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virtual screening #110

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199 changes: 199 additions & 0 deletions virtual-screening/docking_autodock_vina_batch.wic
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steps:
download_pdb.wic:
in:
#pdb_id: !ii 1r4l # ACE2
#pdb_id: !ii 1ntp # trypsin
pdb_id: !ii 1uao # chignolin (for speed)
#pdb_id: !ii 6us9 # Influenza A M2
#pdb_id: !ii 2rlf # Influenza A M2
setup_pdb.wic:
in:
input_pdb_path: !* protein.pdb
pdb_path: !ii pdb.pdbqt
box_path: !ii box.pdb
box_buffer: !ii 20 # Angstroms
water_type: !ii spce
forcefield: !ii amber99sb-ildn
out:
- pdb_path: !& pdb.pdbqt
- box_path: !& box.pdb

download_smiles_ligand_db.wic:
in:
path: !ii https://smacc.mml.unc.edu/ncats_target_based_curated.xlsx
# query syntax: `column name` 'column value'
query: !ii "`Standard Type` == 'Kd' and `duplicate-type-classifier` == 'unique'"
#query: !ii "`Standard Type` == 'Kd' and `Target` == 'Matrix protein 2' and `Outcome` == 'Active'"
max_row: !ii 1 #25 # Use 1 for CI
smiles_column: !ii SMILES
binding_data_column: !ii Standard Value
convert_Kd_dG: !ii True
output_txt_path: !ii binding_data.txt
out:
- output_txt_path: !& binding_data.txt

assign_partial_charges.wic:
scatter: [input_path]
in:
# NOTE: input_path is currently only necessary
# due to a limitation of the inlineing implementation.
input_path: !* ligand_conformers.sdf
# NOTE: cwltool uses the CLI args to determine caching. In batch mode, the
# ligands are passed (as CLI args) to vina all at once. Thus, if you want to
# incrementally increase the number of ligands, the previous results will NOT be cached!

autodock_vina_batch:
in:
input_receptor_pdbqt_path: !* pdb.pdbqt
input_box_path: !* box.pdb
out:
- output_log_path: !& vina.log
- output_batch_pdbqt_path: !& ligand_decoys_1D.pdbqt

split_pdbqt:
scatter: [input_path]
in:
input_path: !* ligand_decoys_1D.pdbqt
out:
- output_pdb_path: !& ligand_decoys_2D.pdbqt

duplicate:
scatter: [input_pdbqt_array_path]
in:
input_pdbqt_singleton_path: !* pdb.pdbqt
input_pdbqt_array_path: !* ligand_decoys_2D.pdbqt
out:
- output_pdbqt_path: !& receptor_dup_2D.pdbqt

autodock_vina_filter:
in:
input_ligand_pdbqt_path: !* ligand_decoys_2D.pdbqt
input_receptor_pdbqt_path: !* receptor_dup_2D.pdbqt
input_log_path: !* vina.log
input_txt_path: !* binding_data.txt
docking_score_cutoff: !ii -1.0
max_num_poses_per_ligand: !ii 1
max_num_poses_total: !ii 1 #25 # Use 1 for CI
out:
- output_ligand_pdbqt_path: !& ligand_filter.pdbqt
- docking_scores: !& docking_scores
- experimental_dGs: !& dGs

gen_topol_params.wic:
in:
input_ligand_pdbqt_path: !* ligand_filter.pdbqt
# NOTE: input_receptor_xyz_path and input_top_zip_path are currently only necessary
# due to a limitation of the inlineing implementation.
input_receptor_xyz_path: !* receptor.xyz
input_top_zip_path: !* receptor.zip
scatter: [input_ligand_pdbqt_path]

stability.wic:
scatter: [crd_path, top_zip_path]
scatterMethod: dotproduct
in:
# NOTE: crd_path and top_zip_path are currently only necessary
# due to a limitation of the inlineing implementation.
crd_path: !* complex_vac.pdb
top_zip_path: !* complex_vac.zip
nsteps: !ii 100000
dt: !ii 0.002
temperature: !ii 298.0
pressure: !ii 1.0
autodock_vina_rescore.wic:
scatter: [input_pdb_path, input_ligand_pdb_path]
scatterMethod: dotproduct
in:
# NOTE: input_pdb_path is currently only necessary
# due to a limitation of the inlineing implementation.
input_pdb_path: !* prod.pdb
input_ligand_pdb_path: !* ligand_GMX.pdb

