├── .codecov.yml ├── .gitattributes ├── .github └── workflows │ └── ci.yaml ├── .gitignore ├── .lgtm.yml ├── .readthedocs.yml ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── LICENSE ├── LICENSE_DATA ├── MANIFEST.in ├── README.md ├── data ├── cdk2 │ ├── 00_data │ │ ├── ligands.yml │ │ └── target.yml │ ├── 01_protein │ │ └── crd │ │ │ └── protein.pdb │ ├── 02_ligands │ │ └── ligands.sdf │ └── 03_edges │ │ ├── kartograf_mapper_lomap_network.yml │ │ ├── kartograf_mapper_lomap_network_no_element_changes.yml │ │ ├── kartograf_mapper_mst_network.yml │ │ ├── kartograf_mapper_mst_network_no_element_changes.yml │ │ ├── kartograf_mapper_radial_network_element_changes.yml │ │ ├── kartograf_mapper_radial_network_no_element_changes.yml │ │ ├── lomap_mapper_lomap_network.yml │ │ ├── lomap_mapper_mst_network.yml │ │ └── lomap_mapper_mst_network_no_element_changes.yml ├── cdk8 │ ├── 00_data │ │ ├── ligands.yml │ │ └── target.yml │ ├── 01_protein │ │ └── crd │ │ │ └── protein.pdb │ ├── 02_ligands │ │ └── ligands.sdf │ └── 03_edges │ │ ├── kartograf_mapper_lomap_network.yml │ │ ├── kartograf_mapper_lomap_network_no_element_changes.yml │ │ ├── kartograf_mapper_mst_network.yml │ │ ├── kartograf_mapper_mst_network_no_element_changes.yml │ │ ├── kartograf_mapper_radial_network_element_changes.yml │ │ ├── kartograf_mapper_radial_network_no_element_changes.yml │ │ ├── lomap_mapper_lomap_network.yml │ │ ├── lomap_mapper_mst_network.yml │ │ └── lomap_mapper_mst_network_no_element_changes.yml ├── cmet │ ├── 00_data │ │ ├── ligands.yml │ │ └── target.yml │ ├── 01_protein │ │ └── crd │ │ │ └── protein.pdb │ ├── 02_ligands │ │ └── ligands.sdf │ └── 03_edges │ │ ├── kartograf_mapper_lomap_network.yml │ │ ├── kartograf_mapper_lomap_network_no_element_changes.yml │ │ ├── kartograf_mapper_mst_network.yml │ │ ├── kartograf_mapper_mst_network_no_element_changes.yml │ │ ├── kartograf_mapper_radial_network_element_changes.yml │ │ ├── kartograf_mapper_radial_network_no_element_changes.yml │ │ ├── lomap_mapper_lomap_network.yml │ │ ├── lomap_mapper_mst_network.yml │ │ └── lomap_mapper_mst_network_no_element_changes.yml ├── eg5 │ ├── 00_data │ │ ├── ligands.yml │ │ └── target.yml │ ├── 01_protein │ │ └── crd │ │ │ ├── cofactor.sdf │ │ │ └── protein.pdb │ ├── 02_ligands │ │ └── ligands.sdf │ └── 03_edges │ │ ├── kartograf_mapper_lomap_network.yml │ │ ├── kartograf_mapper_lomap_network_no_element_changes.yml │ │ ├── kartograf_mapper_mst_network.yml │ │ ├── kartograf_mapper_mst_network_no_element_changes.yml │ │ ├── kartograf_mapper_radial_network_element_changes.yml │ │ ├── kartograf_mapper_radial_network_no_element_changes.yml │ │ ├── lomap_mapper_lomap_network.yml │ │ ├── lomap_mapper_mst_network.yml │ │ └── lomap_mapper_mst_network_no_element_changes.yml ├── hif2a │ ├── 00_data │ │ ├── ligands.yml │ │ └── target.yml │ ├── 01_protein │ │ └── crd │ │ │ └── protein.pdb │ ├── 02_ligands │ │ └── ligands.sdf │ └── 03_edges │ │ ├── kartograf_mapper_lomap_network.yml │ │ ├── kartograf_mapper_lomap_network_no_element_changes.yml │ │ ├── kartograf_mapper_mst_network.yml │ │ ├── kartograf_mapper_mst_network_no_element_changes.yml │ │ ├── kartograf_mapper_radial_network_element_changes.yml │ │ ├── kartograf_mapper_radial_network_no_element_changes.yml │ │ ├── lomap_mapper_lomap_network.yml │ │ ├── lomap_mapper_mst_network.yml │ │ └── lomap_mapper_mst_network_no_element_changes.yml ├── mcl1 │ ├── 00_data │ │ ├── ligands.yml │ │ └── target.yml │ ├── 01_protein │ │ └── crd │ │ │ └── protein.pdb │ ├── 02_ligands │ │ └── ligands.sdf │ └── 03_edges │ │ ├── kartograf_mapper_lomap_network.yml │ │ ├── kartograf_mapper_lomap_network_no_element_changes.yml │ │ ├── kartograf_mapper_mst_network.yml │ │ ├── kartograf_mapper_mst_network_no_element_changes.yml │ │ ├── kartograf_mapper_radial_network_element_changes.yml │ │ ├── kartograf_mapper_radial_network_no_element_changes.yml │ │ ├── lomap_mapper_lomap_network.yml │ │ ├── lomap_mapper_mst_network.yml │ │ └── lomap_mapper_mst_network_no_element_changes.yml ├── p38 │ ├── 00_data │ │ ├── ligands.yml │ │ └── target.yml │ ├── 01_protein │ │ └── crd │ │ │ └── protein.pdb │ ├── 02_ligands │ │ └── ligands.sdf │ └── 03_edges │ │ ├── kartograf_mapper_lomap_network.yml │ │ ├── kartograf_mapper_lomap_network_no_element_changes.yml │ │ ├── kartograf_mapper_mst_network.yml │ │ ├── kartograf_mapper_mst_network_no_element_changes.yml │ │ ├── kartograf_mapper_radial_network_element_changes.yml │ │ ├── kartograf_mapper_radial_network_no_element_changes.yml │ │ ├── lomap_mapper_lomap_network.yml │ │ ├── lomap_mapper_mst_network.yml │ │ └── lomap_mapper_mst_network_no_element_changes.yml ├── pde2 │ ├── 00_data │ │ ├── ligands.yml │ │ └── target.yml │ ├── 01_protein │ │ └── crd │ │ │ └── protein.pdb │ ├── 02_ligands │ │ └── ligands.sdf │ └── 03_edges │ │ ├── kartograf_mapper_lomap_network.yml │ │ ├── kartograf_mapper_lomap_network_no_element_changes.yml │ │ ├── kartograf_mapper_mst_network.yml │ │ ├── kartograf_mapper_mst_network_no_element_changes.yml │ │ ├── kartograf_mapper_radial_network_element_changes.yml │ │ ├── kartograf_mapper_radial_network_no_element_changes.yml │ │ ├── lomap_mapper_lomap_network.yml │ │ ├── lomap_mapper_mst_network.yml │ │ └── lomap_mapper_mst_network_no_element_changes.yml ├── pfkfb3 │ ├── 00_data │ │ ├── ligands.yml │ │ └── target.yml │ ├── 01_protein │ │ └── crd │ │ │ ├── cofactor.sdf │ │ │ └── protein.pdb │ ├── 02_ligands │ │ └── ligands.sdf │ └── 03_edges │ │ ├── kartograf_mapper_lomap_network.yml │ │ ├── kartograf_mapper_lomap_network_no_element_changes.yml │ │ ├── kartograf_mapper_mst_network.yml │ │ ├── kartograf_mapper_mst_network_no_element_changes.yml │ │ ├── kartograf_mapper_radial_network_element_changes.yml │ │ ├── kartograf_mapper_radial_network_no_element_changes.yml │ │ ├── lomap_mapper_lomap_network.yml │ │ ├── lomap_mapper_mst_network.yml │ │ └── lomap_mapper_mst_network_no_element_changes.yml ├── ptp1b │ ├── 00_data │ │ ├── ligands.yml │ │ └── target.yml │ ├── 01_protein │ │ └── crd │ │ │ └── protein.pdb │ ├── 02_ligands │ │ └── ligands.sdf │ └── 03_edges │ │ ├── kartograf_mapper_lomap_network.yml │ │ ├── kartograf_mapper_lomap_network_no_element_changes.yml │ │ ├── kartograf_mapper_mst_network.yml │ │ ├── kartograf_mapper_mst_network_no_element_changes.yml │ │ ├── kartograf_mapper_radial_network_element_changes.yml │ │ ├── kartograf_mapper_radial_network_no_element_changes.yml │ │ ├── lomap_mapper_lomap_network.yml │ │ ├── lomap_mapper_mst_network.yml │ │ └── lomap_mapper_mst_network_no_element_changes.yml ├── shp2 │ ├── 00_data │ │ ├── ligands.yml │ │ └── target.yml │ ├── 01_protein │ │ └── crd │ │ │ └── protein.pdb │ ├── 02_ligands │ │ └── ligands.sdf │ └── 03_edges │ │ ├── kartograf_mapper_lomap_network.yml │ │ ├── kartograf_mapper_lomap_network_no_element_changes.yml │ │ ├── kartograf_mapper_mst_network.yml │ │ ├── kartograf_mapper_mst_network_no_element_changes.yml │ │ ├── kartograf_mapper_radial_network_element_changes.yml │ │ ├── kartograf_mapper_radial_network_no_element_changes.yml │ │ ├── lomap_mapper_lomap_network.yml │ │ ├── lomap_mapper_mst_network.yml │ │ └── lomap_mapper_mst_network_no_element_changes.yml ├── syk │ ├── 00_data │ │ ├── ligands.yml │ │ └── target.yml │ ├── 01_protein │ │ └── crd │ │ │ └── protein.pdb │ ├── 02_ligands │ │ └── ligands.sdf │ └── 03_edges │ │ ├── kartograf_mapper_lomap_network.yml │ │ ├── kartograf_mapper_lomap_network_no_element_changes.yml │ │ ├── kartograf_mapper_mst_network.yml │ │ ├── kartograf_mapper_mst_network_no_element_changes.yml │ │ ├── kartograf_mapper_radial_network_element_changes.yml │ │ ├── kartograf_mapper_radial_network_no_element_changes.yml │ │ ├── lomap_mapper_lomap_network.yml │ │ ├── lomap_mapper_mst_network.yml │ │ └── lomap_mapper_mst_network_no_element_changes.yml ├── targets.yml ├── thrombin │ ├── 00_data │ │ ├── ligands.yml │ │ └── target.yml │ ├── 01_protein │ │ └── crd │ │ │ └── protein.pdb │ ├── 02_ligands │ │ └── ligands.sdf │ └── 03_edges │ │ ├── kartograf_mapper_lomap_network.yml │ │ ├── kartograf_mapper_lomap_network_no_element_changes.yml │ │ ├── kartograf_mapper_mst_network.yml │ │ ├── kartograf_mapper_mst_network_no_element_changes.yml │ │ ├── kartograf_mapper_radial_network_element_changes.yml │ │ ├── kartograf_mapper_radial_network_no_element_changes.yml │ │ ├── lomap_mapper_lomap_network.yml │ │ ├── lomap_mapper_mst_network.yml │ │ └── lomap_mapper_mst_network_no_element_changes.yml ├── tnks2 │ ├── 00_data │ │ ├── ligands.yml │ │ └── target.yml │ ├── 01_protein │ │ └── crd │ │ │ └── protein.pdb │ ├── 02_ligands │ │ └── ligands.sdf │ └── 03_edges │ │ ├── kartograf_mapper_lomap_network.yml │ │ ├── kartograf_mapper_lomap_network_no_element_changes.yml │ │ ├── kartograf_mapper_mst_network.yml │ │ ├── kartograf_mapper_mst_network_no_element_changes.yml │ │ ├── kartograf_mapper_radial_network_element_changes.yml │ │ ├── kartograf_mapper_radial_network_no_element_changes.yml │ │ ├── lomap_mapper_lomap_network.yml │ │ ├── lomap_mapper_mst_network.yml │ │ └── lomap_mapper_mst_network_no_element_changes.yml └── tyk2 │ ├── 00_data │ ├── ligands.yml │ └── target.yml │ ├── 01_protein │ └── crd │ │ └── protein.pdb │ ├── 02_ligands │ └── ligands.sdf │ └── 03_edges │ ├── kartograf_mapper_lomap_network.yml │ ├── kartograf_mapper_lomap_network_no_element_changes.yml │ ├── kartograf_mapper_mst_network.yml │ ├── kartograf_mapper_mst_network_no_element_changes.yml │ ├── kartograf_mapper_radial_network_element_changes.yml │ ├── kartograf_mapper_radial_network_no_element_changes.yml │ ├── lomap_mapper_lomap_network.yml │ ├── lomap_mapper_mst_network.yml │ └── lomap_mapper_mst_network_no_element_changes.yml ├── docs ├── Makefile ├── README.md ├── _config.yml ├── _static │ └── README.md ├── _templates │ └── README.md ├── api.rst ├── conf.py ├── contributions.rst ├── data.rst ├── examples │ └── 01-protein-ligand-benchmark.ipynb ├── figures │ └── examples_graph.png ├── file_tree.txt ├── index.rst ├── install.rst └── make.bat ├── environment.yml ├── examples ├── Edges.ipynb └── Ligands.ipynb ├── plbenchmark ├── __init__.py ├── _version.py ├── edges.py ├── ligands.py ├── metadata.py ├── sample_data │ ├── 2020-08-26_mcl1_sample │ │ ├── 00_data │ │ │ ├── edges.yml │ │ │ ├── ligands.yml │ │ │ └── target.yml │ │ ├── 01_protein │ │ │ └── crd │ │ │ │ └── protein.pdb │ │ └── 02_ligands │ │ │ ├── lig_23 │ │ │ └── crd │ │ │ │ └── lig_23.sdf │ │ │ ├── lig_26 │ │ │ └── crd │ │ │ │ └── lig_26.sdf │ │ │ ├── lig_27 │ │ │ └── crd │ │ │ │ └── lig_27.sdf │ │ │ ├── lig_28 │ │ │ └── crd │ │ │ │ └── lig_28.sdf │ │ │ ├── lig_29 │ │ │ └── crd │ │ │ │ └── lig_29.sdf │ │ │ ├── lig_30 │ │ │ └── crd │ │ │ │ └── lig_30.sdf │ │ │ ├── lig_31 │ │ │ └── crd │ │ │ │ └── lig_31.sdf │ │ │ ├── lig_32 │ │ │ └── crd │ │ │ │ └── lig_32.sdf │ │ │ ├── lig_33 │ │ │ └── crd │ │ │ │ └── lig_33.sdf │ │ │ ├── lig_34 │ │ │ └── crd │ │ │ │ └── lig_34.sdf │ │ │ ├── lig_35 │ │ │ └── crd │ │ │ │ └── lig_35.sdf │ │ │ ├── lig_36 │ │ │ └── crd │ │ │ │ └── lig_36.sdf │ │ │ ├── lig_37 │ │ │ └── crd │ │ │ │ └── lig_37.sdf │ │ │ ├── lig_38 │ │ │ └── crd │ │ │ │ └── lig_38.sdf │ │ │ └── lig_39 │ │ │ └── crd │ │ │ └── lig_39.sdf │ └── targets.yml ├── targets.py ├── tests │ ├── __init__.py │ ├── test_PLBenchmarks.py │ ├── test_edges.py │ ├── test_ligands.py │ ├── test_targets.py │ └── test_utils.py └── utils.py ├── preparation ├── cli-commands.txt ├── docking │ ├── glide-dock_SP_CDK2 │ │ ├── glide-dock_SP_CDK2.in │ │ ├── glide-dock_SP_CDK2.reflig.maegz │ │ └── glide-dock_SP_CDK2.sh │ ├── glide-dock_SP_CDK8 │ │ ├── glide-dock_SP_CDK8.in │ │ ├── glide-dock_SP_CDK8.reflig.maegz │ │ └── glide-dock_SP_CDK8.sh │ ├── glide-dock_SP_EG5 │ │ ├── glide-dock_SP_EG5.in │ │ ├── glide-dock_SP_EG5.reflig.maegz │ │ └── glide-dock_SP_EG5.sh │ ├── glide-dock_SP_HIF2a │ │ ├── glide-dock_SP_HIF2a.in │ │ ├── glide-dock_SP_HIF2a.reflig.maegz │ │ └── glide-dock_SP_HIF2a.sh │ ├── glide-dock_SP_MCL1 │ │ ├── glide-dock_SP_MCL1.in │ │ ├── glide-dock_SP_MCL1.reflig.maegz │ │ └── glide-dock_SP_MCL1.sh │ ├── glide-dock_SP_P38 │ │ ├── glide-dock_SP_P38.in │ │ ├── glide-dock_SP_P38.reflig.maegz │ │ └── glide-dock_SP_P38.sh │ ├── glide-dock_SP_PDE2 │ │ ├── glide-dock_SP_PDE2.in │ │ ├── glide-dock_SP_PDE2.reflig.maegz │ │ └── glide-dock_SP_PDE2.sh │ ├── glide-dock_SP_PFKFB3 │ │ ├── glide-dock_SP_PFKFB3.in │ │ ├── glide-dock_SP_PFKFB3.reflig.maegz │ │ └── glide-dock_SP_PFKFB3.sh │ ├── glide-dock_SP_PTP1B │ │ ├── glide-dock_SP_PTP1B.in │ │ ├── glide-dock_SP_PTP1B.reflig.maegz │ │ └── glide-dock_SP_PTP1B.sh │ ├── glide-dock_SP_SHP2 │ │ ├── glide-dock_SP_SHP2.in │ │ ├── glide-dock_SP_SHP2.reflig.maegz │ │ └── glide-dock_SP_SHP2.sh │ ├── glide-dock_SP_SYK │ │ ├── glide-dock_SP_SYK.in │ │ ├── glide-dock_SP_SYK.reflig.maegz │ │ └── glide-dock_SP_SYK.sh │ ├── glide-dock_SP_TNKS2 │ │ ├── glide-dock_SP_TNKS2.in │ │ ├── glide-dock_SP_TNKS2.reflig.maegz │ │ └── glide-dock_SP_TNKS2.sh │ ├── glide-dock_SP_TYK2 │ │ ├── glide-dock_SP_TYK2.in │ │ ├── glide-dock_SP_TYK2.reflig.maegz │ │ └── glide-dock_SP_TYK2.sh │ ├── glide-dock_SP_cMET │ │ ├── glide-dock_SP_cMET.in │ │ ├── glide-dock_SP_cMET.reflig.maegz │ │ └── glide-dock_SP_cMET.sh │ └── glide-dock_SP_thrombin │ │ ├── glide-dock_SP_thrombin.in │ │ ├── glide-dock_SP_thrombin.reflig.maegz │ │ └── glide-dock_SP_thrombin.sh ├── glide-grids │ ├── glide-grid_CDK2-1H1Q │ │ ├── glide-grid_CDK2-1H1Q.in │ │ ├── glide-grid_CDK2-1H1Q.maegz │ │ └── glide-grid_CDK2-1H1Q.sh │ ├── glide-grid_CDK8-5HNB │ │ ├── glide-grid_CDK8-5HNB.in │ │ ├── glide-grid_CDK8-5HNB.maegz │ │ └── glide-grid_CDK8-5HNB.sh │ ├── glide-grid_EG5-3L9H │ │ ├── glide-grid_EG5-3L9H.in │ │ ├── glide-grid_EG5-3L9H.maegz │ │ └── glide-grid_EG5-3L9H.sh │ ├── glide-grid_HIF2a-5TBM │ │ ├── glide-grid_HIF2a-5TBM.in │ │ ├── glide-grid_HIF2a-5TBM.maegz │ │ └── glide-grid_HIF2a-5TBM.sh │ ├── glide-grid_MCL1-4HW3 │ │ ├── glide-grid_MCL1-4HW3.in │ │ ├── glide-grid_MCL1-4HW3.maegz │ │ └── glide-grid_MCL1-4HW3.sh │ ├── glide-grid_P38-3FLY │ │ ├── glide-grid_P38-3FLY.in │ │ ├── glide-grid_P38-3FLY.maegz │ │ └── glide-grid_P38-3FLY.sh │ ├── glide-grid_PDE2-4D08 │ │ ├── glide-grid_PDE2-4D08.in │ │ ├── glide-grid_PDE2-4D08.maegz │ │ └── glide-grid_PDE2-4D08.sh │ ├── glide-grid_PFKFB3-6HVI │ │ ├── glide-grid_PFKFB3-6HVI.in │ │ ├── glide-grid_PFKFB3-6HVI.maegz │ │ └── glide-grid_PFKFB3-6HVI.sh │ ├── glide-grid_PTP1B-2QBS │ │ ├── glide-grid_PTP1B-2QBS.in │ │ ├── glide-grid_PTP1B-2QBS.maegz │ │ └── glide-grid_PTP1B-2QBS.sh │ ├── glide-grid_SHP2-5EHR │ │ ├── glide-grid_SHP2-5EHR.in │ │ ├── glide-grid_SHP2-5EHR.maegz │ │ └── glide-grid_SHP2-5EHR.sh │ ├── glide-grid_SYK-4PV0 │ │ ├── glide-grid_SYK-4PV0.in │ │ ├── glide-grid_SYK-4PV0.maegz │ │ └── glide-grid_SYK-4PV0.sh │ ├── glide-grid_TNKS2-4UI5 │ │ ├── glide-grid_TNKS2-4UI5.in │ │ ├── glide-grid_TNKS2-4UI5.maegz │ │ └── glide-grid_TNKS2-4UI5.sh │ ├── glide-grid_TYK2-4GIH │ │ ├── glide-grid_TYK2-4GIH.in │ │ ├── glide-grid_TYK2-4GIH.maegz │ │ └── glide-grid_TYK2-4GIH.sh │ ├── glide-grid_cMET-4R1Y │ │ ├── glide-grid_cMET-4R1Y.in │ │ ├── glide-grid_cMET-4R1Y.maegz │ │ └── glide-grid_cMET-4R1Y.sh │ ├── glide-grid_galectin-5E89 │ │ ├── glide-grid_galectin-5E89.in │ │ ├── glide-grid_galectin-5E89.maegz │ │ └── glide-grid_galectin-5E89.sh │ └── glide-grid_thrombin-2ZFF │ │ ├── glide-grid_thrombin-2ZFF.in │ │ ├── glide-grid_thrombin-2ZFF.maegz │ │ └── glide-grid_thrombin-2ZFF.sh ├── ligand-prep │ ├── ligprep_cdk2 │ │ ├── ligprep_cdk2.inp │ │ ├── ligprep_cdk2.sh │ │ └── ligprep_cdk2.smi │ ├── ligprep_cdk8 │ │ ├── ligprep_cdk8.inp │ │ ├── ligprep_cdk8.sh │ │ └── ligprep_cdk8.smi │ ├── ligprep_cmet │ │ ├── ligprep_cmet.inp │ │ ├── ligprep_cmet.sh │ │ └── ligprep_cmet.smi │ ├── ligprep_eg5 │ │ ├── ligprep_eg5.inp │ │ ├── ligprep_eg5.sh │ │ └── ligprep_eg5.smi │ ├── ligprep_hif2a │ │ ├── ligprep_hif2a.inp │ │ ├── ligprep_hif2a.sh │ │ └── ligprep_hif2a.smi │ ├── ligprep_jnk1 │ │ ├── ligprep_jnk1.inp │ │ ├── ligprep_jnk1.sh │ │ └── ligprep_jnk1.smi │ ├── ligprep_mcl1 │ │ ├── ligprep_mcl1.inp │ │ ├── ligprep_mcl1.sh │ │ └── ligprep_mcl1.smi │ ├── ligprep_p38 │ │ ├── ligprep_p38.inp │ │ ├── ligprep_p38.sh │ │ └── ligprep_p38.smi │ ├── ligprep_pde2 │ │ ├── ligprep_pde2.inp │ │ ├── ligprep_pde2.sh │ │ └── ligprep_pde2.smi │ ├── ligprep_pfkfb3 │ │ ├── ligprep_pfkfb3.inp │ │ ├── ligprep_pfkfb3.sh │ │ └── ligprep_pfkfb3.smi │ ├── ligprep_ptp1b │ │ ├── ligprep_ptp1b.inp │ │ ├── ligprep_ptp1b.sh │ │ └── ligprep_ptp1b.smi │ ├── ligprep_shp2 │ │ ├── ligprep_shp2.inp │ │ ├── ligprep_shp2.sh │ │ └── ligprep_shp2.smi │ ├── ligprep_syk │ │ ├── ligprep_syk.inp │ │ ├── ligprep_syk.sh │ │ └── ligprep_syk.smi │ ├── ligprep_thrombin_recurated │ │ ├── ligprep_thrombin_recurated.csv │ │ ├── ligprep_thrombin_recurated.inp │ │ └── ligprep_thrombin_recurated.sh │ ├── ligprep_tnks2 │ │ ├── ligprep_tnks2.inp │ │ ├── ligprep_tnks2.sh │ │ └── ligprep_tnks2.smi │ └── ligprep_tyk2 │ │ ├── ligprep_tyk2.inp │ │ ├── ligprep_tyk2.sh │ │ └── ligprep_tyk2.smi ├── mappers │ └── perses-mapper.py └── prep-methods.pdf ├── setup.cfg ├── setup.py └── versioneer.py /.codecov.yml: -------------------------------------------------------------------------------- 1 | # Codecov configuration to make it a bit less noisy 2 | coverage: 3 | status: 4 | patch: false 5 | project: 6 | default: 7 | threshold: 50% 8 | comment: 9 | layout: "header" 10 | require_changes: false 11 | branches: null 12 | behavior: default 13 | flags: null 14 | paths: null 15 | 16 | ignore: 17 | - "plbenchmark/tests/" # ignore test files 18 | - "plbenchmark/sample_data" # ignore sample data 19 | - "plbenchmark/_version.py" 20 | 21 | -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/.gitattributes -------------------------------------------------------------------------------- /.github/workflows/ci.yaml: -------------------------------------------------------------------------------- 1 | name: "CI" 2 | on: 3 | pull_request: 4 | branches: 5 | - main 6 | push: 7 | branches: 8 | - main 9 | schedule: 10 | # At 07:00 UTC on Monday and Thursday. 