +2vta +4cq0 +1jk7 +4bfp +5jjs +4m5i +1dmt +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +6br2 +6aol +5h7h +5zml +2ynr +3il6 +5am0 +3okp +3rqf +2zu3 +5iui +3w54 +3r0y +4az2 +3kry +4whz +1t4s +4k9g +5fni +6q4q +2xvd +6au9 +3prz +2ccu +3fsj +5aib +5tr6 +1pxh +4ks3 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +1xm4 +4e6c +3r0h +3px8 +1ke8 +6mdq +1n0t +1w2x +3m9f +3wkc +4yzm +4oo9 +5uch +5szb +3tv4 +4oon +5xhs +2h2g +3qmk +6h7j +2vtr +3t3d +5sz9 +3rsv +4xc2 +2zq1 +4o75 +4uxb +4x63 +4x1r +1ke7 +1fpp +1nyy +Waring: Missing or wrong elements: B +5a4t +3nw7 +6iyv +6aeh +6i16 +6g46 +3qd0 +2g00 +6apu +6cb5 +5nge +2ff2 +6drt +5tur +6g9n +5lvx +4gcj +3p4f +4od7 +6f3f +5ekj +1xom +3g2j +2cmf +1xqc +2qoh +6aad +4mqp +3o6l +6au2 +1ind +6n3l +6dry +6e0r +4u0s +4nms +1m9n +5vqu +3uwl +5awj +3wzq +5i40 +3hlo +4ycn +3fdm +3r92 +6c67 +2v86 +5nf6 +5lmb +4h4m +6afg +4m5o +5ddc +1au2 +4z1n +3lp2 +6c8x +Waring: Missing or wrong elements: B +1n9a +6cd8 +5vwk +5l72 +3zev +5fsl +5hlw +2qki +5cav +6fmf +3c6w +6hzd +3wcb +4agd +4cix +4bpj +2yq6 +4yc9 +4e5j +5mlw +5aei +6ind +5k0f +3p4w +1hk2 +1h26 +1osg +3bmn +6oac +1ct8 +5yve +6edl +4b80 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +5ei4 +5bot +2xqq +4n9d +2zpk +2r3i +2pj0 +3f3t +2byp +5icy +5eml +6hcw +5edi +3kl6 +5m6u +6hks +5unp +1fig +2buc +4j0y +3kig +5ekn +6gbe +5j8i +1mm7 +1owk +3psl +3qtr +3u6w +6gdg +6n69 +6hmr +2xv1 +6g9s +4bkz +4kn4 +4osf +6h4p +2krd +3zmz +6qft +5mjb +5ald +5b5o +4mzo +4avu +2r3m +1o8b +1yrs +4pnk +4wrs +3tg5 +3p8h +6o9x +5tuy +4di2 +4nyj +1dmb +6hdo +5fqp +4zy5 +6hsk +3zc6 +1g4j +1sre +5tbp +1r5h +5q0l +5o9h +1kmv +5gic +5v5o +6qxj +1q6j +2ndg +5yco +6dtn +4i6q +1slg +4bie +1hty +5gsw +4gv1 +5ly2 +5dp9 +2kmx +6jjm +5aag +1bb0 +5x02 +5qan +2b7f +5tzh +4ewo +5ho7 +4mzs +4qz2 +3hqh +2qch +1bmn +5myo +4oaz +1r0x +5d0j +3ncr +3tne +6f3d +3ioi +3g9n +3nw5 +3jyj +5mob +5jt2 +6cf6 +3f66 +5ih6 +4kp6 +2jjr +5vom +6axb +3il5 +2k3w +5a4e +4rwk +3tic +6me2 +1ebg +4tpm +5lwn +4pyn +1utz +5wg8 +2bba +5l2y +5f0h +2r3j +2q6c +2fes +6agt +3c43 +1kvo +5xs2 +4yv1 +5yun +6d4q +5afj +3gwt +2jk7 +3f88 +1npa +4nk3 +5th7 +5m29 +5wzv +6c9n +5o1g +3bux +5qar +4q15 +5ogk +5kmf +5c4u +3nzc +4oow +4y2v +4nnw +3ukr +2j9l +5whc +4pte +2os9 +2aia +4yv2 +5uwl +3rul +2bub +2w17 +1dbj +6bib +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +3d27 +3rum +1uyg +5lcj +3lc5 +3nfl +1h1p +6h4t +2c6o +1mui +1toi +1bmk +4d8a +6iam +6rfj +3p7a +4gfn +3vf8 +4cff +4uwl +3fu5 +4n7y +4u01 +4nb3 +5g3w +5osd +2o9r +3dc2 +6ib2 +4qvx +6bik +5al4 +6ds0 +6huu +5ab9 +5mos +3skk +Waring: Missing or wrong elements: B +4he9 +2oj9 +5e3g +4awg +1p6d +4bg6 +4b6u +1ozv +4dr9 +3vjk +3cj3 +4unr +3b78 +1ocn +4r1e +4i80 +6a73 +4l8m +5o4s +6g7f +4led +1rhu +3gyn +6p3p +6h76 +3o6m +6dxx +1ugp +3lbl +1jlx +5aqo +3hdm +1tmm +5n2x +1zkk +3uol +4ztm +5h13 +2uw7 +3tgs +1uxa +5ivt +4yab +2g0g +2j50 +5kw2 +4rlk +3fhr +5wg3 +2uw6 +6k0j +6em7 +5ur5 +6gip +2ay6 +5epk +1kti +5y48 +2wd3 +5jz9 +3pix +4nka +2qn1 +2i1m +2agv +1rww +6joe +4nq6 +5oxg +6fv2 +5nhl +5elq +5o1i +5dri +2uzl +3rxi +6m9t +5twz +6npt +5f3z +3itu +1h1r +3zmh +5wb6 +4pd6 +3dvp +6mso +2nxm +4gtt +3iqq +5igk +1csi +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +centreofmass.sh: line 112: 2117278 Segmentation fault (core dumped) $LEDOCK input.txt +5iis +1e37 +5fdp +3a1t +3poz +4rfy +2h5d +Waring: Missing or wrong elements: B +2aa6 +4g8o +5w7u +4bde +4wq3 +3sdi +5gn6 +4djs +3d32 +4l7f +6goo +3kjq +5q0g +6at0 +4k5n +4tzq +3e0p +5xpp +4ede +6afj +5alp +5gx7 +3lpj +4ikt +3d1v +4k6y +1o79 +3lmp +4h5c +4xjr +4qyg +6uim +2w71 +2yde +4l7b +5ybe +5lqf +3lbk +4ge7 +4uwh +6g47 +2jdo +1ke0 +Waring: Missing or wrong elements: B +4e3n +Waring: Missing or wrong elements: B +2g9u +6o8i +4n6y +4wrq +2cem +5fbe +6e5s +4mr5 +1bmm +3caj +1nd5 +3kpv +4eev +1uk0 +6c28 +3rz3 +5l6i +4mnq +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +1c2t +6sde +3ogm +1jqd +5oua +5ixt +6euv +5y5t +3lnk +6a3n +3s00 +2a4w +3rwq +4lh5 +1x7b +6h4o +1ywr +5inh +Waring: Missing or wrong elements: B +6jsf +1fw0 +3u15 +4gtv +4eh6 +2wa3 +5swg +1y3g +1uod +4hnn +5adr +4jsr +5vdv +2p33 +4jnm +1u59 +4xkb +6qfv +2mkr +3nwe +6e4u +2uw0 +4qps +6d28 +2vd7 +3sow +4k8a +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +3c4c +3oeu +5hip +5ar0 +3gk2 +3o0e +6buu +4b6e +3vyf +4qkd +6pf6 +2koh +3f0r +3r00 +5lmk +1a3e +3k5d +5l26 +5bmm +5t6f +1axr +6rj3 +4o76 +4ib5 +6ak5 +5a3q +4uvb +3w32 +5qa7 +6ami +1nl4 +1fpy +5ctb +3q3b +4du8 +6dih +2it4 +3d9l +4ixu +Waring: Missing or wrong elements: B +6r49 +3abu +3i7b +6p14 +4ui7 +3kpw +4dhn +3kwf +2ydo +5nvc +4jv9 +5cls +4mwu +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2vxj +4eo4 +3oct +4u5l +5du4 +1cqp +5vnb +5nuu +5vkf +3upz +3u51 +3fum +2ig0 +4zly +5ti6 +4ycv +4rx7 +5j3s +5yr4 +4xg7 +4q9z +3pa4 +4gj9 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4ydf +5xmr +3v4v +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4rvl +3fh5 +1fwu +4u0m +3l17 +5vil +3uoj +3mp6 +3c10 +4bic +4igk +3obx +5tx5 +1rsi +4rcd +2ksa +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +5nr8 +6oi8 +6hzp +5iep +2kfh +5qby +1qw7 +4oba +5y3o +5ggj +6hv7 +5a2s +1lhf +Waring: Missing or wrong elements: B +3sgx +4u5j +4kmd +1xn2 +5w4v +5o4t +4ok6 +5dif +5e2n +3l3a +3vrt +6rj2 +2wtj +6plg +3inh +2wzz +5svz +6oe3 +4hnf +2nq7 +4k3m +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +3aw0 +5u2f +1ld8 +2qbx +6cco +3pa3 +3efj +1b42 +5fdz +3k3b +3tiy +1o4e +6nfn +3qip +1qaq +4avw +1af6 +5eh0 +1h79 +4an3 +2q11 +5jf3 +5etq +2ha4 +2pv2 +5zee +3rxe +6e59 +1mj7 +4y2t +3blt +1g2a +4mwe +4ce2 +6m9c +4h3c +3w5t +5yjp +4wno +2fah +3p8e +4gbz +3rcj +3fzc +2ovq +5mzg +6fzf +4kjv +3co9 +5ai8 +4pre +1wbn +1h3b +2w1c +2z52 +5iv4 +4ory +3rkb +3neg +1t08 +3n4c +6rn9 +4ipf +5v9p +3dcs +3lp0 +4mep +4hdc +4eym +2peh +4eg7 +1o37 +6bhi +4gtr +5v7i +5hh6 +2psj +3mle +5wyq +4k3r +2c57 +3t6r +4wf6 +5c42 +2h8h +5ai4 +2bks +2vvo +5hg5 +5yvt +3vrv +5mt0 +5j47 +5vfd +4ui4 +5m39 +3feg +2fuu +2avi +4rxd +6br3 +3cqu +3wk8 +6fgq +6i9a +6i0x +2jkq +3e6k +Waring: Missing or wrong elements: B +4dem +4mnw +6bw8 +4l09 +3iet +1oh4 +6ewk +6mum +6e3z +5khj +4wmx +4xyf +5l2o +2c6n +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2h2e +6hu2 +3rl8 +5akk +5wuu +4axa +1vyz +2vtl +8hvp +5kjn +5etv +5xbt +4urm +4g9c +2no3 +3qqu +4d1s +2xpc +5ut0 +3wyk +5nfa +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +4p4e +5kww +3rth +4ppc +4ai8 +5dhs +4at5 +6s7k +5e80 +6eks +5dda +4l33 +2g96 +5y6e +1q6m +3bm6 +Waring: Missing or wrong elements: B +4yve +4ikn +3nnw +6qts +6rvf +Waring: Missing or wrong elements: B +1dx6 +1a1c +2br6 +4x3i +4q1a +1bky +5ick +3ue4 +1hkj +4x7k +5ak0 +4aa1 +6knh +2ow0 +1kv2 +3ern +2jmj +3iut +6ilq +4i5h +5kde +1ru1 +4ncg +5tdr +5f4r +1w0y +5tol +5g1n +3d25 +4ty8 +4mzl +4w9e +5k32 +6cq0 +3chr +4zts +4n7g +4a2a +1o9e +4msl +6eaa +3s0o +6bgu +3mvh +5zdg +4pra +2who +1ze8 +3s56 +4ouj +4m3f +2jko +6hx8 +5naw +2yhy +5nar +3zh8 +2bmv +6m8d +6nrj +5nin +5ufo +4o36 +1fl6 +6hth +3dcq +1i9l +5v5y +3hv6 +5he4 +4gw1 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +5jgb +4crj +4ie5 +1npv +5ypy +1pxk +1xpc +6mmo +5z4h +5ou2 +4mw0 +5h3q +3cid +1we2 +1uye +6kjf +2o9j +4hgs +4no6 +3udv +4wy7 +5ove +5m0d +5lwe +3odu +3szm +4urx +5fqb +Waring: Missing or wrong elements: B +4c9w +6eda +6g91 +3sm1 +4btl +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +6cjj +2jb6 +4cqf +3dpk +4a9n +5v88 +5wf5 +5diq +1uvs +4d2w +4hlm +1uy9 +6f5w +5yf1 +3mmr +Waring: Missing or wrong elements: B +5lzg +3ik1 +2kce +3t3g +2vcb +1rdj +6a93 +5jrq +5nn0 +2ncz +4o4g +1eb1 +6di1 +4ir6 +3ncg +5g10 +4u45 +2qfo +5myl +6ea2 +1wxz +2rm0 +2p8o +Waring: Missing or wrong elements: V +6axq +5fcw +1v79 +3kqw +4li0 +4fyo +6bec +2w0z +4pnm +3kck +4xpj +3vvz +3t03 +4rac +4l02 +4joe +3qcj +2bdj +3q6k +3s74 +5d3s +2cgu +5y1y +6cer +1f4y +4l0v +4phw +2xxw +2ltv +2o4h +5hf1 +1qkn +4yc8 +3prf +2xp3 +3lpu +3l08 +5kks +5hvy +3k7f +4p44 +6d1u +3uh4 +2mwo +5fi2 +1hrn +5tt8 +6ra1 +4nro +2m0v +5jq8 +5hna +1y6a +4amz +3twv +1uu9 +2hmh +5uvc +2ie4 +3t3i +5fow +6i97 +3lpt +3aya +5yp5 +4mm7 +5kpk +4qo4 +4la7 +5xjm +3ctj +5nhp +3hyf +1jmq +5h0e +5hbe +3my1 +2zm3 +5hj9 +Waring: Missing or wrong elements: B +6mzq +2y2h +Waring: Missing or wrong elements: B +6ea1 +5awt +4nzo +2bgr +3ntp +6anl +4ufg +3rv9 +5eom +4oz1 +3phe +4hyb +4cc7 +4ba3 +4umt +5kgn +4uzd +3zjt +Waring: Missing or wrong elements: B +4pkw +4zdu +1swn +5tzg +6c3n +2v0n +3m1s +Waring: Missing or wrong elements: R +5ugh +3hyg +5i24 +3nc4 +3kvx +3tcp +2az9 +2aw1 +6dne +3doy +2csm +3rqg +3wqv +5hbj +5nhv +5div +1jyi +6gxy +5a0c +1pdq +6bsl +3h06 +3u1i +5ehe +4cbt +1hxk +4mk7 +4kne +1yz3 +5hh5 +6f6s +5ho6 +3hc8 +5ei6 +3bys +1gag +3eu7 +5jf2 +2y2j +Waring: Missing or wrong elements: B +4e35 +3m5a +4odm +6gy5 +6co4 +3lqi +5c20 +1c8v +5e8w +6g28 +4fcb +6n92 +6cn8 +4uxj +2a4q +4k3o +5c4k +2gmv +4pji +5arf +1v41 +2z8e +5l8n +4e3f +4q3s +Waring: Missing or wrong elements: B +3bb1 +1iht +2fr8 +3sie +4ez5 +2kbr +1etz +6q39 +Waring: Missing or wrong elements: B +6n3z +5acw +5f6d +2pyi +2lko +5t66 +Waring: Missing or wrong elements: B +4wnm +5jv0 +3ejs +4gb9 +5anq +3syr +3lgl +4nrm +3ohf +3r2a +2pj3 +4gk2 +5gmi +4odn +5t5g +5nwh +4x7i +3k3a +2ilp +6qz7 +5fiv +4gd6 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +3tam +5mkx +2wf3 +5o91 +2m0u +5mnb +3hy7 +3s7b +1pwq +3dp3 +3pkb +2p98 +5oxn +6n4t +3o9g +4tk4 +2o9v +1ugw +4p2t +3ex3 +3zbf +6e5b +Waring: Missing or wrong elements: B +3nga +6n0p +1czk +5u4g +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +6pt3 +5hfc +5n2d +4i32 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +5c7c +5uiq +1nj1 +1qq9 +5he2 +2wqb +2y1o +1lf8 +4nks +4im0 +4erq +2y68 +1ett +2nd0 +5dhq +5ywy +6b4w +5qcl +3ezv +6bny +3oxc +5ur6 +4gh6 +5w5k +3pup +Waring: Missing or wrong elements: R +6bgg +3rti +2lpr +Waring: Missing or wrong elements: B +3uqp +2y54 +3tfk +4yo6 +2ccs +1bbz +3arz +5l2n +2vnm +4kab +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +3bf1 +6gqm +4gui +6ckc +5i94 +4ej2 +3v8t +3p9t +3dxm +1snk +5d7a +2i1r +4x7l +4lp0 +3pd4 +4xy2 +3g4f +5wbz +4wku +Waring: Missing or wrong elements: B +4pku +5mfr +4bcj +1zhk +4o7f +6bmx +5am3 +4o70 +4alw +4bqw +5f67 +3o3j +5mrd +3zzf +1h9l +6d59 +5thi +3zya +4o0j +2pjc +5o7n +6cct +3gpj +4twt +5elf +4kzc +6oqn +2xi7 +5a85 +6hpg +1u3q +3d4l +2j83 +3s3k +2a3x +5wou +2boi +5nt4 +3be2 +6m88 +6q8c +6eyz +2y34 +6afd +3msc +1ove +1svh +6b2q +4oq5 +2ew6 +3eou +2uw8 +2qlm +6df7 +1q0b +4rt0 +3t4h +5g0q +2jq9 +2oji +2i5j +6d6u +5uwi +3d7m +2kfx +6q8k +3zlq +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +3qnj +4c8r +3vp1 +2nng +2zg1 +1upk +6hov +4caf +4l0b +4mw7 +4yik +6q7v +3ck8 +2anm +1tkx +2i0d +5np8 +4hbx +5auu +3vby +5zef +5tg6 +Waring: Missing or wrong elements: B +5dxb +3unj +5q0j +4bqx +6bj3 +3bm9 +4lge +1xud +6oyw +3hvc +6qyl +2x6j +3oaw +4yrr +6g97 +2ff1 +5uy8 +2ow2 +2vti +4fll +4xe0 +4mse +4ue1 +1j4k +5n9s +5uuu +2y36 +4oq6 +3b8q +1q3w +1o4p +5ke0 +4e5i +4yw7 +6e83 +2g2r +5dv2 +1zom +6b33 +3wut +4a4e +3ooz +4dk7 +4io8 +1o4r +4ob2 +Waring: Missing or wrong elements: B +4mqu +1sfi +5vc5 +3t5i +2ojf +4ztn +4j1i +6qfw +4qmt +5wdc +1pig +4kju +5can +4iwd +3vsx +5nb6 +5a8x +5tg1 +4bhi +4ocv +4cfx +1w6r +3vws +4pyv +4uil +6dgy +5yc1 +1ci7 +3ueo +3l5e +2xui +1xbb +2ql9 +2x3t +3zs1 +1mik +4cmt +5y86 +5uyu +3as1 +5mz3 +6fns +6mil +6bfw +2v0z +1rek +6mul +4uvw +4w53 +5k8v +1r10 +2lyb +5i56 +4oas +2qv7 +3moe +3lnz +5z1e +2g79 +4nw5 +5w9g +4hej +4kp0 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +3py0 +4hcu +2ds1 +2w1i +3i6m +4egh +5h2u +4ejn +3qj9 +2oc0 +5ndd +3uph +3dz2 +4mzk +3o4l +3uhm +2wxd +2auz +2l75 +6ak6 +4op1 +5aqh +3pxe +1c85 +5lgo +3mbz +5k8o +6n3o +4gsy +3i4a +4umr +2ohv +4eop +5dhf +4l1a +4yl1 +6g8p +4z3v +2cia +5may +5cei +5emm +3mtb +3l81 +2cmc +4ehe +2qrh +4mk1 +5a3r +3l6f +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4j3u +4jyu +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +5fxs +4yrt +6asz +5l6o +4y5i +3zot +5tqu +5d7r +5u9i +6fyk +3m17 +3n7s +4tk5 +5hg7 +6ak4 +4feq +5bpe +4mb9 +3pj2 +6ez6 +4zsp +2iw6 +4inu +5nad +2xd6 +4ps5 +3up7 +5eyz +1jqe +5km0 +5yyb +7gch +6nng +5fap +6rr0 +4bcf +4k2f +3pvw +6ei4 +5zu0 +5v84 +1ag9 +4b70 +2og8 +5abh +2piy +1zuc +1uj0 +6gmq +1o6q +5alk +4g3e +2vc7 +5ypw +4dx9 +3bsc +5dsx +4wkt +Waring: Missing or wrong elements: B +5kql +5k5s +5xvu +5ek0 +6gch +5ksv +2xx5 +3jq8 +5wad +Waring: Missing or wrong elements: B +4a6v +2h5a +2cct +5cw8 +5w0q +6rn6 +3hs9 +5nwz +5ets +1hy7 +3dbd +6miq +5vo2 +1sc8 +3ccc +1gjd +2hyy +4pl3 +6keb +5gv2 +1o0o +3sou +4bdj +4jlg +5ku9 +4pm0 +2qh6 +5qj3 +1o3e +4ps1 +6axk +2ykb +1oxg +3kqs +3pch +6pyc +6s90 +4d2p +1tfq +2oqs +1uyd +4pnr +1you +6c98 +5fun +5toz +6imb +3p55 +3kyg +6rfi +4ucd +4huo +5a5r +2jst +4nxo +4qzs +3ika +3cpb +2bzz +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +1xr8 +5un1 +6bfx +4c5w +2fie +3fty +5tyj +Waring: Missing or wrong elements: B +2wxi +4cqe +4z2j +4gao +3br9 +6pvx +5vs6 +6eox +5i8b +4bw1 +6i8l +5q0n +3tpu +4hxm +4erz +3gwx +6tl2 +5xup +6r7k +1uyc +3ddp +1e9h +4nj3 +4j53 +3vb4 +5dro +4bzs +6mdb +4ksq +5td7 +4h36 +2xaj +1lb6 +2ay7 +5n20 +6u8l +5kcv +4qta +3bpr +1r6z +5sxn +4lh7 +2k00 +2f71 +5y7k +4mx9 +3wgw +5ea4 +1ukt +4exg +4eh7 +3aig +6qw8 +4dhs +5mno +4j0p +4pkv +2opb +3smq +5vcx +2jdv +4xx4 +6fi5 +3oad +3twj +6ufn +5t1i +3sad +4rvt +5n21 +1ujj +4r93 +5e1o +4pvo +4ezo +4dt2 +4dce +4ucu +5i5z +4deb +3s2p +4qc1 +3wuv +1g5s +1tg5 +4n4s +6dvm +1rry +4kba +5i4v +1noj +2bbb +2o9a +1i00 +5eb3 +4u0b +3kd7 +4kc1 +1o2y +4mz4 +2x5o +4u5t +4jn4 +4tww +5he3 +4ee0 +5wrs +4j1c +1ezf +4flk +3hio +4yec +6dgz +5xms +5jhd +1gym +3kjn +4yxd +5akl +3eig +4bds +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4dtk +2uz6 +5ofw +5q1b +4jai +5ap0 +2ity +2ay3 +2x4u +2az5 +4p6e +6c7r +1p02 +Waring: Missing or wrong elements: B +6afl +2zxb +1pmn +4eol +2oic +2qd9 +6baw +4btm +4az3 +5w14 +Waring: Missing or wrong elements: B +4bky +3nf8 +2xf0 +5mxv +4b85 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2xag +1y4z +2zjf +3nzi +Waring: Missing or wrong elements: B +3ked +5d29 +5ajo +3bjc +6bqd +3zha +5ckr +5mql +3kfc +5est +Waring: Missing or wrong elements: B +5zgg +3d3p +3pwh +2q6b +4jvb +3cth +3f82 +3g6z +2aox +4bi0 +4own +4ww8 +1yid +2y8l +4at3 +5etu +5k0t +6mx3 +1guw +4uwf +2xne +5f4u +4lte +4pzx +5opc +6aaq +1fvv +1h1b +3djf +5waf +Waring: Missing or wrong elements: B +3g2l +1hqh +2khh +4j03 +6ezh +2zb0 +4u3f +5v7w +5zz2 +5a6n +1juy +3hrf +5z1s +1bzf +4hyh +5iu4 +6huc +4xmo +1t4j +2xoi +3ppk +2bmc +6c2t +4omd +3fyj +5jin +3ccn +3qvu +1zh7 +4p0x +3ryw +3zpt +4z7i +1v3x +1qxy +3heg +4r07 +3upx +5x4m +1jm4 +4h3b +4bfr +1xot +5iq6 +3que +4iz0 +4bd3 +5tv3 +4jyv +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +6a04 +3qio +1ni1 +3cgy +5agu +1rdi +4ce3 +6f34 +2wtd +6f6u +3ovz +2g78 +6oxx +5qap +4mt9 +5tgy +Waring: Missing or wrong elements: Z +4pr5 +4oc4 +5v8q +4pns +4wvt +5mja +5xvw +5i12 +2x7d +5u5l +4psq +5eld +6hmb +6aa5 +4bzo +4zjc +5bml +2x2l +5a3s +3tct +4j5b +3qi4 +6d40 +6dk1 +4okg +5knv +1dbk +6bij +3ayd +5alo +3o86 +Waring: Missing or wrong elements: B +3cso +1ax1 +4wk7 +5eel +5j3v +2fme +6b5i +5m6m +6npm +2c6i +4jbs +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4dcd +4pli +2v85 +4dxj +1u2r +4e9c +5c26 +4uro +1hiv +4bdh +5yy9 +1rti +3d9o +1oir +6hkn +2piz +6h4x +4euv +6aoy +3e73 +5mli +3are +1inh +6bkx +2c9t +4zs9 +6aah +4cby +3zlk +2y8i +5sy3 +4ie2 +Waring: Missing or wrong elements: B +3tv8 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +3eu5 +5x9o +6b5t +4c73 +5ni0 +2of2 +2kup +6gjy +2n14 +3qcl +5auw +2rg6 +1n5z +3kqt +4i10 +5ne1 +Waring: Missing or wrong elements: B +6fyp +5ewz +6ez9 +4qsm +5iz9 +4wgi +2mwp +2pjb +5dls +5qax +3mks +5gvp +5nr7 +3pcb +6ar4 +3t4n +2r9b +3qpo +2va5 +3fi3 +2lsv +4wkv +Waring: Missing or wrong elements: B +2i0j +3vtc +2emt +4lv1 +Waring: Missing or wrong elements: B +3fy0 +Waring: Missing or wrong elements: R +6e91 +4es0 +5usq +5mar +4frj +5m4i +4l6s +4os2 +1ylv +4tkf +1c3b +Waring: Missing or wrong elements: B +3nzw +2hy0 +2uzn +4e9d +6e1a +2jnp +3kqd +5ali +4bbg +4qvy +Waring: Missing or wrong elements: B +3f5p +5ugd +1i90 +3gxz +5j74 +2bb7 +6nzf +4nrt +6afa +4b77 +4k19 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +6g9k +5kkt +3meu +2gnj +5ni7 +1eol +4j86 +6c5h +6oy2 +4hys +3wk6 +4rse +2w70 +6b8j +3ktr +2fzz +2vwz +1rxp +1tka +5i8c +5wzs +5m3b +5khd +6nel +4z0u +4bfz +3lpb +6oko +3q4l +2f18 +3o64 +4avg +5m1z +6b95 +4xkx +5zh5 +4xdo +6dnp +6jsn +2llq +3bl9 +2brg +3r21 +3s9y +6cje +5u6k +5jf6 +4xyn +6fvm +4j5e +3wke +6rrm +6cd4 +4e20 +5ghv +3gl6 +5w4r +5jdi +6n77 +4oq3 +6c5q +3da6 +5ty8 +3qt7 +2o5d +3sl1 +Waring: Missing or wrong elements: B +5hff +5oq7 +3nzx +5qik +4gvc +3sn8 +4url +2anl +4kio +4c4f +5hls +6ow2 +6ccx +5g53 +2pj5 +6hot +1br8 +4zpe +4fhh +6eip +3lzb +5c29 +4od0 +5ih2 +5jcj +3l9n +4zs2 +2z3z +Waring: Missing or wrong elements: B +1klg +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2uue +3c72 +4hy4 +1q66 +3k5u +1qca +3upy +4fic +3k84 +6n7c +5lp6 +6f6i +5os3 +1nhx +2ria +4zw3 +3ogx +4gq6 +4myh +2fde +4wk2 +4yqv +3h22 +4awj +6d3g +6g6y +6b7c +2woq +3ske +1ov3 +4jr5 +4jdf +6hkm +1tyn +3twu +3rl3 +1mf4 +5vdk +6bef +1c50 +5mky +4c6z +1hyz +Waring: Missing or wrong elements: A +2q15 +2y56 +3t3v +2h03 +2ych +3ti1 +3d3x +6fnx +4qt0 +3fck +1bl4 +1mwt +5g11 +4ff8 +5t2d +4ogt +4u4s +6kqi +6min +5orz +4xhe +6bw5 +3lxg +6mom +5a09 +6iik +2q2n +4l3p +1jt1 +2rt5 +4unq +1u3s +6d4v +4b6q +6ed6 +5adq +5mm9 +3lfn +5j87 +3u0p +3gf2 +2r3k +4piq +3wmb +6q6m +5q14 +3wk9 +6cdg +2ooz +3t0t +4emt +3hha +3q7j +4i7c +5uqx +4zg7 +1ad8 +6abk +1yvh +3rmf +4zyq +2n3k +5wfm +5lj1 +5ivf +1fdq +5khi +5npe +4urn +5k0j +2bgd +6sy7 +2pj1 +6jz0 +2ea2 +2frd +4ms0 +2f6y +2ntf +3gds +4gee +6ft7 +3opp +6pgp +3tsd +5owh +4rfz +1zd5 +1xur +3tv6 +6bh3 +3hvg +2z9g +1h0r +2hai +6aps +2srt +5ai1 +1akq +5fat +4n8e +1mxu +2pl9 +6poh +6gop +4o4k +5ml2 +6op0 +4nru +3mvm +4rg0 +1yys +6i4x +5ndb +5ct1 +4y8y +5zdp +1jbd +5vqy +2lk1 +1mdl +1ayu +6mhb +4u0x +Waring: Missing or wrong elements: B +2jo9 +6e3m +2xx2 +5l2i +5fi6 +6abp +2vie +5xyz +4jmh +1iau +3dz5 +2y0j +2ipo +4r91 +4uwg +2ci9 +4p4t +3eor +6hgx +5m4c +2fm5 +1hk5 +3nsh +6eo8 +4bgm +5tqs +4xua +5aer +2zx9 +3fuk +2i0h +2jbk +1qpl +4hgl +3u7m +2jbu +3uat +1zaj +1bmb +3dow +5bnr +5hg8 +2gh7 +3hb8 +1ke5 +5fus +5l6j +4hww +Waring: Missing or wrong elements: B +2eum +1cin +1pau +2isv +5wzr +4u0e +1m5d +1ntv +1nyx +2wgi +3wpn +3k5k +6hmy +5n7g +6mlf +5emj +2v3e +3u0t +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4jls +5w19 +2y59 +Waring: Missing or wrong elements: B +4ono +5fwj +3loo +2lkk +5efb +3uvx +6da4 +5tus +6ipj +4u2w +3ztx +1anf +1tyr +4byi +3uib +4w9w +2eep +Waring: Missing or wrong elements: B +1azl +5lyw +5bns +1t1r +2gg2 +5ehp +5mae +5ewj +6n82 +2isc +3ttn +3ij0 +6o0h +5eob +1ndj +4dgb +5qa6 +4bnx +3cwk +2az8 +3wq6 +2qe2 +1xs7 +3qzt +4dgg +2pmc +4lbo +4zz0 +6cvy +5ti5 +3r8u +5a4l +1y2k +5j9y +1o4q +3r01 +1qnh +1rgl +4qtc +4ce1 +5fqs +2r3h +4g8l +3wth +5umw +3bki +5oug +6fu1 +2ovx +4dbn +6gz9 +5wi0 +1riw +2h44 +3l5d +5v5d +5t3n +2a25 +1z3c +6jsg +6sze +3hnb +1k08 +4fci +3wns +3fun +4bdi +2xyn +2g6p +6e06 +3e7b +2dua +6i8z +1bim +6h5w +1rm8 +3jsw +1f40 +1c3i +4egi +1gx4 +5hjc +1i7i +1xh6 +2aa9 +5lo5 +2ito +2l11 +2b1p +5uxm +6hv2 +2lbv +1tkc +2c8x +3cib +2pja +6g3o +1kna +6mjj +3fud +3ro0 +5w4w +3v31 +4l23 +5two +6sfc +1x9d +3f35 +6ox0 +2wxo +1bwn +3wkd +3uw9 +6pnm +4kbk +1i41 +1x76 +3f38 +5jzy +4nud +1q63 +5ung +3mv5 +5x79 +5ti3 +4qmv +4r6v +4qvw +Waring: Missing or wrong elements: B +6e4t +6jn3 +Waring: Missing or wrong elements: B +4lpg +3g0b +2vo7 +4zyu +1ahx +3ls4 +6a8n +6hld +3n7h +6v1c +2cm7 +4u7o +4cxy +5hhx +5y93 +5al5 +2mov +6hbm +3zls +5w73 +4x1s +5e1e +4ze6 +5w12 +Waring: Missing or wrong elements: B +2kdh +6ic6 +1y91 +1nym +Waring: Missing or wrong elements: B +4u0i +1tt1 +4q3r +Waring: Missing or wrong elements: B +1lkx +4g1f +2l65 +6jpj +4ps3 +3fqs +3wiz +6q8p +2j2i +3adt +5lgr +6q92 +Waring: Missing or wrong elements: B +4f14 +2jqi +6m8b +1lek +6fgy +4fab +3u2k +5uwf +4yih +1ujk +3e8r +1g05 +4gjb +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2qft +3hfz +2wks +4ef4 +1pmx +3fal +6j8q +Waring: Missing or wrong elements: B +5xst +1is0 +2x38 +2vqm +4eh3 +4r7m +5vqv +5c1x +1p2a +2y2n +Waring: Missing or wrong elements: B +6dik +5ap2 +2f6v +4nmo +6g86 +2aie +2oa0 +1d6n +3ual +1cka +5fdd +3sdk +6aom +5oah +4o72 +2h02 +3n1w +4ufe +1kdw +Waring: Missing or wrong elements: B +5enf +2vtn +6gzl +2qic +3e6v +Waring: Missing or wrong elements: B +6hrx +3ny3 +6o3y +3h0v +2xnm +3pxy +4h2m +3cp9 +5gtr +5jf7 +3kf7 +4ycw +1nqc +6moo +1g49 +3hv4 +5aae +5buj +4b8p +6buv +5mi7 +4xnw +5f1c +4u0n +6qhr +5ap1 +1hc9 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +5fqt +6gxa +3mvl +3v2o +4ohm +3ry8 +3ued +6mtu +5npb +3g6h +5w5u +1i7m +4uff +6fqu +4ht6 +1wqv +1ih0 +3qai +6hhh +2nwn +4bcb +3dg8 +5o1s +4j2c +5w1w +4p4s +3fz1 +6j8r +Waring: Missing or wrong elements: B +3pkc +2wu6 +5dhr +3fl9 +5anw +6mmc +3avf +2h13 +4mjr +4wlb +1fyr +1biw +4na7 +4ud7 +3rm8 +4b3u +4ez3 +4j06 +3e62 +5f94 +4hzw +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +3f7u +1uj6 +3mz3 +5lqq +3vbq +5vsk +1mqj +2ohl +3lxo +4bch +3kmm +5bnj +2qrg +3t9t +6c9r +6i15 +5ygi +3shb +6f8g +5tzc +5w4e +3g3m +2ye9 +2gg0 +6fse +2b1q +6e6j +5maj +5gn7 +1u0h +5l6p +2igv +6d4u +5w0e +4l2f +4lsj +4jg7 +5trr +4pnt +3cpj +1bzh +1yy4 +5mra +3qlc +6a6k +3gcq +4oc6 +4j4o +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +1f9e +4qwg +5vc6 +3mpm +3p5k +6f55 +5koq +1oq5 +3tki +6ps9 +5xyy +6inz +1h39 +4m7x +2yjx +4mwv +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +1u6q +3va4 +1pus +6c0n +4jvq +5y0x +2onz +4os7 +2ewp +4qvl +Waring: Missing or wrong elements: B +5e8r +3sym +5ggl +3zm4 +2gv2 +4xrq +5twh +3eta +2xpb +6c7j +2w0d +2wei +4zsr +3oy3 +4g69 +4h1m +4heu +4ucr +5xsu +6gcw +5zwi +5db2 +5c7d +4bkj +5sy2 +4zph +4dho +6cqt +3tnh +4g93 +3r6t +3ua8 +3wf8 +3ipx +6c42 +4hvh +4xv1 +5f4n +1him +3vs3 +3tpx +5kos +1rlp +3qd3 +2wxf +2c02 +3e0q +3d7f +6huv +4qq4 +1j07 +4yl3 +3umo +5izm +5lpl +1kak +2byh +1n1t +2k62 +3tv7 +4h4e +3qar +4uvu +5aln +1z9h +5juz +6bqk +2x8e +4no9 +4eos +4pni +4o24 +5ldo +4f70 +1tze +4a7b +2wf4 +4wh9 +2p93 +4iks +1j5i +6mob +4uit +4len +Waring: Missing or wrong elements: B +1ymx +6seo +3eyg +3p44 +Waring: Missing or wrong elements: R +4knb +1zkl +3l6x +3h98 +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +2wl4 +2ooh +4xx9 +2uw5 +1opi +1q83 +3n49 +5zhn +5jv1 +5j7b +1au0 +4nrk +3jzs +6c0r +3k5i +6nk0 +4dvf +1v2p +3lpf +5tq4 +3kwz +6et8 +5fsm +3el7 +1okw +1aqj +3lc3 +4rx8 +1axs +1ws5 +3nfk +2w97 +5j8x +Waring: Missing or wrong elements: B +1n1g +3ljj +2chx +2jaj +6pl2 +4why +5ztn +4pqn +5t2i +2vew +4w4z +2p8n +6cea +5obj +3v3b +3dxh +1jtq +4d88 +3wyy +2jkm +1pf7 +5uv5 +3vjs +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +6s4u +3sh0 +1e03 +6sfi +4glx +6fer +4hod +3cde +5oqw +5tyo +Waring: Missing or wrong elements: B +4mgv +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4dgr +1h4n +4pkt +6f9r +6fr0 +1iem +Waring: Missing or wrong elements: B +5aes +4cl9 +6g4m +6gvx +4pml +6fi1 +6iql +2v5x +4fil +5alf +6gcl +1h07 +4l1u +4k78 +2vci +4a4c +3k0k +5lvn +6qxu +3aje +3x1k +5kcx +3f6h +5adt +3uh2 +6n4b +6sal +5i3m +3wti +1xgj +2x6w +4krs +1cwc +2fx9 +5tyl +Waring: Missing or wrong elements: B +4qq5 +2yig +4x6j +3pka +5l0c +6cwi +1czc +3run +6i3s +4b0g +1ft4 +3n2e +5azg +2n06 +2or4 +2lzg +2gm9 +1rt2 +3sjt +Waring: Missing or wrong elements: B +3u0d +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +1mfg +5kgw +3uef +4qqc +5wxo +4k8o +4ywa +4wj5 +6bfn +6das +6bgx +4yvc +3rkz +3c7p +6q6f +4wj7 +3ptg +6klk +3kr2 +5tq3 +5fwa +Waring: Missing or wrong elements: U +5ovg +1o32 +4j8m +3wc5 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +1ryf +6sdd +4wx7 +5tpc +4tn2 +1p93 +1xp0 +1bap +1mcz +5jha +5jur +3ecn +4c4n +5fb0 +2h23 +4jx7 +5yjk +5zyi +2w8f +6eb1 +3gz9 +1h8s +3w2o +2uzj +4j51 +4tnw +5svk +1q95 +5qad +4yat +5eym +5jim +3hav +2cbr +3psd +5h09 +2xtn +4y4v +3h0a +3ipb +5c8m +5ubt +4x8n +6evo +5zun +3pty +4jfv +1okx +4ac3 +1qj6 +5ais +3mnu +Waring: Missing or wrong elements: B +6ccm +2xto +3v4x +5ne3 +6em6 +5y6g +4o4y +2ydj +4eox +3ipa +4bdc +6d1m +3ldw +6cq5 +4aw5 +3nus +1auj +Waring: Missing or wrong elements: B +3wzp +4i0f +4i7f +3ctq +6enx +6mod +5cgv +6g4n +4yv9 +1pfy +1nnb +5vb9 +6ocq +5os0 +6azk +4qz6 +4mds +5bui +4y29 +5lay +6h50 +3d9n +3cy2 +6g2a +3gfe +1yy6 +5hn7 +3zm6 +3hqw +2pzi +5id0 +4b71 +1h37 +3ska +1utc +3hpt +1axz +2n27 +1dm2 +4iut +6oa1 +1irs +4ybm +5hkh +4kn7 +4bo2 +2vtj +2ycs +2k46 +6nsp +5wa4 +4kiq +5dxg +3wav +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +5u48 +Waring: Missing or wrong elements: B +6npi +2bmg +5abg +3dux +2vcx +6r7r +3sv6 +4w4v +2xas +2qcf +3v7c +5n4t +4u0u +6qz6 +5tuq +4qab +4cli +5jf4 +1o0d +1ol1 +8lpr +Waring: Missing or wrong elements: B +2etm +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2jdl +5csh +3mag +3lhj +1y1m +5vpm +6euz +2q2c +3msk +1skj +1ax2 +5ut4 +5apr +4ge2 +5qck +3dkf +5opv +5w7i +5lpm +3g76 +4l0l +5mka +2qlb +2vth +4dwb +6pka +4aph +5u1q +4uw1 +1wum +4uy1 +3ghe +6fa2 +6nvi +4yrg +2ajd +Waring: Missing or wrong elements: B +4jht +1fq7 +1ysg +3hab +4xh2 +6jn5 +Waring: Missing or wrong elements: B +2r9m +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4yti +4bis +2gvz +5mtx +5zjz +2b53 +4o7a +6biv +5a1f +4urv +6h4s +3cwj +6qg4 +2rg5 +5w86 +6dzv +4wn0 +1j81 +4kza +4mw1 +2nxl +6mjq +5lca +5sys +2ql5 +5iub +2gz7 +3src +3dwb +3r2f +4hz5 +4j8t +5jr2 +3rwc +3gxy +4pde +3hvh +1mzc +5gmm +5ihc +1oxq +5jo0 +5amn +4p75 +1vgc +Waring: Missing or wrong elements: B +2gbf +5l97 +1vcu +1r1i +1aqc +3v1r +2xiz +3udn +5etl +1awh +6pf5 +5cal +3hdn +3uzc +3g15 +5kk8 +3tdu +4m7b +1wb0 +4b1c +3qs1 +4k5l +4qms +5a0e +3pp7 +2xwe +1utt +4mjo +6pic +6pk7 +5dg6 +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +3hfj +3txo +1doj +4od9 +3iqg +4oym +6hx5 +1fo2 +3qi3 +5u69 +2c5n +1prl +4o1d +6gn1 +5ntk +5t23 +2j4z +5wg5 +4ju7 +5zyj +4gz3 +2qc6 +5to8 +4uj9 +3jzq +4bzn +5o0a +5y59 +1yly +Waring: Missing or wrong elements: B +3c6u +5zjy +6gfy +2yjc +2uze +6ow7 +5epy +5tco +4li6 +1ao8 +5gs4 +1maw +4g2j +1m5e +5toe +5lu2 +6fex +5t2t +6r1x +1qcp +3bmq +6fdc +1wok +5v13 +4ufu +5q0x +3iny +1i43 +4foc +4cfv +1yk7 +4hso +4mic +1njb +5oy3 +2clm +2xj0 +6skd +Waring: Missing or wrong elements: B +1ywh +4uyn +5zeq +2ai7 +1tpz +5orb +1f9g +2qmd +4fgx +2ycf +4mx1 +2qzx +6hzu +2cng +5hmy +1xp9 +3vfj +3d9v +1a5h +6m8w +6ceh +6f5m +3rxa +5v86 +5svx +4tw9 +6imd +4r95 +1t13 +3u3u +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2vip +3zmu +4mzh +6npf +5v83 +5a4q +6jmf +1w10 +5c3k +3nij +1y3a +5u5t +1zxc +4i0r +3n5e +5vee +2wou +5ief +5wvd +3rik +4l10 +3d9k +5fos +4pf3 +3ly2 +5lc0 +Waring: Missing or wrong elements: B +5vfm +4ie3 +Waring: Missing or wrong elements: B +4u44 +4a9t +4mpe +3lce +4mq1 +5k51 +2cgv +4obz +6itj +5w99 +4qg7 +6ovz +3r7b +1qi0 +6bh0 +3oqk +4ofb +5xg4 +1a5v +4fmq +3faa +2pj6 +2qp6 +5a5d +3tjm +5f0c +3qkl +2vj6 +3qa2 +6iuo +3d7g +3p76 +4ux6 +6oxy +6pm9 +6eq6 +5hgc +4ctk +4dv9 +6n55 +6f7b +4w9s +4pl5 +5uz0 +2xba +3m8p +5l4f +3ary +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2wkt +3uwk +4lpb +4zyc +5es1 +6nrg +4oee +3i7i +6f9t +5nwg +5uc1 +1l2z +5t1k +1l5s +4iu1 +6eq4 +2jbl +3r2y +4oi6 +4bid +5lpj +4h39 +6i0p +1qj1 +5uci +6dkp +4pkb +2ylq +5ypo +1b4d +5xiw +2bxu +6peu +2euf +5du6 +5apj +3eov +5q16 +4abj +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2op3 +3v7s +4g3g +2pe2 +5nzm +2pj8 +1z4n +3byu +4o3u +5cfb +2w2i +6hwu +6q9u +4o7d +6chl +1klu +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +6r8p +3tdc +2yiv +6biy +2znu +3v66 +3s9t +1py1 +6bo6 +5abe +5ggp +3elm +3rup +1g42 +2hw2 +5tvn +5k0x +3l9m +2q8g +6ps3 +4gpl +4qsh +4wxi +5am2 +2xwy +3vb5 +3f81 +2fl5 +1a86 +1n7m +5j58 +4fpf +5n87 +4b1d +1onp +6i5i +3zmm +6i1r +3e85 +4ear +2yis +2hs2 +2mip +2b52 +2i4t +4j5c +6pf4 +6hvi +3uvk +6hk7 +4qbm +3vw9 +6pvy +3mb6 +2ohr +1i9o +1nkm +1a52 +4q1s +3vqh +6fav +5agv +5tri +6a94 +5yba +2f10 +6jax +4meo +2c68 +4acf +5mte +6md7 +6ma1 +3nal +1zub +4j73 +2a29 +3qkv +5a8z +4trw +2xs0 +5abw +4ngr +4dds +3sxu +2uup +5dh3 +3bum +3ap7 +1abt +6cnk +3dp1 +4nxs +2xru +5dts +1tsi +5cuh +6czv +6r0k +2azc +4yy6 +5ech +4m5j +6cn6 +1xuc +1w6j +6pfj +2ybp +2dxs +4ocz +1tft +6f8t +6hlb +2jkk +4ngs +1ikv +3hv3 +2hd1 +4uvx +4hlk +5m34 +4pd8 +1rne +5lpd +3muk +3oui +1g6r +2qry +2clf +5ncy +6oh2 +6bvb +5arg +4ojr +4l2k +1ha2 +1jut +6f6n +3olf +5wzw +2itk +6fvl +4jfl +3vbw +4prh +2gbi +2a5u +1hlf +6mxe +5fb1 +4qjo +4k9h +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4c0r +6e5x +4l7j +4j3m +1orw +3byo +4zjw +5twl +3dkg +3wk5 +2r7b +5l7k +3oxi +4otf +6q8b +1fsg +2q6h +4pid +4euc +3rl7 +6qat +1owd +6fjf +5emb +4eft +2y9q +5cfa +6kdi +4ay5 +3mxc +2n1g +6g33 +5zku +4gsc +6fg6 +2jfh +6er3 +3mn8 +4tmp +1z3j +6ft8 +6ocz +4k2y +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +5m0s +3ncq +1los +4pmt +3c4e +6q36 +4nmt +3eht +6j7l +5nqe +4n1u +2ftd +5a9u +6pdj +4f20 +1w1v +4lp9 +1ba8 +3sx9 +1gcz +4e81 +3jzo +5als +4uvv +5alx +4prn +5ivn +6fnt +2qq7 +5okt +1me8 +4xuc +4zuq +3k26 +3qiz +6fap +1x11 +3bl7 +5g22 +4q18 +4kqr +5i59 +6o6g +3uxg +6ic5 +3hq5 +1mm6 +1pwy +1k03 +1hp0 +5ok6 +4qh8 +4yv0 +2q96 +1xdd +5ous +4lw1 +4ded +5vo6 +3fuj +5fkj +4i31 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +3wcl +5cs5 +3dbs +6mvu +3eka +3ur9 +4ydn +4pg3 +5wbr +4gm8 +5of0 +4qsx +4c66 +1g9t +6fkz +2q95 +5ak5 +4mww +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +1jq3 +3qti +5f6u +1utp +3aqa +3pcu +1els +4x7h +1tys +5t8q +4bcd +2ykj +6gu3 +5nvf +6o7g +1gnj +4zg6 +6a03 +2zzu +5mev +2waj +2w12 +6f5h +4mzj +2rcw +3hmv +4zk5 +6i41 +5o5h +4a6w +4pov +6o2p +3udq +4z7n +1ilh +3gpo +6dzq +4l7l +6p8y +3lcd +5vad +4ohk +1zgv +1zyj +2fw3 +2qlj +6oxl +5a0a +1u9v +5k7h +2gfa +6iar +5jh6 +6j63 +6c0u +2jup +3ivh +5a6h +4tjw +4umj +4hv3 +5aaa +5ism +1yw7 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4bh3 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +1c6y +4zud +3zmv +2g1q +6hzc +6fo9 +6g8q +5zuj +2w5i +4gtp +5y0g +4y83 +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +6rmm +4wzv +2oz5 +6eu6 +1h61 +4bbh +4mp7 +4jju +2xaf +4dpf +4yxu +4ty1 +5fjx +3tn8 +6ipl +4gne +5t2p +5wfc +5vdq +4i9s +4qxs +4esi +3k8d +2xaq +4bhn +6exm +6djj +5etf +6nzk +4xx3 +1hq5 +Waring: Missing or wrong elements: B +2y77 +1ny0 +Waring: Missing or wrong elements: B +6fh7 +5k00 +4z2l +1kl5 +6f22 +4clp +3d6q +6aaj +3ot8 +3l5c +4dhq +4o44 +3wt5 +2wf1 +5o3r +4v11 +6qk8 +6me3 +1rgj +1k2v +4hyi +1kc5 +5d9p +3igv +5f04 +1oky +6e7m +3h21 +6n9t +6coj +3v04 +4nyt +5w0l +6as6 +4dea +3ns9 +2nno +1bkm +4ezw +4k4f +2p1c +6n53 +4zx9 +4md6 +4zx8 +6etg +5nho +6ibv +Waring: Missing or wrong elements: B +5mi9 +5avi +3m93 +6mo4 +5nhj +4nah +5q0o +6m9f +3tdz +2r2b +1h7a +6arj +3d45 +1w1g +5yy4 +2o9k +5y8c +3ekq +1s26 +4mbf +3ftv +6gmx +5tx3 +6q6y +2hj4 +3svv +2xtk +3vap +3spk +4q07 +2x7x +5elz +2oqv +5zwe +3plu +4yuy +5h08 +3ftz +1rin +4lwh +5t4h +6i10 +5lyx +4h2j +1sqi +3r93 +4nxr +5f3t +6aqf +5lh8 +2uzb +5ayy +3pj3 +6fbv +6h51 +6p5v +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +2vd0 +6q9y +2r3p +5l3g +4mvh +5yof +4hra +4ge9 +3dgl +2fm0 +4x7q +6cgt +6dtw +5vsd +5i8p +6fyi +1pwp +2h1h +4aom +5nmg +5hk2 +4zz1 +5t4e +4nau +6m8e +6iph +3qtf +5wlt +3kze +3u7l +5n69 +6g9d +2xn6 +5v5e +5nf5 +4mgb +1dg9 +6hhi +2gde +4c6v +1u8t +5y5u +6qxa +6qtx +5ak4 +6evp +6a84 +5nra +6h4y +6g8i +2a2g +5kpm +6gr7 +4qo9 +4j8b +1sqp +1okv +3efk +5wio +3qc4 +4b4q +5wzt +2bdl +4qiy +1ggn +6hd4 +1fta +3e4a +4iq6 +5knr +1ewj +3fui +6ibx +2ow3 +6cus +4a22 +4a0j +6alz +3h6z +3vbv +3wdc +5u2j +1il5 +3nw6 +5wzu +2y6c +4loj +5wb3 +3kaf +6f4n +4wy3 +3oe0 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +5yr5 +6pnn +6ev0 +5qim +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +4x9w +3rt6 +5ii1 +5x27 +5myk +4xgz +1g9b +5zys +6dcy +4y64 +6f09 +5eie +6bc9 +3qri +5vgi +5sxk +5g6u +5e8a +6d5w +6p1l +4wr7 +4qxj +5d11 +6fo7 +6p8x +6f1w +4mka +5orx +6jn6 +Waring: Missing or wrong elements: B +4n8d +5i9i +2x85 +6ib0 +1tcw +4jxw +4mx0 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +1lf9 +1d5r +1i8i +1inq +2y3p +4gto +5b6g +4fmu +2y58 +6uf0 +4x1f +4lp6 +4acd +5wag +Waring: Missing or wrong elements: B +4ycl +2vev +4bi2 +5nf9 +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +4g16 +4jlj +5a2j +3k54 +1sqb +1yvx +5doh +5qbv +4m84 +3dv1 +5lhi +3d20 +4mw2 +5dia +3kag +6gih +2lsp +3el0 +2vte +6e3s +3voz +4xm6 +1a37 +6itp +2ork +5yea +4j79 +4r6e +2oc1 +4f6v +5osy +3chf +3i90 +3wci +3tkm +2xdw +3iuc +4joo +3ft8 +3qs5 +4ezj +3k23 +4p0b +1oj5 +5k05 +1njf +3ocg +6f26 +2oyl +2qcn +1pye +3er5 +4b60 +4qlt +3d2r +1d4w +1gsf +4h3i +2c0o +2hwo +6rk4 +3qck +2fo4 +6hvv +5ngu +3kbz +6b1f +3ckt +6hro +5ml8 +2l8r +6q9o +4d2s +4o0v +5g3n +4wsk +4hl5 +4ux9 +3g9e +2y7k +6ft3 +3g5y +3iqh +2r5b +2ym5 +3c4f +1m74 +5u6c +5q17 +5t8r +6i68 +5i22 +6c2x +1xmu +4jve +4og7 +4rxe +5x5g +1j1a +5i2z +3ibc +3u8d +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +5drs +2r3f +6s0e +2y2p +Waring: Missing or wrong elements: B +3vi5 +5tdw +3kr5 +3k3e +4yrc +1n95 +4utn +6boy +5ap3 +2rc8 +1ow6 +3p1d +4rj3 +5npr +5lsx +3zzh +5o22 +6bbv +6dim +2oht +7gpb +1o43 +1q9d +6pf3 +4ryc +1jlq +4xh6 +2znt +5yg3 +1bq3 +5op6 +4pio +5wle +5cqx +6di0 +4c1c +4ap0 +5u4e +Waring: Missing or wrong elements: B +5lgq +4hbn +4q6r +3kjf +6rna +6ce8 +1g1e +5tkd +2i47 +5oul +6cwf +5ox5 +5z89 +6g8m +5d10 +2n9x +5cpr +6n4e +3wd2 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4lq9 +6sen +1lhd +Waring: Missing or wrong elements: B +3iu7 +5ak6 +5ll4 +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +2wnl +5ijp +5osk +5mf6 +5v2q +3lw0 +5y0z +5dms +4d63 +3wkb +2w0p +4x2s +3k05 +1q4x +4kpx +5fpi +6cyc +4ttv +5j9z +4gj8 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2gpp +4mwb +1ca8 +5o3q +3zeb +2wl5 +3fkt +2lgf +4avt +3lqj +4uce +4m3d +4px6 +2p3d +3i7c +3zy2 +4y5h +4k0u +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +1oxn +4mrd +5olk +4mmf +6f8r +4jg1 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4acu +5oui +4idv +6mhd +3p2k +5bqi +6s1s +Waring: Missing or wrong elements: B +5yqo +1rhj +5ow8 +4x3t +3wt7 +2b2v +5tq1 +6eg9 +5duf +2qm7 +3sfh +2xow +2g9x +4loq +1qhr +1ynd +2w7x +1sqq +5byy +1puq +6k05 +3vzg +4n5t +3e51 +2x8d +6hm7 +5xof +3qs6 +3nf9 +4mdq +6j6m +2aov +4qh7 +4m7y +6u9v +3avz +2wd1 +4csj +6dxg +6ikm +4o9s +2qf6 +3kqy +2b54 +4bgh +3kvw +5q19 +1o45 +1uu8 +5qaq +3i28 +4k5o +2w1g +4wmu +3n0h +6hf5 +6e7w +2hdq +3o2m +4c4i +4qhp +6qff +2iv9 +3bh8 +6boe +4d0w +2evm +6q5b +1y2d +4tyb +3fh8 +6p3w +1p03 +Waring: Missing or wrong elements: B +5dpa +3lq8 +1oe0 +1uyk +1czo +1ent +4wag +3efw +2duv +4fcr +3w69 +6gg8 +6p7p +5gmj +5y3n +2w6t +2x4r +4ewr +2ez5 +6e2m +4n4t +1cs4 +1rs4 +5zla +5b5b +6b0v +6drz +5ul5 +6f8v +2ym4 +3pz3 +1o4a +3svj +5cte +1npw +3o9b +1w51 +6npv +5ov9 +3new +1fax +2q7y +4bw4 +4f8j +5aux +1r58 +2c2l +5lj0 +5gwz +5m2q +1pip +3nrm +4mcv +3p4r +3wka +6atv +4n6h +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +5z9e +5fqr +3pjc +2ha5 +4ool +6h4w +6g2n +6h96 +5k48 +4fyh +2hzi +2gm1 +5fue +5ttg +1bmq +4itj +2chw +2ko7 +6ul8 +6o8u +1rst +2asu +5hog +3r7r +2q3z +4ahv +6fug +3hr1 +5vll +6qzh +6ehh +5dlz +4hg7 +3iqi +6beb +5c11 +5ory +3px9 +1utr +4flh +5f4p +5lub +1rhq +2n0w +4xii +3hqr +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +1gj7 +4ajo +3nti +4fjz +5n9k +5aqr +3srv +5fpp +5t97 +4z68 +6dvl +4twy +5nx2 +6g3y +5wbf +5un9 +5m7m +4nan +5db3 +1mqd +4jzf +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +3b8z +4yff +3uvq +6cki +4el5 +2hk5 +3rj7 +Waring: Missing or wrong elements: R +5iuh +4bib +1iky +1k3q +1u65 +3shz +6hvj +5icz +3fcl +4x8t +1w7x +5jyo +3qzq +6o9b +5urj +3m53 +5mri +2lwi +1qjb +4lts +3isw +2ad5 +4hlh +1bzs +6cz3 +3nnu +4hs6 +2yir +4u0d +6qeg +5a5s +3q7p +5am5 +6ey7 +3gjs +4y6p +3ft2 +6nem +2x2c +4kom +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4gs6 +5nev +1jfh +4rn2 +3w55 +4bio +5li3 +3h2n +2ay9 +2c1n +6h9v +1nju +1b2m +6ba7 +2vnn +2chz +3l38 +2xg5 +5zk5 +3u2q +4iqt +4ark +2ms4 +4aj2 +1fls +5vzy +1x8b +4mw6 +6fzm +6jwa +3f36 +6dud +3t0l +1gt5 +2oqi +5dk4 +2wxn +3uix +5nxq +5xag +3eoc +6f3e +3r9h +2o3p +3bgl +2i72 +Waring: Missing or wrong elements: B +5f37 +2qiq +2axi +5lxp +3uqg +5w8v +1ikw +5gow +3qch +2xxy +4e5d +1k9r +3okv +2jg8 +3iwy +6m8a +3uik +2xix +4ohp +1fq4 +5zah +4x68 +1tnj +4e3h +3kb7 +1vwf +6hzv +6d07 +4qxt +2q70 +1ing +4kpz +4ufd +5cf8 +3nan +4ehr +6fa5 +4i0s +6hry +4oyp +6max +5dtw +1wss +3u78 +3iw8 +2xa4 +2x24 +3erd +6ffh +2l98 +2c5o +4ov5 +5aab +3soq +5y2f +4dht +4g8r +2igx +6ajh +5eol +5t37 +1zsr +1fsy +Waring: Missing or wrong elements: B +5zr3 +1n8v +16pk +1x78 +5ddb +5jek +5he7 +5thn +4yb6 +5klp +5ega +6pii +4zxy +4xg8 +1iew +6udy +5xhz +6h41 +6bh5 +5gso +3f69 +6o50 +6e8k +6ck6 +4ddy +2owb +1apw +3qrk +2vpg +5eqq +1o2t +1rv1 +3zmj +6dge +5tl9 +3s3i +6b31 +3gk4 +3w8o +4w9q +2vgp +3ia6 +3jpx +6gmd +4yll +1joc +1tr7 +5jdc +1x70 +3kqb +6qsz +4e3d +4no8 +2gdo +5wdj +5ukj +4izm +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: B @ HSE-------------- +------------Warning: Missing Parameters for Residue: B @ HSE-------------- +------------Warning: Missing Parameters for Residue: B @ HSE-------------- +------------Warning: Missing Parameters for Residue: B @ HSE-------------- +------------Warning: Missing Parameters for Residue: C @ HSE-------------- +------------Warning: Missing Parameters for Residue: C @ HSE-------------- +------------Warning: Missing Parameters for Residue: C @ HSE-------------- +------------Warning: Missing Parameters for Residue: C @ HSE-------------- +5uwp +5aia +3rv6 +4wm9 +3g4g +6ipm +2nv7 +5i0l +6eo0 +5myr +5u4a +Waring: Missing or wrong elements: B +1gux +4usj +3b2t +3pd2 +5qa5 +4lbl +6mwe +5vlk +5ivj +4hs8 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4tpp +6f8b +3b5j +5i83 +2np8 +1om9 +1hdt +5qat +6pgx +Waring: Missing or wrong elements: T +1lvk +Waring: Missing or wrong elements: B +1xmy +5nat +5xzr +5klr +1ch8 +3hrb +3aza +3ao1 +4xv3 +4j0s +4qme +4wyo +4mz5 +3kme +1tog +3gjd +5dyw +5mmn +4hxq +Waring: Missing or wrong elements: B +4gvd +3m8q +2jt6 +5q0z +5u6v +2nw4 +2gph +3lkj +2pri +5izl +3uda +4lv3 +Waring: Missing or wrong elements: B +6c3e +2g19 +5t18 +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +5oq6 +2ea4 +5kzi +2brp +5fq9 +Waring: Missing or wrong elements: B +4gw6 +5bqg +5k1v +2fq6 +1vea +3imy +4dk5 +4pce +6f86 +4l7d +6bj2 +4oeg +3ugc +4el0 +3rtm +2vgc +Waring: Missing or wrong elements: B +6n93 +1xlx +1zm7 +4xtm +2viz +4acg +4ebv +6hu1 +5vqz +6imi +4j1k +2gd8 +2ei6 +2ieh +1i33 +2obj +5vp0 +3jqf +3sv7 +2mpm +2hob +4uua +3atw +5ggn +3agm +4i6f +4zxx +3skh +4dxg +4yur +4pnn +2xlc +2yof +4aa5 +4ps8 +6k4x +4gs8 +3chd +3gp0 +2aq7 +6qw7 +3krl +5gvm +4psx +6bfa +3zjc +3al3 +5j7g +3nth +2r6y +6bxy +1c7e +2kwn +3dp2 +4mbc +3p0g +6p11 +2qju +6b7d +1swi +4tk2 +4bcq +5q0r +4oru +5auv +5ajx +5v4b +4au7 +3ohh +2o4s +1mzs +5h9s +1a46 +5glu +4ggl +3mrv +6qdx +4d8e +5kx7 +1em6 +5ccm +1b5g +6s88 +2jbj +4lgu +5b4k +1o3h +2w76 +3is9 +3u8w +5ofx +2wa4 +2a4r +5tks +4dfu +5u7j +6ccl +4pyo +5kpl +6c7d +2wk2 +3dt1 +5ejw +4x3e +5nhy +4aa2 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4mk0 +2e9v +5cyi +5gn5 +2xn7 +5wbk +3juq +4qht +3uo9 +1g37 +6o3x +4byj +3zmi +5c13 +3r02 +4kfp +5ljj +5lg3 +4k67 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4nzm +3sdg +2c8y +1wax +2hdu +1h9z +2fx7 +3lfs +3eqb +4i1r +3shy +4uu7 +2m3m +5y5n +5j1w +3d4f +5vk0 +5wh5 +2c9d +3hbo +3igg +2c3j +5enc +4d89 +5a7j +6ax1 +2df6 +3rxb +4k6v +4kai +Waring: Missing or wrong elements: B +1o3k +6h0u +5ct7 +6f4x +2y67 +2jsd +3diw +2kff +2x8i +6n3k +4frk +3jqg +5urm +4edy +6gva +6g9h +4fr3 +5j1v +1f28 +3bwk +6b3v +3et7 +1ywi +1q5l +2flu +4x1p +3ckr +4jrv +3rxj +2lyw +4zom +2xct +1rhr +5tho +4w5j +1vwn +5ujo +Waring: Missing or wrong elements: R +4cd8 +2exc +4e3m +Waring: Missing or wrong elements: B +5z68 +1lol +5kzp +2xg3 +5ixq +5ful +4jjg +4r5w +1yw8 +1ckb +2q9n +4cpu +4kwp +5mav +4bgy +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +6r5f +5dya +2x81 +1kfy +5bms +2a3i +5jnn +4m8t +3qxh +4i7d +1qng +1yvf +3ril +3jsi +4z2k +3py1 +4de3 +3wym +1fbm +4uvc +5lck +2x2k +6d3z +4tw8 +4lqy +2xez +5xih +4k63 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2vcg +6ck3 +2r0y +1uy6 +3c1x +1k2i +2c5x +4bti +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +6oip +1uyf +2qfu +6hjj +4meq +4hw2 +1kf0 +2r9s +3d9p +4fbx +3dcv +5iu6 +4lil +4xv2 +4mgc +4nw7 +5q1e +5alr +5f1l +4ciy +5o4z +2mnz +1qti +6dm8 +3s3o +6biz +5iha +4dcv +1ths +5h5s +4twd +2y57 +6b7f +3q5u +5vlp +4lg6 +2l3r +5tkb +3rk9 +4pnl +4f3h +5wfz +4uub +3vfq +6aum +3h0w +3v4j +4edu +3az8 +2w85 +6gu4 +4j82 +4wmy +3dba +6g5j +4kv9 +5u9d +3s3r +4uco +3pm1 +5nsp +1aku +6q89 +4tsz +6jib +6htz +3cho +1hs6 +2obo +3rse +3l9h +4uva +6ela +5teg +3t1l +5wbl +3q4k +1jdj +6clv +4ehv +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +2zjv +5km2 +5olb +5erg +4lv2 +Waring: Missing or wrong elements: B +2zif +6fbw +6bid +4i0t +5khg +3ut5 +4c4e +5hng +4lh2 +6mqm +1kcs +1a0q +4tkn +5wr7 +5iyv +2z7r +1qf4 +3uvl +5lz8 +6fii +6q7a +4lqg +3oyp +5uxn +5kam +1f47 +1lf3 +5jan +3chp +3pke +5i0b +5gmp +3fq7 +4c1m +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +5ncz +1c3r +2nmy +2r02 +2iwu +3r0w +5hyx +4qz4 +2iw8 +3tge +4qr3 +3frg +1shd +4rx9 +4op2 +6pit +5b5p +1y2e +6jjz +4frs +4j8s +1t49 +3mbp +6fdu +6afh +2y6d +4pjt +5pzn +4wvs +4y38 +1pmu +5uac +3k98 +4kva +6c8c +4x1n +6g8n +4jck +5e3d +3eq7 +2gnh +3wfg +5ett +2qhr +1nlo +5zhm +4ris +4y2y +4x7n +3max +4oz3 +5zqp +3sl0 +Waring: Missing or wrong elements: B +4zyt +4eki +3iad +3c3o +3v3l +1ow4 +2azm +4w7p +6iiv +4idz +4zx5 +5agt +Waring: Missing or wrong elements: B +2ieo +6dlj +2pjt +5zdc +3ti5 +2eg8 +3we4 +5hmh +3oof +1xh7 +4ra5 +5n9n +6h7z +4qwx +4tyt +4hxr +1y2f +2xkc +5uhi +5emk +3t3h +5ktw +4j1e +3db8 +5swf +5v35 +2qqs +5znr +2zsc +3atk +5aok +6e4f +5zk9 +2q8i +4x6k +2xln +Waring: Missing or wrong elements: B +6oyh +2f3e +3n5k +4jgv +3l1n +3v49 +4e3j +Waring: Missing or wrong elements: B +4wnp +5kj0 +3gzn +5egs +3hf6 +4kw6 +2f4b +4jps +4m5n +1h1q +5f88 +3q5h +4fl3 +5kv9 +5dgz +4j84 +5oh1 +4wwn +4rxc +6bsx +3ens +1gz9 +1iq1 +6aqo +4ckr +4f6s +5npd +1mqi +1ogu +5n7x +2fb8 +6bqj +4o37 +5nt0 +4hze +Waring: Missing or wrong elements: B +4qn7 +3jzf +5wkm +4nct +3ds0 +4iu0 +Waring: Missing or wrong elements: B +4oar +3iiy +5v41 +1p5e +4ayx +1xm6 +4mib +4l52 +1exw +4mma +3fea +1my8 +Waring: Missing or wrong elements: B +6fgf +4zyw +2qhd +6c0t +1o4n +5hgq +2yi5 +4x47 +2o9i +3lil +3uqf +1zp5 +5x4o +5ar4 +6bmv +5t1u +4zh2 +1pf8 +3piz +5nhf +4dt6 +4is6 +2zis +5cvd +3d7b +3khj +5xv7 +1ka7 +3wax +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +Waring: Missing or wrong elements: B +5a6a +5ap6 +4pvv +1ym2 +3qw7 +4mho +6v5l +5o4y +5ekh +2d06 +3wk7 +5zh4 +6oie +1g4k +3dla +6q73 +2igw +1lrt +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +2yj9 +4oex +1pum +2ydi +4yht +4mw5 +5mny +6esy +3btc +2vl1 +3as2 +6nvh +4v0i +5vsb +5fas +2qtu +3vnt +1g9s +4g0c +5lx6 +5w6e +6db3 +1a2c +2w87 +1n2v +5cs2 +4zga +6fdt +5etm +3l5b +4bb2 +5ni8 +5am4 +3r7n +2pjl +2aoj +5c0m +4znx +2y1w +1b6m +2w77 +5lsc +4jfw +1f0q +5bve +2v11 +5tz3 +2z92 +3nc9 +1jje +3unk +5o0j +5zh3 +1wva +Waring: Missing or wrong elements: B +1dzp +5ieg +6n6o +3hau +2hrp +4f1q +3q43 +2prj +4hkp +4p45 +2ww2 +5op2 +3iw7 +3b2w +5yzd +3mqf +2ada +2ga2 +2l12 +6h1h +4w50 +6oah +5j6d +1qtn +4qwk +6ar9 +2wxk +2wi2 +3mj1 +2yiw +5dy5 +1v2v +5hdv +5all +5fdr +2ica +3e63 +1hgj +6ft9 +1pu8 +6c7g +2f0z +4lh3 +5xmt +13gs +5db0 +5mk3 +6kdx +6ncj +4x8p +6s7s +1xbc +1clu +4x49 +4wt6 +4gts +4aof +4int +4rvm +3rzb +9lpr +Waring: Missing or wrong elements: B +4xyc +5iop +3gwu +3q2a +5tjx +2o7n +3i5n +1g2m +4z6i +2tsr +4ybs +6nfo +5tyr +3kdt +4d8c +2vxa +3q3k +6g4z +3ine +3lbj +5j4v +4eg5 +2ll6 +1pzj +6uyx +2p9a +5ans +4n7j +6qme +3udr +3hdk +1f8a +2pr9 +5izk +4w4x +2ndo +1lq2 +5ze6 +5aen +5tig +5gwy +4amx +5iok +5f3e +5w6i +4ln7 +5hx6 +6fym +1llb +4gk7 +6pht +Waring: Missing or wrong elements: B +6ee6 +2pvn +6oxt +4xqb +2hug +3g7l +5h0b +4jg6 +1azx +5w1v +6f8w +6nm4 +4g0l +1gz4 +4bci +4xe1 +3dda +3v6r +6hwv +5cgc +6qra +5tln +3w5e +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4qwj +6ap7 +4ge4 +6cdc +5dgj +5qam +4pyy +6mdd +2vu3 +4eh2 +5hk9 +6cef +4ybj +3ind +5nu5 +3pjg +6me1 +6chn +4i2z +6qm7 +3s7m +3qrj +3m54 +1t7r +3jwr +2nnk +2xk7 +6bbu +3tv5 +6jsz +5gu4 +6mim +4mk5 +5m63 +1cim +2o65 +3sv9 +3rey +5qak +3d8y +5y8z +5iu8 +2ajl +5iu7 +2adm +5nfb +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +Waring: Missing or wrong elements: U +2l0i +1x7r +6eww +2zu4 +3hx3 +6n7y +4k72 +2iyf +6hv0 +5lsy +5up0 +6pml +5epp +4k10 +5ji6 +2loz +4ruu +4pl0 +5ovh +3mg8 +3pi5 +2w54 +6ggd +2qn3 +5ipa +6aqq +1bdl +4fvr +3ppo +3qsd +4a50 +5yu9 +5k5n +1jjk +4hy0 +5hlm +4fe9 +2j9n +4dmn +2pvw +5hm3 +2bdf +3ti8 +3o57 +4ogi +5c84 +1eed +1pk0 +3aav +5w3i +3wv3 +2a2x +4i1c +4cu1 +3ufa +6fgl +3kga +5c6v +1hww +1uxb +2gej +6jno +5npf +5f9e +5zkb +1w2g +4nni +4wr8 +5xhr +4lkj +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4mg7 +4r18 +5bue +4mrf +5mon +5u5k +3qcf +2w3o +1tnl +5o83 +4cwb +9hvp +1rs2 +4jft +3rv3 +2bua +5cxi +4mx5 +5tzo +3khv +4mh7 +4ztr +4ddl +5uwm +3g1m +5q10 +1qpf +4b9w +1amn +4dpu +4yt6 +3v3v +3a2c +4aua +5vdr +5qa4 +1cj1 +2v12 +1wug +1nde +4xsx +2kgi +7hvp +1hti +3stj +2bve +1xoe +5t4v +3g8i +3t7g +4nym +5yv5 +5oq5 +5mwz +4z6h +5qaf +3n1v +2wf0 +5z95 +3uli +1zzz +1o41 +1tvo +4ith +4k69 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +3hdz +1a7x +5opu +5ctc +3ewh +4xsy +4g3f +3er3 +Waring: Missing or wrong elements: * +4yyi +5ax3 +6gi6 +2qn2 +4x34 +2zxa +1zeo +4x60 +4ep2 +6hck +5mqx +6h7l +4ks5 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +3lcv +5zqr +3gb2 +5zmq +3r91 +5iez +4j4n +6e05 +5tgc +5v8p +4mk8 +1dtt +5y8w +4j1p +3rxp +3rg2 +4ocp +1tet +6fky +4kb7 +Waring: Missing or wrong elements: B +5aiv +4hhz +5fgk +2ph6 +2xu4 +5syn +1h3a +4j1h +3ad7 +3guz +5q1d +4mg8 +4n84 +6g6x +220l +6eea +4p4i +6aej +2gnl +4aif +5qil +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +5nq5 +6drg +2g72 +3hac +5knx +6cve +5x13 +5f32 +2wxm +5f3c +1o39 +6njz +6dql +3az9 +4r6w +5aki +6qz8 +4ega +3wnt +2qrq +2q9m +1o3g +6st3 +1rbo +2fys +1gwq +4hct +6hvt +3bim +2aof +4h5d +1ets +1al7 +2pze +4acx +1h28 +5mnx +4ibm +6sd9 +4e1n +5a6i +2vwu +5szc +1juq +5q0f +3axk +6b5a +2wmv +4d8n +3fmr +2jc0 +5fi7 +3ff6 +4q9m +2c4w +3pj1 +3wk4 +4inh +6q9q +1q6k +6mo2 +3uyt +2xk1 +Waring: Missing or wrong elements: B +5byz +5c6p +1oy7 +3saz +5gp7 +6fty +3sff +3sfi +3zpr +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +4aoc +1owj +5axq +4myq +4nhc +4bek +1i8j +6i78 +5zms +1kds +Waring: Missing or wrong elements: B +4ayt +5tci +5aix +3krr +4q1n +3tf7 +6bvh +5f02 +4ir5 +2fjn +1z6q +1tou +6uii +4lc7 +3f3v +6fzj +4qgh +2hvc +3h52 +2ymt +2io6 +3oe6 +4rn1 +1h24 +1a5g +2c9b +3fi2 +1qja +3zw3 +3oe8 +4ys7 +4hxl +4e8w +5knj +4iku +5diu +4lpf +5dry +5igq +2w0x +2hmb +6mt5 +6ink +1q4l +3p4q +3wd9 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +6fmk +4dmy +6cqz +1ek1 +5ops +4h1e +3sji +4rrr +3zrc +4fob +4mbi +2hpa +6k1q +3zhz +1ow8 +5zk7 +6qxd +2ima +1v2m +2r0u +3rxo +4ybt +6r0u +6ms1 +3met +2c3k +4odf +4j3j +5duc +6f7q +4ntj +5zfi +3odi +4e1m +3gxt +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +6cjy +3anq +4msk +4pn1 +6df2 +6s07 +4iti +4b0c +3ifp +1gzg +4qwi +4fem +5akz +3fxb +5ngt +3mpt +4imz +2pcu +4xhv +2eh8 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +6mbp +4nrl +5ol3 +4u7q +6uvp +6cec +1py2 +5dv4 +3sbh +4bqy +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +3s53 +3f7z +2ha0 +1gui +6q8a +4nmp +4yjl +2q80 +2qzk +5c5h +4pgc +5vdp +3qpn +2cne +3mg0 +Waring: Missing or wrong elements: B +2xk3 +6psb +2p8h +6f08 +1npz +1ftl +5hlb +4u0g +3img +1l5r +6bed +6bgz +5ncq +2avv +6ps6 +3rq7 +4uwk +6pya +4n9b +5oae +6npu +3kx1 +6uhv +2a3a +5nvh +4x3h +6f6d +3jxw +3zkf +6fau +2b8v +1lt6 +4qvp +Waring: Missing or wrong elements: B +5huy +1qj7 +4r3b +4ks2 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +3dkj +1py5 +2xh5 +6ert +Waring: Missing or wrong elements: B +4oel +5l4h +4mnx +4lno +1xo2 +1o2u +5l15 +5nhh +3ig7 +3hy9 +4kil +6aec +1m5b +1bqm +3erk +6g92 +3zmg +2qmf +4nhy +5qaj +4yoi +4u68 +3ms7 +3c1k +5qqo +5tiu +2i40 +3qci +5b0x +4bo4 +2hz4 +3q4j +2psx +1fsw +Waring: Missing or wrong elements: B +4bb4 +5d7c +4xs2 +3tyv +3gv6 +5dtr +5tzd +5uzk +4fiv +4pzh +2xk8 +4c68 +3ehw +3o9f +2ozr +4pge +4z7f +3k3j +1k3t +6ohd +1qvu +2xwd +3dng +4ab8 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2wxp +3sl8 +5uir +5l9h +4tw6 +5bnm +3q4b +3h91 +3uvw +1wbs +4oyk +3at4 +2vr3 +4kz0 +3h0b +3tku +4ona +1a9u +6oin +1d2s +2yoj +1qpb +6uwp +4w9x +5tc0 +3m3r +3q77 +6e3g +5m9d +5qa9 +3le6 +6hy7 +4gv8 +3sax +4lmu +3szb +3hwn +1w22 +2ja3 +3dtc +5mk9 +4bj9 +5em7 +4edz +6fvn +6gin +5ake +4pkr +4kip +3k3g +5hld +3kl8 +4x6s +6drx +6c7b +3uvo +6bln +3gnv +4zuo +6fel +5kup +5c7a +3arn +3sl4 +3cyu +6emu +6o9d +2zyn +3rvi +4q1b +1xdg +4abv +5n49 +3fxw +4py4 +3ej5 +2ceo +1oqp +4b7n +5fp0 +5k0b +3ggv +3dpc +4yp1 +4kql +1o2k +3w2q +3r42 +4gjc +5mtw +1j4p +4pp9 +6fn9 +4ob1 +Waring: Missing or wrong elements: B +5w94 +5tob +2c6l +6c5f +4hmq +5da3 +6bcr +6hky +1wv7 +1czq +5hm0 +4c71 +6ega +4ajk +1pcg +2xcg +1q9m +6rvk +Waring: Missing or wrong elements: B +6e9l +4re3 +3iit +2jbv +2wsx +6uvy +6r7d +2vl8 +1fv9 +3s2o +1urg +5i38 +4m3b +5mxo +2oh4 +4xnv +6o68 +4nal +6qwi +6k4t +4hvs +3nrz +3chc +2yit +5trj +4m48 +5eg4 +3pdc +5unf +6apt +4d1d +2hdx +1g9c +5gjg +3w1f +1dub +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +centreofmass.sh: line 120: 2940952 Segmentation fault (core dumped) $LEDOCK input.txt +6bau +4hzt +3n3l +5q1g +6hjk +1cwb +2aig +4e5g +2xyr +3vf9 +3thb +1yt9 +4i9z +4pgd +4hy5 +6i5j +4yyn +2wi1 +3qd4 +1oth +3ken +5q0w +2e93 +5uwn +6ilz +2onc +6qxs +3mw1 +6f3g +3lbz +1o5m +3fv8 +5m4q +3bze +1yye +5f3i +3t3y +3tdh +4anb +3dcw +1g6s +1w7h +3f9n +6rw1 +Waring: Missing or wrong elements: B +5ez0 +3gqo +1tuf +1cil +3uo6 +1btn +3g90 +5nwb +3gur +5wev +4fgt +2c8w +6ps1 +5jcb +6eh2 +3t0w +4kzb +5xii +------------Warning: Missing Parameters for Residue: C @ HSE-------------- +------------Warning: Missing Parameters for Residue: C @ HSE-------------- +5q0s +5ktx +3v8w +5c85 +6qad +5mhp +1rrw +4o0t +1e06 +5g2n +4rhu +6hva +4jbo +5ur9 +1bcj +4k3q +2oq6 +6bgy +6i96 +6me4 +6rhe +1zpb +6nfz +6o57 +4zup +6axl +6iup +4mdt +1pyw +6ct7 +3s7a +2iw9 +3f39 +5o7e +6qha +3sgv +3sm0 +5n58 +5t35 +5hcl +4htp +3vry +1zkn +5v4q +2fx8 +6bic +1oeb +5tnt +5ezz +3skg +4apo +1ppw +6egs +3ilq +4pci +4to8 +1xoz +1i48 +4gkc +3nin +4mm4 +1l7x +6cha +Waring: Missing or wrong elements: B +4aqc +2g5t +4azy +5l6h +5u4f +Waring: Missing or wrong elements: B +Waring: Missing or wrong elements: B +4hva +4fz6 +6ffe +6nkp +7lpr +Waring: Missing or wrong elements: B +5t1s +4dwg +5fao +3g0c +4drk +4lwc +4ch2 +2hz0 +4g55 +6hwz +5wgq +4gj6 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +6gfx +1ugy +6rln +4an2 +4g2l +2lcs +4eyj +1y2h +6aak +4tk1 +3otf +4k75 +5f2s +6byk +6b1o +5knt +3k48 +6b67 +4txc +2pgj +5akw +2flb +4i47 +5yz7 +5v3r +2r6n +2w8g +3msj +4trz +5al2 +5ml3 +3afk +1sle +2viq +2ohp +6oco +5prc +4muw +4men +4tju +4anq +5vrl +Waring: Missing or wrong elements: B +5wkl +3v30 +2h9p +2wig +6eji +3tia +5a0b +6e5g +4gw5 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2ks9 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +3i81 +2veu +5b6c +4bo1 +6nvj +6fc6 +5ajc +6nzg +1ljt +3sjo +4fse +4csy +6c9p +5ku3 +4mzf +5b4l +6fu5 +6qac +5ddf +4yee +1nok +5yql +4rqz +1q41 +5eje +2va6 +3t19 +2jle +2yak +Waring: Missing or wrong elements: R +6hhp +2b7a +3c5u +5ytu +2rqu +6rj6 +5t4b +5wf3 +1ll4 +5kdf +2d41 +2vvt +5w84 +4i7b +2qlf +3rx7 +2f3r +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +Waring: Missing or wrong elements: A +1i6v +5afl +1p0y +3eid +3eqs +5urk +6bfd +2xcn +Waring: Missing or wrong elements: B +3dxj +3p9j +4wmv +5mt4 +2f1a +3wdz +1p28 +5w88 +3uvu +3fr2 +1waw +4i33 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +5v2p +6do3 +5kbf +6qtw +Processing 6c5k +Processing 6faw +Processing 5k4x +Processing 6aji +Processing 1wbw +Processing 5i5x +Processing 4o42 +Processing 2osm +Processing 5qag +Processing 6gjd +Processing 6gu7 +Processing 5hlp +Processing 2a0t +Processing 4enx +Processing 4puk +Processing 2b1z +Processing 4ym4 +Processing 6pek +Processing 5xig +Processing 2itz +Processing 1w2h +Processing 4mwy +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +Processing 3cl2 +Processing 2g1y +Processing 5hes +Processing 5tw2 +Processing 5ng9 +Processing 5nba +Processing 5cao +Processing 5fb7 +Processing 1vkj +Processing 2oo8 +Processing 5t52 +Processing 3exf +Processing 4ynk +Processing 6nzt +Processing 2etk +Processing 1n9m +Processing 4k43 +Processing 5y0f +Processing 6g9m +Processing 5ngf +Processing 1ero +Waring: Missing or wrong elements: B +Processing 2gg9 +Processing 3avb +Processing 6gge +Processing 3vp4 +Processing 4x69 +Processing 3ixj +Processing 4lww +Processing 4rj6 +Processing 2fix +Processing 5ntp +Processing 4i6b +Processing 4btw +Processing 5zty +Processing 5wmt +Processing 4jj8 +Processing 4hni +Processing 3bzi +Processing 2yln +Processing 2o48 +Processing 1zky +Processing 2rf2 +Processing 5n1v +Processing 3jq9 +Processing 3lj7 +Processing 4gg5 +Processing 1hk3 +Processing 6cyg +Processing 2ykc +Processing 1juf +Processing 2hrm +Processing 1gt1 +Processing 4zz2 +Processing 6a80 +Processing 1jd6 +Processing 4afj +Processing 1swk +Processing 6qrd +Processing 3ixg +Waring: Missing or wrong elements: B +Processing 3d94 +Processing 2cfd +Waring: Missing or wrong elements: R +Processing 5ty1 +Processing 6gy0 +Processing 4z2p +Processing 4kby +Processing 5d1j +Processing 1xlz +Processing 6qh9 +Processing 1lhc +Waring: Missing or wrong elements: B +Processing 4oti +Processing 4wvl +Processing 4yym +Processing 2fgh +Processing 5eto +Processing 1ule +Processing 1zz3 +Processing 4his +Processing 2e9c +Processing 5k5c +Processing 6d4r +Processing 3bbt +Processing 5ylu +Processing 6jse +Processing 2q72 +Processing 2z4y +Processing 2uzv +Processing 2l6j +Processing 2pfy +Processing 6qrg +Processing 6gxw +Processing 4ykn +Processing 3jy9 +Processing 5wii +Processing 1a4m +Processing 1hyv +Waring: Missing or wrong elements: A +Processing 2vwf +Processing 3apc +Processing 5xpl +Processing 1uvr +Processing 1pr1 +Processing 5o0e +Processing 4no1 +Waring: Missing or wrong elements: B +Processing 6fne +Processing 4luo +Processing 6pys +Processing 2a4g +Processing 2vcq +Processing 6i76 +Processing 4yv8 +Processing 3jzi +Processing 2h9t +Processing 5hda +Processing 2hds +Processing 2ydk +Processing 3hu2 +Processing 2b1r +Processing 6fdp +Processing 5f95 +Processing 3pcc +Processing 6pxc +Processing 3kxz +Processing 5gx6 +Processing 5vkm +Processing 4lm5 +Processing 5alh +Processing 5nx9 +Processing 4xta +Processing 6frf +Processing 3o9c +Processing 3r5j +Processing 4yw2 +Processing 3mrx +Processing 5d1w +Processing 6gy1 +Processing 6hbn +Processing 5ot3 +Waring: Missing or wrong elements: B +Processing 2fr3 +Processing 6dq8 +Processing 4p7m +Processing 5j5r +Processing 5d12 +Processing 3cgf +Processing 4bpi +Processing 3o8h +Processing 5kit +Processing 6m89 +Processing 1p04 +Waring: Missing or wrong elements: B +Processing 3zo1 +Processing 6oou +Processing 5y6f +Processing 5lhh +Processing 4lnp +Processing 4qmo +Processing 6djd +Processing 4ww6 +Processing 1a1b +Processing 4hcz +Processing 3ma3 +Processing 4ifh +Processing 3vv7 +Processing 3od0 +Processing 4m5h +Processing 2nqg +Processing 3me9 +Processing 3vbg +Processing 4b4n +Processing 6do4 +Processing 5qb1 +Processing 2ndf +Processing 2aou +Processing 1u32 +Processing 5qaw +Processing 4luv +Processing 2jdk +Processing 2vx0 +Processing 3njq +Processing 4pnw +Processing 4qyo +Processing 4rrv +Processing 3csl +Processing 3hwx +Processing 1vjy +Processing 3f07 +Processing 1g9d +Processing 2r6w +Processing 4o13 +Processing 4li7 +Processing 1ryh +Processing 2xuf +Processing 3cen +Processing 3pkn +Processing 1wbv +Processing 3c0z +Processing 6md4 +Processing 5owt +Processing 2rgp +Processing 1cp6 +Waring: Missing or wrong elements: B +Processing 2c93 +Processing 6dji +Processing 3hvk +Processing 4u58 +Processing 4jj7 +Processing 4hlw +Processing 6by8 +Processing 3vb6 +Processing 2q93 +Processing 5h21 +Processing 5vqx +Processing 6jt3 +Processing 3hiw +Processing 2yne +Processing 3c9e +Processing 5u00 +Processing 5vp1 +Processing 5q0t +Processing 1o48 +Processing 4inb +Processing 5d1t +Processing 3vye +Processing 5wfw +Processing 5t4u +Processing 2wti +Processing 3u4i +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +Processing 2ama +Processing 1xos +Processing 3fzt +Processing 3dek +Processing 1xon +Processing 5jog +Processing 4bnv +Processing 3o1e +Processing 6prt +Processing 2gtv +Processing 3nf6 +Processing 4py1 +Processing 2bcd +Processing 6qs5 +Processing 1fq8 +Processing 4hrc +Processing 5pzm +Processing 6qhg +Processing 4mu7 +Processing 4zim +Processing 2l8j +Processing 5hjb +Processing 6htr +Processing 3qo9 +Processing 1noi +Processing 3p3j +Waring: Missing or wrong elements: R +Processing 5ixf +Processing 5cnj +Processing 1qfs +Processing 2xhr +Processing 6aee +Processing 3qbh +Processing 4ydq +Processing 4ufz +Processing 3qcy +Processing 6mxd +Processing 4zur +Processing 2k0x +Processing 3qs8 +Processing 4dhf +Processing 5u6d +Processing 1d3v +Waring: Missing or wrong elements: B +Processing 6bu0 +Processing 6c8p +Processing 5izq +Processing 1pxm +Processing 4bs4 +Processing 4dtt +Processing 3vg1 +Processing 5w0i +Processing 3zlw +Processing 5jaz +Processing 5k76 +Processing 5mi6 +Processing 6do5 +Processing 3sz1 +Processing 2hf8 +Processing 3oy1 +Processing 5fdo +Processing 5nb7 +Processing 3qsb +Processing 4e4x +Processing 5lvf +Processing 2xz5 +Processing 5cy3 +Processing 4anw +Processing 5cf6 +Processing 5ea3 +Processing 4y16 +Processing 2xdm +Waring: Missing or wrong elements: B +Processing 5isl +Processing 2yjb +Processing 1lhe +Waring: Missing or wrong elements: B +Processing 5kgx +Processing 4lrh +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +Processing 5kdr +Processing 5mxr +Processing 3dnt +Processing 3mj5 +Processing 5usz +Processing 3pp0 +Processing 1agw +Processing 6cf5 +Processing 1jiz +Processing 1y3w +Processing 5kjm +Processing 2vio +Processing 6h7n +Processing 3vi7 +Processing 5aqt +Processing 6k5t +Processing 3pz1 +Processing 4jr0 +Processing 4brx +Processing 6gj7 +Processing 3oe9 +Processing 3clp +Processing 3osw +Processing 3ggc +Processing 5em8 +Processing 4prb +Processing 5mxx +Processing 5vdu +Processing 1sqc +Processing 4bw2 +Processing 2go4 +Processing 4oue +Processing 3hjo +Processing 5ier +Processing 1r6n +Processing 5u6b +Processing 4yhz +Processing 1jik +Processing 1lxf +Processing 5c7f +Processing 3uvn +Processing 5wa1 +Processing 3np7 +Processing 5mgg +Processing 3e1r +Processing 5ivz +Processing 2fts +Processing 3o0g +Processing 3r22 +Processing 3zmt +Processing 6fvo +Processing 6u80 +Processing 5yc2 +Processing 5nme +Processing 5vqr +Processing 4mvx +Processing 6c7e +Processing 2h2h +Processing 5ceo +Processing 3r4o +Processing 3h85 +Processing 5svl +Processing 2p0x +Processing 1g3f +Processing 6pvu +Processing 1jld +Processing 4wz8 +Processing 4n1t +Processing 6n54 +Processing 1mwn +Processing 5jk3 +Processing 2i2b +Processing 3fyz +Processing 3atv +Processing 2vin +Processing 6aud +Processing 6oht +Processing 4qt2 +Processing 3odk +Processing 3tiz +Processing 3km4 +Processing 2xzc +Processing 1exv +Processing 5wxg +Processing 4lnw +Processing 4l5j +Processing 4tk3 +Processing 5n53 +Processing 2v0c +Waring: Missing or wrong elements: B +Processing 4e93 +Processing 4jpa +Processing 2xk6 +Processing 1w14 +Processing 6hcv +Processing 3dz6 +Processing 2zns +Processing 1ol2 +Processing 3zrk +Processing 5g43 +Processing 1b9s +Processing 5djr +Processing 4qga +Processing 5a8y +Processing 5d6f +Processing 5i89 +Processing 5e0m +Processing 6qg7 +Processing 3ctr +Processing 6sfk +Processing 6ftn +Processing 4zt6 +Processing 5izu +Processing 4dli +Processing 3dv5 +Processing 6hu3 +Processing 4n8r +Processing 4knr +Processing 3ka2 +Processing 6ocu +Processing 2pe1 +Processing 2y06 +Processing 2il2 +Processing 5icp +Processing 3k16 +Processing 5nsx +Processing 4pdk +Processing 3zsz +Processing 4nak +Processing 5i23 +Processing 5eak +Processing 1o2g +Processing 5f6v +Processing 1i91 +Processing 6ccy +Processing 4uv8 +Processing 1lqd +Processing 1yyy +Processing 2qt9 +Processing 3l2y +Processing 4man +Processing 5zo7 +Processing 2gga +Processing 5vrp +Processing 6ibs +Waring: Missing or wrong elements: B +Processing 3c45 +Processing 3dgq +Processing 5a6b +Processing 3asx +Processing 4quo +Processing 4jk6 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +Processing 2wij +Processing 1m7q +Processing 6qfq +Processing 3axm +Processing 3vyd +Processing 6oir +Processing 4wnk +Processing 4j6i +Processing 3uvp +Processing 4f3i +Processing 3l7a +Processing 4hrd +Processing 5idp +Processing 6nri +Processing 1q1m +Processing 6s9x +Processing 2h42 +Processing 3bv3 +Processing 2h96 +Processing 3tiw +Processing 3iiw +Processing 4wkc +Processing 3pdh +Processing 4nus +Processing 1rpa +Processing 5jpt +Processing 4dro +Processing 4jvi +Processing 5etp +Processing 5ajp +Processing 1s3k +Processing 5n70 +Processing 5law +Processing 6hlz +Processing 4cae +Processing 1n3w +Processing 4w9n +Processing 1o47 +Processing 6bnt +Processing 2fjp +Processing 2ltz +Processing 4guj +Processing 6tyz +Processing 4y6r +Processing 4jmx +Processing 5t2b +Processing 4kvm +Processing 4q4i +Processing 6qtr +Processing 3g4l +Processing 1ppx +Processing 3cgo +Processing 4cc2 +Processing 1xge +Processing 4zjj +Processing 4odp +Processing 5ohj +Processing 3vhe +Processing 4dn0 +Processing 6bs5 +Processing 6g9f +Processing 1inc +Processing 2zmj +Processing 4hzz +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +Processing 4wph +Processing 5lgu +Processing 1o4b +Processing 2zo3 +Processing 6u26 +Processing 6iso +Processing 3qpp +Processing 4lwe +Processing 3kn0 +Processing 1pq6 +Processing 4pz8 +Processing 6nzr +Processing 3zov +Processing 3bym +Processing 4ng9 +Processing 2qwg +Processing 5ely +Processing 4eoy +Processing 2x4s +Processing 4pmp +Processing 4cfe +Processing 2x6e +Processing 4jok +Processing 4l6q +Waring: Missing or wrong elements: B +Processing 4d1y +Processing 4usi +Processing 6m8y +Processing 1hqf +Processing 4y3b +Processing 1gj4 +Processing 6azl +Processing 2hwi +Processing 3haw +Processing 1i7c +Processing 3a73 +Processing 3wi6 +Processing 1pg2 +Processing 2bow +Processing 4mji +Processing 5m0m +Processing 3zlv +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +Processing 2zhd +Processing 4m5g +Processing 4kn2 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +Processing 1xt3 +Processing 3bt9 +Processing 4fhi +Processing 4ii9 +Processing 6n0m +Processing 5gwa +Processing 4zyy +Processing 4dma +Processing 4qp8 +Processing 4wp7 +Processing 3rah +Processing 4c36 +Processing 4j2t +Processing 4lmn +Processing 6nzh +Processing 2ggu +Processing 2f8i +Processing 5n55 +Processing 6skb +Waring: Missing or wrong elements: B +Processing 3itz +Processing 1m5f +Processing 1tl3 +Processing 3qcq +Processing 5jat +Processing 4ifi +Processing 5tyh +Processing 3lk1 +Processing 4aj1 +Processing 6cjp +Processing 3gws +Processing 4tlr +Processing 3qqk +Processing 1zhl +Processing 2pj4 +Processing 5e0g +Processing 2h9n +Processing 6n3e +Processing 3mg4 +Processing 3so9 +Processing 3as0 +Processing 4hup +Processing 3evf +Processing 4d09 +Processing 4daw +Waring: Missing or wrong elements: R +Processing 2zg3 +Processing 5alt +Processing 6mlw +Processing 3jzg +Processing 1gu1 +Processing 3udj +Processing 2d2v +Processing 2gg8 +Processing 6eru +Processing 4u03 +Processing 2iws +Processing 5ab1 +Processing 6c7f +Processing 1jg0 +Processing 2yex +Processing 5afk +Processing 3ij1 +Processing 5ea5 +Processing 3owd +Processing 5he0 +Processing 4e28 +Processing 3zn1 +Processing 5dhp +Processing 4yhf +Processing 6guf +Processing 1xxi +Processing 6itq +Processing 4b6c +Processing 3k3i +Processing 4oty +Processing 5wcl +Processing 3sv8 +Processing 4j58 +Processing 1w1t +Processing 5nve +Processing 3bx5 +Processing 3mea +Processing 3whw +Waring: Missing or wrong elements: R +Processing 5zqu +Processing 1n43 +Processing 2vwy +Processing 4azp +Processing 3el8 +Processing 3my5 +Processing 4rwl +Processing 1r5w +Processing 5mng +Processing 6e49 +Processing 1w80 +Processing 3g86 +Processing 4hiq +Processing 6prg +Processing 4ery +Processing 2q94 +Processing 4k3k +Processing 1jpl +Processing 2xl3 +Processing 5ivs +Processing 4gtm +Processing 1dzj +Processing 1h5u +Processing 5jq9 +Processing 3mj2 +Processing 6h75 +Processing 2w16 +Processing 4zhm +Processing 2c5y +Processing 2qnz +Processing 6eb2 +Processing 5heb +Processing 