scatter_plot:
in:
xs: !* dGs
ys: !* docking_scores
ys2: !* docking_rescores
wic:
graphviz:
label: Virtual Screening Demo
steps:
(1, download_pdb.wic):
wic:
inlineable: False
(2, setup_pdb.wic):
wic:
inlineable: True
graphviz:
label: Setup PDB
(3, download_smiles_ligand_db.wic):
wic:
inlineable: True
(4, assign_partial_charges.wic):
wic:
inlineable: False
(5, autodock_vina_batch):
wic:
graphviz:
label: Docking
(6, split_pdbqt):
wic:
graphviz:
label: Extract Docking\nPoses
(7, duplicate):
wic:
graphviz:
label: Duplicate Receptor PDBQT
(8, autodock_vina_filter):
wic:
graphviz:
label: Apply Docking\nScore Cutoff
(9, gen_topol_params.wic):
wic:
inlineable: False
(10, stability.wic):
wic:
inlineable: False
steps:
(1, setup.wic):
wic:
steps:
(4, genion):
out:
- output_top_zip_path: !& genion_complex.zip
(2, basic.wic):
wic:
steps:
(3, prod.wic):
wic:
steps:
(2, grompp):
in:
input_top_zip_path: !* genion_complex.zip
(3, mdrun):
# NOTE: If there are multiple anchors / multiple outputs
# in the original source file, you must overload ALL of them.
# (because the entire list gets replaced)
out:
- output_crd_path: !& prod_complex.gro # overload prod.gro
- output_trr_path: !& prod.trr
- output_edr_path: !& prod.edr
(4, cwl_subinterpreter_analysis.wic):
wic:
implementation: complex
(3, analysis.wic):
wic:
steps:
(1, analysis_realtime.wic):
wic:
implementation: complex
(2, analysis_final.wic):
wic:
implementation: complex
(11, autodock_vina_rescore.wic):
wic:
inlineable: False
(12, scatter_plot):
wic:
graphviz:
label: Plot Experimental\nvs Predicted Binding
175 changes: 175 additions & 0 deletions virtual-screening/docking_autodock_vina_filter.wic
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Original file line number Diff line number Diff line change
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steps:
download_pdb.wic:
in:
#pdb_id: !ii 1r4l # ACE2
#pdb_id: !ii 1ntp # trypsin
pdb_id: !ii 1uao # chignolin (for speed)
#pdb_id: !ii 6us9 # Influenza A M2
#pdb_id: !ii 2rlf # Influenza A M2

setup_pdb.wic:
in:
input_pdb_path: !* protein.pdb
pdb_path: !ii pdb.pdbqt
box_path: !ii box.pdb
box_buffer: !ii 20 # Angstroms
water_type: !ii spce
forcefield: !ii amber99sb-ildn
out:
- pdb_path: !& pdb.pdbqt
- box_path: !& box.pdb
# For some reason, this step is not cached by --cachedir, but use it for the CI.
#- download_ligand_database_xlsx:
# in:
# database: !ii /ncats_target_based_curated.xlsx # SMACC ligand database
download_smiles_ligand_db.wic:
in:
path: !ii https://smacc.mml.unc.edu/ncats_target_based_curated.xlsx
# query syntax: `column name` 'column value'
query: !ii "`Standard Type` == 'Kd' and `duplicate-type-classifier` == 'unique'"
max_row: !ii 1 #25 # Use 1 for CI
smiles_column: !ii SMILES
binding_data_column: !ii Standard Value
convert_Kd_dG: !ii True
output_txt_path: !ii binding_data.txt
out:
- output_txt_path: !& binding_data.txt