11 | - cron: "0 7 * * 1,4" 12 | 13 | concurrency: 14 | # Cancel out any previous workflows within the same PR 15 | group: "${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}" 16 | cancel-in-progress: True 17 | 18 | defaults: 19 | run: 20 | shell: bash -l {0} 21 | 22 | jobs: 23 | tests: 24 | if: "github.repository == 'openforcefield/protein-ligand-benchmark'" 25 | runs-on: ${{ matrix.OS }}-latest 26 | name: "tests" 27 | strategy: 28 | fail-fast: False 29 | matrix: 30 | os: ['ubuntu', 'macos'] 31 | python-versions: [3.8, 3.9] 32 | 33 | steps: 34 | - uses: actions/checkout@v3 35 | 36 | - uses: conda-incubator/setup-miniconda@v2 37 | with: 38 | auto-update-conda: True 39 | use-mamba: True 40 | python-version: ${{ matrix.python-version }} 41 | miniforge-variant: Mambaforge 42 | environment-file: environment.yml 43 | activate-environment: plbenchmark 44 | 45 | - name: "install" 46 | run: python setup.py develop --no-deps 47 | 48 | - name: "test imports" 49 | run: | 50 | python -Ic "import plbenchmark" 51 | 52 | - name: "environment information" 53 | run: | 54 | mamba info -a 55 | mamba list 56 | 57 | - name: "run tests" 58 | run: | 59 | pytest -v --nbval-lax --cov=plbenchmark --cov-report=xml plbenchmark/tests/ examples/ docs/examples/ 60 | 61 | - name: "codecov" 62 | if: "github.event != 'schedule'" 63 | uses: codecov/codecov-action@v2 64 | with: 65 | token: ${{ secrets.CODECOV_TOKEN }} 66 | file: coverage.xml 67 | fail_ci_if_error: True 68 | verbose: True 69 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | *$py.class 5 | 6 | # C extensions 7 | *.so 8 | 9 | # Distribution / packaging 10 | .Python 11 | env/ 12 | build/ 13 | develop-eggs/ 14 | dist/ 15 | downloads/ 16 | eggs/ 17 | .eggs/ 18 | lib/ 19 | lib64/ 20 | parts/ 21 | sdist/ 22 | var/ 23 | wheels/ 24 | *.egg-info/ 25 | .installed.cfg 26 | *.egg 27 | 28 | # PyInstaller 29 | # Usually these files are written by a python script from a template 30 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 31 | *.manifest 32 | *.spec 33 | 34 | # Installer logs 35 | pip-log.txt 36 | pip-delete-this-directory.txt 37 | 38 | # Unit test / coverage reports 39 | htmlcov/ 40 | .tox/ 41 | .coverage 42 | .coverage.* 43 | .cache 44 | .pytest_cache 45 | nosetests.xml 46 | coverage.xml 47 | *.cover 48 | .hypothesis/ 49 | 50 | # Translations 51 | *.mo 52 | *.pot 53 | 54 | # Django stuff: 55 | *.log 56 | local_settings.py 57 | 58 | # Flask stuff: 59 | instance/ 60 | .webassets-cache 61 | 62 | # Scrapy stuff: 63 | .scrapy 64 | 65 | # Sphinx documentation 66 | docs/_build/ 67 | 68 | # PyBuilder 69 | target/ 70 | 71 | # Jupyter Notebook 72 | .ipynb_checkpoints 73 | 74 | # pyenv 75 | .python-version 76 | 77 | # celery beat schedule file 78 | celerybeat-schedule 79 | 80 | # SageMath parsed files 81 | *.sage.py 82 | 83 | # dotenv 84 | .env 85 | 86 | # virtualenv 87 | .venv 88 | venv/ 89 | ENV/ 90 | 91 | # Spyder project settings 92 | .spyderproject 93 | .spyproject 94 | 95 | # Rope project settings 96 | .ropeproject 97 | 98 | # mkdocs documentation 99 | /site 100 | 101 | # mypy 102 | .mypy_cache/ 103 | 104 | # MacOS 105 | *.DS_Store 106 | 107 | #*# 108 | *~ 109 | *# 110 | 111 | mdout.mdp 112 | tpr.tpr 113 | -------------------------------------------------------------------------------- /.lgtm.yml: -------------------------------------------------------------------------------- 1 | # Configure LGTM for this package 2 | 3 | extraction: 4 | python: # Configure Python 5 | python_setup: # Configure the setup 6 | version: 3 # Specify Version 3 7 | path_classifiers: 8 | library: 9 | - versioneer.py # Set Versioneer.py to an external "library" (3rd party code) 10 | generated: 11 | - plbenchmark/_version.py 12 | test: 13 | - "plbenchmark/tests/*.py" 14 | docs: 15 | - docs 16 | -------------------------------------------------------------------------------- /.readthedocs.yml: -------------------------------------------------------------------------------- 1 | # .readthedocs.yml 2 | # Read the Docs configuration file 3 | # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details 4 | 5 | # Required 6 | version: 2 7 | 8 | # Build documentation in the docs/ directory with Sphinx 9 | sphinx: 10 | configuration: docs/conf.py 11 | 12 | # Build documentation with MkDocs 13 | #mkdocs: 14 | # configuration: mkdocs.yml 15 | 16 | # Optionally build your docs in additional formats such as PDF and ePub 17 | formats: all 18 | 19 | python: 20 | version: 3.8 21 | 22 | conda: 23 | environment: environment.yml 24 | -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- 1 | cff-version: 1.2.0 2 | title: 'Protein-Ligand Benchmark Dataset for Free Energy Calculations' 3 | message: "If you use this software, please cite both the article from preferred-citation and the software itself." 4 | type: dataset 5 | authors: 6 | - given-names: David F. 7 | family-names: Hahn 8 | email: dhahn3@its.jnj.com 9 | affiliation: "Computational Chemistry, Janssen Research & Development" 10 | orcid: 'https://orcid.org/0000-0003-2830-6880' 11 | - given-names: Jeffrey R. 12 | family-names: Wagner 13 | affiliation: "Software Scientist, Open Force Field Initiative" 14 | orcid: 'https://orcid.org/0000-0001-6448-0873' 15 | preferred-citation: 16 | title: "Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks." 17 | authors: 18 | - given-names: David F. 19 | family-names: Hahn 20 | email: dhahn3@its.jnj.com 21 | affiliation: "Computational Chemistry, Janssen Research & Development" 22 | orcid: 'https://orcid.org/0000-0003-2830-6880' 23 | - given-names: Christopher I. 24 | family-names: Bayly 25 | affiliation: OpenEye Scientific Software 26 | orcid: 'https://orcid.org/0000-0001-9145-6457' 27 | - given-names: Hannah E. 28 | family-names: Bruce Macdonald 29 | orcid: 'https://orcid.org/0000-0002-5562-6866' 30 | - given-names: John D. 31 | family-names: Chodera 32 | email: john.chodera@choderalab.org 33 | orcid: 'https://orcid.org/0000-0003-0542-119X' 34 | affiliation: "Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center" 35 | - given-names: Vytautas 36 | family-names: Gapsys 37 | orcid: 'https://orcid.org/0000-0002-6761-7780' 38 | - given-names: Antonia S. J. S. 39 | family-names: Mey 40 | orcid: 'https://orcid.org/0000-0001-7512-5252' 41 | - given-names: David L. 42 | family-names: Mobley 43 | affiliation: "Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine." 44 | orcid: 'https://orcid.org/0000-0002-1083-5533' 45 | - given-names: Laura 46 | family-names: Perez Benito 47 | orcid: 'https://orcid.org/0000-0001-9607-9048' 48 | - given-names: Christina E. M. 49 | family-names: Schindler 50 | - given-names: Gary 51 | family-names: Tresadern 52 | orcid: 'https://orcid.org/0000-0002-4801-1644' 53 | - given-names: Gregory L. 54 | family-names: Warren 55 | orcid: 'https://orcid.org/0000-0003-4017-0162' 56 | type: article 57 | repository-code: "https://github.com/openforcefield/protein-ligand-benchmark" 58 | doi: 10.5281/zenodo.4813735 59 | -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- 1 | # Contributor Covenant Code of Conduct 2 | 3 | ## Our Pledge 4 | 5 | In the interest of fostering an open and welcoming environment, we as 6 | contributors and maintainers pledge to making participation in our project and 7 | our community a harassment-free experience for everyone, regardless of age, 8 | body size, disability, ethnicity, gender identity and expression, level of 9 | experience, nationality, personal appearance, race, religion, or sexual 10 | identity and orientation. 11 | 12 | ## Our Standards 13 | 14 | Examples of behavior that contributes to creating a positive environment include: 15 | 16 | * Using welcoming and inclusive language 17 | * Being respectful of differing viewpoints and experiences 18 | * Gracefully accepting constructive criticism 19 | * Focusing on what is best for the community 20 | * Showing empathy towards other community members 21 | 22 | Examples of unacceptable behavior by participants include: 23 | 24 | * The use of sexualized language or imagery and unwelcome sexual attention or advances 25 | * Trolling, insulting/derogatory comments, and personal or political attacks 26 | * Public or private harassment 27 | * Publishing others' private information, such as a physical or electronic address, without explicit permission 28 | * Other conduct which could reasonably be considered inappropriate in a professional setting 29 | 30 | ## Our Responsibilities 31 | 32 | Project maintainers are responsible for clarifying the standards of acceptable 33 | behavior and are expected to take appropriate and fair corrective action in 34 | response to any instances of unacceptable behavior. 35 | 36 | Project maintainers have the right and responsibility to remove, edit, or 37 | reject comments, commits, code, wiki edits, issues, and other contributions 38 | that are not aligned to this Code of Conduct, or to ban temporarily or 39 | permanently any contributor for other behaviors that they deem inappropriate, 40 | threatening, offensive, or harmful. 41 | 42 | Moreover, project maintainers will strive to offer feedback and advice to 43 | ensure quality and consistency of contributions to the code. Contributions 44 | from outside the group of project maintainers are strongly welcomed but the 45 | final decision as to whether commits are merged into the codebase rests with 46 | the team of project maintainers. 47 | 48 | ## Scope 49 | 50 | This Code of Conduct applies both within project spaces and in public spaces 51 | when an individual is representing the project or its community. Examples of 52 | representing a project or community include using an official project e-mail 53 | address, posting via an official social media account, or acting as an 54 | appointed representative at an online or offline event. Representation of a 55 | project may be further defined and clarified by project maintainers. 56 | 57 | ## Enforcement 58 | 59 | Instances of abusive, harassing, or otherwise unacceptable behavior may be 60 | reported by contacting the project team at 'davidfriedrichhahn@gmail.com'. The project team will 61 | review and investigate all complaints, and will respond in a way that it deems 62 | appropriate to the circumstances. The project team is obligated to maintain 63 | confidentiality with regard to the reporter of an incident. Further details of 64 | specific enforcement policies may be posted separately. 65 | 66 | Project maintainers who do not follow or enforce the Code of Conduct in good 67 | faith may face temporary or permanent repercussions as determined by other 68 | members of the project's leadership. 69 | 70 | ## Attribution 71 | 72 | This Code of Conduct is adapted from the [Contributor Covenant][homepage], 73 | version 1.4, available at 74 | [http://contributor-covenant.org/version/1/4][version] 75 | 76 | [homepage]: http://contributor-covenant.org 77 | [version]: http://contributor-covenant.org/version/1/4/ 78 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | 2 | MIT License 3 | 4 | Copyright (c) 2019 David F. Hahn 5 | 6 | Permission is hereby granted, free of charge, to any person obtaining a copy 7 | of this software and associated documentation files (the "Software"), to deal 8 | in the Software without restriction, including without limitation the rights 9 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 10 | copies of the Software, and to permit persons to whom the Software is 11 | furnished to do so, subject to the following conditions: 12 | 13 | The above copyright notice and this permission notice shall be included in all 14 | copies or substantial portions of the Software. 15 | 16 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 17 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 18 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 19 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 20 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 21 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 22 | SOFTWARE. 23 | -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include LICENSE 2 | include MANIFEST.in 3 | include versioneer.py 4 | 5 | graft plbenchmark 6 | prune plbenchmark/data 7 | global-exclude *.py[cod] __pycache__ *.so -------------------------------------------------------------------------------- /data/cdk2/00_data/ligands.yml: -------------------------------------------------------------------------------- 1 | lig_17: 2 | measurement: 3 | comment: Table 2, entry 17 4 | doi: 10.1021/jm0311442 5 | error: 4.8 6 | type: ic50 7 | unit: uM 8 | value: 6.8 9 | name: lig_17 10 | smiles: '[H][C]1=[N][C]2=[C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])[N]=[C]([N]([H])[C]3=[C]([H])[C]([H])=[C]([H])[C]([Br])=[C]3[H])[N]=[C]2[N]1[H]' 11 | lig_1h1q: 12 | measurement: 13 | comment: Table 2, entry 2 14 | doi: 10.1021/jm0311442 15 | error: 0.03 16 | type: ic50 17 | unit: uM 18 | value: 0.97 19 | name: lig_1h1q 20 | smiles: '[H][C]1=[N][C]2=[C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])[N]=[C]([N]([H])[C]3=[C]([H])[C]([H])=[C]([H])[C]([H])=[C]3[H])[N]=[C]2[N]1[H]' 21 | lig_1h1r: 22 | measurement: 23 | comment: Table 2, entry 15 24 | doi: 10.1021/jm0311442 25 | error: 0.3 26 | type: ic50 27 | unit: uM 28 | value: 2.3 29 | name: lig_1h1r 30 | smiles: '[H]c1c(c(c(c(c1[H])Cl)[H])N([H])c2nc3c(c(n2)OC([H])([H])C4(C(C(C(C(C4([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])N=C(N3[H])[H])[H]' 31 | lig_1oi9: 32 | measurement: 33 | comment: Table 2, entry 25 34 | doi: 10.1021/jm0311442 35 | error: 0.001 36 | type: ic50 37 | unit: uM 38 | value: 0.069 39 | name: lig_1oi9 40 | smiles: '[H][O][C]1=[C]([H])[C]([H])=[C]([N]([H])[C]2=[N][C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])=[C]3[N]=[C]([H])[N]([H])[C]3=[N]2)[C]([H])=[C]1[H]' 41 | lig_1oiu: 42 | measurement: 43 | comment: Table 3, entry 3 44 | doi: 10.1021/jm0311442 45 | error: 0.04 46 | type: ic50 47 | unit: uM 48 | value: 0.21 49 | name: lig_1oiu 50 | smiles: '[H][C]1=[N][C]2=[C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])[N]=[C]([N]([H])[C]3=[C]([H])[C]([S](=[O])(=[O])[N]([H])[H])=[C]([H])[C]([H])=[C]3[H])[N]=[C]2[N]1[H]' 51 | lig_1oiy: 52 | measurement: 53 | comment: Table 3, entry 34 54 | doi: 10.1021/jm0311442 55 | error: 0.033 56 | type: ic50 57 | unit: uM 58 | value: 0.064 59 | name: lig_1oiy 60 | smiles: '[H][C]1=[N][C]2=[C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])[N]=[C]([N]([H])[C]3=[C]([H])[C]([H])=[C]([C](=[O])[N]([H])[H])[C]([H])=[C]3[H])[N]=[C]2[N]1[H]' 61 | lig_20: 62 | measurement: 63 | comment: Table 2, entry 20 64 | doi: 10.1021/jm0311442 65 | error: 0.1 66 | type: ic50 67 | unit: uM 68 | value: 0.4 69 | name: lig_20 70 | smiles: '[H][O][C]([H])([H])[C]1=[C]([H])[C]([H])=[C]([H])[C]([N]([H])[C]2=[N][C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])=[C]3[N]=[C]([H])[N]([H])[C]3=[N]2)=[C]1[H]' 71 | lig_21: 72 | measurement: 73 | comment: Table 2, entry 21 74 | doi: 10.1021/jm0311442 75 | error: 0.2 76 | type: ic50 77 | unit: uM 78 | value: 1.8 79 | name: lig_21 80 | smiles: '[H][C]1=[N][C]2=[C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])[N]=[C]([N]([H])[C]3=[C]([H])[C]([H])=[C]([H])[C]([O][C]([H])([H])[H])=[C]3[H])[N]=[C]2[N]1[H]' 81 | lig_22: 82 | measurement: 83 | comment: Table 2, entry 22 84 | doi: 10.1021/jm0311442 85 | error: 0.1 86 | type: ic50 87 | unit: uM 88 | value: 1.7 89 | name: lig_22 90 | smiles: '[H][C]1=[N][C]2=[C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])[N]=[C]([N]([H])[C]3=[C]([H])[C]([H])=[C]([H])[C]([S][C]([H])([H])[H])=[C]3[H])[N]=[C]2[N]1[H]' 91 | lig_26: 92 | measurement: 93 | comment: Table 2, entry 26 94 | doi: 10.1021/jm0311442 95 | error: 0.03 96 | type: ic50 97 | unit: uM 98 | value: 0.65 99 | name: lig_26 100 | smiles: '[H][C]1=[N][C]2=[C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])[N]=[C]([N]([H])[C]3=[C]([H])[C]([H])=[C]([O][C]([H])([H])[H])[C]([H])=[C]3[H])[N]=[C]2[N]1[H]' 101 | -------------------------------------------------------------------------------- /data/cdk2/00_data/target.yml: -------------------------------------------------------------------------------- 1 | alternate: 2 | iridium_classifier: HT 3 | iridium_score: 0.31 4 | pdb: 3DDQ 5 | associated_sets: 6 | - Schrodinger JACS 7 | comments: '' 8 | date: 2019-12-13 9 | dpi: 0.28 10 | id: 6 11 | iridium_classifier: MT 12 | iridium_score: 0.87 13 | name: cdk2 14 | netcharge: -2 e 15 | pdb: 1H1Q 16 | references: 17 | calculation: 18 | - 10.1021/ja512751q 19 | - 10.1021/acs.jcim.9b00105 20 | - 10.1039/C9SC03754C 21 | measurement: 22 | - 10.1021/ci5004027 23 | -------------------------------------------------------------------------------- /data/cdk8/00_data/target.yml: -------------------------------------------------------------------------------- 1 | alternate: 2 | iridium_classifier: HT 3 | iridium_score: 0.33 4 | pdb: 5XS2 5 | associated_sets: 6 | - Merck KGgA fep-benchmark 7 | comments: 8 | - ligands with different net charges 9 | date: 2020-07-01 10 | dpi: 0.22 11 | id: 15 12 | iridium_classifier: MT 13 | iridium_score: 0.74 14 | name: cdk8 15 | netcharge: null 16 | pdb: 5HNB 17 | references: 18 | calculation: null 19 | measurement: null 20 | -------------------------------------------------------------------------------- /data/cmet/00_data/ligands.yml: -------------------------------------------------------------------------------- 1 | lig_CHEMBL3402744_300_4: 2 | charge: 0.0 3 | measurement: 4 | doi: 5 | - 10.1016/j.bmcl.2015.02.002 6 | error: -1 7 | type: ic50 8 | unit: nM 9 | value: 300 10 | name: lig_CHEMBL3402744_300_4 11 | smiles: '[H][C]1=[C]([H])[C]([c]2[c]([H])[c]([F])[c]([H])[c]([F])[c]2[H])=[N][N]([C]([H])([H])[c]2[c]([H])[c]([H])[c]([H])[c]([N]([H])[C](=[O])[O][C]([H])([H])[H])[c]2[H])[C]1=[O]' 12 | lig_CHEMBL3402745_200_5: 13 | charge: 0.0 14 | measurement: 15 | doi: 16 | - 10.1016/j.bmcl.2015.02.002 17 | error: -1 18 | type: ic50 19 | unit: nM 20 | value: 200 21 | name: lig_CHEMBL3402745_200_5 22 | smiles: '[H][C]1=[C]([H])[C]([c]2[c]([H])[c]([F])[c]([H])[c]([F])[c]2[H])=[N][N]([C]([H])([H])[c]2[c]([H])[c]([H])[c]([H])[c]([N]([H])[C](=[O])[O][C]([H])([H])[C]([H])([H])[H])[c]2[H])[C]1=[O]' 23 | lig_CHEMBL3402749_500_9: 24 | charge: 0.0 25 | measurement: 26 | doi: 27 | - 10.1016/j.bmcl.2015.02.002 28 | error: -1 29 | type: ic50 30 | unit: nM 31 | value: 500 32 | name: lig_CHEMBL3402749_500_9 33 | smiles: '[H][C]1=[C]([C]([H])([H])[H])[O][C]([c]2[c]([H])[c]([H])[c]([H])[c]([C]([H])([H])[N]3[N]=[C]([c]4[c]([H])[c]([F])[c]([H])[c]([F])[c]4[H])[C]([H])=[C]([H])[C]3=[O])[c]2[H])=[N]1' 34 | lig_CHEMBL3402754_40_14: 35 | charge: 0.0 36 | measurement: 37 | doi: 38 | - 10.1016/j.bmcl.2015.02.002 39 | error: -1 40 | type: ic50 41 | unit: nM 42 | value: 40 43 | name: lig_CHEMBL3402754_40_14 44 | smiles: '[H][C]1=[C]([H])[C]([c]2[c]([H])[c]([F])[c]([H])[c]([F])[c]2[H])=[N][N]([C]([H])([H])[c]2[c]([H])[c]([H])[c]([H])[c](-[c]3[n][c]([H])[c]([C]([H])([H])[H])[c]([H])[n]3)[c]2[H])[C]1=[O]' 45 | lig_CHEMBL3402761_1_21: 46 | charge: 0.0 47 | measurement: 48 | doi: 49 | - 10.1016/j.bmcl.2015.02.002 50 | error: -1 51 | type: ic50 52 | unit: nM 53 | value: 1 54 | name: lig_CHEMBL3402761_1_21 55 | smiles: '[H][C]1=[C]([H])[C]([c]2[c]([H])[c]([H])[c]([H])[c]([C]#[N])[c]2[H])=[N][N]([C]([H])([H])[c]2[c]([H])[c]([H])[c]([H])[c](-[c]3[n][c]([H])[c]([O][C]([H])([H])[C]([H])([H])[N]4[C]([H])([H])[C]([H])([H])[O][C]([H])([H])[C]4([H])[H])[c]([H])[n]3)[c]2[H])[C]1=[O]' 