3bjm +Processing 4z1s +Processing 3tt0 +Processing 5n1y +Processing 5hka +Processing 2y5l +Processing 6d4o +Processing 2fs9 +Processing 2z4w +Processing 2ael +Processing 4cnh +Processing 2jiu +Processing 4mwq +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +Processing 4k6t +Processing 1nzl +Processing 4qna +Processing 3wp1 +Processing 6oy0 +Processing 3qbn +Processing 5n8v +Processing 4ktc +Processing 3dy6 +Processing 6c4u +Processing 2ylp +Processing 4x6h +Processing 5t28 +Processing 1tl7 +Processing 3ah8 +Processing 4deg +Processing 4fli +Processing 2iiv +Processing 2puy +Processing 6b1e +Processing 4hvg +Processing 5qcm +Processing 4fns +Processing 5etr +Processing 4z22 +Processing 4li8 +Processing 6awn +Processing 1lvc +Processing 6msn +Processing 2ow9 +Processing 5kqg +Processing 1ld7 +Processing 1p10 +Waring: Missing or wrong elements: B +Processing 6h7m +Processing 4xhk +Processing 3omc +Processing 6cyh +Processing 4prd +Processing 5kre +Processing 4hvi +Processing 6ps4 +Processing 6s89 +Processing 4ke0 +Processing 1yvz +Processing 3nwb +Processing 1bdr +Processing 5ou1 +Processing 5jf5 +Processing 5l0h +Processing 1t5a +Processing 6tld +Processing 5ti2 +Processing 2w3k +Processing 4bvb +Processing 3rtn +Processing 5hu0 +Processing 2oi9 +Processing 4kup +Processing 1qm5 +Processing 3snl +Processing 1m21 +Processing 2zx5 +Processing 2mwy +Processing 3mxr +Waring: Missing or wrong elements: B +Processing 5dtq +Processing 5hfu +Processing 6pi7 +Processing 6fby +Processing 3v7d +Processing 3w0l +Processing 2mc1 +Processing 5nkk +Processing 5lrg +Processing 5wei +Processing 5dva +Processing 5f1u +Processing 6djc +Processing 5hln +Processing 2bro +Processing 3g70 +Processing 4z0d +Processing 4ybi +Processing 5l96 +Processing 3oxz +Processing 4uuq +Processing 4e3b +Processing 4x13 +Processing 3mww +Processing 4cfu +Processing 4x3u +Processing 4lwv +Processing 1ybg +Processing 2qrp +Processing 6hrt +Processing 6ps5 +Processing 1g3m +Processing 6pi1 +Processing 5y7z +Processing 5ugc +Processing 4og5 +Processing 2gvd +Processing 4cpx +Processing 4ivt +Processing 4abk +Processing 2gni +Processing 4bo8 +Processing 3daj +Processing 5vse +Processing 2wfg +Waring: Missing or wrong elements: B +Processing 4d83 +Processing 1h2u +Processing 3eks +Processing 4c35 +Processing 1n8u +Processing 3oyn +Processing 4pxf +Processing 6f7c +Processing 5vex +Processing 1tv6 +Processing 4muk +Processing 2x6f +Processing 4qmw +Processing 1p05 +Waring: Missing or wrong elements: B +Processing 4btt +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +Processing 1bl7 +Processing 6mt6 +Processing 5bvw +Processing 5u7i +Processing 5ahu +Processing 6qre +Processing 3vi2 +Processing 1zyr +Processing 3c1n +Processing 3l3x +Processing 2pzy +Processing 3ti4 +Processing 6b4h +Processing 2j4k +Processing 1hte +Processing 6mr5 +Processing 6ggg +Processing 3fpm +Processing 6q35 +Waring: Missing or wrong elements: B +Processing 6qcg +Processing 3omm +Processing 4uiv +Processing 3mvj +Processing 3npa +Processing 6uyy +Processing 2an5 +Processing 2xzw +Processing 4zsm +Processing 4cgj +Processing 3ouh +Processing 4qhc +Processing 4qiz +Processing 5im3 +Processing 1kr3 +Processing 1bo5 +Processing 2h2j +Processing 1gi8 +Processing 3ral +Processing 1yxd +Processing 4ycu +Processing 1o4f +Processing 1z6f +Waring: Missing or wrong elements: B +Processing 5o5m +Waring: Missing or wrong elements: B +Processing 5v1y +Processing 5t6z +Processing 4zy2 +Processing 5k6a +Processing 6oy1 +Processing 6oxq +Processing 4mlx +Processing 4r4q +Processing 4urk +Processing 3opr +Processing 3bcn +Processing 3gbq +Processing 5ws3 +Processing 1sj0 +Processing 7kme +Processing 3sh1 +Processing 6htc +Processing 4puj +Processing 6o3w +Processing 5gnk +Processing 5akj +Processing 6moa +Processing 4gm3 +Processing 4op3 +Processing 5alj +Processing 4dcy +Processing 3fk1 +Processing 2ai8 +Processing 2ym7 +Processing 2pt9 +Processing 4hbp +Processing 1vr1 +Processing 6jij +Processing 3avi +Processing 2nm1 +Processing 1e8h +Processing 2wi5 +Processing 3mt9 +Processing 5uga +Processing 3n7r +Processing 3bi0 +Processing 3mta +Processing 1h3c +Processing 1lxh +Processing 1ftj +Processing 4o1l +Processing 4mti +Processing 4ikr +Processing 2qu5 +Processing 4eh8 +Processing 5ecv +Processing 4jlh +Processing 4ok3 +Processing 6g22 +Processing 4qye +Processing 2xp2 +Processing 4nwk +Processing 2mpa +Processing 6bnk +Processing 3nef +Processing 2v83 +Processing 6f23 +Processing 1oai +Processing 4nmv +Processing 1y2j +Processing 5q15 +Processing 3hv7 +Processing 2zdx +Processing 5v8v +Processing 3n5j +Processing 6h7f +Processing 5ok3 +Processing 3chg +Processing 5yyz +Processing 5o55 +Processing 3t0m +Processing 3dnj +Processing 1ayv +Processing 6g15 +Processing 5i86 +Processing 4j1f +Processing 4z2o +Processing 4mcc +Processing 5ow1 +Processing 6ai9 +Processing 3s68 +Processing 1qx1 +Processing 5n8e +Processing 5h7g +Processing 5ybi +Processing 4d62 +Processing 2rip +Processing 6htp +Processing 6gxu +Processing 6qed +Processing 1i8z +Processing 2fum +Processing 3amb +Processing 4yqm +Processing 3egk +Processing 2ygu +Processing 3fe7 +Processing 1vik +Processing 6iin +Processing 3fdn +Processing 6p3u +Processing 4gwi +Processing 4olh +Processing 2hxl +Processing 6ew7 +Processing 1mmp +Processing 5hd0 +Processing 2g6q +Processing 4g11 +Processing 5e0h +Processing 6rjp +Processing 3o87 +Waring: Missing or wrong elements: B +Processing 6c1s +Processing 4i0d +Processing 4wuy +Processing 4mga +Processing 2lo6 +Processing 5aqk +Processing 5mw4 +Processing 2xgs +Processing 4xhl +Processing 3ewz +Processing 1erq +Waring: Missing or wrong elements: B +Processing 3tyq +Processing 1c12 +Processing 4xcu +Processing 2q2z +Processing 4fi9 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +Processing 2pj9 +Processing 2c4f +Processing 5vio +Processing 4ydg +Processing 2ywp +Processing 5fnj +Processing 6sq0 +Processing 5vqe +Processing 5vzu +Processing 4joa +Processing 5a00 +Processing 3vru +Processing 4jfz +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +Processing 3abt +Processing 1flm +Processing 2o7v +Processing 6apz +Processing 1vyq +Processing 4xtt +Processing 4jjs +Processing 4hyf +Processing 5wae +Waring: Missing or wrong elements: B +Processing 2vwv +Processing 3i8t +Processing 1vyj +Processing 4xsz +Processing 3vf3 +Processing 3d1g +Processing 5zde +Processing 4nrp +Processing 5u3b +Processing 5el2 +Processing 6oxu +Processing 2pmk +Processing 6ar2 +Processing 1yms +Waring: Missing or wrong elements: B +Processing 5moo +Processing 3e16 +Processing 3pj8 +Processing 6h4r +Processing 4zun +Processing 4uyd +Processing 5t2g +Processing 4hpy +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +Processing 2p3o +Processing 3doz +Processing 1htg +Processing 5zh2 +Processing 4xbb +Processing 3ho2 +Processing 6miv +Processing 4e8z +Processing 6i5y +Processing 2rgu +Processing 7abp +Processing 7prc +Processing 6qw9 +Processing 1om2 +Processing 3vo3 +Processing 3arr +Processing 5hvp +Processing 4dpi +Processing 3og7 +Processing 3e64 +Processing 5gmu +Processing 4ay6 +Processing 4x8g +Processing 3adu +Processing 1evh +Processing 5h9q +Processing 5c8k +Processing 1xzx +Processing 6hdq +Processing 4uau +Processing 2ze1 +Processing 6mep +Processing 4hwb +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +Processing 4b78 +Processing 4qw7 +Processing 2yol +Processing 5w7x +Processing 1uv5 +Processing 2xkd +Processing 1h6e +Processing 4wi1 +Processing 6afe +Processing 3hhk +Processing 4xxs +Processing 4d85 +Processing 1vij +Processing 2oph +Processing 4aa4 +Processing 3g2k +Processing 4htx +Processing 1i5d +Processing 6bhe +Processing 4zyz +Processing 5w13 +Waring: Missing or wrong elements: B +Processing 1ym4 +Processing 6fv1 +Processing 4xjs +Processing 6hhj +Processing 5dxe +Processing 4c1g +Processing 1y3y +Processing 3ds1 +Processing 1zm6 +Processing 3vid +Processing 5ekx +Processing 4hv7 +Processing 6g1w +Processing 2a3w +Processing 4ln2 +Processing 2fl2 +Processing 3zxe +Processing 6q9w +Processing 3cvk +Processing 4dru +Processing 5x28 +Processing 5yr6 +Processing 1ycm +Processing 4d08 +Processing 5x26 +Processing 2o2u +Processing 4y8z +Processing 2i03 +Processing 6ps0 +Processing 4asy +Processing 5eif +Processing 3upi +Processing 4mwc +Processing 5gid +Processing 4og8 +Processing 2z97 +Processing 4eoi +Processing 3wcg +Processing 6b1j +Processing 5y53 +Processing 3cn0 +Processing 3krw +Processing 2r3n +Processing 3u4h +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +Processing 4i9o +Processing 6fyv +Processing 1agm +Processing 4d2d +Processing 2bw7 +Processing 6oxr +Processing 2wzx +Processing 3h2o +Processing 3o0j +Waring: Missing or wrong elements: B +Processing 4rcg +Processing 5u4c +Waring: Missing or wrong elements: B +Processing 3g5v +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +Processing 5t68 +Processing 2vur +Processing 6dvn +Processing 3g4i +Processing 5jau +Processing 1ztq +Processing 5ceh +Processing 3qk5 +Processing 2g70 +Processing 4qz0 +Processing 3c94 +Processing 6b27 +Processing 4b13 +Processing 2zva +Processing 1gsz +Processing 2y8o +Processing 3eky +Processing 4bo9 +Processing 5mqt +Processing 6ott +Processing 2nxd +Processing 5d7x +Processing 6fjm +Processing 4uuh +Processing 3cbp +Processing 2q8y +Processing 6b1x +Processing 6d4a +Processing 6ew6 +Processing 1ke6 +Processing 4wwo +Processing 4k3p +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +------------Warning: Missing Parameters for Residue: A @ HSE-------------- +Processing 4tzm +Processing 4oyo +Processing 3oyl +Processing 2vts +Processing 4tx6 +Processing 5oq4 +Processing 4oyt +Processing 4uiw +Processing 2y71 +Processing 1ibc +Processing 6erw +Processing 4rj7 +Processing 2ofv +Processing 3evc +Processing 5cqj +Processing 5luu +Processing 6cv8 +Processing 6rtn +Waring: Missing or wrong elements: B +Processing 1xog +2z4b +4qvn +Waring: Missing or wrong elements: B +6qwa +4dgn +1eub +5vew +3sgt +5tyi +5kq5 +4awq +3umx +4e1z +3ns7 +2yim +5nxv +4zla +2nns +1mns +6h9x +3qxd +5ttu +3lkh +5jmw +6cqf +1xz8 +3ti6 +4bo5 +6bh2 +6h12 +4aa7 +3uzd +4y46 +5mym +3aru +2wi4 +5i2r +4p6g +4yb7 +2clx +1kne +2q1j +4k64 +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +------------Warning: Missing Parameters for Residue: CYX @ HG-------------- +2hwp +3fsm +1cx9 +5os1 +5w85 +4ie7 +4u91 diff --git a/utils/ledock/refined-set-com.txt b/utils/ledock/refined-set-com.txt new file mode 100644 index 0000000..44d73b3 --- /dev/null +++ b/utils/ledock/refined-set-com.txt @@ -0,0 +1,5316 @@ +6ayo -33.035 7.272 95.517 +2pqc -129.588 31.015 126.050 +1oyt 16.824 -12.394 21.850 +2q1q -4.539 3.676 14.056 +2yix 3.144 12.352 31.744 +1upf 9.797 95.564 