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Merge in COM/icolos from development to master * commit 'db781044d8efbba5e3f5a3f7d20fa136abc184ad': (36 commits) udpate changelog for 1.7 release fix some asserts in unit tests fix but in citation generator when no tty connected to process add serial partition for slurm execution bug fix in slurm executor when handling binary locations bug fix in slurm executor when handling binary locations bug fix in slurm executor small fix in pdb2gmx when parametrising multiple ligand components improvement for debug logging in pdb2gmx minor citation formatting changes additional papers for citation generator add initial citation generator + header art for stdout parametrise threads for gmx mmgbsa calculation under MPI fix syntax in water posre block for gromacs topol small formatting improvements for gromacs topol fixed some iterator-related issues with circular imports, small improvements to logging and gromacs topology handling small method name change for gromacs update example gromacs MD workflows final updates to gromacs classes Finalized "CCDC"/"Gold" initial implementation. ...
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| __pycache__ | ||
| pip-wheel-metadata | ||
| *.pyc | ||
| package.json | ||
| .vscode | ||
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| Original file line number | Diff line number | Diff line change |
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| { | ||
| "workflow": { | ||
| "header": { | ||
| "workflow_id": "Gold docking", | ||
| "description": "Runs docking using CCDC's GOLD and a pre-defined receptor file.", | ||
| "environment": { | ||
| "export": [ | ||
| ] | ||
| }, | ||
| "global_variables": { | ||
| "smiles": "another_mol:Nc1ccc(cc1N)C(F)(F)F;failure:CXXC;aspirin:O=C(C)Oc1ccccc1C(=O)O", | ||
| "cavity_mol2_path": "{package_dir}/../IcolosData/molecules/1UYD/PU8_reference_ligand.mol2", | ||
| "receptor_path": "{package_dir}/../IcolosData/Gold/1UYD_protein.mol2" | ||
| } | ||
| }, | ||
| "steps": [{ | ||
| "step_id": "rdkit_embedding", | ||
| "type": "embedding", | ||
| "settings": { | ||
| "arguments": { | ||
| "flags": ["-epik"], | ||
| "parameters": { | ||
| "protonate": true, | ||
| "method": "rdkit" | ||
| } | ||
| }, | ||
| "additional": { | ||
| } | ||
| }, | ||
| "input": { | ||
| "compounds": [{ | ||
| "source": "{smiles}", | ||
| "source_type": "string" | ||
| } | ||
| ] | ||
| } | ||
| }, { | ||
| "step_id": "Gold", | ||
| "type": "gold_docking", | ||
| "execution": { | ||
| "prefix_execution": "module load ccdc", | ||
| "parallelization": { | ||
| "cores": 4 | ||
| }, | ||
| "failure_policy": { | ||
| "n_tries": 3 | ||
| } | ||
| }, | ||
| "settings": { | ||
| "arguments": { | ||
| "flags": [], | ||
| "parameters": { | ||
| } | ||
| }, | ||
| "additional": { | ||
| "configuration": { | ||
| "AUTOMATIC SETTINGS": { | ||
| "autoscale": 0.5 | ||
| }, | ||
| "FLOOD FILL": { | ||
| "cavity_file": "{cavity_mol2_path}" | ||
| }, | ||
| "PROTEIN DATA": { | ||
| "protein_datafile": "{receptor_path}" | ||
| } | ||
| }, | ||
| "grid_ids": ["1UYD"] | ||
| } | ||
| }, | ||
| "input": { | ||
| "compounds": [{ | ||
| "source": "rdkit_embedding", | ||
| "source_type": "step" | ||
| } | ||
| ] | ||
| }, | ||
| "writeout": [ | ||
| { | ||
| "compounds": { | ||
| "category": "conformers" | ||
| }, | ||
| "destination": { | ||
| "resource": "{package_dir}/tests/junk/gold_docked_conformers.sdf", | ||
| "type": "file", | ||
| "format": "SDF" | ||
| } | ||
| }, | ||
| { | ||
| "compounds": { | ||
| "category": "conformers", | ||
| "selected_tags": ["docking_score", "grid_id"], | ||
| "aggregation": { | ||
| "mode": "best_per_compound", | ||
| "key": "docking_score", | ||
| "highest_is_best": true | ||
| } | ||
| }, | ||
| "destination": { | ||
| "resource": "{package_dir}/tests/junk/gold_docked_conformers.csv", | ||
| "type": "file", | ||
| "format": "CSV" | ||
| } | ||
| } | ||
| ] | ||
| } | ||
| ] | ||
| } | ||
| } |
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