56 | -------------------------------------------------------------------------------- /data/cmet/00_data/target.yml: -------------------------------------------------------------------------------- 1 | alternate: 2 | iridium_classifier: '' 3 | iridium_score: '' 4 | pdb: '' 5 | associated_sets: 6 | - Merck KGaA fep-benchmark 7 | comments: '' 8 | date: 2019-12-13 9 | dpi: '' 10 | id: 7 11 | iridium_classifier: '' 12 | iridium_score: '' 13 | name: cmet 14 | netcharge: 6 e 15 | pdb: 4R1Y 16 | references: 17 | calculation: 18 | - 10.1021/acs.jcim.0c00900 19 | - 10.1039/C9SC03754C 20 | measurement: 21 | - 10.1016/j.bmcl.2015.02.002 22 | -------------------------------------------------------------------------------- /data/cmet/03_edges/kartograf_mapper_lomap_network.yml: -------------------------------------------------------------------------------- 1 | remarks: Kartograph mapper, Lomap scorer, Lomap network, allow element changes 2 | planner: openfe v0.14 lomap network 3 | edges: 4 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402749_500_9: 5 | ligand_a: lig_CHEMBL3402745_200_5 6 | ligand_b: lig_CHEMBL3402749_500_9 7 | atom mapping: {0: 37, 3: 35, 7: 25, 11: 29, 15: 33, 19: 18, 20: 19, 23: 15, 25: 13, 8 | 27: 11, 42: 41, 1: 36, 2: 34, 4: 22, 5: 23, 6: 24, 8: 26, 9: 27, 10: 28, 12: 30, 9 | 13: 31, 14: 32, 16: 21, 17: 20, 18: 17, 21: 16, 22: 14, 24: 12, 26: 10, 28: 9, 10 | 41: 40, 43: 38, 44: 39} 11 | score: {value: '0.111', method: Lomap default scorer} 12 | mapper: Kartograf (atom_map_hydrogens=True) 13 | remarks: null 14 | edge_lig_CHEMBL3402754_40_14_lig_CHEMBL3402761_1_21: 15 | ligand_a: lig_CHEMBL3402754_40_14 16 | ligand_b: lig_CHEMBL3402761_1_21 17 | atom mapping: {0: 0, 3: 3, 7: 7, 9: 9, 11: 11, 15: 16, 19: 21, 20: 20, 23: 24, 18 | 25: 26, 27: 28, 32: 57, 35: 36, 39: 33, 42: 60, 1: 1, 2: 2, 4: 4, 5: 5, 6: 6, 19 | 8: 8, 10: 10, 12: 12, 13: 13, 14: 15, 16: 17, 17: 18, 18: 19, 21: 22, 22: 23, 20 | 24: 25, 26: 27, 28: 29, 29: 30, 30: 58, 31: 56, 33: 34, 34: 35, 38: 32, 40: 31, 21 | 41: 59, 43: 61, 44: 62} 22 | score: {value: '0.287', method: Lomap default scorer} 23 | mapper: Kartograf (atom_map_hydrogens=True) 24 | remarks: null 25 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402744_300_4: 26 | ligand_a: lig_CHEMBL3402745_200_5 27 | ligand_b: lig_CHEMBL3402744_300_4 28 | atom mapping: {0: 0, 3: 3, 19: 19, 20: 20, 23: 23, 25: 25, 27: 27, 30: 30, 35: 36, 29 | 36: 37, 37: 35, 42: 39, 1: 1, 2: 2, 4: 4, 16: 16, 17: 17, 18: 18, 21: 21, 22: 22, 30 | 24: 24, 26: 26, 28: 28, 29: 29, 31: 31, 32: 32, 33: 33, 34: 34, 41: 38, 43: 40, 31 | 44: 41} 32 | score: {value: '0.183', method: Lomap default scorer} 33 | mapper: Kartograf (atom_map_hydrogens=True) 34 | remarks: null 35 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402761_1_21: 36 | ligand_a: lig_CHEMBL3402745_200_5 37 | ligand_b: lig_CHEMBL3402761_1_21 38 | atom mapping: {0: 0, 3: 3, 7: 7, 9: 9, 11: 11, 15: 16, 19: 21, 20: 20, 23: 24, 39 | 25: 26, 27: 28, 42: 60, 1: 1, 2: 2, 4: 4, 5: 5, 6: 6, 8: 8, 10: 10, 12: 12, 40 | 13: 13, 14: 15, 16: 17, 17: 18, 18: 19, 21: 22, 22: 23, 24: 25, 26: 27, 28: 29, 41 | 41: 59, 43: 61, 44: 62} 42 | score: {value: '0.030', method: Lomap default scorer} 43 | mapper: Kartograf (atom_map_hydrogens=True) 44 | remarks: null 45 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402754_40_14: 46 | ligand_a: lig_CHEMBL3402745_200_5 47 | ligand_b: lig_CHEMBL3402754_40_14 48 | atom mapping: {0: 0, 3: 3, 7: 7, 11: 11, 15: 15, 19: 19, 20: 20, 23: 23, 25: 25, 49 | 27: 27, 42: 42, 1: 1, 2: 2, 4: 4, 5: 5, 6: 6, 8: 8, 9: 9, 10: 10, 12: 12, 13: 13, 50 | 14: 14, 16: 16, 17: 17, 18: 18, 21: 21, 22: 22, 24: 24, 26: 26, 28: 28, 41: 41, 51 | 43: 43, 44: 44} 52 | score: {value: '0.100', method: Lomap default scorer} 53 | mapper: Kartograf (atom_map_hydrogens=True) 54 | remarks: null 55 | edge_lig_CHEMBL3402744_300_4_lig_CHEMBL3402749_500_9: 56 | ligand_a: lig_CHEMBL3402744_300_4 57 | ligand_b: lig_CHEMBL3402749_500_9 58 | atom mapping: {0: 37, 3: 35, 19: 18, 20: 19, 23: 15, 25: 13, 27: 11, 39: 41, 1: 36, 59 | 2: 34, 4: 22, 16: 21, 17: 20, 18: 17, 21: 16, 22: 14, 24: 12, 26: 10, 28: 9, 60 | 38: 40, 40: 38, 41: 39} 61 | score: {value: '0.025', method: Lomap default scorer} 62 | mapper: Kartograf (atom_map_hydrogens=True) 63 | remarks: null 64 | edge_lig_CHEMBL3402744_300_4_lig_CHEMBL3402754_40_14: 65 | ligand_a: lig_CHEMBL3402744_300_4 66 | ligand_b: lig_CHEMBL3402754_40_14 67 | atom mapping: {0: 0, 3: 3, 19: 19, 20: 20, 23: 23, 25: 25, 27: 27, 39: 42, 1: 1, 68 | 2: 2, 4: 4, 16: 16, 17: 17, 18: 18, 21: 21, 22: 22, 24: 24, 26: 26, 28: 28, 69 | 38: 41, 40: 43, 41: 44} 70 | score: {value: '0.022', method: Lomap default scorer} 71 | mapper: Kartograf (atom_map_hydrogens=True) 72 | remarks: null 73 | -------------------------------------------------------------------------------- /data/cmet/03_edges/kartograf_mapper_lomap_network_no_element_changes.yml: -------------------------------------------------------------------------------- 1 | remarks: Kartograf mapper, Lomap scorer, Lomap network, no element changes 2 | planner: openfe v1.0.1 lomap network 3 | edges: 4 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402754_40_14: 5 | ligand_a: lig_CHEMBL3402745_200_5 6 | ligand_b: lig_CHEMBL3402754_40_14 7 | atom mapping: {0: 0, 3: 3, 7: 7, 11: 11, 15: 15, 19: 19, 20: 20, 23: 23, 25: 25, 8 | 27: 27, 42: 42, 1: 1, 2: 2, 4: 4, 5: 5, 6: 6, 8: 8, 9: 9, 10: 10, 12: 12, 13: 13, 9 | 14: 14, 16: 16, 17: 17, 18: 18, 21: 21, 22: 22, 24: 24, 26: 26, 28: 28, 41: 41, 10 | 43: 43, 44: 44} 11 | score: {value: '0.100', method: Lomap default scorer} 12 | mapper: Kartograf (atom_map_hydrogens=True) 13 | remarks: null 14 | edge_lig_CHEMBL3402744_300_4_lig_CHEMBL3402754_40_14: 15 | ligand_a: lig_CHEMBL3402744_300_4 16 | ligand_b: lig_CHEMBL3402754_40_14 17 | atom mapping: {0: 0, 3: 3, 19: 19, 20: 20, 23: 23, 25: 25, 27: 27, 39: 42, 1: 1, 18 | 2: 2, 4: 4, 16: 16, 17: 17, 18: 18, 21: 21, 22: 22, 24: 24, 26: 26, 28: 28, 19 | 38: 41, 40: 43, 41: 44} 20 | score: {value: '0.022', method: Lomap default scorer} 21 | mapper: Kartograf (atom_map_hydrogens=True) 22 | remarks: null 23 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402761_1_21: 24 | ligand_a: lig_CHEMBL3402745_200_5 25 | ligand_b: lig_CHEMBL3402761_1_21 26 | atom mapping: {0: 0, 3: 3, 7: 7, 11: 11, 15: 16, 19: 21, 20: 20, 23: 24, 25: 26, 27 | 27: 28, 42: 60, 1: 1, 2: 2, 4: 4, 5: 5, 6: 6, 8: 8, 10: 10, 12: 12, 14: 15, 28 | 16: 17, 17: 18, 18: 19, 21: 22, 22: 23, 24: 25, 26: 27, 28: 29, 41: 59, 43: 61, 29 | 44: 62} 30 | score: {value: '0.030', method: Lomap default scorer} 31 | mapper: Kartograf (atom_map_hydrogens=True) 32 | remarks: null 33 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402744_300_4: 34 | ligand_a: lig_CHEMBL3402745_200_5 35 | ligand_b: lig_CHEMBL3402744_300_4 36 | atom mapping: {0: 0, 3: 3, 19: 19, 20: 20, 23: 23, 25: 25, 27: 27, 30: 30, 35: 36, 37 | 36: 37, 42: 39, 1: 1, 2: 2, 4: 4, 16: 16, 17: 17, 18: 18, 21: 21, 22: 22, 24: 24, 38 | 26: 26, 28: 28, 29: 29, 31: 31, 32: 32, 33: 33, 34: 34, 41: 38, 43: 40, 44: 41} 39 | score: {value: '0.183', method: Lomap default scorer} 40 | mapper: Kartograf (atom_map_hydrogens=True) 41 | remarks: null 42 | edge_lig_CHEMBL3402744_300_4_lig_CHEMBL3402749_500_9: 43 | ligand_a: lig_CHEMBL3402744_300_4 44 | ligand_b: lig_CHEMBL3402749_500_9 45 | atom mapping: {0: 37, 3: 35, 19: 18, 20: 19, 23: 15, 25: 13, 27: 11, 39: 41, 1: 36, 46 | 2: 34, 4: 22, 16: 21, 17: 20, 18: 17, 21: 16, 22: 14, 24: 12, 26: 10, 28: 9, 47 | 38: 40, 40: 38, 41: 39} 48 | score: {value: '0.025', method: Lomap default scorer} 49 | mapper: Kartograf (atom_map_hydrogens=True) 50 | remarks: null 51 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402749_500_9: 52 | ligand_a: lig_CHEMBL3402745_200_5 53 | ligand_b: lig_CHEMBL3402749_500_9 54 | atom mapping: {0: 37, 3: 35, 7: 25, 11: 29, 15: 33, 19: 18, 20: 19, 23: 15, 25: 13, 55 | 27: 11, 42: 41, 1: 36, 2: 34, 4: 22, 5: 23, 6: 24, 8: 26, 9: 27, 10: 28, 12: 30, 56 | 13: 31, 14: 32, 16: 21, 17: 20, 18: 17, 21: 16, 22: 14, 24: 12, 26: 10, 28: 9, 57 | 41: 40, 43: 38, 44: 39} 58 | score: {value: '0.111', method: Lomap default scorer} 59 | mapper: Kartograf (atom_map_hydrogens=True) 60 | remarks: null 61 | edge_lig_CHEMBL3402754_40_14_lig_CHEMBL3402761_1_21: 62 | ligand_a: lig_CHEMBL3402754_40_14 63 | ligand_b: lig_CHEMBL3402761_1_21 64 | atom mapping: {0: 0, 3: 3, 7: 7, 11: 11, 15: 16, 19: 21, 20: 20, 23: 24, 25: 26, 65 | 27: 28, 32: 57, 39: 33, 42: 60, 1: 1, 2: 2, 4: 4, 5: 5, 6: 6, 8: 8, 10: 10, 66 | 12: 12, 14: 15, 16: 17, 17: 18, 18: 19, 21: 22, 22: 23, 24: 25, 26: 27, 28: 29, 67 | 29: 30, 30: 58, 31: 56, 33: 34, 38: 32, 40: 31, 41: 59, 43: 61, 44: 62} 68 | score: {value: '0.247', method: Lomap default scorer} 69 | mapper: Kartograf (atom_map_hydrogens=True) 70 | remarks: null 71 | -------------------------------------------------------------------------------- /data/cmet/03_edges/kartograf_mapper_mst_network.yml: -------------------------------------------------------------------------------- 1 | remarks: Kartograph mapper, Lomap scorer, MST network 2 | planner: openfe v0.14 lomap network 3 | edges: 4 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402744_300_4: 5 | ligand_a: lig_CHEMBL3402745_200_5 6 | ligand_b: lig_CHEMBL3402744_300_4 7 | atom mapping: {0: 0, 3: 3, 19: 19, 20: 20, 23: 23, 25: 25, 27: 27, 30: 30, 35: 36, 8 | 36: 37, 37: 35, 42: 39, 1: 1, 2: 2, 4: 4, 16: 16, 17: 17, 18: 18, 21: 21, 22: 22, 9 | 24: 24, 26: 26, 28: 28, 29: 29, 31: 31, 32: 32, 33: 33, 34: 34, 41: 38, 43: 40, 10 | 44: 41} 11 | score: {value: '0.183', method: Lomap default scorer} 12 | mapper: Kartograf (atom_map_hydrogens=True) 13 | remarks: null 14 | edge_lig_CHEMBL3402754_40_14_lig_CHEMBL3402761_1_21: 15 | ligand_a: lig_CHEMBL3402754_40_14 16 | ligand_b: lig_CHEMBL3402761_1_21 17 | atom mapping: {0: 0, 3: 3, 7: 7, 9: 9, 11: 11, 15: 16, 19: 21, 20: 20, 23: 24, 18 | 25: 26, 27: 28, 32: 57, 35: 36, 39: 33, 42: 60, 1: 1, 2: 2, 4: 4, 5: 5, 6: 6, 19 | 8: 8, 10: 10, 12: 12, 13: 13, 14: 15, 16: 17, 17: 18, 18: 19, 21: 22, 22: 23, 20 | 24: 25, 26: 27, 28: 29, 29: 30, 30: 58, 31: 56, 33: 34, 34: 35, 38: 32, 40: 31, 21 | 41: 59, 43: 61, 44: 62} 22 | score: {value: '0.287', method: Lomap default scorer} 23 | mapper: Kartograf (atom_map_hydrogens=True) 24 | remarks: null 25 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402754_40_14: 26 | ligand_a: lig_CHEMBL3402745_200_5 27 | ligand_b: lig_CHEMBL3402754_40_14 28 | atom mapping: {0: 0, 3: 3, 7: 7, 11: 11, 15: 15, 19: 19, 20: 20, 23: 23, 25: 25, 29 | 27: 27, 42: 42, 1: 1, 2: 2, 4: 4, 5: 5, 6: 6, 8: 8, 9: 9, 10: 10, 12: 12, 13: 13, 30 | 14: 14, 16: 16, 17: 17, 18: 18, 21: 21, 22: 22, 24: 24, 26: 26, 28: 28, 41: 41, 31 | 43: 43, 44: 44} 32 | score: {value: '0.100', method: Lomap default scorer} 33 | mapper: Kartograf (atom_map_hydrogens=True) 34 | remarks: null 35 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402749_500_9: 36 | ligand_a: lig_CHEMBL3402745_200_5 37 | ligand_b: lig_CHEMBL3402749_500_9 38 | atom mapping: {0: 37, 3: 35, 7: 25, 11: 29, 15: 33, 19: 18, 20: 19, 23: 15, 25: 13, 39 | 27: 11, 42: 41, 1: 36, 2: 34, 4: 22, 5: 23, 6: 24, 8: 26, 9: 27, 10: 28, 12: 30, 40 | 13: 31, 14: 32, 16: 21, 17: 20, 18: 17, 21: 16, 22: 14, 24: 12, 26: 10, 28: 9, 41 | 41: 40, 43: 38, 44: 39} 42 | score: {value: '0.111', method: Lomap default scorer} 43 | mapper: Kartograf (atom_map_hydrogens=True) 44 | remarks: null 45 | -------------------------------------------------------------------------------- /data/cmet/03_edges/kartograf_mapper_mst_network_no_element_changes.yml: -------------------------------------------------------------------------------- 1 | remarks: Kartograf mapper, Lomap scorer, MST network, no element changes 2 | planner: openfe v.1.0.1 lomap network 3 | edges: 4 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402754_40_14: 5 | ligand_a: lig_CHEMBL3402745_200_5 6 | ligand_b: lig_CHEMBL3402754_40_14 7 | atom mapping: {0: 0, 3: 3, 7: 7, 11: 11, 15: 15, 19: 19, 20: 20, 23: 23, 25: 25, 8 | 27: 27, 42: 42, 1: 1, 2: 2, 4: 4, 5: 5, 6: 6, 8: 8, 9: 9, 10: 10, 12: 12, 13: 13, 9 | 14: 14, 16: 16, 17: 17, 18: 18, 21: 21, 22: 22, 24: 24, 26: 26, 28: 28, 41: 41, 10 | 43: 43, 44: 44} 11 | score: {value: '0.100', method: Lomap default scorer} 12 | mapper: Kartograf (atom_map_hydrogens=True) 13 | remarks: null 14 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402744_300_4: 15 | ligand_a: lig_CHEMBL3402745_200_5 16 | ligand_b: lig_CHEMBL3402744_300_4 17 | atom mapping: {0: 0, 3: 3, 19: 19, 20: 20, 23: 23, 25: 25, 27: 27, 30: 30, 35: 36, 18 | 36: 37, 42: 39, 1: 1, 2: 2, 4: 4, 16: 16, 17: 17, 18: 18, 21: 21, 22: 22, 24: 24, 19 | 26: 26, 28: 28, 29: 29, 31: 31, 32: 32, 33: 33, 34: 34, 41: 38, 43: 40, 44: 41} 20 | score: {value: '0.183', method: Lomap default scorer} 21 | mapper: Kartograf (atom_map_hydrogens=True) 22 | remarks: null 23 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402749_500_9: 24 | ligand_a: lig_CHEMBL3402745_200_5 25 | ligand_b: lig_CHEMBL3402749_500_9 26 | atom mapping: {0: 37, 3: 35, 7: 25, 11: 29, 15: 33, 19: 18, 20: 19, 23: 15, 25: 13, 27 | 27: 11, 42: 41, 1: 36, 2: 34, 4: 22, 5: 23, 6: 24, 8: 26, 9: 27, 10: 28, 12: 30, 28 | 13: 31, 14: 32, 16: 21, 17: 20, 18: 17, 21: 16, 22: 14, 24: 12, 26: 10, 28: 9, 29 | 41: 40, 43: 38, 44: 39} 30 | score: {value: '0.111', method: Lomap default scorer} 31 | mapper: Kartograf (atom_map_hydrogens=True) 32 | remarks: null 33 | edge_lig_CHEMBL3402754_40_14_lig_CHEMBL3402761_1_21: 34 | ligand_a: lig_CHEMBL3402754_40_14 35 | ligand_b: lig_CHEMBL3402761_1_21 36 | atom mapping: {0: 0, 3: 3, 7: 7, 11: 11, 15: 16, 19: 21, 20: 20, 23: 24, 25: 26, 37 | 27: 28, 32: 57, 39: 33, 42: 60, 1: 1, 2: 2, 4: 4, 5: 5, 6: 6, 8: 8, 10: 10, 38 | 12: 12, 14: 15, 16: 17, 17: 18, 18: 19, 21: 22, 22: 23, 24: 25, 26: 27, 28: 29, 39 | 29: 30, 30: 58, 31: 56, 33: 34, 38: 32, 40: 31, 41: 59, 43: 61, 44: 62} 40 | score: {value: '0.247', method: Lomap default scorer} 41 | mapper: Kartograf (atom_map_hydrogens=True) 42 | remarks: null 43 | -------------------------------------------------------------------------------- /data/cmet/03_edges/kartograf_mapper_radial_network_element_changes.yml: -------------------------------------------------------------------------------- 1 | remarks: Kartograf mapper, Lomap scorer, Radial network, element changes 2 | planner: openfe v0.14 radial network 3 | edges: 4 | edge_lig_CHEMBL3402744_300_4_lig_CHEMBL3402761_1_21: 5 | ligand_a: lig_CHEMBL3402744_300_4 6 | ligand_b: lig_CHEMBL3402761_1_21 7 | atom mapping: {0: 0, 3: 3, 19: 21, 20: 20, 23: 24, 25: 26, 27: 28, 39: 60, 1: 1, 8 | 2: 2, 4: 4, 16: 17, 17: 18, 18: 19, 21: 22, 22: 23, 24: 25, 26: 27, 28: 29, 9 | 38: 59, 40: 61, 41: 62} 10 | mapper: Kartograf (atom_map_hydrogens=True) 11 | remarks: null 12 | edge_lig_CHEMBL3402744_300_4_lig_CHEMBL3402754_40_14: 13 | ligand_a: lig_CHEMBL3402744_300_4 14 | ligand_b: lig_CHEMBL3402754_40_14 15 | atom mapping: {0: 0, 3: 3, 19: 19, 20: 20, 23: 23, 25: 25, 27: 27, 39: 42, 1: 1, 16 | 2: 2, 4: 4, 16: 16, 17: 17, 18: 18, 21: 21, 22: 22, 24: 24, 26: 26, 28: 28, 17 | 38: 41, 40: 43, 41: 44} 18 | mapper: Kartograf (atom_map_hydrogens=True) 19 | remarks: null 20 | edge_lig_CHEMBL3402744_300_4_lig_CHEMBL3402749_500_9: 21 | ligand_a: lig_CHEMBL3402744_300_4 22 | ligand_b: lig_CHEMBL3402749_500_9 23 | atom mapping: {0: 37, 3: 35, 19: 18, 20: 19, 23: 15, 25: 13, 27: 11, 39: 41, 1: 36, 24 | 2: 34, 4: 22, 16: 21, 17: 20, 18: 17, 21: 16, 22: 14, 24: 12, 26: 10, 28: 9, 25 | 38: 40, 40: 38, 41: 39} 26 | mapper: Kartograf (atom_map_hydrogens=True) 27 | remarks: null 28 | edge_lig_CHEMBL3402744_300_4_lig_CHEMBL3402745_200_5: 29 | ligand_a: lig_CHEMBL3402744_300_4 30 | ligand_b: lig_CHEMBL3402745_200_5 31 | atom mapping: {0: 0, 3: 3, 19: 19, 20: 20, 23: 23, 25: 25, 27: 27, 30: 30, 35: 37, 32 | 36: 35, 37: 36, 39: 42, 1: 1, 2: 2, 4: 4, 16: 16, 17: 17, 18: 18, 21: 21, 22: 22, 33 | 24: 24, 26: 26, 28: 28, 29: 29, 31: 31, 32: 32, 33: 33, 34: 34, 38: 41, 40: 43, 34 | 41: 44} 35 | mapper: Kartograf (atom_map_hydrogens=True) 36 | remarks: null 37 | -------------------------------------------------------------------------------- /data/cmet/03_edges/kartograf_mapper_radial_network_no_element_changes.yml: -------------------------------------------------------------------------------- 1 | remarks: Kartograf mapper, Lomap scorer, Radial network, no element changes 2 | planner: openfe v0.14 radial network 3 | edges: 4 | edge_lig_CHEMBL3402744_300_4_lig_CHEMBL3402754_40_14: 5 | ligand_a: lig_CHEMBL3402744_300_4 6 | ligand_b: lig_CHEMBL3402754_40_14 7 | atom mapping: {0: 0, 3: 3, 19: 19, 20: 20, 23: 23, 25: 25, 27: 27, 39: 42, 1: 1, 8 | 2: 2, 4: 4, 16: 16, 17: 17, 18: 18, 21: 21, 22: 22, 24: 24, 26: 26, 28: 28, 9 | 38: 41, 40: 43, 41: 44} 10 | mapper: Kartograf (atom_map_hydrogens=True) 11 | remarks: null 12 | edge_lig_CHEMBL3402744_300_4_lig_CHEMBL3402761_1_21: 13 | ligand_a: lig_CHEMBL3402744_300_4 14 | ligand_b: lig_CHEMBL3402761_1_21 15 | atom mapping: {0: 0, 3: 3, 19: 21, 20: 20, 23: 24, 25: 26, 27: 28, 39: 60, 1: 1, 16 | 2: 2, 4: 4, 16: 17, 17: 18, 18: 19, 21: 22, 22: 23, 24: 25, 26: 27, 28: 29, 17 | 38: 59, 40: 61, 41: 62} 18 | mapper: Kartograf (atom_map_hydrogens=True) 19 | remarks: null 20 | edge_lig_CHEMBL3402744_300_4_lig_CHEMBL3402745_200_5: 21 | ligand_a: lig_CHEMBL3402744_300_4 22 | ligand_b: lig_CHEMBL3402745_200_5 23 | atom mapping: {0: 0, 3: 3, 19: 19, 20: 20, 23: 23, 25: 25, 27: 27, 30: 30, 36: 35, 24 | 37: 36, 39: 42, 1: 1, 2: 2, 4: 4, 16: 16, 17: 17, 18: 18, 21: 21, 22: 22, 24: 24, 25 | 26: 26, 28: 28, 29: 29, 31: 31, 32: 32, 33: 33, 34: 34, 38: 41, 40: 43, 41: 44} 26 | mapper: Kartograf (atom_map_hydrogens=True) 27 | remarks: null 28 | edge_lig_CHEMBL3402744_300_4_lig_CHEMBL3402749_500_9: 29 | ligand_a: lig_CHEMBL3402744_300_4 30 | ligand_b: lig_CHEMBL3402749_500_9 31 | atom mapping: {0: 37, 3: 35, 19: 18, 20: 19, 23: 15, 25: 13, 27: 11, 39: 41, 1: 36, 32 | 2: 34, 4: 22, 16: 21, 17: 20, 18: 17, 21: 16, 22: 14, 24: 12, 26: 10, 28: 9, 33 | 38: 40, 40: 38, 41: 39} 34 | mapper: Kartograf (atom_map_hydrogens=True) 35 | remarks: null 36 | -------------------------------------------------------------------------------- /data/cmet/03_edges/lomap_mapper_lomap_network.yml: -------------------------------------------------------------------------------- 1 | remarks: Lomap network graph, Lomap mapper, Lomap scorer 2 | planner: openfe v0.14 Lomap network 3 | edges: 4 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402761_1_21: 5 | ligand_a: lig_CHEMBL3402745_200_5 6 | ligand_b: lig_CHEMBL3402761_1_21 7 | atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 8 | 11: 11, 12: 12, 13: 13, 14: 15, 15: 16, 16: 17, 17: 18, 18: 19, 19: 21, 20: 20, 9 | 21: 22, 22: 23, 23: 24, 24: 25, 25: 26, 26: 27, 27: 28, 28: 29, 41: 59, 42: 60, 10 | 43: 61, 44: 62} 11 | score: {value: '0.030', method: Lomap default scorer} 12 | mapper: LomapAtomMapper 13 | remarks: null 14 | edge_lig_CHEMBL3402754_40_14_lig_CHEMBL3402761_1_21: 15 | ligand_a: lig_CHEMBL3402754_40_14 16 | ligand_b: lig_CHEMBL3402761_1_21 17 | atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 18 | 11: 11, 12: 12, 13: 13, 14: 15, 15: 16, 16: 17, 17: 18, 18: 19, 19: 21, 20: 20, 19 | 21: 22, 22: 23, 23: 24, 24: 25, 25: 26, 26: 27, 27: 28, 28: 29, 29: 30, 30: 58, 20 | 31: 56, 32: 57, 33: 34, 34: 35, 35: 36, 38: 32, 39: 33, 40: 31, 41: 59, 42: 60, 21 | 43: 61, 44: 62} 22 | score: {value: '0.287', method: Lomap default scorer} 23 | mapper: LomapAtomMapper 24 | remarks: null 25 | edge_lig_CHEMBL3402744_300_4_lig_CHEMBL3402749_500_9: 26 | ligand_a: lig_CHEMBL3402744_300_4 27 | ligand_b: lig_CHEMBL3402749_500_9 28 | atom mapping: {0: 37, 1: 36, 2: 34, 3: 35, 4: 22, 16: 21, 17: 20, 18: 17, 19: 18, 29 | 20: 19, 21: 16, 22: 14, 23: 15, 24: 12, 25: 13, 26: 10, 27: 11, 28: 9, 38: 40, 30 | 39: 41, 40: 38, 41: 39} 31 | score: {value: '0.025', method: Lomap default scorer} 32 | mapper: LomapAtomMapper 33 | remarks: null 34 | edge_lig_CHEMBL3402744_300_4_lig_CHEMBL3402754_40_14: 35 | ligand_a: lig_CHEMBL3402744_300_4 36 | ligand_b: lig_CHEMBL3402754_40_14 37 | atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 38 | 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 38: 41, 39: 42, 39 | 40: 43, 41: 44} 40 | score: {value: '0.022', method: Lomap default scorer} 41 | mapper: LomapAtomMapper 42 | remarks: null 43 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402749_500_9: 44 | ligand_a: lig_CHEMBL3402745_200_5 45 | ligand_b: lig_CHEMBL3402749_500_9 46 | atom mapping: {0: 37, 1: 36, 2: 34, 3: 35, 4: 22, 5: 23, 6: 24, 7: 25, 8: 26, 47 | 9: 27, 10: 28, 11: 29, 12: 30, 13: 31, 14: 32, 15: 33, 16: 21, 17: 20, 18: 17, 48 | 19: 18, 20: 19, 21: 16, 22: 14, 23: 15, 24: 12, 25: 13, 26: 10, 27: 11, 28: 9, 49 | 41: 40, 42: 41, 43: 38, 44: 39} 50 | score: {value: '0.111', method: Lomap default scorer} 51 | mapper: LomapAtomMapper 52 | remarks: null 53 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402744_300_4: 54 | ligand_a: lig_CHEMBL3402745_200_5 55 | ligand_b: lig_CHEMBL3402744_300_4 56 | atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 57 | 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, 58 | 31: 31, 32: 32, 33: 33, 34: 34, 35: 36, 36: 37, 37: 35, 41: 38, 42: 39, 43: 40, 59 | 44: 41} 60 | score: {value: '0.183', method: Lomap default scorer} 61 | mapper: LomapAtomMapper 62 | remarks: null 63 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402754_40_14: 64 | ligand_a: lig_CHEMBL3402745_200_5 65 | ligand_b: lig_CHEMBL3402754_40_14 66 | atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 67 | 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 68 | 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 41: 41, 42: 42, 69 | 43: 43, 44: 44} 70 | score: {value: '0.100', method: Lomap default scorer} 71 | mapper: LomapAtomMapper 72 | remarks: null 73 | -------------------------------------------------------------------------------- /data/cmet/03_edges/lomap_mapper_mst_network.yml: -------------------------------------------------------------------------------- 1 | remarks: MST lomap scorer lomap mapper 2 | planner: openfe v1.0.1 MST 3 | edges: 4 | edge_lig_CHEMBL3402754_40_14_lig_CHEMBL3402761_1_21: 5 | ligand_a: lig_CHEMBL3402754_40_14 6 | ligand_b: lig_CHEMBL3402761_1_21 7 | atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 8 | 11: 11, 12: 12, 13: 13, 14: 15, 15: 16, 16: 17, 17: 18, 18: 19, 19: 21, 20: 20, 9 | 21: 22, 22: 23, 23: 24, 24: 25, 25: 26, 26: 27, 27: 28, 28: 29, 29: 30, 30: 58, 10 | 31: 56, 32: 57, 33: 34, 34: 35, 35: 36, 38: 32, 39: 33, 40: 31, 41: 59, 42: 60, 11 | 43: 61, 44: 62} 12 | score: {value: '0.287', method: Lomap scorer} 13 | mapper: Lomap mapper 14 | remarks: null 15 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402744_300_4: 16 | ligand_a: lig_CHEMBL3402745_200_5 17 | ligand_b: lig_CHEMBL3402744_300_4 18 | atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 19 | 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, 20 | 31: 31, 32: 32, 33: 33, 34: 34, 35: 36, 36: 37, 37: 35, 41: 38, 42: 39, 43: 40, 21 | 44: 41} 22 | score: {value: '0.183', method: Lomap scorer} 23 | mapper: Lomap mapper 24 | remarks: null 25 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402754_40_14: 26 | ligand_a: lig_CHEMBL3402745_200_5 27 | ligand_b: lig_CHEMBL3402754_40_14 28 | atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 29 | 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 30 | 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 41: 41, 42: 42, 31 | 43: 43, 44: 44} 32 | score: {value: '0.100', method: Lomap scorer} 33 | mapper: Lomap mapper 34 | remarks: null 35 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402749_500_9: 36 | ligand_a: lig_CHEMBL3402745_200_5 37 | ligand_b: lig_CHEMBL3402749_500_9 38 | atom mapping: {0: 37, 1: 36, 2: 34, 3: 35, 4: 22, 5: 23, 6: 24, 7: 25, 8: 26, 39 | 9: 27, 10: 28, 11: 29, 12: 30, 13: 31, 14: 32, 15: 33, 16: 21, 17: 20, 18: 17, 40 | 19: 18, 20: 19, 21: 16, 22: 14, 23: 15, 24: 12, 25: 13, 26: 10, 27: 11, 28: 9, 41 | 41: 40, 42: 41, 43: 38, 44: 39} 42 | score: {value: '0.111', method: Lomap scorer} 43 | mapper: Lomap mapper 44 | remarks: null 45 | -------------------------------------------------------------------------------- /data/cmet/03_edges/lomap_mapper_mst_network_no_element_changes.yml: -------------------------------------------------------------------------------- 1 | remarks: MST lomap scorer lomap mapper 2 | planner: openfe v1.0.1 MST 3 | edges: 4 | edge_lig_CHEMBL3402754_40_14_lig_CHEMBL3402761_1_21: 5 | ligand_a: lig_CHEMBL3402754_40_14 6 | ligand_b: lig_CHEMBL3402761_1_21 7 | atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 10: 10, 11: 11, 8 | 12: 12, 14: 15, 15: 16, 16: 17, 17: 18, 18: 19, 19: 21, 20: 20, 21: 22, 22: 23, 9 | 23: 24, 24: 25, 25: 26, 26: 27, 27: 28, 28: 29, 29: 30, 30: 58, 31: 56, 32: 57, 10 | 33: 34, 38: 32, 39: 33, 40: 31, 41: 59, 42: 60, 43: 61, 44: 62} 11 | score: {value: '0.247', method: Lomap scorer} 12 | mapper: Lomap mapper 13 | remarks: null 14 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402744_300_4: 15 | ligand_a: lig_CHEMBL3402745_200_5 16 | ligand_b: lig_CHEMBL3402744_300_4 17 | atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 18 | 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, 19 | 31: 31, 32: 32, 33: 33, 34: 34, 35: 36, 36: 37, 41: 38, 42: 39, 43: 40, 44: 41} 20 | score: {value: '0.183', method: Lomap scorer} 21 | mapper: Lomap mapper 22 | remarks: null 23 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402754_40_14: 24 | ligand_a: lig_CHEMBL3402745_200_5 25 | ligand_b: lig_CHEMBL3402754_40_14 26 | atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 27 | 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 28 | 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 41: 41, 42: 42, 29 | 43: 43, 44: 44} 30 | score: {value: '0.100', method: Lomap scorer} 31 | mapper: Lomap mapper 32 | remarks: null 33 | edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402749_500_9: 34 | ligand_a: lig_CHEMBL3402745_200_5 35 | ligand_b: lig_CHEMBL3402749_500_9 36 | atom mapping: {0: 37, 1: 36, 2: 34, 3: 35, 4: 22, 5: 23, 6: 24, 7: 25, 8: 26, 37 | 9: 27, 10: 28, 11: 29, 12: 30, 13: 31, 14: 32, 15: 33, 16: 21, 17: 20, 18: 17, 38 | 19: 18, 20: 19, 21: 16, 22: 14, 23: 15, 24: 12, 25: 13, 26: 10, 27: 11, 28: 9, 39 | 41: 40, 42: 41, 43: 38, 44: 39} 40 | score: {value: '0.111', method: Lomap scorer} 41 | mapper: Lomap mapper 42 | remarks: null 43 | -------------------------------------------------------------------------------- /data/eg5/00_data/target.yml: -------------------------------------------------------------------------------- 1 | alternate: 2 | iridium_classifier: HT 3 | iridium_score: 0.32 4 | pdb: 2X7C 5 | associated_sets: 6 | - Merck KGgA fep-benchmark 7 | comments: 8 | - ligands with different net charges 9 | - cofactor 10 | - stereocenter uncertainty (tetravalent nitrogen for lig_CHEMBL1084935) 11 | date: 2020-06-19 12 | dpi: 0.18 13 | id: 14 14 | iridium_classifier: MT 15 | iridium_score: 0.88 16 | name: eg5 17 | netcharge: null 18 | pdb: 3L9H 19 | references: 20 | calculation: null 21 | measurement: null 22 | -------------------------------------------------------------------------------- /data/eg5/01_protein/crd/cofactor.sdf: -------------------------------------------------------------------------------- 1 | 3L9H 2 | 3D 3 | Schrodinger Suite 2021-1. 4 | 39 41 0 0 1 0 999 V2000 5 | 17.7103 1.3810 16.7258 P 0 0 0 0 0 0 6 | 16.2918 1.9380 16.9415 O 0 0 0 0 0 0 7 | 17.7048 -0.1381 16.4765 O 0 5 0 0 0 0 8 | 18.4945 2.1622 15.6604 O 0 5 0 0 0 0 9 | 20.1704 1.9553 18.6598 P 0 0 0 0 0 0 10 | 21.0614 1.4768 17.5414 O 0 0 0 0 0 0 11 | 20.2345 3.3559 19.2252 O 0 5 0 0 0 0 12 | 18.5522 1.6400 18.2257 O 0 0 0 0 0 0 13 | 20.3327 0.8377 19.9634 O 0 0 0 0 0 0 14 | 19.5869 1.0879 21.1452 C 0 0 0 0 0 0 15 | 20.4613 1.1653 22.4074 C 0 0 1 0 0 0 16 | 21.0911 -0.0950 22.5958 O 0 0 0 0 0 0 17 | 21.6078 2.1760 22.3912 C 0 0 1 0 0 0 18 | 21.7761 2.7834 23.6633 O 0 0 0 0 0 0 19 | 22.8150 1.3580 21.9342 C 0 0 1 0 0 0 20 | 24.0771 1.7580 22.4399 O 0 0 0 0 0 0 21 | 22.4830 -0.0283 22.4899 C 0 0 2 0 0 0 22 | 22.9954 -1.1724 21.6426 N 0 0 0 0 0 0 23 | 22.4947 -1.6440 20.4842 C 0 0 0 0 0 0 24 | 23.2096 -2.5994 19.9459 N 0 0 0 0 0 0 25 | 24.2457 -2.7439 20.7874 C 0 0 0 0 0 0 26 | 25.3696 -3.6002 20.7533 C 0 0 0 0 0 0 27 | 25.5873 -4.5319 19.7432 N 0 0 0 0 0 0 28 | 26.2748 -3.5190 21.7663 N 0 0 0 0 0 0 29 | 26.0465 -2.6305 22.7424 C 0 0 0 0 0 0 30 | 25.0272 -1.7702 22.8844 N 0 0 0 0 0 0 31 | 24.1457 -1.8743 21.8585 C 0 0 0 0 0 0 32 | 18.9006 0.2596 21.2825 H 0 0 0 0 0 0 33 | 18.9668 1.9826 21.0671 H 0 0 0 0 0 0 34 | 19.7967 1.3439 23.2547 H 0 0 0 0 0 0 35 | 21.4113 2.9719 21.6708 H 0 0 0 0 0 0 36 | 22.6054 3.2689 23.6516 H 0 0 0 0 0 0 37 | 22.8340 1.3030 20.8442 H 0 0 0 0 0 0 38 | 24.3615 2.5656 21.9940 H 0 0 0 0 0 0 39 | 22.8770 -0.1608 23.5002 H 0 0 0 0 0 0 40 | 21.5746 -1.2447 20.0891 H 0 0 0 0 0 0 41 | 26.3917 -5.1389 19.8129 H 0 0 0 0 0 0 42 | 24.9075 -4.6313 19.0027 H 0 0 0 0 0 0 43 | 26.7890 -2.6030 23.5264 H 0 0 0 0 0 0 44 | 1 2 2 0 0 0 45 | 1 3 1 0 0 0 46 | 1 4 1 0 0 0 47 | 1 8 1 0 0 0 48 | 5 6 2 0 0 0 49 | 5 7 1 0 0 0 50 | 5 8 1 0 0 0 51 | 5 9 1 0 0 0 52 | 9 10 1 0 0 0 53 | 10 11 1 0 0 0 54 | 10 28 1 0 0 0 55 | 10 29 1 0 0 0 56 | 11 12 1 0 0 0 57 | 11 13 1 0 0 0 58 | 11 30 1 0 0 0 59 | 12 17 1 0 0 0 60 | 13 14 1 0 0 0 61 | 13 15 1 0 0 0 62 | 13 31 1 0 0 0 63 | 14 32 1 0 0 0 64 | 15 16 1 0 0 0 65 | 15 17 1 0 0 0 66 | 15 33 1 0 0 0 67 | 16 34 1 0 0 0 68 | 17 18 1 0 0 0 69 | 17 35 1 0 0 0 70 | 18 19 1 0 0 0 71 | 18 27 1 0 0 0 72 | 19 20 2 0 0 0 73 | 19 36 1 0 0 0 74 | 20 21 1 0 0 0 75 | 21 22 1 0 0 0 76 | 21 27 2 0 0 0 77 | 22 23 1 0 0 0 78 | 22 24 2 0 0 0 79 | 23 37 1 0 0 0 80 | 23 38 1 0 0 0 81 | 24 25 1 0 0 0 82 | 25 26 2 0 0 0 83 | 25 39 1 0 0 0 84 | 26 27 1 0 0 0 85 | M CHG 3 3 -1 4 -1 7 -1 86 | M END 87 | $$$$ 88 | -------------------------------------------------------------------------------- /data/hif2a/00_data/target.yml: -------------------------------------------------------------------------------- 1 | alternate: 2 | iridium_classifier: HT 3 | iridium_score: 0.30 4 | pdb: 5TBM 5 | associated_sets: 6 | - Merck KGgA fep-benchmark 7 | comments: null 8 | date: 2020-07-03 9 | dpi: 0.17 10 | id: 16 11 | iridium_classifier: HT 12 | iridium_score: 0.35 13 | name: hif2a 14 | netcharge: null 15 | pdb: 5TBM 16 | references: 17 | calculation: null 18 | measurement: null 19 | -------------------------------------------------------------------------------- /data/mcl1/00_data/target.yml: -------------------------------------------------------------------------------- 1 | alternate: 2 | iridium_classifier: HT 3 | iridium_score: 0.3 4 | pdb: 6O6F 5 | associated_sets: 6 | - Schrodinger JACS 7 | comments: hydrophobic interactions contributing to binding 8 | date: 2019-12-13 9 | dpi: 0.26 10 | id: 9 11 | iridium_classifier: HT 12 | iridium_score: 0.41 13 | name: mcl1 14 | netcharge: 4 e 15 | pdb: 4HW3 16 | references: 17 | calculation: 18 | - 10.1021/ja512751q 19 | - 10.1021/acs.jcim.9b00105 20 | - 10.1039/C9SC03754C 21 | measurement: 22 | - 10.1021/jm301448p 23 | -------------------------------------------------------------------------------- /data/p38/00_data/target.yml: -------------------------------------------------------------------------------- 1 | alternate: 2 | iridium_classifier: HT 3 | iridium_score: 0.3 4 | pdb: 6SFI 5 | associated_sets: 6 | - Schrodinger JACS 7 | comments: 8 | - inversion of a stereocenter in one mutation 9 | - Some ligands are not well aligned 10 | date: 2019-12-09 11 | dpi: 0.12 12 | id: 4 13 | iridium_classifier: HT 14 | iridium_score: 0.6 15 | name: p38 16 | netcharge: -5 e 17 | pdb: 3FLY 18 | references: 19 | calculation: 20 | - 10.1021/ja512751q 21 | - 10.1021/acs.jcim.9b00105 22 | - 10.1039/C9SC03754C 23 | measurement: 24 | - 10.1021/jm101423y 25 | -------------------------------------------------------------------------------- /data/pde2/00_data/target.yml: -------------------------------------------------------------------------------- 1 | alternate: 2 | iridium_classifier: HT 3 | iridium_score: 0.29 4 | pdb: 6C7E 5 | associated_sets: 6 | - Janssen 7 | comments: 8 | - Some ligands are not well aligned 9 | dpi: 0.07 10 | id: 2 11 | iridium_classifier: MT 12 | iridium_score: 0.3 13 | name: pde2 14 | netcharge: -8 e 15 | pdb: 6EZF 16 | references: 17 | calculation: 18 | - 10.1038/s41598-018-23039-5 19 | - 10.1039/C9SC03754C 20 | measurement: 21 | - 10.1021/ml500262u 22 | - 10.1021/ja404449g 23 | -------------------------------------------------------------------------------- /data/pfkfb3/00_data/target.yml: -------------------------------------------------------------------------------- 1 | alternate: 2 | iridium_classifier: HT 3 | iridium_score: 0.36 4 | pdb: 6HVH 5 | associated_sets: 6 | - Merck KGgA fep-benchmark 7 | comments: 8 | - cofactor 9 | date: 2020-07-06 10 | dpi: 0.11 11 | id: 17 12 | iridium_classifier: HT 13 | iridium_score: 0.31 14 | name: pfkfb3 15 | netcharge: null 16 | pdb: 6HVI 17 | references: 18 | calculation: null 19 | measurement: null 20 | -------------------------------------------------------------------------------- /data/pfkfb3/01_protein/crd/cofactor.sdf: -------------------------------------------------------------------------------- 1 | F6P 2 | -OEChem-12082315173D 3 | 4 | 27 27 0 1 0 0 0 0 0999 V2000 5 | 58.0051 68.4855 268.5575 O 0 0 0 0 0 0 0 0 0 0 0 0 6 | 58.8930 67.7950 269.4113 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 60.2803 68.4383 269.4215 C 0 0 2 0 0 0 0 0 0 0 0 0 8 | 61.1024 67.6811 270.2199 O 0 0 0 0 0 0 0 0 0 0 0 0 9 | 60.3389 69.9030 269.9143 C 0 0 1 0 0 0 0 0 0 0 0 0 10 | 60.3862 70.0476 271.3256 O 0 0 0 0 0 0 0 0 0 0 0 0 11 | 61.5671 70.4146 269.1666 C 0 0 2 0 0 0 0 0 0 0 0 0 12 | 61.5922 71.8146 269.0028 O 0 0 0 0 0 0 0 0 0 0 0 0 13 | 61.4880 69.6797 267.8322 C 0 0 2 0 0 0 0 0 0 0 0 0 14 | 60.7312 68.5020 268.0989 O 0 0 0 0 0 0 0 0 0 0 0 0 15 | 62.8335 69.3225 267.1836 C 0 0 0 0 0 0 0 0 0 0 0 0 16 | 62.6150 68.8338 265.8771 O 0 0 0 0 0 0 0 0 0 0 0 0 17 | 62.6147 69.9073 264.4928 P 0 0 0 0 0 0 0 0 0 0 0 0 18 | 62.0190 69.0931 263.3355 O 0 0 0 0 0 0 0 0 0 0 0 0 19 | 64.0872 70.2758 264.2574 O 0 5 0 0 0 0 0 0 0 0 0 0 20 | 61.7551 71.1268 264.8507 O 0 5 0 0 0 0 0 0 0 0 0 0 21 | 57.1551 68.0616 268.5741 H 0 0 0 0 0 0 0 0 0 0 0 0 22 | 58.4867 67.8068 270.4334 H 0 0 0 0 0 0 0 0 0 0 0 0 23 | 58.9845 66.7549 269.0651 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | 61.9703 68.0670 270.2378 H 0 0 0 0 0 0 0 0 0 0 0 0 25 | 59.4557 70.4272 269.5204 H 0 0 0 0 0 0 0 0 0 0 0 0 26 | 60.4205 70.9704 271.5489 H 0 0 0 0 0 0 0 0 0 0 0 0 27 | 62.4683 70.0781 269.7001 H 0 0 0 0 0 0 0 0 0 0 0 0 28 | 62.3787 72.0648 268.5323 H 0 0 0 0 0 0 0 0 0 0 0 0 29 | 60.9328 70.3159 267.1273 H 0 0 0 0 0 0 0 0 0 0 0 0 30 | 63.4673 70.2204 267.1373 H 0 0 0 0 0 0 0 0 0 0 0 0 31 | 63.3357 68.5498 267.7842 H 0 0 0 0 0 0 0 0 0 0 0 0 32 | 1 2 1 0 0 0 0 33 | 2 3 1 0 0 0 0 34 | 3 4 1 0 0 0 0 35 | 3 5 1 0 0 0 0 36 | 3 10 1 0 0 0 0 37 | 5 6 1 0 0 0 0 38 | 5 7 1 0 0 0 0 39 | 7 8 1 0 0 0 0 40 | 7 9 1 0 0 0 0 41 | 9 10 1 0 0 0 0 42 | 9 11 1 0 0 0 0 43 | 11 12 1 0 0 0 0 44 | 12 13 1 0 0 0 0 45 | 13 14 2 0 0 0 0 46 | 13 15 1 0 0 0 0 47 | 13 16 1 0 0 0 0 48 | 1 17 1 0 0 0 0 49 | 2 18 1 0 0 0 0 50 | 2 19 1 0 0 0 0 51 | 4 20 1 0 0 0 0 52 | 5 21 1 0 0 0 0 53 | 6 22 1 0 0 0 0 54 | 7 23 1 0 0 0 0 55 | 8 24 1 0 0 0 0 56 | 9 25 1 0 0 0 0 57 | 11 26 1 0 0 0 0 58 | 11 27 1 0 0 0 0 59 | M CHG 2 15 -1 16 -1 60 | M END 61 | $$$$ 62 | POP 63 | -OEChem-12082315173D 64 | 65 | 9 8 0 0 0 0 0 0 0999 V2000 66 | 94.1200 47.6630 260.3200 O 0 0 0 0 0 0 0 0 0 0 0 0 67 | 92.3940 47.6350 260.3690 P 0 0 0 0 0 0 0 0 0 0 0 0 68 | 95.3590 48.5050 259.4720 P 0 0 0 0 0 0 0 0 0 0 0 0 69 | 91.9180 47.4410 258.9220 O 0 5 0 0 0 0 0 0 0 0 0 0 70 | 91.9380 48.9800 260.9620 O 0 5 0 0 0 0 0 0 0 0 0 0 71 | 92.0860 46.4270 261.2630 O 0 0 0 0 0 0 0 0 0 0 0 0 72 | 95.9420 47.5170 258.4470 O 0 5 0 0 0 0 0 0 0 0 0 0 73 | 96.3750 48.8880 260.5590 O 0 5 0 0 0 0 0 0 0 0 0 0 74 | 94.6990 49.7150 258.8030 O 0 0 0 0 0 0 0 0 0 0 0 0 75 | 1 2 1 0 0 0 0 76 | 1 3 1 0 0 0 0 77 | 2 4 1 0 0 0 0 78 | 2 5 1 0 0 0 0 79 | 2 6 2 0 0 0 0 80 | 3 7 1 0 0 0 0 81 | 3 8 1 0 0 0 0 82 | 3 9 2 0 0 0 0 83 | M CHG 4 4 -1 5 -1 7 -1 8 -1 84 | M END 85 | $$$$ 86 | -------------------------------------------------------------------------------- /data/ptp1b/00_data/target.yml: -------------------------------------------------------------------------------- 1 | alternate: 2 | iridium_classifier: HT 3 | iridium_score: 0.32 4 | pdb: 2HB1 5 | associated_sets: 6 | - Schrodinger JACS 7 | comments: 8 | - Charges in binding site; electrostatic interactions contribute to binding 9 | - Some ligands are not well aligned 10 | date: 2019-12-12 11 | dpi: 0.15 12 | id: 5 13 | iridium_classifier: MT 14 | iridium_score: 0.33 15 | name: ptp1b 16 | netcharge: -6 e 17 | pdb: 2QBS 18 | references: 19 | calculation: 20 | - 10.1021/ja512751q 21 | - 10.1021/acs.jcim.9b00105 22 | - 10.1039/C9SC03754C 23 | measurement: 24 | - 10.1021/jm0702478 25 | -------------------------------------------------------------------------------- /data/shp2/00_data/target.yml: -------------------------------------------------------------------------------- 1 | alternate: 2 | iridium_classifier: MT 3 | iridium_score: 0.33 4 | pdb: 5EHP 5 | associated_sets: 6 | - Merck KGgA fep-benchmark 7 | comments: 8 | - Some ligands are not well aligned 9 | date: 2020-07-30 10 | dpi: 0.1 11 | id: 19 12 | iridium_classifier: MT 13 | iridium_score: 0.32 14 | name: shp2 15 | netcharge: null 16 | pdb: 5EHR 17 | references: 18 | calculation: null 19 | measurement: null 20 | -------------------------------------------------------------------------------- /data/syk/00_data/target.yml: -------------------------------------------------------------------------------- 1 | alternate: 2 | iridium_classifier: HT 3 | iridium_score: 0.3 4 | pdb: 4PX6 5 | associated_sets: 6 | - Merck KGgA fep-benchmark 7 | comments: 8 | - ligands with different net charges 9 | - Protonation state uncertainty for some ligands (lig_CHEMBL3265030_n and lig_CHEMBL3265035) 10 | date: 2020-08-11 11 | dpi: null 12 | id: 20 13 | iridium_classifier: MT 14 | iridium_score: 0.69 15 | name: syk 16 | netcharge: null 17 | pdb: 4PV0 18 | references: 19 | calculation: null 20 | measurement: null 21 | -------------------------------------------------------------------------------- /data/targets.yml: -------------------------------------------------------------------------------- 1 | bace: 2 | date: 2020-02-04 3 | dir: bace 4 | name: bace 5 | bace_hunt: 6 | date: 2020-02-05 7 | dir: bace_hunt 8 | name: bace_hunt 9 | bace_p2: 10 | date: 2020-02-06 11 | dir: bace_p2 12 | name: bace_p2 13 | cdk2: 14 | date: 2019-12-13 15 | dir: cdk2 16 | name: cdk2 17 | cdk8: 18 | date: 2020-07-01 19 | dir: cdk8 20 | name: cdk8 21 | cmet: 22 | date: 2019-12-13 23 | dir: cmet 24 | name: cmet 25 | eg5: 26 | date: 2020-06-19 27 | dir: eg5 28 | name: eg5 29 | galectin: 30 | date: 2019-12-13 31 | dir: galectin 32 | name: galectin 33 | hif2a: 34 | date: 2020-07-03 35 | dir: hif2a 36 | name: hif2a 37 | jnk1: 38 | date: 2019-09-23 39 | dir: jnk1 40 | name: jnk1 41 | mcl1: 42 | date: 2019-12-13 43 | dir: mcl1 44 | name: mcl1 45 | p38: 46 | date: 2019-12-09 47 | dir: p38 48 | name: p38 49 | pde10: 50 | date: 2020-07-10 51 | dir: pde10 52 | name: pde10 53 | pde2: 54 | date: 2019-09-23 55 | dir: pde2 56 | name: pde2 57 | pfkfb3: 58 | date: 2020-07-06 59 | dir: pfkfb3 60 | name: pfkfb3 61 | ptp1b: 62 | date: 2019-12-12 63 | dir: ptp1b 64 | name: ptp1b 65 | shp2: 66 | date: 2020-07-30 67 | dir: shp2 68 | name: shp2 69 | syk: 70 | date: 2020-08-11 71 | dir: syk 72 | name: syk 73 | thrombin: 74 | date: 2019-09-23 75 | dir: thrombin 76 | name: thrombin 77 | tnks2: 78 | date: 2020-08-12 79 | dir: tnks2 80 | name: tnks2 81 | tyk2: 82 | date: 2020-02-07 83 | dir: tyk2 84 | name: tyk2 85 | -------------------------------------------------------------------------------- /data/thrombin/00_data/target.yml: -------------------------------------------------------------------------------- 1 | alternate: 2 | iridium_classifier: HT 3 | iridium_score: 0.31 4 | pdb: 3LXP 5 | associated_sets: 6 | - Schrodinger JACS 7 | comments: 8 | - expulsion of a single water molecule from the active site contributing to binding 9 | - ligands with different net charges 10 | - Protonation state uncertainty for some ligands (primary amine) 11 | date: 2019-09-23 12 | dpi: 0.15 13 | id: 3 14 | iridium_classifier: HT 15 | iridium_score: 0.3 16 | name: thrombin 17 | netcharge: -1 e 18 | pdb: 2ZFF 19 | references: 20 | calculation: 21 | - 10.1021/ja512751q 22 | - 10.1021/acs.jcim.9b00105 23 | - 10.1039/C9SC03754C 24 | measurement: 25 | - 10.1016/j.jmb.2009.04.051 26 | -------------------------------------------------------------------------------- /data/tnks2/00_data/target.yml: -------------------------------------------------------------------------------- 1 | alternate: 2 | iridium_classifier: HT 3 | iridium_score: 0.27 4 | pdb: 4PC9 5 | associated_sets: 6 | - Merck KGgA fep-benchmark 7 | comments: 8 | - ligands with different net charges 9 | - Protonation state uncertainty (lig_7) 10 | date: 2020-08-12 11 | dpi: 0.08 12 | id: 21 13 | iridium_classifier: HT 14 | iridium_score: 0.29 15 | name: tnks2 16 | netcharge: null 17 | pdb: 4UI5 18 | references: 19 | calculation: null 20 | measurement: null 21 | -------------------------------------------------------------------------------- /data/tyk2/00_data/ligands.yml: -------------------------------------------------------------------------------- 1 | lig_ejm_31: 2 | measurement: 3 | comment: Table 4, entry 31 4 | doi: 10.1016/j.ejmech.2013.03.070 5 | error: 0.029 6 | type: ki 7 | unit: uM 8 | value: 0.096 9 | name: lig_ejm_31 10 | smiles: '[H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)C([H])([H])[H])[H])[H])Cl)[H]' 11 | lig_ejm_42: 12 | measurement: 13 | comment: Table 4, entry 42 14 | doi: 10.1016/j.ejmech.2013.03.070 15 | error: 0.019 16 | type: ki 17 | unit: uM 18 | value: 0.064 19 | name: lig_ejm_42 20 | smiles: '[H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)C([H])([H])C([H])([H])[H])[H])[H])Cl)[H]' 21 | lig_ejm_43: 22 | measurement: 23 | comment: Table 4, entry 43 24 | doi: 10.1016/j.ejmech.2013.03.070 25 | error: 0.25 26 | type: ki 27 | unit: uM 28 | value: 0.84 29 | name: lig_ejm_43 30 | smiles: '[H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)C([H])(C([H])([H])[H])C([H])([H])[H])[H])[H])Cl)[H]' 31 | lig_ejm_45: 32 | measurement: 33 | comment: Table 4, entry 45 34 | doi: 10.1016/j.ejmech.2013.03.070 35 | error: 0.028 36 | type: ki 37 | unit: uM 38 | value: 0.094 39 | name: lig_ejm_45 40 | smiles: '[H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)C([H])([H])C3(C(C3([H])[H])([H])[H])[H])[H])[H])Cl)[H]' 41 | lig_ejm_46: 42 | measurement: 43 | comment: Table 4, entry 46 44 | doi: 10.1016/j.ejmech.2013.03.070 45 | error: 0.0014 46 | type: ki 47 | unit: uM 48 | value: 0.0048 49 | name: lig_ejm_46 50 | smiles: '[H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)C3(C(C3([H])[H])([H])[H])[H])[H])[H])Cl)[H]' 51 | lig_ejm_47: 52 | measurement: 53 | comment: Table 4, entry 47 54 | doi: 10.1016/j.ejmech.2013.03.070 55 | error: 0.022 56 | type: ki 57 | unit: uM 58 | value: 0.074 59 | name: lig_ejm_47 60 | smiles: '[H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)C3(C(C(C3([H])[H])([H])[H])([H])[H])[H])[H])[H])Cl)[H]' 61 | lig_ejm_48: 62 | measurement: 63 | comment: Table 4, entry 48 64 | doi: 10.1016/j.ejmech.2013.03.070 65 | error: 0.072 66 | type: ki 67 | unit: uM 68 | value: 0.24 69 | name: lig_ejm_48 70 | smiles: '[H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)C3(C(C(C(C3([H])[H])([H])[H])([H])[H])([H])[H])[H])[H])[H])Cl)[H]' 71 | lig_ejm_50: 72 | measurement: 73 | comment: Table 4, entry 50 74 | doi: 10.1016/j.ejmech.2013.03.070 75 | error: 0.075 76 | type: ki 77 | unit: uM 78 | value: 0.25 79 | name: lig_ejm_50 80 | smiles: '[H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)C([H])([H])O[H])[H])[H])Cl)[H]' 81 | lig_ejm_54: 82 | measurement: 83 | comment: Table 4, entry 54 84 | doi: 10.1016/j.ejmech.2013.03.070 85 | error: 0.0054 86 | type: ki 87 | unit: uM 88 | value: 0.018 89 | name: lig_ejm_54 90 | smiles: '[H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)N([H])C([H])([H])C([H])([H])[H])[H])[H])Cl)[H]' 91 | lig_ejm_55: 92 | measurement: 93 | comment: Table 4, entry 55 94 | doi: 10.1016/j.ejmech.2013.03.070 95 | error: 0.051 96 | type: ki 97 | unit: uM 98 | value: 0.17 99 | name: lig_ejm_55 100 | smiles: '[H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)OC([H])([H])[H])[H])[H])Cl)[H]' 101 | lig_jmc_23: 102 | measurement: 103 | comment: Table 2, entry 23; values for four different enantionmers listed, this 104 | one is for cis 105 | doi: 10.1021/jm400266t 106 | error: 0.75 107 | type: ki 108 | unit: nM 109 | value: 2.5 110 | name: lig_jmc_23 111 | smiles: '[H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)[C@@]3([C@](C3([H])[H])([H])F)[H])[H])[H])Cl)[H]' 112 | lig_jmc_27: 113 | measurement: 114 | comment: Table 2, entry 27; cis enantiomer 115 | doi: 10.1021/jm400266t 116 | error: 1.5 117 | type: ki 118 | unit: nM 119 | value: 5.1 120 | name: lig_jmc_27 121 | smiles: '[H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)[C@@]3([C@](C3([H])[H])([H])Cl)[H])[H])[H])Cl)[H]' 122 | lig_jmc_28: 123 | measurement: 124 | comment: Table 2, entry 28; cis enantiomer 125 | doi: 10.1021/jm400266t 126 | error: 2.6 127 | type: ki 128 | unit: nM 129 | value: 8.5 130 | name: lig_jmc_28 131 | smiles: '[H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)[C@@]3([C@](C3([H])[H])([H])C([H])([H])[H])[H])[H])[H])Cl)[H]' 132 | -------------------------------------------------------------------------------- /data/tyk2/00_data/target.yml: -------------------------------------------------------------------------------- 1 | alternate: 2 | iridium_classifier: HT 3 | iridium_score: 0.31 4 | pdb: 3LXP 5 | associated_sets: 6 | - Schrodinger JACS 7 | comments: '' 8 | date: 2020-02-07 9 | dpi: 0.15 10 | id: 13 11 | iridium_classifier: HT 12 | iridium_score: 0.5 13 | name: tyk2 14 | netcharge: -3 e 15 | pdb: 4GIH 16 | references: 17 | calculation: 18 | - 10.1021/ja512751q 19 | - 10.1039/C9SC03754C 20 | measurement: 21 | - 10.1016/j.ejmech.2013.03.070 22 | - 10.1021/jm400266t 23 | -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line. 5 | SPHINXOPTS = 6 | SPHINXBUILD = sphinx-build 7 | SPHINXPROJ = PLBenchmarks 8 | SOURCEDIR = . 9 | BUILDDIR = _build 10 | 11 | # Put it first so that "make" without argument is like "make help". 12 | help: 13 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 14 | 15 | .PHONY: help Makefile 16 | 17 | # Catch-all target: route all unknown targets to Sphinx using the new 18 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 19 | %: Makefile 20 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 21 | -------------------------------------------------------------------------------- /docs/README.md: -------------------------------------------------------------------------------- 1 | # Compiling ProteinLigandBenchmarks's Documentation 2 | 3 | The docs for this project are built with [Sphinx](http://www.sphinx-doc.org/en/master/). 4 | To compile the docs, first ensure that Sphinx and the ReadTheDocs theme are installed. 5 | 6 | 7 | ```bash 8 | pip install sphinx sphinx_rtd_theme 9 | ``` 10 | 11 | 12 | Once installed, you can use the `Makefile` in this directory to compile static HTML pages by 13 | ```bash 14 | make html 15 | ``` 16 | 17 | The compiled docs will be in the `_build` directory and can be viewed by opening `index.html` (which may itself 18 | be inside a directory called `html/` depending on what version of Sphinx is installed). -------------------------------------------------------------------------------- /docs/_config.yml: -------------------------------------------------------------------------------- 1 | theme: jekyll-theme-minimal -------------------------------------------------------------------------------- /docs/_static/README.md: -------------------------------------------------------------------------------- 1 | # Static Doc Directory 2 | 3 | Add any paths that contain custom static files (such as style sheets) here, 4 | relative to the `conf.py` file's directory. 5 | They are copied after the builtin static files, 6 | so a file named "default.css" will overwrite the builtin "default.css". 7 | 8 | The path to this folder is set in the Sphinx `conf.py` file in the line: 9 | ```python 10 | templates_path = ['_static'] 11 | ``` 12 | 13 | ## Examples of file to add to this directory 14 | * Custom Cascading Style Sheets 15 | * Custom JavaScript code 16 | * Static logo images 17 | -------------------------------------------------------------------------------- /docs/_templates/README.md: -------------------------------------------------------------------------------- 1 | # Templates Doc Directory 2 | 3 | Add any paths that contain templates here, relative to 4 | the `conf.py` file's directory. 5 | They are copied after the builtin template files, 6 | so a file named "page.html" will overwrite the builtin "page.html". 7 | 8 | The path to this folder is set in the Sphinx `conf.py` file in the line: 9 | ```python 10 | html_static_path = ['_templates'] 11 | ``` 12 | 13 | ## Examples of file to add to this directory 14 | * HTML extensions of stock pages like `page.html` or `layout.html` 15 | -------------------------------------------------------------------------------- /docs/api.rst: -------------------------------------------------------------------------------- 1 | API Documentation 2 | ================= 3 | 4 | .. toctree:: 5 | :maxdepth: 1 6 | 7 | Targets 8 | ----------------- 9 | 10 | .. toctree:: 11 | :maxdepth: 1 12 | 13 | .. automodule:: plbenchmark.targets 14 | :members: 15 | 16 | Ligands 17 | ----------------- 18 | .. toctree:: 19 | :maxdepth: 1 20 | 21 | .. automodule:: plbenchmark.ligands 22 | :members: 23 | 24 | Edges 25 | ----------------- 26 | .. toctree:: 27 | :maxdepth: 1 28 | 29 | .. automodule:: plbenchmark.edges 30 | :members: 31 | 32 | Utils 33 | ----------------- 34 | .. toctree:: 35 | :maxdepth: 1 36 | 37 | .. automodule:: plbenchmark.utils 38 | :members: 39 | 40 | 41 | 42 | -------------------------------------------------------------------------------- /docs/contributions.rst: -------------------------------------------------------------------------------- 1 | Contributions 2 | ============= 3 | 4 | .. toctree:: 5 | :maxdepth: 1 6 | 7 | 8 | * **Authors** David Hahn 9 | * **Data Contributors** The authors of the following publications, especially Vytautas Gapsys and Christina E. M. Schindler. 10 | * `V. Gapsys et al., Large scale relative protein ligand binding affinities using non-equilibrium alchemy, Chem. Sci., 2020,11, 1140-1152 `_ 11 | * `Christina E. M. Schindler et al., Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects, J. Chem. Inf. Model. 2020, 60, 11, 5457–5474 `_ 12 | * `Laura Perez Benito et al., Predicting Activity Cliffs with Free-Energy Perturbation, J. Chem. Theory Comput. 2019, 15, 3, 1884–1895 `_ 13 | * **Discussions and Suggestions** Christopher I. Bayly, Marko Breznik, Hannah E. Bruce Macdonald, John D.Chodera, Katharina Meier, Antonia S. J. S. Mey, David L. Mobley, Laura Perez Benito, Gary Tresadern, Gregory L. Warren and all members of the Open Force Field Initiative 14 | * **Code review and discussions** Matt Thompson, Jeffrey Wagner 15 | 16 | Related Publication 17 | ------------------- 18 | The `preprint `_ on "Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks" provides accompanying information to this benchmark dataset and how to use it for alchemical free energy calculations. 19 | For any suggestions of improvements please raise an issue in its `GitHub repository `_. 20 | -------------------------------------------------------------------------------- /docs/data.rst: -------------------------------------------------------------------------------- 1 | Data 2 | ==== 3 | 4 | Data file tree and file description 5 | ----------------------------------- 6 | 7 | .. toctree:: 8 | :maxdepth: 1 9 | 10 | The data is organized as follows: 11 | 12 | .. literalinclude:: file_tree.txt 13 | 14 | -------------------------------------------------------------------------------- /docs/figures/examples_graph.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/docs/figures/examples_graph.png -------------------------------------------------------------------------------- /docs/file_tree.txt: -------------------------------------------------------------------------------- 1 | data 2 | ├── targets.yml # list of all targets and their directories 3 | ├── _ # directory for target 1 4 | │ ├── 00_data # metadata for target 1 5 | │ │ ├── edges.yml # edges/perturbations 6 | │ │ ├── ligands.yml # ligands and activities 7 | │ │ └── target.yml # target 8 | │ ├── 01_protein # protein data 9 | │ │ ├── crd # coordinates 10 | │ │ │ ├── cofactors_crystalwater.pdb # cofactors and cyrstal waters 11 | │ │ │ └── protein.pdb # aminoacid residues 12 | │ │ └── top # topology(s) 13 | │ │ │ └── amber99sb-star-ildn-mut.ff # force field spec. 14 | │ │ │ ├── cofactors_crystalwater.top# Gromacs TOP file of cofactors and crystal water 15 | │ │ │ ├── protein.top # Gromacs TOP file of amino acid residues 16 | │ │ │ └── *.itp # Gromacs ITP file(s) to be included in TOP files 17 | │ └── 02_ligands # ligands 18 | │ ├── lig_ # ligand 1 19 | │ │ ├── crd # coordinates 20 | │ │ │ └── lig_.sdf # SDF file 21 | │ │ └── top # topology(s) 22 | │ │ └── openff-1.0.0.offxml # force field spec. 23 | │ │ ├── fflig_.itp # Gromacs ITP file : atom types 24 | │ │ ├── lig_.itp # Gromacs ITP file 25 | │ │ ├── lig_.top # Gromacs TOP file 26 | │ │ └── posre_lig_.itp # Gromacs ITP file : position restraint file 27 | │ ├── lig_ # ligand 2 28 | │ … 29 | │ └── 03_hybrid # edges (perturbations) 30 | │ ├── edge__ # edge between ligand 1 and ligand 2 31 | │ │ └── water # edge in water 32 | │ │ ├── crd # coordinates 33 | │ │ │ ├── mergedA.pdb # merged conf based on coords of ligand 1 34 | │ │ │ ├── mergedB.pdb # merged conf based on coords of ligand 2 35 | │ │ │ ├── pairs.dat # atom mapping 36 | │ │ │ └── score.dat # similarity score 37 | │ │ └── top # topology(s) 38 | │ │ └── openff-1.0.0.offxml # force field spec. 39 | │ │ ├── ffmerged.itp # Gromacs ITP file 40 | │ │ ├── ffMOL.itp # Gromacs ITP file 41 | │ │ └── merged.itp # Gromacs ITP file 42 | │ … 43 | ├── _ # directory for target 2 44 | … 45 | -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- 1 | .. plbenchmarks documentation master file, created by 2 | sphinx-quickstart on Thu Mar 15 13:55:56 2018. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | Protein-Ligand Benchmarks for Free Energy Calculations 7 | ====================================================== 8 | 9 | .. toctree:: 10 | :maxdepth: 2 11 | :caption: Contents: 12 | 13 | install 14 | Getting Started 15 | data 16 | contributions 17 | api 18 | 19 | Indices and tables 20 | ================== 21 | 22 | * :ref:`genindex` 23 | * :ref:`modindex` 24 | * :ref:`search` 25 | -------------------------------------------------------------------------------- /docs/install.rst: -------------------------------------------------------------------------------- 1 | Installing the Protein Ligand Benchmark Set 2 | =========================================== 3 | 4 | The Protein Ligand Benchmark Set is currently only installable from source. 5 | 6 | Installation from Source 7 | ------------------------ 8 | 9 | .. toctree:: 10 | :maxdepth: 1 11 | 12 | The repository uses `git-lfs (large file storage) `_ for the storage of all the data file. Ideally git-lfs is installed first before cloning the repository. 