46.604 +2zy1 17.118 54.694 36.668 +4i8n -11.553 39.859 35.421 +2xn3 9.409 6.370 23.469 +3g1v 8.683 1.554 3.379 +2vvv -4.297 8.808 22.573 +1s19 11.577 23.005 34.308 +3vhd -12.792 -3.651 -10.083 +3ekv 19.512 30.044 14.155 +4crb 24.706 10.070 53.144 +6gjj -2.474 17.923 -6.182 +1gi1 28.983 12.833 19.509 +3e5u 9.992 -23.355 16.996 +3pwd 23.648 7.279 18.998 +5dw2 11.748 5.748 0.310 +1b3g 2.772 19.183 14.822 +2xog 38.435 3.077 16.074 +4w9j 12.084 53.672 89.386 +185l 27.299 6.304 4.157 +6rot 16.495 -12.622 23.029 +4xtx -3.827 -4.138 10.997 +1w11 31.481 9.449 28.400 +3ozs -19.950 29.490 9.838 +5lvd 12.439 39.749 -7.280 +3si4 17.187 -12.504 22.478 +5sz7 0.045 7.203 85.336 +6mln 2.240 -1.196 -10.347 +1bwa -9.268 16.024 27.911 +3rsx 69.832 50.027 10.439 +1k1y 1.406 54.739 93.811 +2pyy 55.930 22.029 34.224 +3coy 14.782 10.031 1.563 +5n2z 11.695 -40.273 6.206 +3n3j -3.721 5.353 14.182 +5zkc 183.603 27.656 525.750 +3hl8 33.971 2.531 57.312 +3f7i 78.746 61.910 15.276 +1c1r 45.067 22.760 50.028 +1ydd -5.636 2.962 15.201 +5om2 4.496 -18.177 -15.253 +1rpj 3.921 7.663 11.625 +4qer -5.851 21.986 5.292 +4bi7 2.292 -18.547 -23.804 +5kly -30.964 6.121 -26.697 +5nk8 122.311 14.621 45.676 +6b7a -34.773 -34.661 56.076 +3c8b 26.637 22.430 55.393 +4cp5 49.626 -50.786 75.457 +3uuo 4.724 12.732 43.719 +6dz3 86.946 160.333 175.489 +5ufp 24.619 -0.220 -10.277 +4aq6 17.890 42.655 -2.092 +5n6s -7.202 -9.798 6.614 +3n7a 44.326 6.661 26.328 +3bgs 14.753 11.242 57.731 +3g32 -5.737 52.718 11.743 +4cu8 39.776 -46.220 6.638 +6c9s 4.953 4.309 11.680 +5oh3 24.608 17.189 -7.921 +3v3q -12.407 24.122 6.694 +3usx -34.910 -22.036 -40.916 +5xmx 2.778 -1.146 50.251 +4yyt -1.642 4.342 85.348 +1bnn -4.187 4.801 14.881 +5vij 18.729 106.252 378.924 +6gl8 16.054 2.055 16.161 +6mnc 23.093 -3.948 -29.343 +3jvs 30.257 -3.289 20.164 +1x8d 10.753 32.033 8.721 +5nih -31.678 85.970 32.460 +5otz -113.031 -175.649 309.021 +5nki -99.667 -14.603 45.662 +1b6h 2.703 18.852 14.632 +4m8h 62.610 46.996 30.799 +2jfz 14.629 59.745 38.235 +4xmb 3.945 0.788 -23.017 +1vyg 12.038 32.063 6.821 +1hxw 10.828 23.099 3.751 +4uac 27.359 64.872 25.471 +2rkm 5.268 19.572 15.735 +1efy 39.493 22.694 20.430 +4c5d -14.992 -25.998 -13.791 +4ykj 8.847 60.575 44.791 +2nt7 48.183 10.420 3.040 +1q1g 8.743 4.494 92.829 +3o4k 15.246 20.618 -22.573 +5ldp -23.258 -2.470 23.018 +4b6p 29.308 46.022 7.240 +2exm 102.885 99.931 80.450 +4k7i 12.326 7.787 40.758 +6d5h 35.152 30.548 22.826 +4gkm -28.156 -32.471 7.848 +1usi 29.209 8.992 48.343 +3zdv -8.948 17.605 23.850 +3b26 0.554 9.911 0.201 +1pdz 30.846 69.815 12.705 +1jvu 36.828 0.587 24.009 +5ehv 19.335 6.295 13.651 +4jyb 62.285 4.451 46.528 +2nn7 -18.025 1.485 -17.524 +1b5j 2.896 18.812 14.900 +3hub 20.685 2.763 -23.700 +5k8s 18.689 -20.176 -15.124 +1ebw 13.206 22.928 5.548 +1ugx 36.993 33.434 25.714 +6nsv -6.502 7.467 3.769 +4ncn -11.681 18.632 10.874 +6fnr 7.924 14.890 15.413 +5m23 -11.956 23.943 6.200 +6t1i -0.727 15.702 16.479 +6h77 19.590 4.030 25.469 +4qtl -4.690 3.637 13.292 +3nyd 22.969 -2.202 -21.371 +6mli 17.732 1.486 -10.434 +4k3n 84.691 72.927 31.059 +4gue 33.642 5.186 9.071 +5e8f 7.590 -17.311 10.773 +3ppp -29.197 -30.750 9.271 +1qb1 12.133 39.758 12.939 +6edr -12.425 -1.432 -0.501 +1szd -9.649 33.132 -42.271 +3mhc -5.282 4.786 13.535 +4luz -9.888 12.148 -22.600 +3nsn 34.809 2.710 13.880 +4ks4 205.599 72.380 -125.004 +4lm4 4.078 12.945 44.386 +6bs4 -44.376 46.690 11.180 +1qaw 16.343 60.564 32.778 +6ma5 -0.045 -45.819 15.238 +4bny 7.517 -1.041 34.405 +4cs9 101.561 26.845 169.627 +2qnp 17.508 22.961 -5.886 +1m2p 23.964 5.755 18.094 +3s76 15.412 1.821 16.050 +1ajx 12.935 23.057 5.550 +3prs -1.529 4.300 9.236 +1o2j 43.987 -1.416 30.905 +4q4p 107.426 18.616 17.913 +1nhz -2.230 12.396 3.388 +3hu3 20.989 47.897 -11.341 +4q7p 15.536 1.606 15.562 +4m2w 16.822 3.601 14.795 +2brm 3.371 -4.973 18.762 +3uil -36.789 -21.806 -41.379 +5ipj -22.600 -35.018 -1.441 +5cqt 4.809 9.158 1.482 +1siv 3.105 11.351 40.217 +6mku 2.529 -1.043 -10.361 +3k8c 39.673 29.076 13.008 +3st5 15.968 22.677 16.781 +6d1j 49.533 11.665 45.745 +2weo 5.426 -4.099 15.832 +1bma 38.147 20.495 37.620 +5mgk -107.480 41.000 27.711 +5avf 24.759 142.834 144.656 +4rra 14.810 -2.532 -3.095 +4m0e -17.124 -42.404 25.598 +5qtt 41.207 -19.715 29.324 +5l4j -43.689 -0.441 69.372 +1phw 4.253 -8.216 41.915 +1e3v 3.277 -8.554 85.265 +4ca5 13.890 -6.957 -21.138 +2qhz 19.798 31.036 14.397 +3iub 15.463 10.083 0.569 +4std 103.048 90.904 29.148 +5mod 4.537 141.170 353.101 +5f5z 61.410 79.573 78.188 +2vba 40.910 69.773 64.662 +3zk6 21.131 49.516 1.260 +4xit 3.404 -10.850 -25.354 +4ly9 37.591 -23.576 16.599 +5lyr 3.747 23.091 6.351 +5x54 -9.146 17.734 -0.427 +4ibc 2.736 20.937 1.333 +4rqk -11.707 16.327 -9.944 +5ey0 -2.756 -1.065 -23.932 +2yge 22.773 -34.406 -4.744 +6o5u 110.567 -16.493 -7.889 +2c97 -21.242 0.816 3.339 +2qrl 45.496 54.776 18.174 +3bpc 29.498 -2.944 3.237 +4ayp -29.377 -13.191 -11.556 +6ghj 23.696 18.160 -4.130 +4q6e -3.734 5.490 14.711 +3ozg 64.234 36.315 75.274 +5b2d 8.961 -48.095 -29.328 +1o0m 36.836 0.622 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+4cwn 2.608 11.133 25.415 +5oss -19.240 -29.403 -5.381 +5op4 1.519 -4.260 19.784 +2gh9 23.112 16.130 22.864 +1hii 15.311 30.907 12.535 +4ipj 97.347 -20.774 52.642 +5n17 1.330 -27.280 -28.340 +1pxo 12.225 -8.304 11.552 +5n2t 11.805 40.092 -6.308 +6gj8 14.339 16.121 -21.307 +3u8l -7.145 25.323 31.317 +3nhi -6.610 -0.889 18.061 +3lgs 23.754 -8.666 11.055 +6fuh 5.592 7.665 1.710 +5l9o 42.026 -67.586 32.669 +4re2 8.795 12.036 12.151 +5f1h 7.939 -4.255 4.766 +4qge 76.258 50.987 40.343 +5c28 3.592 13.176 42.552 +6poi 39.529 10.435 3.094 \ No newline at end of file diff --git a/utils/misc.py b/utils/misc.py new file mode 100644 index 0000000..d5eaf52 --- /dev/null +++ b/utils/misc.py @@ -0,0 +1,109 @@ +import os +import time +import random +import logging +import torch +import numpy as np +import pickle +import yaml +from easydict import EasyDict +from logging import Logger +from tqdm.auto import tqdm + + +class BlackHole(object): + def __setattr__(self, name, value): + pass + def __call__(self, *args, **kwargs): + return self + def __getattr__(self, name): + return self + + +def load_config(path): + fmt = path.split(".")[-1] + if fmt == "yml": + with open(path, 'r') as f: + return EasyDict(yaml.safe_load(f)) + elif fmt == "pkl": + with open(path, 'rb') as f: + return EasyDict(pickle.load(f)) + else: + raise FileTypeNotRecognised("Please use either .yml or .pkl data source.") + + +def get_logger(name, log_dir=None): + logger = logging.getLogger(name) + logger.setLevel(logging.DEBUG) + formatter = logging.Formatter('[%(asctime)s::%(name)s::%(levelname)s] %(message)s') + + stream_handler = logging.StreamHandler() + stream_handler.setLevel(logging.DEBUG) + stream_handler.setFormatter(formatter) + logger.addHandler(stream_handler) + + if log_dir is not None: + file_handler = logging.FileHandler(os.path.join(log_dir, 'log.txt')) + file_handler.setLevel(logging.DEBUG) + file_handler.setFormatter(formatter) + logger.addHandler(file_handler) + + return logger + + +def get_new_log_dir(root='./logs', prefix='', tag=''): + fn = time.strftime('%Y_%m_%d__%H_%M_%S', time.localtime()) + if prefix != '': + fn = prefix + '_' + fn + if tag != '': + fn = fn + '_' + tag + log_dir = os.path.join(root, fn) + os.makedirs(log_dir) + return log_dir + + +def seed_all(seed): + torch.manual_seed(seed) + np.random.seed(seed) + random.seed(seed) + + +def log_hyperparams(writer, args): + from torch.utils.tensorboard.summary import hparams + vars_args = {k:v if isinstance(v, str) else repr(v) for k, v in vars(args).items()} + exp, ssi, sei = hparams(vars_args, {}) + writer.file_writer.add_summary(exp) + writer.file_writer.add_summary(ssi) + writer.file_writer.add_summary(sei) + + +def int_tuple(argstr): + return tuple(map(int, argstr.split(','))) + + +def str_tuple(argstr): + return tuple(argstr.split(',')) + +def unique(x, dim=None): + """Unique elements of x and indices of those unique elements + https://github.com/pytorch/pytorch/issues/36748#issuecomment-619514810 + + e.g. + + unique(tensor([ + [1, 2, 3], + [1, 2, 4], + [1, 2, 3], + [1, 2, 5] + ]), dim=0) + => (tensor([[1, 2, 3], + [1, 2, 4], + [1, 2, 5]]), + tensor([0, 1, 3])) + """ + unique, inverse = torch.unique( + x, sorted=True, return_inverse=True, dim=dim) + perm = torch.arange(inverse.size(0), dtype=inverse.dtype, + device=inverse.device) + inverse, perm = inverse.flip([0]), perm.flip([0]) + return unique, inverse.new_empty(unique.size(dim)).scatter_(0, inverse, perm) \ No newline at end of file diff --git a/utils/train.py b/utils/train.py new file mode 100644 index 0000000..cbd20ea --- /dev/null +++ b/utils/train.py @@ -0,0 +1,52 @@ +import copy +import warnings +import numpy as np +import torch +import torch.nn as nn +from torch_geometric.data import Data, Batch + +def repeat_data(data: Data, num_repeat) -> Batch: + datas = [copy.deepcopy(data) for i in range(num_repeat)] + return Batch.from_data_list(datas) + + +def repeat_batch(batch: Batch, num_repeat) -> Batch: + datas = batch.to_data_list() + new_data = [] + for i in range(num_repeat): + new_data += copy.deepcopy(datas) + return Batch.from_data_list(new_data) + + +def inf_iterator(iterable): + iterator = iterable.__iter__() + while True: + try: + yield iterator.__next__() + except StopIteration: + iterator = iterable.__iter__() + + +def get_optimizer(cfg, model): + if cfg.type == 'adam': + return torch.optim.Adam( + model.parameters(), + lr=cfg.lr, + weight_decay=cfg.weight_decay, + betas=(cfg.beta1, cfg.beta2, ) + ) + else: + raise NotImplementedError('Optimizer not supported: %s' % cfg.type) + + +def get_scheduler(cfg, optimizer): + if cfg.type == 'plateau': + return torch.optim.lr_scheduler.ReduceLROnPlateau( + optimizer, + factor=cfg.factor, + patience=cfg.patience, + min_lr=cfg.min_lr + ) + else: + raise NotImplementedError('Scheduler not supported: %s' % cfg.type) + diff --git a/utils/trial.py b/utils/trial.py new file mode 100644 index 0000000..9a76d34 --- /dev/null +++ b/utils/trial.py @@ -0,0 +1,24 @@ +import biopandas.pdb as bpdb +import oddt +from PLInteraction import * + +protein_path = '../example/7cff_protein.pdb' +ligand_path = '../example/7cff_ligand.sdf' + +ppdb = bpdb.PandasPdb() +ppdb.read_pdb(protein_path) + +atom_df = ppdb.df['ATOM'][ppdb.df['ATOM']['element_symbol'] != 'H'] +list_atom_name = atom_df['atom_name'].tolist() + +protein = next(oddt.toolkits.ob.readfile('pdb', protein_path)) +protein.removeh() +protein.protein = True + +ligand = next(oddt.toolkits.ob.readfile('sdf', ligand_path)) +ligand.removeh() + + +#get_bonds_protein_ligand(protein, ligand, 4.0, list_atom_name) +alpha, beta, gamma, delta = get_bonds_protein_ligand(protein, ligand, 4.0, list_atom_name) +