refactor pdbfixer

PolusAI · Jun 10, 2024 · e674a37 · e674a37
1 parent 23fb84d
commit e674a37
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Showing 18 changed files with 36 additions and 29 deletions.
diff --git a/utils/pdbfixer-plugin/Dockerfile b/utils/pdbfixer-plugin/Dockerfile
diff --git a/utils/pdbfixer-plugin/.bumpversion.cfg → ...ure-change/pdbfixer-tool/.bumpversion.cfg b/utils/pdbfixer-plugin/.bumpversion.cfg → ...ure-change/pdbfixer-tool/.bumpversion.cfg
diff --git a/utils/pdbfixer-plugin/.dockerignore → ...ucture-change/pdbfixer-tool/.dockerignore b/utils/pdbfixer-plugin/.dockerignore → ...ucture-change/pdbfixer-tool/.dockerignore
diff --git a/utils/pdbfixer-plugin/.gitignore → ...structure-change/pdbfixer-tool/.gitignore b/utils/pdbfixer-plugin/.gitignore → ...structure-change/pdbfixer-tool/.gitignore
diff --git a/utils/pdbfixer-plugin/CHANGELOG.md → ...ructure-change/pdbfixer-tool/CHANGELOG.md b/utils/pdbfixer-plugin/CHANGELOG.md → ...ructure-change/pdbfixer-tool/CHANGELOG.md
diff --git a/utils/pre-process/structure-change/pdbfixer-tool/Dockerfile b/utils/pre-process/structure-change/pdbfixer-tool/Dockerfile
@@ -0,0 +1,31 @@
+# docker build -f Dockerfile -t mrbrandonwalker/pdbfixer-tool .
+
+FROM condaforge/mambaforge
+
+ENV EXEC_DIR="/opt/executables"
+ENV POLUS_LOG="INFO"
+RUN mkdir -p ${EXEC_DIR}
+
+
+# Work directory defined in the base container
+# WORKDIR ${EXEC_DIR}
+
+COPY pyproject.toml ${EXEC_DIR}
+COPY VERSION ${EXEC_DIR}
+COPY README.md ${EXEC_DIR}
+COPY CHANGELOG.md ${EXEC_DIR}
+
+# Install needed packages here
+# errors installing pdbfixer from poetry so using conda
+COPY environment.yml ${EXEC_DIR}
+RUN mamba env create -f ${EXEC_DIR}/environment.yml
+RUN echo "source activate project_env" > ~/.bashrc
+ENV PATH /opt/conda/envs/env/bin:$PATH
+
+COPY src ${EXEC_DIR}/src
+
+ADD Dockerfile .
+
+RUN conda run -n project_env pip install ${EXEC_DIR} --no-cache-dir
+
+CMD ["--help"]
diff --git a/utils/pdbfixer-plugin/README.md → .../structure-change/pdbfixer-tool/README.md b/utils/pdbfixer-plugin/README.md → .../structure-change/pdbfixer-tool/README.md
@@ -12,7 +12,7 @@ This plugin takes 9 input arguments and 1 output argument:
 | input_helper_pdb_path | Template input PDB path | Input | File | File |
 | pdbid | PDB id from RCSB? | Input | string | string |
 | url | URL to retrieve PDB from | Input | string | string |
-| output_pdb_path |  | Input | string | string |
+| output_pdb_path | Output protein file path name | Input | string | string |
 | add_atoms | What missing atoms to add, all, heavy or none | Input | string | string |
 | add_residues | If set to True, adds missing residue | Input | boolean | boolean |
 | replace_nonstandard | Replace nonstandard residues with standard equivalents | Input | boolean | boolean |

diff --git a/utils/pdbfixer-plugin/VERSION → ...ss/structure-change/pdbfixer-tool/VERSION b/utils/pdbfixer-plugin/VERSION → ...ss/structure-change/pdbfixer-tool/VERSION
diff --git a/utils/pdbfixer-plugin/environment.yml → ...ture-change/pdbfixer-tool/environment.yml b/utils/pdbfixer-plugin/environment.yml → ...ture-change/pdbfixer-tool/environment.yml
diff --git a/utils/pdbfixer-plugin/ict.yml → ...ss/structure-change/pdbfixer-tool/ict.yml b/utils/pdbfixer-plugin/ict.yml → ...ss/structure-change/pdbfixer-tool/ict.yml
@@ -1,11 +1,12 @@
 specVersion: 0.1.0
 name: labshare/pdbfixer
 version: 0.1.0
-container: polusai/pdbfixer-plugin:0.1.0
+container: polusai/pdbfixer-tool:0.1.0
 entrypoint: ""
 title: pdbfixer
 description: Fix pdbfiles.
-author: Data Scientist ([email protected])
+author: Brandon Walker, Nazanin Donyapour
+contact: [email protected], [email protected]
 repository: https://github.com/labshare/mmtools
 documentation: https://ncats.nih.gov/preclinical/core/informatics
 citation:

diff --git a/utils/pdbfixer-plugin/pdb_fixer.cwl → ...ucture-change/pdbfixer-tool/pdb_fixer.cwl b/utils/pdbfixer-plugin/pdb_fixer.cwl → ...ucture-change/pdbfixer-tool/pdb_fixer.cwl
@@ -12,7 +12,7 @@ baseCommand: ["python", "-m", "polus.mm.utils.pdbfixer"]
 
 hints:
   DockerRequirement:
-    dockerPull: mrbrandonwalker/pdbfixer
+    dockerPull: mrbrandonwalker/pdbfixer-tool
 
 inputs:
   input_pdb_path:

diff --git a/utils/pdbfixer-plugin/pyproject.toml → ...cture-change/pdbfixer-tool/pyproject.toml b/utils/pdbfixer-plugin/pyproject.toml → ...cture-change/pdbfixer-tool/pyproject.toml
diff --git a/...n/src/polus/mm/utils/pdbfixer/__init__.py → ...l/src/polus/mm/utils/pdbfixer/__init__.py b/...n/src/polus/mm/utils/pdbfixer/__init__.py → ...l/src/polus/mm/utils/pdbfixer/__init__.py
diff --git a/...n/src/polus/mm/utils/pdbfixer/__main__.py → ...l/src/polus/mm/utils/pdbfixer/__main__.py b/...n/src/polus/mm/utils/pdbfixer/__main__.py → ...l/src/polus/mm/utils/pdbfixer/__main__.py
diff --git a/...n/src/polus/mm/utils/pdbfixer/pdbfixer.py → ...l/src/polus/mm/utils/pdbfixer/pdbfixer.py b/...n/src/polus/mm/utils/pdbfixer/pdbfixer.py → ...l/src/polus/mm/utils/pdbfixer/pdbfixer.py
diff --git a/utils/pdbfixer-plugin/tests/1msn_protein.pdb → ...ange/pdbfixer-tool/tests/1msn_protein.pdb b/utils/pdbfixer-plugin/tests/1msn_protein.pdb → ...ange/pdbfixer-tool/tests/1msn_protein.pdb
diff --git a/utils/pdbfixer-plugin/tests/__init__.py → ...re-change/pdbfixer-tool/tests/__init__.py b/utils/pdbfixer-plugin/tests/__init__.py → ...re-change/pdbfixer-tool/tests/__init__.py
diff --git a/utils/pdbfixer-plugin/tests/test_pdbfixer.py → ...ange/pdbfixer-tool/tests/test_pdbfixer.py b/utils/pdbfixer-plugin/tests/test_pdbfixer.py → ...ange/pdbfixer-tool/tests/test_pdbfixer.py