13 | 14 | :: 15 | 16 | conda create -n plbenchmark python=3.7 git-lfs 17 | conda activate plbenchmark 18 | git lfs clone https://github.com/openforcefield/protein-ligand-benchmark.git 19 | cd protein-ligand-benchmark 20 | conda env update --file environment.yml 21 | pip install -e . 22 | 23 | -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- 1 | @ECHO OFF 2 | 3 | pushd %~dp0 4 | 5 | REM Command file for Sphinx documentation 6 | 7 | if "%SPHINXBUILD%" == "" ( 8 | set SPHINXBUILD=sphinx-build 9 | ) 10 | set SOURCEDIR=. 11 | set BUILDDIR=_build 12 | set SPHINXPROJ=plbenchmarks 13 | 14 | if "%1" == "" goto help 15 | 16 | %SPHINXBUILD% >NUL 2>NUL 17 | if errorlevel 9009 ( 18 | echo. 19 | echo.The 'sphinx-build' command was not found. Make sure you have Sphinx 20 | echo.installed, then set the SPHINXBUILD environment variable to point 21 | echo.to the full path of the 'sphinx-build' executable. Alternatively you 22 | echo.may add the Sphinx directory to PATH. 23 | echo. 24 | echo.If you don't have Sphinx installed, grab it from 25 | echo.http://sphinx-doc.org/ 26 | exit /b 1 27 | ) 28 | 29 | %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% 30 | goto end 31 | 32 | :help 33 | %SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% 34 | 35 | :end 36 | popd 37 | -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- 1 | name: plbenchmark 2 | channels: 3 | - conda-forge 4 | dependencies: 5 | # Base depends 6 | - python 7 | - pip 8 | 9 | # Testing 10 | - pytest 11 | - pytest-cov 12 | - codecov 13 | - nbval 14 | - coverage 15 | 16 | - pyyaml 17 | - numpy 18 | - matplotlib 19 | - pandas 20 | - rdkit 21 | - networkx 22 | - openff-units 23 | - scipy 24 | - openff-toolkit<=0.11 25 | - requests 26 | - git-lfs 27 | - nbsphinx 28 | -------------------------------------------------------------------------------- /plbenchmark/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | ProteinLigandBenchmarks 3 | Protein-Ligand Benchmark Dataset for testing Parameters and Methods of Free Energy Calculations. 4 | """ 5 | 6 | # Add imports here 7 | 8 | # Handle versioneer 9 | from ._version import get_versions 10 | 11 | versions = get_versions() 12 | __version__ = versions["version"] 13 | __git_revision__ = versions["full-revisionid"] 14 | del get_versions, versions 15 | -------------------------------------------------------------------------------- /plbenchmark/metadata.py: -------------------------------------------------------------------------------- 1 | """ 2 | targets.py 3 | Functions and classes for handling the target data. 4 | """ 5 | 6 | import os 7 | import shutil 8 | import yaml 9 | import numpy as np 10 | import pandas as pd 11 | 12 | from . import __path__, targets, ligands, edges, utils 13 | 14 | 15 | def clean_yaml_file(path): 16 | if os.path.exists(path): 17 | count = 1 18 | bk_path = f"{path}.bk.{count}" 19 | while os.path.exists(bk_path): 20 | count += 1 21 | bk_path = f"{path}.bk.{count}" 22 | shutil.copy(path, bk_path) 23 | with open(path, "r") as file: 24 | yaml_dict = [d for d in yaml.full_load_all(file)] 25 | print(yaml_dict) 26 | with open(path, "w") as file: 27 | if len(yaml_dict) == 1: 28 | file.write(yaml.dump(yaml_dict[0])) 29 | else: 30 | file.write(yaml.dump_all(yaml_dict)) 31 | else: 32 | raise ValueError(f"Path for file {path} not found.") 33 | 34 | 35 | def clean_metadata(): 36 | clean_yaml_file(os.path.join(targets.data_path, "targets.yml")) 37 | for target in targets.target_dict: 38 | clean_yaml_file( 39 | os.path.join(targets.get_target_data_path(target), "target.yml") 40 | ) 41 | 42 | clean_yaml_file( 43 | os.path.join(targets.get_target_data_path(target), "ligands.yml") 44 | ) 45 | 46 | clean_yaml_file(os.path.join(targets.get_target_data_path(target), "edges.yml")) 47 | -------------------------------------------------------------------------------- /plbenchmark/sample_data/2020-08-26_mcl1_sample/00_data/edges.yml: -------------------------------------------------------------------------------- 1 | edge_28_35: 2 | ligand_a: lig_28 3 | ligand_b: lig_35 4 | name: edge_28_35 5 | edge_30_27: 6 | ligand_a: lig_30 7 | ligand_b: lig_27 8 | name: edge_30_27 9 | edge_31_35: 10 | ligand_a: lig_31 11 | ligand_b: lig_35 12 | name: edge_31_35 13 | edge_33_27: 14 | ligand_a: lig_33 15 | ligand_b: lig_27 16 | name: edge_33_27 17 | edge_35_33: 18 | ligand_a: lig_35 19 | ligand_b: lig_33 20 | name: edge_35_33 21 | edge_35_37: 22 | ligand_a: lig_35 23 | ligand_b: lig_37 24 | name: edge_35_37 25 | edge_39_32: 26 | ligand_a: lig_39 27 | ligand_b: lig_32 28 | name: edge_39_32 29 | -------------------------------------------------------------------------------- /plbenchmark/sample_data/2020-08-26_mcl1_sample/00_data/target.yml: -------------------------------------------------------------------------------- 1 | associated_sets: 2 | - Schrodinger JACS 3 | comments: hydrophobic interactions contributing to binding 4 | date: 2020-08-21 5 | fullname: Induced myeloid leukemia cell differentiation protein Mcl-1 6 | id: 99 7 | ligands: 8 | - lig_23 9 | - lig_26 10 | - lig_27 11 | - lig_28 12 | - lig_29 13 | - lig_30 14 | - lig_31 15 | - lig_32 16 | - lig_33 17 | - lig_34 18 | - lig_35 19 | - lig_36 20 | - lig_37 21 | - lig_38 22 | - lig_39 23 | name: mcl1_sample 24 | netcharge: xx 25 | pdb: 4HW3 26 | references: 27 | calculation: 28 | - 10.1021/ja512751q 29 | - 10.1021/acs.jcim.9b00105 30 | measurement: null 31 | -------------------------------------------------------------------------------- /plbenchmark/sample_data/2020-08-26_mcl1_sample/02_ligands/lig_23/crd/lig_23.sdf: -------------------------------------------------------------------------------- 1 | lig_23 2 | -OEChem-01312017293D 3 | 4 | 43 46 0 0 0 0 0 0 0999 V2000 5 | 3.8100 -50.0800 6.4300 O 0 5 0 0 0 0 0 0 0 0 0 0 6 | 2.9400 -49.1700 6.5100 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 3.2800 -47.9700 6.6700 O 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1.5200 -49.6100 6.4100 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1.0100 -51.1700 6.8300 S 0 0 0 0 0 0 0 0 0 0 0 0 10 | -0.6500 -51.0200 6.4700 C 0 0 0 0 0 0 0 0 0 0 0 0 11 | -1.7400 -51.8800 6.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | -1.5900 -52.9000 6.8900 H 0 0 0 0 0 0 0 0 0 0 0 0 13 | -3.0100 -51.4600 6.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 14 | -3.8500 -52.1300 6.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 15 | -3.1800 -50.1500 5.7300 C 0 0 0 0 0 0 0 0 0 0 0 0 16 | -4.1700 -49.8000 5.4500 H 0 0 0 0 0 0 0 0 0 0 0 0 17 | -2.1000 -49.2800 5.6300 C 0 0 0 0 0 0 0 0 0 0 0 0 18 | -2.2500 -48.2700 5.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 19 | -0.8300 -49.7000 6.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 20 | 0.3700 -48.9100 5.9700 C 0 0 0 0 0 0 0 0 0 0 0 0 21 | 0.4000 -47.4900 5.5200 C 0 0 0 0 0 0 0 0 0 0 0 0 22 | 1.1900 -47.3900 4.7800 H 0 0 0 0 0 0 0 0 0 0 0 0 23 | -0.5600 -47.2600 5.0600 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | 0.6500 -46.4800 6.6000 C 0 0 0 0 0 0 0 0 0 0 0 0 25 | 0.5300 -45.4900 6.1500 H 0 0 0 0 0 0 0 0 0 0 0 0 26 | 1.6900 -46.6000 6.9200 H 0 0 0 0 0 0 0 0 0 0 0 0 27 | -0.2000 -46.5200 7.8200 C 0 0 0 0 0 0 0 0 0 0 0 0 28 | 0.1100 -45.7300 8.5100 H 0 0 0 0 0 0 0 0 0 0 0 0 29 | -0.0800 -47.4900 8.3100 H 0 0 0 0 0 0 0 0 0 0 0 0 30 | -1.5300 -46.3400 7.5000 O 0 0 0 0 0 0 0 0 0 0 0 0 31 | -2.5500 -46.4800 8.4100 C 0 0 0 0 0 0 0 0 0 0 0 0 32 | -2.3800 -47.2600 9.5300 C 0 0 0 0 0 0 0 0 0 0 0 0 33 | -1.4400 -47.7700 9.7100 H 0 0 0 0 0 0 0 0 0 0 0 0 34 | -3.4400 -47.3800 10.4300 C 0 0 0 0 0 0 0 0 0 0 0 0 35 | -3.3200 -47.9800 11.3100 H 0 0 0 0 0 0 0 0 0 0 0 0 36 | -4.6500 -46.7300 10.2000 C 0 0 0 0 0 0 0 0 0 0 0 0 37 | -5.4700 -46.8300 10.9100 H 0 0 0 0 0 0 0 0 0 0 0 0 38 | -4.8100 -45.9500 9.0700 C 0 0 0 0 0 0 0 0 0 0 0 0 39 | -3.7500 -45.8300 8.1700 C 0 0 0 0 0 0 0 0 0 0 0 0 40 | -3.9100 -45.0200 7.0200 C 0 0 0 0 0 0 0 0 0 0 0 0 41 | -3.0900 -44.9200 6.3200 H 0 0 0 0 0 0 0 0 0 0 0 0 42 | -5.1100 -44.3600 6.7600 C 0 0 0 0 0 0 0 0 0 0 0 0 43 | -5.2200 -43.7500 5.8800 H 0 0 0 0 0 0 0 0 0 0 0 0 44 | -6.1800 -44.4900 7.6500 C 0 0 0 0 0 0 0 0 0 0 0 0 45 | -7.1100 -43.9800 7.4600 H 0 0 0 0 0 0 0 0 0 0 0 0 46 | -6.0400 -45.2700 8.8000 C 0 0 0 0 0 0 0 0 0 0 0 0 47 | -6.8700 -45.3700 9.4900 H 0 0 0 0 0 0 0 0 0 0 0 0 48 | 17 18 1 0 0 0 0 49 | 17 19 1 0 0 0 0 50 | 13 14 1 0 0 0 0 51 | 11 12 1 0 0 0 0 52 | 16 17 1 0 0 0 0 53 | 17 20 1 0 0 0 0 54 | 11 13 2 0 0 0 0 55 | 13 15 1 0 0 0 0 56 | 9 11 1 0 0 0 0 57 | 38 39 1 0 0 0 0 58 | 15 16 1 0 0 0 0 59 | 4 16 2 0 0 0 0 60 | 6 15 2 0 0 0 0 61 | 20 21 1 0 0 0 0 62 | 9 10 1 0 0 0 0 63 | 7 9 2 0 0 0 0 64 | 36 37 1 0 0 0 0 65 | 2 4 1 0 0 0 0 66 | 4 5 1 0 0 0 0 67 | 1 2 1 0 0 0 0 68 | 6 7 1 0 0 0 0 69 | 5 6 1 0 0 0 0 70 | 2 3 2 0 0 0 0 71 | 7 8 1 0 0 0 0 72 | 20 22 1 0 0 0 0 73 | 20 23 1 0 0 0 0 74 | 36 38 2 0 0 0 0 75 | 38 40 1 0 0 0 0 76 | 35 36 1 0 0 0 0 77 | 40 41 1 0 0 0 0 78 | 23 26 1 0 0 0 0 79 | 26 27 1 0 0 0 0 80 | 40 42 2 0 0 0 0 81 | 23 25 1 0 0 0 0 82 | 23 24 1 0 0 0 0 83 | 27 35 2 0 0 0 0 84 | 34 35 1 0 0 0 0 85 | 27 28 1 0 0 0 0 86 | 34 42 1 0 0 0 0 87 | 42 43 1 0 0 0 0 88 | 32 34 2 0 0 0 0 89 | 28 29 1 0 0 0 0 90 | 28 30 2 0 0 0 0 91 | 30 32 1 0 0 0 0 92 | 32 33 1 0 0 0 0 93 | 30 31 1 0 0 0 0 94 | M CHG 1 1 -1 95 | M END 96 | $$$$ 97 | -------------------------------------------------------------------------------- /plbenchmark/sample_data/2020-08-26_mcl1_sample/02_ligands/lig_26/crd/lig_26.sdf: -------------------------------------------------------------------------------- 1 | lig_26 2 | -OEChem-01312017293D 3 | 4 | 43 46 0 0 0 0 0 0 0999 V2000 5 | 3.8100 -50.0800 6.4300 O 0 5 0 0 0 0 0 0 0 0 0 0 6 | 2.9400 -49.1700 6.5100 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 3.2800 -47.9700 6.6700 O 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1.5200 -49.6100 6.4100 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1.0100 -51.1700 6.8300 O 0 0 0 0 0 0 0 0 0 0 0 0 10 | -0.6500 -51.0200 6.4700 C 0 0 0 0 0 0 0 0 0 0 0 0 11 | -1.7400 -51.8800 6.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | -1.5900 -52.9000 6.8900 H 0 0 0 0 0 0 0 0 0 0 0 0 13 | -3.0100 -51.4600 6.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 14 | -3.8500 -52.1300 6.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 15 | -3.1800 -50.1500 5.7300 C 0 0 0 0 0 0 0 0 0 0 0 0 16 | -4.1700 -49.8000 5.4500 H 0 0 0 0 0 0 0 0 0 0 0 0 17 | -2.1000 -49.2800 5.6300 C 0 0 0 0 0 0 0 0 0 0 0 0 18 | -2.2500 -48.2700 5.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 19 | -0.8300 -49.7000 6.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 20 | 0.3700 -48.9100 5.9700 C 0 0 0 0 0 0 0 0 0 0 0 0 21 | 0.4000 -47.4900 5.5200 C 0 0 0 0 0 0 0 0 0 0 0 0 22 | 1.1900 -47.3900 4.7800 H 0 0 0 0 0 0 0 0 0 0 0 0 23 | -0.5600 -47.2600 5.0600 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | 0.6500 -46.4800 6.6000 C 0 0 0 0 0 0 0 0 0 0 0 0 25 | 0.5300 -45.4900 6.1500 H 0 0 0 0 0 0 0 0 0 0 0 0 26 | 1.6900 -46.6000 6.9200 H 0 0 0 0 0 0 0 0 0 0 0 0 27 | -0.2000 -46.5200 7.8200 C 0 0 0 0 0 0 0 0 0 0 0 0 28 | 0.0400 -45.6700 8.4600 H 0 0 0 0 0 0 0 0 0 0 0 0 29 | 0.0000 -47.4400 8.3700 H 0 0 0 0 0 0 0 0 0 0 0 0 30 | -1.5400 -46.4700 7.4900 O 0 0 0 0 0 0 0 0 0 0 0 0 31 | -2.5500 -46.5300 8.4200 C 0 0 0 0 0 0 0 0 0 0 0 0 32 | -3.7500 -45.9100 8.1800 C 0 0 0 0 0 0 0 0 0 0 0 0 33 | -4.7500 -46.0000 9.1500 C 0 0 0 0 0 0 0 0 0 0 0 0 34 | -4.5400 -46.7000 10.3500 C 0 0 0 0 0 0 0 0 0 0 0 0 35 | -5.3300 -46.7500 11.0900 H 0 0 0 0 0 0 0 0 0 0 0 0 36 | -3.3200 -47.3200 10.5600 C 0 0 0 0 0 0 0 0 0 0 0 0 37 | -3.1500 -47.8600 11.4800 H 0 0 0 0 0 0 0 0 0 0 0 0 38 | -2.3200 -47.2400 9.5900 C 0 0 0 0 0 0 0 0 0 0 0 0 39 | -1.3800 -47.7300 9.7600 H 0 0 0 0 0 0 0 0 0 0 0 0 40 | -5.9900 -45.3600 8.9200 C 0 0 0 0 0 0 0 0 0 0 0 0 41 | -6.7700 -45.4300 9.6600 H 0 0 0 0 0 0 0 0 0 0 0 0 42 | -6.2300 -44.6600 7.7400 C 0 0 0 0 0 0 0 0 0 0 0 0 43 | -7.1900 -44.1800 7.5800 H 0 0 0 0 0 0 0 0 0 0 0 0 44 | -5.2300 -44.5700 6.7700 C 0 0 0 0 0 0 0 0 0 0 0 0 45 | -5.4200 -44.0200 5.8500 H 0 0 0 0 0 0 0 0 0 0 0 0 46 | -4.0000 -45.1800 6.9700 C 0 0 0 0 0 0 0 0 0 0 0 0 47 | -3.2300 -45.1100 6.2200 H 0 0 0 0 0 0 0 0 0 0 0 0 48 | 17 18 1 0 0 0 0 49 | 17 19 1 0 0 0 0 50 | 13 14 1 0 0 0 0 51 | 11 12 1 0 0 0 0 52 | 16 17 1 0 0 0 0 53 | 17 20 1 0 0 0 0 54 | 11 13 2 0 0 0 0 55 | 13 15 1 0 0 0 0 56 | 9 11 1 0 0 0 0 57 | 40 41 1 0 0 0 0 58 | 15 16 1 0 0 0 0 59 | 4 16 2 0 0 0 0 60 | 6 15 2 0 0 0 0 61 | 20 21 1 0 0 0 0 62 | 9 10 1 0 0 0 0 63 | 7 9 2 0 0 0 0 64 | 42 43 1 0 0 0 0 65 | 2 4 1 0 0 0 0 66 | 4 5 1 0 0 0 0 67 | 1 2 1 0 0 0 0 68 | 6 7 1 0 0 0 0 69 | 5 6 1 0 0 0 0 70 | 2 3 2 0 0 0 0 71 | 7 8 1 0 0 0 0 72 | 20 22 1 0 0 0 0 73 | 20 23 1 0 0 0 0 74 | 40 42 2 0 0 0 0 75 | 38 40 1 0 0 0 0 76 | 28 42 1 0 0 0 0 77 | 23 26 1 0 0 0 0 78 | 26 27 1 0 0 0 0 79 | 38 39 1 0 0 0 0 80 | 36 38 2 0 0 0 0 81 | 23 25 1 0 0 0 0 82 | 23 24 1 0 0 0 0 83 | 27 28 2 0 0 0 0 84 | 28 29 1 0 0 0 0 85 | 27 34 1 0 0 0 0 86 | 29 36 1 0 0 0 0 87 | 36 37 1 0 0 0 0 88 | 29 30 2 0 0 0 0 89 | 34 35 1 0 0 0 0 90 | 32 34 2 0 0 0 0 91 | 30 32 1 0 0 0 0 92 | 30 31 1 0 0 0 0 93 | 32 33 1 0 0 0 0 94 | M CHG 1 1 -1 95 | M END 96 | $$$$ 97 | -------------------------------------------------------------------------------- /plbenchmark/sample_data/2020-08-26_mcl1_sample/02_ligands/lig_27/crd/lig_27.sdf: -------------------------------------------------------------------------------- 1 | lig_27 2 | -OEChem-01312017293D 3 | 4 | 38 40 0 0 0 0 0 0 0999 V2000 5 | 3.8100 -50.0800 6.4300 O 0 5 0 0 0 0 0 0 0 0 0 0 6 | 2.9400 -49.1700 6.5100 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 3.2800 -47.9700 6.6700 O 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1.5200 -49.6100 6.4100 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1.0100 -51.1700 6.8300 N 0 0 0 0 0 0 0 0 0 0 0 0 10 | 1.5300 -51.9500 7.1800 H 0 0 0 0 0 0 0 0 0 0 0 0 11 | -0.6500 -51.0200 6.4700 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | -1.7400 -51.8800 6.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 13 | -1.5900 -52.9000 6.8900 H 0 0 0 0 0 0 0 0 0 0 0 0 14 | -3.0100 -51.4600 6.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 15 | -3.8500 -52.1300 6.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 16 | -3.1800 -50.1500 5.7300 C 0 0 0 0 0 0 0 0 0 0 0 0 17 | -4.1700 -49.8000 5.4500 H 0 0 0 0 0 0 0 0 0 0 0 0 18 | -2.1000 -49.2800 5.6300 C 0 0 0 0 0 0 0 0 0 0 0 0 19 | -2.2500 -48.2700 5.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 20 | -0.8300 -49.7000 6.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 21 | 0.3700 -48.9100 5.9700 C 0 0 0 0 0 0 0 0 0 0 0 0 22 | 0.4000 -47.4900 5.5200 C 0 0 0 0 0 0 0 0 0 0 0 0 23 | 1.2600 -47.3600 4.8600 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | -0.5200 -47.2900 4.9700 H 0 0 0 0 0 0 0 0 0 0 0 0 25 | 0.5100 -46.4700 6.6100 C 0 0 0 0 0 0 0 0 0 0 0 0 26 | 0.4000 -45.4900 6.1500 H 0 0 0 0 0 0 0 0 0 0 0 0 27 | 1.5100 -46.5600 7.0400 H 0 0 0 0 0 0 0 0 0 0 0 0 28 | -0.4600 -46.5400 7.7500 C 0 0 0 0 0 0 0 0 0 0 0 0 29 | -0.1100 -45.8900 8.5500 H 0 0 0 0 0 0 0 0 0 0 0 0 30 | -0.5100 -47.5600 8.1100 H 0 0 0 0 0 0 0 0 0 0 0 0 31 | -1.7200 -46.1400 7.3400 O 0 0 0 0 0 0 0 0 0 0 0 0 32 | -2.8000 -46.1300 8.1700 C 0 0 0 0 0 0 0 0 0 0 0 0 33 | -2.7900 -46.8600 9.3500 C 0 0 0 0 0 0 0 0 0 0 0 0 34 | -1.9300 -47.4400 9.6300 H 0 0 0 0 0 0 0 0 0 0 0 0 35 | -3.9200 -46.8200 10.1600 C 0 0 0 0 0 0 0 0 0 0 0 0 36 | -3.9200 -47.3900 11.0900 H 0 0 0 0 0 0 0 0 0 0 0 0 37 | -5.0500 -46.0800 9.8100 C 0 0 0 0 0 0 0 0 0 0 0 0 38 | -5.9200 -46.0600 10.4600 H 0 0 0 0 0 0 0 0 0 0 0 0 39 | -5.0400 -45.3600 8.6300 C 0 0 0 0 0 0 0 0 0 0 0 0 40 | -5.9100 -44.7800 8.3400 H 0 0 0 0 0 0 0 0 0 0 0 0 41 | -3.9100 -45.3800 7.8100 C 0 0 0 0 0 0 0 0 0 0 0 0 42 | -3.9000 -44.8100 6.8900 H 0 0 0 0 0 0 0 0 0 0 0 0 43 | 18 19 1 0 0 0 0 44 | 18 20 1 0 0 0 0 45 | 14 15 1 0 0 0 0 46 | 12 13 1 0 0 0 0 47 | 17 18 1 0 0 0 0 48 | 18 21 1 0 0 0 0 49 | 12 14 2 0 0 0 0 50 | 14 16 1 0 0 0 0 51 | 10 12 1 0 0 0 0 52 | 16 17 1 0 0 0 0 53 | 4 17 2 0 0 0 0 54 | 7 16 2 0 0 0 0 55 | 21 22 1 0 0 0 0 56 | 10 11 1 0 0 0 0 57 | 8 10 2 0 0 0 0 58 | 2 4 1 0 0 0 0 59 | 4 5 1 0 0 0 0 60 | 1 2 1 0 0 0 0 61 | 7 8 1 0 0 0 0 62 | 5 7 1 0 0 0 0 63 | 2 3 2 0 0 0 0 64 | 8 9 1 0 0 0 0 65 | 21 23 1 0 0 0 0 66 | 21 24 1 0 0 0 0 67 | 5 6 1 0 0 0 0 68 | 37 38 1 0 0 0 0 69 | 24 27 1 0 0 0 0 70 | 27 28 1 0 0 0 0 71 | 24 26 1 0 0 0 0 72 | 24 25 1 0 0 0 0 73 | 28 37 2 0 0 0 0 74 | 35 37 1 0 0 0 0 75 | 28 29 1 0 0 0 0 76 | 35 36 1 0 0 0 0 77 | 33 35 2 0 0 0 0 78 | 29 30 1 0 0 0 0 79 | 29 31 2 0 0 0 0 80 | 31 33 1 0 0 0 0 81 | 33 34 1 0 0 0 0 82 | 31 32 1 0 0 0 0 83 | M CHG 1 1 -1 84 | M END 85 | $$$$ 86 | -------------------------------------------------------------------------------- /plbenchmark/sample_data/2020-08-26_mcl1_sample/02_ligands/lig_28/crd/lig_28.sdf: -------------------------------------------------------------------------------- 1 | lig_28 2 | -OEChem-01312017293D 3 | 4 | 41 43 0 0 0 0 0 0 0999 V2000 5 | 3.8100 -50.0800 6.4300 O 0 5 0 0 0 0 0 0 0 0 0 0 6 | 2.9400 -49.1700 6.5100 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 3.2800 -47.9700 6.6700 O 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1.5200 -49.6100 6.4100 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1.0100 -51.1700 6.8300 N 0 0 0 0 0 0 0 0 0 0 0 0 10 | 1.5300 -51.9500 7.1800 H 0 0 0 0 0 0 0 0 0 0 0 0 11 | -0.6500 -51.0200 6.4700 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | -1.7400 -51.8800 6.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 13 | -1.5900 -52.9000 6.8900 H 0 0 0 0 0 0 0 0 0 0 0 0 14 | -3.0100 -51.4600 6.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 15 | -3.8500 -52.1300 6.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 16 | -3.1800 -50.1500 5.7300 C 0 0 0 0 0 0 0 0 0 0 0 0 17 | -4.1700 -49.8000 5.4500 H 0 0 0 0 0 0 0 0 0 0 0 0 18 | -2.1000 -49.2800 5.6300 C 0 0 0 0 0 0 0 0 0 0 0 0 19 | -2.2500 -48.2700 5.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 20 | -0.8300 -49.7000 6.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 21 | 0.3700 -48.9100 5.9700 C 0 0 0 0 0 0 0 0 0 0 0 0 22 | 0.4000 -47.4900 5.5200 C 0 0 0 0 0 0 0 0 0 0 0 0 23 | 1.1900 -47.3900 4.7800 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | -0.5600 -47.2600 5.0600 H 0 0 0 0 0 0 0 0 0 0 0 0 25 | 0.6500 -46.4800 6.6000 C 0 0 0 0 0 0 0 0 0 0 0 0 26 | 0.6300 -45.5000 6.1300 H 0 0 0 0 0 0 0 0 0 0 0 0 27 | 1.6500 -46.6700 6.9900 H 0 0 0 0 0 0 0 0 0 0 0 0 28 | -0.2800 -46.4300 7.7600 C 0 0 0 0 0 0 0 0 0 0 0 0 29 | -0.0300 -45.5900 8.4000 H 0 0 0 0 0 0 0 0 0 0 0 0 30 | -0.1900 -47.3600 8.3300 H 0 0 0 0 0 0 0 0 0 0 0 0 31 | -1.5900 -46.2900 7.3300 O 0 0 0 0 0 0 0 0 0 0 0 0 32 | -2.6600 -46.2600 8.