ligand_modeling_docking.wic:
scatter: [sdf_path]
in:
# NOTE: sdf_path is currently only necessary
# due to a limitation of the inlineing implementation.
sdf_path: !* ligand_conformers.sdf

duplicate:
scatter: [input_pdbqt_array_path]
in:
input_pdbqt_singleton_path: !* pdb.pdbqt
input_pdbqt_array_path: !* ligand_nested_split.pdbqt
out:
- output_pdbqt_path: !& receptor_dup_2D.pdbqt

autodock_vina_filter:
in:
input_log_paths: !* vina.log # NOTE: plural
input_txt_path: !* binding_data.txt
docking_score_cutoff: !ii -1.0
max_num_poses_per_ligand: !ii 1
max_num_poses_total: !ii 1 #25 # Use 1 for CI
input_ligand_pdbqt_path: !* ligand_nested_split.pdbqt # 2D Array type
input_receptor_pdbqt_path: !* receptor_dup_2D.pdbqt
out:
- output_ligand_pdbqt_path: !& ligand_filter.pdbqt
- docking_scores: !& docking_scores
- experimental_dGs: !& dGs
gen_topol_params.wic:
in:
input_ligand_pdbqt_path: !* ligand_filter.pdbqt
# NOTE: input_receptor_xyz_path and input_top_zip_path are currently only necessary
# due to a limitation of the inlineing implementation.
input_receptor_xyz_path: !* receptor.xyz
input_top_zip_path: !* receptor.zip
scatter: [input_ligand_pdbqt_path]
stability.wic:
scatter: [crd_path, top_zip_path]
scatterMethod: dotproduct
in:
# NOTE: crd_path and top_zip_path are currently only necessary
# due to a limitation of the inlineing implementation.
crd_path: !* complex_vac.pdb
top_zip_path: !* complex_vac.zip
nsteps: !ii 100000
dt: !ii 0.002
temperature: !ii 298.0
pressure: !ii 1.0
autodock_vina_rescore.wic:
scatter: [input_pdb_path, input_ligand_pdb_path]
scatterMethod: dotproduct
in:
# NOTE: input_pdb_path is currently only necessary
# due to a limitation of the inlineing implementation.
input_pdb_path: !* prod.pdb
input_ligand_pdb_path: !* ligand_GMX.pdb
scatter_plot:
in:
xs: !* dGs
ys: !* docking_scores
ys2: !* docking_rescores

wic:
graphviz:
label: Virtual Screening Demo
steps:
(1, download_pdb.wic):
wic:
inlineable: False

(2, setup_pdb.wic):
wic:
inlineable: True
graphviz:
label: Setup PDB
(3, download_smiles_ligand_db.wic):
wic:
inlineable: True
(4, ligand_modeling_docking.wic):
wic:
inlineable: False
(5, duplicate):
wic:
graphviz:
label: Duplicate Receptor PDBQT
(6, autodock_vina_filter):
wic:
graphviz:
label: Apply Docking\nScore Cutoff
(7, gen_topol_params.wic):
wic:
inlineable: False
(8, stability.wic):
wic:
inlineable: False
steps:
(1, setup.wic):
wic:
steps:
(4, genion):
out:
- output_top_zip_path: !& genion_complex.zip
(2, basic.wic):
wic:
steps:
(3, prod.wic):
wic:
steps:
(2, grompp):
in:
input_top_zip_path: !* genion_complex.zip
(3, mdrun):
# NOTE: If there are multiple anchors / multiple outputs
# in the original source file, you must overload ALL of them.
# (because the entire list gets replaced)
out:
- output_crd_path: !& prod_complex.gro # overload prod.gro
- output_trr_path: !& prod.trr
- output_edr_path: !& prod.edr
(4, cwl_subinterpreter_analysis.wic):
wic:
implementation: complex
(3, analysis.wic):
wic:
steps:
(1, analysis_realtime.wic):
wic:
implementation: complex
(2, analysis_final.wic):
wic:
implementation: complex
(9, autodock_vina_rescore.wic):
wic:
inlineable: False
(10, scatter_plot):
wic:
graphviz:
label: Plot Experimental\nvs Predicted Binding
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