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 33 | -2.6200 -46.9200 9.3900 C 0 0 0 0 0 0 0 0 0 0 0 0 34 | -1.7400 -47.4900 9.6800 H 0 0 0 0 0 0 0 0 0 0 0 0 35 | -3.7300 -46.8600 10.2300 C 0 0 0 0 0 0 0 0 0 0 0 0 36 | -3.7000 -47.3800 11.1800 H 0 0 0 0 0 0 0 0 0 0 0 0 37 | -4.8700 -46.1400 9.8700 C 0 0 0 0 0 0 0 0 0 0 0 0 38 | -5.7200 -46.1000 10.5400 H 0 0 0 0 0 0 0 0 0 0 0 0 39 | -4.8900 -45.4700 8.6600 C 0 0 0 0 0 0 0 0 0 0 0 0 40 | -5.7700 -44.9100 8.3700 H 0 0 0 0 0 0 0 0 0 0 0 0 41 | -3.8000 -44.8300 6.5700 C 0 0 0 0 0 0 0 0 0 0 0 0 42 | -2.8500 -44.9900 6.0500 H 0 0 0 0 0 0 0 0 0 0 0 0 43 | -3.9400 -43.7700 6.7500 H 0 0 0 0 0 0 0 0 0 0 0 0 44 | -4.6200 -45.2100 5.9600 H 0 0 0 0 0 0 0 0 0 0 0 0 45 | -3.7800 -45.5300 7.8200 C 0 0 0 0 0 0 0 0 0 0 0 0 46 | 18 19 1 0 0 0 0 47 | 18 20 1 0 0 0 0 48 | 14 15 1 0 0 0 0 49 | 12 13 1 0 0 0 0 50 | 17 18 1 0 0 0 0 51 | 18 21 1 0 0 0 0 52 | 12 14 2 0 0 0 0 53 | 14 16 1 0 0 0 0 54 | 10 12 1 0 0 0 0 55 | 37 40 1 0 0 0 0 56 | 16 17 1 0 0 0 0 57 | 4 17 2 0 0 0 0 58 | 7 16 2 0 0 0 0 59 | 37 38 1 0 0 0 0 60 | 21 22 1 0 0 0 0 61 | 10 11 1 0 0 0 0 62 | 8 10 2 0 0 0 0 63 | 2 4 1 0 0 0 0 64 | 4 5 1 0 0 0 0 65 | 1 2 1 0 0 0 0 66 | 7 8 1 0 0 0 0 67 | 5 7 1 0 0 0 0 68 | 2 3 2 0 0 0 0 69 | 8 9 1 0 0 0 0 70 | 37 39 1 0 0 0 0 71 | 37 41 1 0 0 0 0 72 | 21 23 1 0 0 0 0 73 | 21 24 1 0 0 0 0 74 | 5 6 1 0 0 0 0 75 | 24 27 1 0 0 0 0 76 | 27 28 1 0 0 0 0 77 | 24 26 1 0 0 0 0 78 | 24 25 1 0 0 0 0 79 | 28 41 2 0 0 0 0 80 | 35 41 1 0 0 0 0 81 | 28 29 1 0 0 0 0 82 | 35 36 1 0 0 0 0 83 | 33 35 2 0 0 0 0 84 | 29 30 1 0 0 0 0 85 | 29 31 2 0 0 0 0 86 | 31 33 1 0 0 0 0 87 | 33 34 1 0 0 0 0 88 | 31 32 1 0 0 0 0 89 | M CHG 1 1 -1 90 | M END 91 | $$$$ 92 | -------------------------------------------------------------------------------- /plbenchmark/sample_data/2020-08-26_mcl1_sample/02_ligands/lig_29/crd/lig_29.sdf: -------------------------------------------------------------------------------- 1 | lig_29 2 | -OEChem-01312015113D 3 | 4 | 41 43 0 0 0 0 0 0 0999 V2000 5 | 3.8100 -50.0800 6.4300 O 0 5 0 0 0 0 0 0 0 0 0 0 6 | 2.9400 -49.1700 6.5100 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 3.2800 -47.9700 6.6700 O 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1.5200 -49.6100 6.4100 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1.0100 -51.1700 6.8300 N 0 0 0 0 0 0 0 0 0 0 0 0 10 | 1.5300 -51.9500 7.1800 H 0 0 0 0 0 0 0 0 0 0 0 0 11 | -0.6500 -51.0200 6.4700 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | -1.7400 -51.8800 6.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 13 | -1.5900 -52.9000 6.8900 H 0 0 0 0 0 0 0 0 0 0 0 0 14 | -3.0100 -51.4600 6.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 15 | -3.8500 -52.1300 6.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 16 | -3.1800 -50.1500 5.7300 C 0 0 0 0 0 0 0 0 0 0 0 0 17 | -4.1700 -49.8000 5.4500 H 0 0 0 0 0 0 0 0 0 0 0 0 18 | -2.1000 -49.2800 5.6300 C 0 0 0 0 0 0 0 0 0 0 0 0 19 | -2.2500 -48.2700 5.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 20 | -0.8300 -49.7000 6.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 21 | 0.3700 -48.9100 5.9700 C 0 0 0 0 0 0 0 0 0 0 0 0 22 | 0.4000 -47.4900 5.5200 C 0 0 0 0 0 0 0 0 0 0 0 0 23 | 1.1900 -47.3900 4.7800 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | -0.5600 -47.2600 5.0600 H 0 0 0 0 0 0 0 0 0 0 0 0 25 | 0.6500 -46.4800 6.6000 C 0 0 0 0 0 0 0 0 0 0 0 0 26 | 0.6300 -45.5000 6.1300 H 0 0 0 0 0 0 0 0 0 0 0 0 27 | 1.6500 -46.6700 6.9900 H 0 0 0 0 0 0 0 0 0 0 0 0 28 | -0.2800 -46.4300 7.7600 C 0 0 0 0 0 0 0 0 0 0 0 0 29 | -0.0300 -45.5900 8.4000 H 0 0 0 0 0 0 0 0 0 0 0 0 30 | -1.5900 -46.2900 7.3300 O 0 0 0 0 0 0 0 0 0 0 0 0 31 | -2.6600 -46.2600 8.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 32 | -2.6200 -46.9200 9.3900 C 0 0 0 0 0 0 0 0 0 0 0 0 33 | -1.4600 -47.6700 9.7700 C 0 0 0 0 0 0 0 0 0 0 0 0 34 | -1.8000 -49.0000 9.9600 F 0 0 0 0 0 0 0 0 0 0 0 0 35 | -0.9400 -47.1600 10.9500 F 0 0 0 0 0 0 0 0 0 0 0 0 36 | -3.7300 -46.8600 10.2300 C 0 0 0 0 0 0 0 0 0 0 0 0 37 | -3.7000 -47.3800 11.1800 H 0 0 0 0 0 0 0 0 0 0 0 0 38 | -4.8700 -46.1400 9.8700 C 0 0 0 0 0 0 0 0 0 0 0 0 39 | -5.7200 -46.1000 10.5400 H 0 0 0 0 0 0 0 0 0 0 0 0 40 | -4.8900 -45.4700 8.6600 C 0 0 0 0 0 0 0 0 0 0 0 0 41 | -5.7700 -44.9100 8.3700 H 0 0 0 0 0 0 0 0 0 0 0 0 42 | -3.7800 -45.5300 7.8200 C 0 0 0 0 0 0 0 0 0 0 0 0 43 | -3.8000 -45.0000 6.8700 H 0 0 0 0 0 0 0 0 0 0 0 0 44 | -0.1884 -47.3538 8.3312 H 0 0 0 0 0 0 0 0 0 0 0 0 45 | -0.5094 -47.5785 8.7738 F 0 0 0 0 0 0 0 0 0 0 0 0 46 | 1 2 1 0 0 0 0 47 | 2 3 2 0 0 0 0 48 | 2 4 1 0 0 0 0 49 | 4 5 1 0 0 0 0 50 | 4 17 2 0 0 0 0 51 | 5 6 1 0 0 0 0 52 | 5 7 1 0 0 0 0 53 | 7 8 2 0 0 0 0 54 | 7 16 1 0 0 0 0 55 | 8 9 1 0 0 0 0 56 | 8 10 1 0 0 0 0 57 | 10 11 1 0 0 0 0 58 | 10 12 2 0 0 0 0 59 | 12 13 1 0 0 0 0 60 | 12 14 1 0 0 0 0 61 | 14 15 1 0 0 0 0 62 | 14 16 2 0 0 0 0 63 | 16 17 1 0 0 0 0 64 | 17 18 1 0 0 0 0 65 | 18 19 1 0 0 0 0 66 | 18 20 1 0 0 0 0 67 | 18 21 1 0 0 0 0 68 | 21 22 1 0 0 0 0 69 | 21 23 1 0 0 0 0 70 | 21 24 1 0 0 0 0 71 | 24 25 1 0 0 0 0 72 | 24 26 1 0 0 0 0 73 | 24 40 1 0 0 0 0 74 | 26 27 1 0 0 0 0 75 | 27 28 2 0 0 0 0 76 | 27 38 1 0 0 0 0 77 | 28 29 1 0 0 0 0 78 | 28 32 1 0 0 0 0 79 | 29 30 1 0 0 0 0 80 | 29 31 1 0 0 0 0 81 | 29 41 1 0 0 0 0 82 | 32 33 1 0 0 0 0 83 | 32 34 2 0 0 0 0 84 | 34 35 1 0 0 0 0 85 | 34 36 1 0 0 0 0 86 | 36 37 1 0 0 0 0 87 | 36 38 2 0 0 0 0 88 | 38 39 1 0 0 0 0 89 | M CHG 1 1 -1 90 | M END 91 | $$$$ 92 | -------------------------------------------------------------------------------- /plbenchmark/sample_data/2020-08-26_mcl1_sample/02_ligands/lig_30/crd/lig_30.sdf: -------------------------------------------------------------------------------- 1 | lig_30 2 | -OEChem-01312017293D 3 | 4 | 41 43 0 0 0 0 0 0 0999 V2000 5 | 3.8100 -50.0800 6.4300 O 0 5 0 0 0 0 0 0 0 0 0 0 6 | 2.9400 -49.1700 6.5100 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 3.2800 -47.9700 6.6700 O 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1.5200 -49.6100 6.4100 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1.0100 -51.1700 6.8300 N 0 0 0 0 0 0 0 0 0 0 0 0 10 | 1.5300 -51.9500 7.1800 H 0 0 0 0 0 0 0 0 0 0 0 0 11 | -0.6500 -51.0200 6.4700 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | -1.7400 -51.8800 6.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 13 | -1.5900 -52.9000 6.8900 H 0 0 0 0 0 0 0 0 0 0 0 0 14 | -3.0100 -51.4600 6.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 15 | -3.8500 -52.1300 6.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 16 | -3.1800 -50.1500 5.7300 C 0 0 0 0 0 0 0 0 0 0 0 0 17 | -4.1700 -49.8000 5.4500 H 0 0 0 0 0 0 0 0 0 0 0 0 18 | -2.1000 -49.2800 5.6300 C 0 0 0 0 0 0 0 0 0 0 0 0 19 | -2.2500 -48.2700 5.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 20 | -0.8300 -49.7000 6.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 21 | 0.3700 -48.9100 5.9700 C 0 0 0 0 0 0 0 0 0 0 0 0 22 | 0.4000 -47.4900 5.5200 C 0 0 0 0 0 0 0 0 0 0 0 0 23 | 1.1900 -47.3900 4.7800 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | -0.5600 -47.2600 5.0600 H 0 0 0 0 0 0 0 0 0 0 0 0 25 | 0.6500 -46.4800 6.6000 C 0 0 0 0 0 0 0 0 0 0 0 0 26 | 0.6300 -45.5000 6.1300 H 0 0 0 0 0 0 0 0 0 0 0 0 27 | 1.6500 -46.6700 6.9900 H 0 0 0 0 0 0 0 0 0 0 0 0 28 | -0.2800 -46.4300 7.7600 C 0 0 0 0 0 0 0 0 0 0 0 0 29 | -0.0300 -45.5900 8.4000 H 0 0 0 0 0 0 0 0 0 0 0 0 30 | -0.1900 -47.3600 8.3300 H 0 0 0 0 0 0 0 0 0 0 0 0 31 | -1.5900 -46.2900 7.3300 O 0 0 0 0 0 0 0 0 0 0 0 0 32 | -2.6600 -46.2600 8.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 33 | -2.6200 -46.9200 9.3900 C 0 0 0 0 0 0 0 0 0 0 0 0 34 | -1.7400 -47.4900 9.6800 H 0 0 0 0 0 0 0 0 0 0 0 0 35 | -3.7300 -46.8600 10.2300 C 0 0 0 0 0 0 0 0 0 0 0 0 36 | -3.7000 -47.5500 11.4800 C 0 0 0 0 0 0 0 0 0 0 0 0 37 | -2.7400 -48.0500 11.6000 H 0 0 0 0 0 0 0 0 0 0 0 0 38 | -4.5000 -48.2800 11.5200 H 0 0 0 0 0 0 0 0 0 0 0 0 39 | -3.8300 -46.8300 12.2900 H 0 0 0 0 0 0 0 0 0 0 0 0 40 | -4.8700 -46.1400 9.8700 C 0 0 0 0 0 0 0 0 0 0 0 0 41 | -5.7200 -46.1000 10.5400 H 0 0 0 0 0 0 0 0 0 0 0 0 42 | -4.8900 -45.4700 8.6600 C 0 0 0 0 0 0 0 0 0 0 0 0 43 | -5.7700 -44.9100 8.3700 H 0 0 0 0 0 0 0 0 0 0 0 0 44 | -3.7800 -45.5300 7.8200 C 0 0 0 0 0 0 0 0 0 0 0 0 45 | -3.8000 -45.0000 6.8700 H 0 0 0 0 0 0 0 0 0 0 0 0 46 | 18 19 1 0 0 0 0 47 | 18 20 1 0 0 0 0 48 | 14 15 1 0 0 0 0 49 | 12 13 1 0 0 0 0 50 | 17 18 1 0 0 0 0 51 | 18 21 1 0 0 0 0 52 | 12 14 2 0 0 0 0 53 | 14 16 1 0 0 0 0 54 | 10 12 1 0 0 0 0 55 | 16 17 1 0 0 0 0 56 | 4 17 2 0 0 0 0 57 | 7 16 2 0 0 0 0 58 | 21 22 1 0 0 0 0 59 | 10 11 1 0 0 0 0 60 | 8 10 2 0 0 0 0 61 | 2 4 1 0 0 0 0 62 | 4 5 1 0 0 0 0 63 | 1 2 1 0 0 0 0 64 | 7 8 1 0 0 0 0 65 | 5 7 1 0 0 0 0 66 | 2 3 2 0 0 0 0 67 | 8 9 1 0 0 0 0 68 | 21 23 1 0 0 0 0 69 | 21 24 1 0 0 0 0 70 | 5 6 1 0 0 0 0 71 | 40 41 1 0 0 0 0 72 | 24 27 1 0 0 0 0 73 | 27 28 1 0 0 0 0 74 | 24 26 1 0 0 0 0 75 | 24 25 1 0 0 0 0 76 | 28 40 2 0 0 0 0 77 | 38 40 1 0 0 0 0 78 | 28 29 1 0 0 0 0 79 | 38 39 1 0 0 0 0 80 | 36 38 2 0 0 0 0 81 | 29 30 1 0 0 0 0 82 | 29 31 2 0 0 0 0 83 | 31 36 1 0 0 0 0 84 | 36 37 1 0 0 0 0 85 | 31 32 1 0 0 0 0 86 | 32 34 1 0 0 0 0 87 | 32 33 1 0 0 0 0 88 | 32 35 1 0 0 0 0 89 | M CHG 1 1 -1 90 | M END 91 | $$$$ 92 | -------------------------------------------------------------------------------- /plbenchmark/sample_data/2020-08-26_mcl1_sample/02_ligands/lig_31/crd/lig_31.sdf: -------------------------------------------------------------------------------- 1 | lig_31 2 | -OEChem-01312017293D 3 | 4 | 41 43 0 0 0 0 0 0 0999 V2000 5 | 3.8100 -50.0800 6.4300 O 0 5 0 0 0 0 0 0 0 0 0 0 6 | 2.9400 -49.1700 6.5100 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 3.2800 -47.9700 6.6700 O 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1.5200 -49.6100 6.4100 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1.0100 -51.1700 6.8300 N 0 0 0 0 0 0 0 0 0 0 0 0 10 | 1.5300 -51.9500 7.1800 H 0 0 0 0 0 0 0 0 0 0 0 0 11 | -0.6500 -51.0200 6.4700 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | -1.7400 -51.8800 6.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 13 | -1.5900 -52.9000 6.8900 H 0 0 0 0 0 0 0 0 0 0 0 0 14 | -3.0100 -51.4600 6.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 15 | -3.8500 -52.1300 6.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 16 | -3.1800 -50.1500 5.7300 C 0 0 0 0 0 0 0 0 0 0 0 0 17 | -4.1700 -49.8000 5.4500 H 0 0 0 0 0 0 0 0 0 0 0 0 18 | -2.1000 -49.2800 5.6300 C 0 0 0 0 0 0 0 0 0 0 0 0 19 | -2.2500 -48.2700 5.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 20 | -0.8300 -49.7000 6.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 21 | 0.3700 -48.9100 5.9700 C 0 0 0 0 0 0 0 0 0 0 0 0 22 | 0.4000 -47.4900 5.5200 C 0 0 0 0 0 0 0 0 0 0 0 0 23 | 1.2300 -47.3700 4.8200 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | -0.5400 -47.2800 5.0200 H 0 0 0 0 0 0 0 0 0 0 0 0 25 | 0.5800 -46.4700 6.6100 C 0 0 0 0 0 0 0 0 0 0 0 0 26 | 0.4600 -45.4900 6.1500 H 0 0 0 0 0 0 0 0 0 0 0 0 27 | 1.6000 -46.5800 6.9800 H 0 0 0 0 0 0 0 0 0 0 0 0 28 | -0.3300 -46.5300 7.7900 C 0 0 0 0 0 0 0 0 0 0 0 0 29 | -0.0600 -45.7300 8.4900 H 0 0 0 0 0 0 0 0 0 0 0 0 30 | -0.2200 -47.5000 8.2800 H 0 0 0 0 0 0 0 0 0 0 0 0 31 | -1.6500 -46.3700 7.4000 O 0 0 0 0 0 0 0 0 0 0 0 0 32 | -2.6800 -46.2900 8.2900 C 0 0 0 0 0 0 0 0 0 0 0 0 33 | -2.6200 -46.9400 9.5000 C 0 0 0 0 0 0 0 0 0 0 0 0 34 | -1.7400 -47.5100 9.7700 H 0 0 0 0 0 0 0 0 0 0 0 0 35 | -3.7000 -46.8300 10.3800 C 0 0 0 0 0 0 0 0 0 0 0 0 36 | -3.6400 -47.4900 11.6400 C 0 0 0 0 0 0 0 0 0 0 0 0 37 | -2.4300 -48.1600 11.7600 F 0 0 0 0 0 0 0 0 0 0 0 0 38 | -4.6800 -48.4000 11.7400 F 0 0 0 0 0 0 0 0 0 0 0 0 39 | -3.7500 -46.5500 12.6600 F 0 0 0 0 0 0 0 0 0 0 0 0 40 | -4.8300 -46.0900 10.0400 C 0 0 0 0 0 0 0 0 0 0 0 0 41 | -5.6600 -46.0200 10.7300 H 0 0 0 0 0 0 0 0 0 0 0 0 42 | -4.8800 -45.4500 8.8200 C 0 0 0 0 0 0 0 0 0 0 0 0 43 | -5.7600 -44.8700 8.5400 H 0 0 0 0 0 0 0 0 0 0 0 0 44 | -3.8000 -45.5400 7.9400 C 0 0 0 0 0 0 0 0 0 0 0 0 45 | -3.8400 -45.0400 6.9900 H 0 0 0 0 0 0 0 0 0 0 0 0 46 | 18 19 1 0 0 0 0 47 | 18 20 1 0 0 0 0 48 | 14 15 1 0 0 0 0 49 | 12 13 1 0 0 0 0 50 | 17 18 1 0 0 0 0 51 | 18 21 1 0 0 0 0 52 | 12 14 2 0 0 0 0 53 | 14 16 1 0 0 0 0 54 | 10 12 1 0 0 0 0 55 | 16 17 1 0 0 0 0 56 | 4 17 2 0 0 0 0 57 | 7 16 2 0 0 0 0 58 | 21 22 1 0 0 0 0 59 | 10 11 1 0 0 0 0 60 | 8 10 2 0 0 0 0 61 | 2 4 1 0 0 0 0 62 | 4 5 1 0 0 0 0 63 | 1 2 1 0 0 0 0 64 | 7 8 1 0 0 0 0 65 | 5 7 1 0 0 0 0 66 | 2 3 2 0 0 0 0 67 | 8 9 1 0 0 0 0 68 | 21 23 1 0 0 0 0 69 | 21 24 1 0 0 0 0 70 | 5 6 1 0 0 0 0 71 | 40 41 1 0 0 0 0 72 | 24 27 1 0 0 0 0 73 | 27 28 1 0 0 0 0 74 | 24 26 1 0 0 0 0 75 | 24 25 1 0 0 0 0 76 | 28 40 2 0 0 0 0 77 | 38 40 1 0 0 0 0 78 | 28 29 1 0 0 0 0 79 | 38 39 1 0 0 0 0 80 | 36 38 2 0 0 0 0 81 | 29 30 1 0 0 0 0 82 | 29 31 2 0 0 0 0 83 | 31 36 1 0 0 0 0 84 | 36 37 1 0 0 0 0 85 | 31 32 1 0 0 0 0 86 | 32 34 1 0 0 0 0 87 | 32 33 1 0 0 0 0 88 | 32 35 1 0 0 0 0 89 | M CHG 1 1 -1 90 | M END 91 | $$$$ 92 | -------------------------------------------------------------------------------- /plbenchmark/sample_data/2020-08-26_mcl1_sample/02_ligands/lig_32/crd/lig_32.sdf: -------------------------------------------------------------------------------- 1 | lig_32 2 | -OEChem-01312017293D 3 | 4 | 41 43 0 0 0 0 0 0 0999 V2000 5 | 3.8100 -50.0800 6.4300 O 0 5 0 0 0 0 0 0 0 0 0 0 6 | 2.9400 -49.1700 6.5100 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 3.2800 -47.9700 6.6700 O 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1.5200 -49.6100 6.4100 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1.0100 -51.1700 6.8300 N 0 0 0 0 0 0 0 0 0 0 0 0 10 | 1.5300 -51.9500 7.1800 H 0 0 0 0 0 0 0 0 0 0 0 0 11 | -0.6500 -51.0200 6.4700 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | -1.7400 -51.8800 6.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 13 | -1.5900 -52.9000 6.8900 H 0 0 0 0 0 0 0 0 0 0 0 0 14 | -3.0100 -51.4600 6.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 15 | -3.8500 -52.1300 6.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 16 | -3.1800 -50.1500 5.7300 C 0 0 0 0 0 0 0 0 0 0 0 0 17 | -4.1700 -49.8000 5.4500 H 0 0 0 0 0 0 0 0 0 0 0 0 18 | -2.1000 -49.2800 5.6300 C 0 0 0 0 0 0 0 0 0 0 0 0 19 | -2.2500 -48.2700 5.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 20 | -0.8300 -49.7000 6.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 21 | 0.3700 -48.9100 5.9700 C 0 0 0 0 0 0 0 0 0 0 0 0 22 | 0.4000 -47.4900 5.5200 C 0 0 0 0 0 0 0 0 0 0 0 0 23 | 1.1900 -47.3900 4.7800 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | -0.5600 -47.2600 5.0600 H 0 0 0 0 0 0 0 0 0 0 0 0 25 | 0.6500 -46.4800 6.6000 C 0 0 0 0 0 0 0 0 0 0 0 0 26 | 0.6300 -45.5000 6.1300 H 0 0 0 0 0 0 0 0 0 0 0 0 27 | 1.6500 -46.6700 6.9900 H 0 0 0 0 0 0 0 0 0 0 0 0 28 | -0.2800 -46.4300 7.7600 C 0 0 0 0 0 0 0 0 0 0 0 0 29 | -0.0300 -45.5900 8.4000 H 0 0 0 0 0 0 0 0 0 0 0 0 30 | -0.1900 -47.3600 8.3300 H 0 0 0 0 0 0 0 0 0 0 0 0 31 | -1.5900 -46.2900 7.3300 O 0 0 0 0 0 0 0 0 0 0 0 0 32 | -2.6600 -46.2600 8.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 33 | -2.6200 -46.9200 9.3900 C 0 0 0 0 0 0 0 0 0 0 0 0 34 | -1.7400 -47.4900 9.6800 H 0 0 0 0 0 0 0 0 0 0 0 0 35 | -3.7300 -46.8600 10.2300 C 0 0 0 0 0 0 0 0 0 0 0 0 36 | -3.7000 -47.3800 11.1800 H 0 0 0 0 0 0 0 0 0 0 0 0 37 | -4.8700 -46.1400 9.8700 C 0 0 0 0 0 0 0 0 0 0 0 0 38 | -5.9900 -46.0900 10.7500 C 0 0 0 0 0 0 0 0 0 0 0 0 39 | -5.7800 -46.6700 11.6500 H 0 0 0 0 0 0 0 0 0 0 0 0 40 | -6.8700 -46.5000 10.2400 H 0 0 0 0 0 0 0 0 0 0 0 0 41 | -6.1900 -45.0500 11.0300 H 0 0 0 0 0 0 0 0 0 0 0 0 42 | -4.8900 -45.4700 8.6600 C 0 0 0 0 0 0 0 0 0 0 0 0 43 | -5.7700 -44.9100 8.3700 H 0 0 0 0 0 0 0 0 0 0 0 0 44 | -3.7800 -45.5300 7.8200 C 0 0 0 0 0 0 0 0 0 0 0 0 45 | -3.8000 -45.0000 6.8700 H 0 0 0 0 0 0 0 0 0 0 0 0 46 | 18 19 1 0 0 0 0 47 | 18 20 1 0 0 0 0 48 | 14 15 1 0 0 0 0 49 | 12 13 1 0 0 0 0 50 | 17 18 1 0 0 0 0 51 | 18 21 1 0 0 0 0 52 | 12 14 2 0 0 0 0 53 | 14 16 1 0 0 0 0 54 | 10 12 1 0 0 0 0 55 | 16 17 1 0 0 0 0 56 | 4 17 2 0 0 0 0 57 | 7 16 2 0 0 0 0 58 | 21 22 1 0 0 0 0 59 | 10 11 1 0 0 0 0 60 | 8 10 2 0 0 0 0 61 | 2 4 1 0 0 0 0 62 | 4 5 1 0 0 0 0 63 | 1 2 1 0 0 0 0 64 | 7 8 1 0 0 0 0 65 | 5 7 1 0 0 0 0 66 | 2 3 2 0 0 0 0 67 | 8 9 1 0 0 0 0 68 | 21 23 1 0 0 0 0 69 | 21 24 1 0 0 0 0 70 | 5 6 1 0 0 0 0 71 | 40 41 1 0 0 0 0 72 | 24 27 1 0 0 0 0 73 | 27 28 1 0 0 0 0 74 | 24 26 1 0 0 0 0 75 | 24 25 1 0 0 0 0 76 | 28 40 2 0 0 0 0 77 | 38 40 1 0 0 0 0 78 | 28 29 1 0 0 0 0 79 | 38 39 1 0 0 0 0 80 | 33 38 2 0 0 0 0 81 | 29 30 1 0 0 0 0 82 | 29 31 2 0 0 0 0 83 | 31 33 1 0 0 0 0 84 | 33 34 1 0 0 0 0 85 | 31 32 1 0 0 0 0 86 | 34 36 1 0 0 0 0 87 | 34 37 1 0 0 0 0 88 | 34 35 1 0 0 0 0 89 | M CHG 1 1 -1 90 | M END 91 | $$$$ 92 | -------------------------------------------------------------------------------- /plbenchmark/sample_data/2020-08-26_mcl1_sample/02_ligands/lig_33/crd/lig_33.sdf: -------------------------------------------------------------------------------- 1 | lig_33 2 | -OEChem-01312017293D 3 | 4 | 38 40 0 0 0 0 0 0 0999 V2000 5 | 3.8100 -50.0800 6.4300 O 0 5 0 0 0 0 0 0 0 0 0 0 6 | 2.9400 -49.1700 6.5100 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 3.2800 -47.9700 6.6700 O 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1.5200 -49.6100 6.4100 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1.0100 -51.1700 6.8300 N 0 0 0 0 0 0 0 0 0 0 0 0 10 | 1.5300 -51.9500 7.1800 H 0 0 0 0 0 0 0 0 0 0 0 0 11 | -0.6500 -51.0200 6.4700 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | -1.7400 -51.8800 6.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 13 | -1.5900 -52.9000 6.8900 H 0 0 0 0 0 0 0 0 0 0 0 0 14 | -3.0100 -51.4600 6.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 15 | -3.8500 -52.1300 6.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 16 | -3.1800 -50.1500 5.7300 C 0 0 0 0 0 0 0 0 0 0 0 0 17 | -4.1700 -49.8000 5.4500 H 0 0 0 0 0 0 0 0 0 0 0 0 18 | -2.1000 -49.2800 5.6300 C 0 0 0 0 0 0 0 0 0 0 0 0 19 | -2.2500 -48.2700 5.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 20 | -0.8300 -49.7000 6.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 21 | 0.3700 -48.9100 5.9700 C 0 0 0 0 0 0 0 0 0 0 0 0 22 | 0.4000 -47.4900 5.5200 C 0 0 0 0 0 0 0 0 0 0 0 0 23 | 1.1900 -47.3900 4.7800 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | -0.5600 -47.2600 5.0600 H 0 0 0 0 0 0 0 0 0 0 0 0 25 | 0.6500 -46.4800 6.6000 C 0 0 0 0 0 0 0 0 0 0 0 0 26 | 0.6300 -45.5000 6.1300 H 0 0 0 0 0 0 0 0 0 0 0 0 27 | 1.6500 -46.6700 6.9900 H 0 0 0 0 0 0 0 0 0 0 0 0 28 | -0.2800 -46.4300 7.7600 C 0 0 0 0 0 0 0 0 0 0 0 0 29 | -0.0300 -45.5900 8.4000 H 0 0 0 0 0 0 0 0 0 0 0 0 30 | -0.1900 -47.3600 8.3300 H 0 0 0 0 0 0 0 0 0 0 0 0 31 | -1.5900 -46.2900 7.3300 O 0 0 0 0 0 0 0 0 0 0 0 0 32 | -2.6600 -46.2600 8.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 33 | -2.6200 -46.9200 9.3900 C 0 0 0 0 0 0 0 0 0 0 0 0 34 | -1.7400 -47.4900 9.6800 H 0 0 0 0 0 0 0 0 0 0 0 0 35 | -3.7300 -46.8600 10.2300 C 0 0 0 0 0 0 0 0 0 0 0 0 36 | -3.7000 -47.3800 11.1800 H 0 0 0 0 0 0 0 0 0 0 0 0 37 | -4.8700 -46.1400 9.8700 C 0 0 0 0 0 0 0 0 0 0 0 0 38 | -6.2500 -46.0800 10.9500 Cl 0 0 0 0 0 0 0 0 0 0 0 0 39 | -4.8900 -45.4700 8.6600 C 0 0 0 0 0 0 0 0 0 0 0 0 40 | -5.7700 -44.9100 8.3700 H 0 0 0 0 0 0 0 0 0 0 0 0 41 | -3.7800 -45.5300 7.8200 C 0 0 0 0 0 0 0 0 0 0 0 0 42 | -3.8000 -45.0000 6.8700 H 0 0 0 0 0 0 0 0 0 0 0 0 43 | 18 19 1 0 0 0 0 44 | 18 20 1 0 0 0 0 45 | 14 15 1 0 0 0 0 46 | 12 13 1 0 0 0 0 47 | 17 18 1 0 0 0 0 48 | 18 21 1 0 0 0 0 49 | 12 14 2 0 0 0 0 50 | 14 16 1 0 0 0 0 51 | 10 12 1 0 0 0 0 52 | 16 17 1 0 0 0 0 53 | 4 17 2 0 0 0 0 54 | 7 16 2 0 0 0 0 55 | 21 22 1 0 0 0 0 56 | 10 11 1 0 0 0 0 57 | 8 10 2 0 0 0 0 58 | 2 4 1 0 0 0 0 59 | 4 5 1 0 0 0 0 60 | 1 2 1 0 0 0 0 61 | 7 8 1 0 0 0 0 62 | 5 7 1 0 0 0 0 63 | 2 3 2 0 0 0 0 64 | 8 9 1 0 0 0 0 65 | 21 23 1 0 0 0 0 66 | 21 24 1 0 0 0 0 67 | 5 6 1 0 0 0 0 68 | 37 38 1 0 0 0 0 69 | 24 27 1 0 0 0 0 70 | 27 28 1 0 0 0 0 71 | 24 26 1 0 0 0 0 72 | 24 25 1 0 0 0 0 73 | 28 37 2 0 0 0 0 74 | 35 37 1 0 0 0 0 75 | 28 29 1 0 0 0 0 76 | 35 36 1 0 0 0 0 77 | 33 35 2 0 0 0 0 78 | 29 30 1 0 0 0 0 79 | 29 31 2 0 0 0 0 80 | 31 33 1 0 0 0 0 81 | 33 34 1 0 0 0 0 82 | 31 32 1 0 0 0 0 83 | M CHG 1 1 -1 84 | M END 85 | $$$$ 86 | -------------------------------------------------------------------------------- /plbenchmark/sample_data/2020-08-26_mcl1_sample/02_ligands/lig_34/crd/lig_34.sdf: -------------------------------------------------------------------------------- 1 | lig_34 2 | -OEChem-01312017293D 3 | 4 | 41 43 0 0 0 0 0 0 0999 V2000 5 | 3.8100 -50.0800 6.4300 O 0 5 0 0 0 0 0 0 0 0 0 0 6 | 2.9400 -49.1700 6.5100 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 3.2800 -47.9700 6.6700 O 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1.5200 -49.6100 6.4100 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1.0100 -51.1700 6.8300 N 0 0 0 0 0 0 0 0 0 0 0 0 10 | 1.5300 -51.9500 7.1800 H 0 0 0 0 0 0 0 0 0 0 0 0 11 | -0.6500 -51.0200 6.4700 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | -1.7400 -51.8800 6.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 13 | -1.5900 -52.9000 6.8900 H 0 0 0 0 0 0 0 0 0 0 0 0 14 | -3.0100 -51.4600 6.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 15 | -3.8500 -52.1300 6.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 16 | -3.1800 -50.1500 5.7300 C 0 0 0 0 0 0 0 0 0 0 0 0 17 | -4.1700 -49.8000 5.4500 H 0 0 0 0 0 0 0 0 0 0 0 0 18 | -2.1000 -49.2800 5.6300 C 0 0 0 0 0 0 0 0 0 0 0 0 19 | -2.2500 -48.2700 5.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 20 | -0.8300 -49.7000 6.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 21 | 0.3700 -48.9100 5.9700 C 0 0 0 0 0 0 0 0 0 0 0 0 22 | 0.4000 -47.4900 5.5200 C 0 0 0 0 0 0 0 0 0 0 0 0 23 | 1.2600 -47.3600 4.8600 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | -0.5200 -47.2900 4.9700 H 0 0 0 0 0 0 0 0 0 0 0 0 25 | 0.5100 -46.4700 6.6100 C 0 0 0 0 0 0 0 0 0 0 0 0 26 | 0.4000 -45.4900 6.1500 H 0 0 0 0 0 0 0 0 0 0 0 0 27 | 1.5100 -46.5600 7.0400 H 0 0 0 0 0 0 0 0 0 0 0 0 28 | -0.4600 -46.5400 7.7500 C 0 0 0 0 0 0 0 0 0 0 0 0 29 | -0.1700 -45.8100 8.5100 H 0 0 0 0 0 0 0 0 0 0 0 0 30 | -0.4300 -47.5400 8.1800 H 0 0 0 0 0 0 0 0 0 0 0 0 31 | -1.7400 -46.2700 7.3100 O 0 0 0 0 0 0 0 0 0 0 0 0 32 | -2.8300 -46.2900 8.1400 C 0 0 0 0 0 0 0 0 0 0 0 0 33 | -2.7700 -46.9300 9.3600 C 0 0 0 0 0 0 0 0 0 0 0 0 34 | -1.8600 -47.4200 9.6800 H 0 0 0 0 0 0 0 0 0 0 0 0 35 | -3.9100 -46.9300 10.1700 C 0 0 0 0 0 0 0 0 0 0 0 0 36 | -3.8700 -47.4300 11.1300 H 0 0 0 0 0 0 0 0 0 0 0 0 37 | -5.0900 -46.3100 9.7700 C 0 0 0 0 0 0 0 0 0 0 0 0 38 | -6.2400 -46.3200 10.6100 C 0 0 0 0 0 0 0 0 0 0 0 0 39 | -5.9500 -47.0200 11.7800 F 0 0 0 0 0 0 0 0 0 0 0 0 40 | -7.2900 -46.9500 9.9500 F 0 0 0 0 0 0 0 0 0 0 0 0 41 | -6.6000 -45.0200 10.9300 F 0 0 0 0 0 0 0 0 0 0 0 0 42 | -5.1300 -45.6700 8.5400 C 0 0 0 0 0 0 0 0 0 0 0 0 43 | -6.0400 -45.1800 8.2100 H 0 0 0 0 0 0 0 0 0 0 0 0 44 | -3.9900 -45.6600 7.7200 C 0 0 0 0 0 0 0 0 0 0 0 0 45 | -4.0200 -45.1500 6.7700 H 0 0 0 0 0 0 0 0 0 0 0 0 46 | 18 19 1 0 0 0 0 47 | 18 20 1 0 0 0 0 48 | 14 15 1 0 0 0 0 49 | 12 13 1 0 0 0 0 50 | 17 18 1 0 0 0 0 51 | 18 21 1 0 0 0 0 52 | 12 14 2 0 0 0 0 53 | 14 16 1 0 0 0 0 54 | 10 12 1 0 0 0 0 55 | 16 17 1 0 0 0 0 56 | 4 17 2 0 0 0 0 57 | 7 16 2 0 0 0 0 58 | 21 22 1 0 0 0 0 59 | 10 11 1 0 0 0 0 60 | 8 10 2 0 0 0 0 61 | 2 4 1 0 0 0 0 62 | 4 5 1 0 0 0 0 63 | 1 2 1 0 0 0 0 64 | 7 8 1 0 0 0 0 65 | 5 7 1 0 0 0 0 66 | 2 3 2 0 0 0 0 67 | 8 9 1 0 0 0 0 68 | 21 23 1 0 0 0 0 69 | 21 24 1 0 0 0 0 70 | 40 41 1 0 0 0 0 71 | 5 6 1 0 0 0 0 72 | 24 27 1 0 0 0 0 73 | 27 28 1 0 0 0 0 74 | 28 40 2 0 0 0 0 75 | 38 40 1 0 0 0 0 76 | 24 26 1 0 0 0 0 77 | 24 25 1 0 0 0 0 78 | 28 29 1 0 0 0 0 79 | 38 39 1 0 0 0 0 80 | 33 38 2 0 0 0 0 81 | 29 30 1 0 0 0 0 82 | 29 31 2 0 0 0 0 83 | 31 33 1 0 0 0 0 84 | 33 34 1 0 0 0 0 85 | 34 36 1 0 0 0 0 86 | 31 32 1 0 0 0 0 87 | 34 37 1 0 0 0 0 88 | 34 35 1 0 0 0 0 89 | M CHG 1 1 -1 90 | M END 91 | $$$$ 92 | -------------------------------------------------------------------------------- /plbenchmark/sample_data/2020-08-26_mcl1_sample/02_ligands/lig_35/crd/lig_35.sdf: -------------------------------------------------------------------------------- 1 | lig_35 2 | -OEChem-01312017303D 3 | 4 | 41 43 0 0 0 0 0 0 0999 V2000 5 | 3.8100 -50.0800 6.4300 O 0 5 0 0 0 0 0 0 0 0 0 0 6 | 2.9400 -49.1700 6.5100 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 3.2800 -47.9700 6.6700 O 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1.5200 -49.6100 6.4100 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1.0100 -51.1700 6.8300 N 0 0 0 0 0 0 0 0 0 0 0 0 10 | 1.5300 -51.9500 7.1800 H 0 0 0 0 0 0 0 0 0 0 0 0 11 | -0.6500 -51.0200 6.4700 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | -1.7400 -51.8800 6.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 13 | -1.5900 -52.9000 6.8900 H 0 0 0 0 0 0 0 0 0 0 0 0 14 | -3.0100 -51.4600 6.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 15 | -3.8500 -52.1300 6.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 16 | -3.1800 -50.1500 5.7300 C 0 0 0 0 0 0 0 0 0 0 0 0 17 | -4.1700 -49.8000 5.4500 H 0 0 0 0 0 0 0 0 0 0 0 0 18 | -2.1000 -49.2800 5.6300 C 0 0 0 0 0 0 0 0 0 0 0 0 19 | -2.2500 -48.2700 5.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 20 | -0.8300 -49.7000 6.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 21 | 0.3700 -48.9100 5.9700 C 0 0 0 0 0 0 0 0 0 0 0 0 22 | 0.4000 -47.4900 5.5200 C 0 0 0 0 0 0 0 0 0 0 0 0 23 | 1.1900 -47.3900 4.7800 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | -0.5600 -47.2600 5.0600 H 0 0 0 0 0 0 0 0 0 0 0 0 25 | 0.6500 -46.4800 6.6000 C 0 0 0 0 0 0 0 0 0 0 0 0 26 | 0.6300 -45.5000 6.1300 H 0 0 0 0 0 0 0 0 0 0 0 0 27 | 1.6500 -46.6700 6.9900 H 0 0 0 0 0 0 0 0 0 0 0 0 28 | -0.2800 -46.4300 7.7600 C 0 0 0 0 0 0 0 0 0 0 0 0 29 | -0.0300 -45.5900 8.4000 H 0 0 0 0 0 0 0 0 0 0 0 0 30 | -0.1900 -47.3600 8.3300 H 0 0 0 0 0 0 0 0 0 0 0 0 31 | -1.5900 -46.2900 7.3300 O 0 0 0 0 0 0 0 0 0 0 0 0 32 | -2.6600 -46.2600 8.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 33 | -2.6200 -46.9200 9.3900 C 0 0 0 0 0 0 0 0 0 0 0 0 34 | -1.7400 -47.4900 9.6800 H 0 0 0 0 0 0 0 0 0 0 0 0 35 | -3.7300 -46.8600 10.2300 C 0 0 0 0 0 0 0 0 0 0 0 0 36 | -3.7000 -47.5500 11.4800 C 0 0 0 0 0 0 0 0 0 0 0 0 37 | -2.7400 -48.0500 11.6000 H 0 0 0 0 0 0 0 0 0 0 0 0 38 | -4.5000 -48.2800 11.5200 H 0 0 0 0 0 0 0 0 0 0 0 0 39 | -3.8300 -46.8300 12.2900 H 0 0 0 0 0 0 0 0 0 0 0 0 40 | -4.8700 -46.1400 9.8700 C 0 0 0 0 0 0 0 0 0 0 0 0 41 | -6.2500 -46.0800 10.9500 Cl 0 0 0 0 0 0 0 0 0 0 0 0 42 | -4.8900 -45.4700 8.6600 C 0 0 0 0 0 0 0 0 0 0 0 0 43 | -5.7700 -44.9100 8.3700 H 0 0 0 0 0 0 0 0 0 0 0 0 44 | -3.7800 -45.5300 7.8200 C 0 0 0 0 0 0 0 0 0 0 0 0 45 | -3.8000 -45.0000 6.8700 H 0 0 0 0 0 0 0 0 0 0 0 0 46 | 18 19 1 0 0 0 0 47 | 18 20 1 0 0 0 0 48 | 14 15 1 0 0 0 0 49 | 12 13 1 0 0 0 0 50 | 17 18 1 0 0 0 0 51 | 18 21 1 0 0 0 0 52 | 12 14 2 0 0 0 0 53 | 14 16 1 0 0 0 0 54 | 10 12 1 0 0 0 0 55 | 16 17 1 0 0 0 0 56 | 4 17 2 0 0 0 0 57 | 7 16 2 0 0 0 0 58 | 21 22 1 0 0 0 0 59 | 10 11 1 0 0 0 0 60 | 8 10 2 0 0 0 0 61 | 2 4 1 0 0 0 0 62 | 4 5 1 0 0 0 0 63 | 1 2 1 0 0 0 0 64 | 7 8 1 0 0 0 0 65 | 5 7 1 0 0 0 0 66 | 2 3 2 0 0 0 0 67 | 8 9 1 0 0 0 0 68 | 21 23 1 0 0 0 0 69 | 21 24 1 0 0 0 0 70 | 5 6 1 0 0 0 0 71 | 40 41 1 0 0 0 0 72 | 24 27 1 0 0 0 0 73 | 27 28 1 0 0 0 0 74 | 24 26 1 0 0 0 0 75 | 24 25 1 0 0 0 0 76 | 28 40 2 0 0 0 0 77 | 38 40 1 0 0 0 0 78 | 28 29 1 0 0 0 0 79 | 38 39 1 0 0 0 0 80 | 36 38 2 0 0 0 0 81 | 29 30 1 0 0 0 0 82 | 29 31 2 0 0 0 0 83 | 31 36 1 0 0 0 0 84 | 36 37 1 0 0 0 0 85 | 31 32 1 0 0 0 0 86 | 32 34 1 0 0 0 0 87 | 32 33 1 0 0 0 0 88 | 32 35 1 0 0 0 0 89 | M CHG 1 1 -1 90 | M END 91 | $$$$ 92 | -------------------------------------------------------------------------------- /plbenchmark/sample_data/2020-08-26_mcl1_sample/02_ligands/lig_36/crd/lig_36.sdf: -------------------------------------------------------------------------------- 1 | lig_36 2 | -OEChem-01312017303D 3 | 4 | 44 46 0 0 0 0 0 0 0999 V2000 5 | 3.8100 -50.0800 6.4300 O 0 5 0 0 0 0 0 0 0 0 0 0 6 | 2.9400 -49.1700 6.5100 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 3.2800 -47.9700 6.6700 O 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1.5200 -49.6100 6.4100 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1.0100 -51.1700 6.8300 N 0 0 0 0 0 0 0 0 0 0 0 0 10 | 1.5300 -51.9500 7.1800 H 0 0 0 0 0 0 0 0 0 0 0 0 11 | -0.6500 -51.0200 6.4700 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | -1.7400 -51.8800 6.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 13 | -1.5900 -52.9000 6.8900 H 0 0 0 0 0 0 0 0 0 0 0 0 14 | -3.0100 -51.4600 6.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 15 | -3.8500 -52.1300 6.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 16 | -3.1800 -50.1500 5.7300 C 0 0 0 0 0 0 0 0 0 0 0 0 17 | -4.1700 -49.8000 5.4500 H 0 0 0 0 0 0 0 0 0 0 0 0 18 | -2.1000 -49.2800 5.6300 C 0 0 0 0 0 0 0 0 0 0 0 0 19 | -2.2500 -48.2700 5.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 20 | -0.8300 -49.7000 6.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 21 | 0.3700 -48.9100 5.9700 C 0 0 0 0 0 0 0 0 0 0 0 0 22 | 0.4000 -47.4900 5.5200 C 0 0 0 0 0 0 0 0 0 0 0 0 23 | 1.2600 -47.3600 4.8600 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | -0.5200 -47.2900 4.9700 H 0 0 0 0 0 0 0 0 0 0 0 0 25 | 0.5100 -46.4700 6.6100 C 0 0 0 0 0 0 0 0 0 0 0 0 26 | 0.4000 -45.4900 6.1500 H 0 0 0 0 0 0 0 0 0 0 0 0 27 | 1.5100 -46.5600 7.0400 H 0 0 0 0 0 0 0 0 0 0 0 0 28 | -0.4600 -46.5400 7.7500 C 0 0 0 0 0 0 0 0 0 0 0 0 29 | -0.2400 -45.7400 8.4600 H 0 0 0 0 0 0 0 0 0 0 0 0 30 | -0.3500 -47.5000 8.2500 H 0 0 0 0 0 0 0 0 0 0 0 0 31 | -1.7500 -46.4000 7.2900 O 0 0 0 0 0 0 0 0 0 0 0 0 32 | -2.8400 -46.3400 8.1300 C 0 0 0 0 0 0 0 0 0 0 0 0 33 | -2.8200 -46.9800 9.3500 C 0 0 0 0 0 0 0 0 0 0 0 0 34 | -1.9500 -47.5500 9.6600 H 0 0 0 0 0 0 0 0 0 0 0 0 35 | -3.9400 -46.8900 10.1700 C 0 0 0 0 0 0 0 0 0 0 0 0 36 | -3.9400 -47.5500 11.4300 C 0 0 0 0 0 0 0 0 0 0 0 0 37 | -2.9900 -48.0600 11.5700 H 0 0 0 0 0 0 0 0 0 0 0 0 38 | -5.0000 -48.5000 11.4800 C 0 0 0 0 0 0 0 0 0 0 0 0 39 | -4.8600 -49.2400 10.6900 H 0 0 0 0 0 0 0 0 0 0 0 0 40 | -5.9600 -47.9900 11.3400 H 0 0 0 0 0 0 0 0 0 0 0 0 41 | -5.0000 -49.0100 12.4400 H 0 0 0 0 0 0 0 0 0 0 0 0 42 | -4.0800 -46.8200 12.2300 H 0 0 0 0 0 0 0 0 0 0 0 0 43 | -5.0700 -46.1700 9.7800 C 0 0 0 0 0 0 0 0 0 0 0 0 44 | -6.4700 -46.0800 10.8300 Cl 0 0 0 0 0 0 0 0 0 0 0 0 45 | -5.0700 -45.5300 8.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 46 | -5.9400 -44.9700 8.2300 H 0 0 0 0 0 0 0 0 0 0 0 0 47 | -3.9500 -45.6100 7.7200 C 0 0 0 0 0 0 0 0 0 0 0 0 48 | -3.9400 -45.1000 6.7700 H 0 0 0 0 0 0 0 0 0 0 0 0 49 | 18 19 1 0 0 0 0 50 | 18 20 1 0 0 0 0 51 | 14 15 1 0 0 0 0 52 | 12 13 1 0 0 0 0 53 | 17 18 1 0 0 0 0 54 | 18 21 1 0 0 0 0 55 | 12 14 2 0 0 0 0 56 | 14 16 1 0 0 0 0 57 | 10 12 1 0 0 0 0 58 | 16 17 1 0 0 0 0 59 | 4 17 2 0 0 0 0 60 | 7 16 2 0 0 0 0 61 | 21 22 1 0 0 0 0 62 | 10 11 1 0 0 0 0 63 | 8 10 2 0 0 0 0 64 | 2 4 1 0 0 0 0 65 | 4 5 1 0 0 0 0 66 | 1 2 1 0 0 0 0 67 | 7 8 1 0 0 0 0 68 | 5 7 1 0 0 0 0 69 | 2 3 2 0 0 0 0 70 | 8 9 1 0 0 0 0 71 | 21 23 1 0 0 0 0 72 | 21 24 1 0 0 0 0 73 | 43 44 1 0 0 0 0 74 | 5 6 1 0 0 0 0 75 | 24 27 1 0 0 0 0 76 | 27 28 1 0 0 0 0 77 | 28 43 2 0 0 0 0 78 | 41 43 1 0 0 0 0 79 | 24 26 1 0 0 0 0 80 | 24 25 1 0 0 0 0 81 | 28 29 1 0 0 0 0 82 | 41 42 1 0 0 0 0 83 | 39 41 2 0 0 0 0 84 | 29 30 1 0 0 0 0 85 | 29 31 2 0 0 0 0 86 | 31 39 1 0 0 0 0 87 | 39 40 1 0 0 0 0 88 | 31 32 1 0 0 0 0 89 | 34 35 1 0 0 0 0 90 | 34 36 1 0 0 0 0 91 | 32 34 1 0 0 0 0 92 | 32 33 1 0 0 0 0 93 | 32 38 1 0 0 0 0 94 | 34 37 1 0 0 0 0 95 | M CHG 1 1 -1 96 | M END 97 | $$$$ 98 | -------------------------------------------------------------------------------- /plbenchmark/sample_data/2020-08-26_mcl1_sample/02_ligands/lig_37/crd/lig_37.sdf: -------------------------------------------------------------------------------- 1 | lig_37 2 | -OEChem-01312017303D 3 | 4 | 44 46 0 0 0 0 0 0 0999 V2000 5 | 3.8100 -50.0800 6.4300 O 0 5 0 0 0 0 0 0 0 0 0 0 6 | 2.9400 -49.1700 6.5100 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 3.2800 -47.9700 6.6700 O 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1.5200 -49.6100 6.4100 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1.0100 -51.1700 6.8300 N 0 0 0 0 0 0 0 0 0 0 0 0 10 | 1.5300 -51.9500 7.1800 H 0 0 0 0 0 0 0 0 0 0 0 0 11 | -0.6500 -51.0200 6.4700 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | -1.7400 -51.8800 6.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 13 | -1.5900 -52.9000 6.8900 H 0 0 0 0 0 0 0 0 0 0 0 0 14 | -3.0100 -51.4600 6.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 15 | -3.8500 -52.1300 6.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 16 | -3.1800 -50.1500 5.7300 C 0 0 0 0 0 0 0 0 0 0 0 0 17 | -4.1700 -49.8000 5.4500 H 0 0 0 0 0 0 0 0 0 0 0 0 18 | -2.1000 -49.2800 5.6300 C 0 0 0 0 0 0 0 0 0 0 0 0 19 | -2.2500 -48.2700 5.2600 H 0 0 0 0 0 0 0 0 0 0 0 0 20 | -0.8300 -49.7000 6.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 21 | 0.3700 -48.9100 5.9700 C 0 0 0 0 0 0 0 0 0 0 0 0 22 | 0.4000 -47.4900 5.5200 C 0 0 0 0 0 0 0 0 0 0 0 0 23 | 1.1900 -47.3900 4.7800 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | -0.5600 -47.2600 5.0600 H 0 0 0 0 0 0 0 0 0 0 0 0 25 | 0.6500 -46.4800 6.6000 C 0 0 0 0 0 0 0 0 0 0 0 0 26 | 0.6300 -45.5000 6.1300 H 0 0 0 0 0 0 0 0 0 0 0 0 27 | 1.6500 -46.6700 6.9900 H 0 0 0 0 0 0 0 0 0 0 0 0 28 | -0.2800 -46.4300 7.7600 C 0 0 0 0 0 0 0 0 0 0 0 0 29 | -0.0300 -45.5900 8.4000 H 0 0 0 0 0 0 0 0 0 0 0 0 30 | -0.1900 -47.3600 8.3300 H 0 0 0 0 0 0 0 0 0 0 0 0 31 | -1.5900 -46.2900 7.3300 O 0 0 0 0 0 0 0 0 0 0 0 0 32 | -2.6600 -46.2600 8.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 33 | -2.6200 -46.9200 9.3900 C 0 0 0 0 0 0 0 0 0 0 0 0 34 | -1.7400 -47.4900 9.6800 H 0 0 0 0 0 0 0 0 0 0 0 0 35 | -3.7300 -46.8600 10.2300 C 0 0 0 0 0 0 0 0 0 0 0 0 36 | -3.7000 -47.5500 11.4800 C 0 0 0 0 0 0 0 0 0 0 0 0 37 | -2.7400 -48.0500 11.6000 H 0 0 0 0 0 0 0 0 0 0 0 0 38 | -4.5000 -48.2800 11.5200 H 0 0 0 0 0 0 0 0 0 0 0 0 39 | -3.8300 -46.8300 12.2900 H 0 0 0 0 0 0 0 0 0 0 0 0 40 | -4.8700 -46.1400 9.8700 C 0 0 0 0 0 0 0 0 0 0 0 0 41 | -6.2500 -46.0800 10.9500 Cl 0 0 0 0 0 0 0 0 0 0 0 0 42 | -4.8900 -45.4700 8.6600 C 0 0 0 0 0 0 0 0 0 0 0 0 43 | -6.0500 -44.7300 8.2700 C 0 0 0 0 0 0 0 0 0 0 0 0 44 | -6.8100 -44.8000 9.0500 H 0 0 0 0 0 0 0 0 0 0 0 0 45 | -6.4500 -45.1400 7.3400 H 0 0 0 0 0 0 0 0 0 0 0 0 46 | -5.7800 -43.6900 8.1300 H 0 0 0 0 0 0 0 0 0 0 0 0 47 | -3.7800 -45.5300 7.8200 C 0 0 0 0 0 0 0 0 0 0 0 0 48 | -3.8000 -45.0000 6.8700 H 0 0 0 0 0 0 0 0 0 0 0 0 49 | 18 19 1 0 0 0 0 50 | 18 20 1 0 0 0 0 51 | 14 15 1 0 0 0 0 52 | 12 13 1 0 0 0 0 53 | 17 18 1 0 0 0 0 54 | 18 21 1 0 0 0 0 55 | 12 14 2 0 0 0 0 56 | 14 16 1 0 0 0 0 57 | 10 12 1 0 0 0 0 58 | 16 17 1 0 0 0 0 59 | 4 17 2 0 0 0 0 60 | 7 16 2 0 0 0 0 61 | 21 22 1 0 0 0 0 62 | 10 11 1 0 0 0 0 63 | 8 10 2 0 0 0 0 64 | 2 4 1 0 0 0 0 65 | 4 5 1 0 0 0 0 66 | 1 2 1 0 0 0 0 67 | 7 8 1 0 0 0 0 68 | 5 7 1 0 0 0 0 69 | 2 3 2 0 0 0 0 70 | 8 9 1 0 0 0 0 71 | 21 23 1 0 0 0 0 72 | 21 24 1 0 0 0 0 73 | 5 6 1 0 0 0 0 74 | 43 44 1 0 0 0 0 75 | 24 27 1 0 0 0 0 76 | 27 28 1 0 0 0 0 77 | 39 41 1 0 0 0 0 78 | 24 26 1 0 0 0 0 79 | 24 25 1 0 0 0 0 80 | 28 43 2 0 0 0 0 81 | 38 43 1 0 0 0 0 82 | 39 42 1 0 0 0 0 83 | 28 29 1 0 0 0 0 84 | 38 39 1 0 0 0 0 85 | 39 40 1 0 0 0 0 86 | 36 38 2 0 0 0 0 87 | 29 30 1 0 0 0 0 88 | 29 31 2 0 0 0 0 89 | 31 36 1 0 0 0 0 90 | 36 37 1 0 0 0 0 91 | 31 32 1 0 0 0 0 92 | 32 34 1 0 0 0 0 93 | 32 33 1 0 0 0 0 94 | 32 35 1 0 0 0 0 95 | M CHG 1 1 -1 96 | M END 97 | $$$$ 98 | -------------------------------------------------------------------------------- /plbenchmark/sample_data/targets.yml: -------------------------------------------------------------------------------- 1 | mcl1_sample: 2 | date: 2020-08-26 3 | dir: 2020-08-26_mcl1_sample 4 | name: mcl1_sample 5 | -------------------------------------------------------------------------------- /plbenchmark/tests/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | Empty init file in case you choose a package besides PyTest such as Nose which may look for such a file 3 | """ 4 | -------------------------------------------------------------------------------- /plbenchmark/tests/test_PLBenchmarks.py: -------------------------------------------------------------------------------- 1 | """ 2 | Unit and regression test for the plbenchmark package. 3 | """ 4 | 5 | # Import package, test suite, and other packages as needed 6 | import plbenchmark 7 | import pytest 8 | import sys 9 | 10 | 11 | def test_plbenchmark_imported(): 12 | """Sample test, will always pass so long as import statement worked""" 13 | assert "plbenchmark" in sys.modules 14 | -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_CDK2/glide-dock_SP_CDK2.in: -------------------------------------------------------------------------------- 1 | CORE_DEFINITION mcssmarts 2 | CORE_POS_MAX_RMSD 0.25 3 | CORE_RESTRAIN True 4 | FORCEFIELD OPLS_2005 5 | GRIDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/grids/glide-grid_CDK2-1H1Q.zip 6 | LIGANDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/prepped_ligs/ligands/ligprep_cdk2-out.sdf 7 | POSE_OUTTYPE ligandlib 8 | PRECISION SP 9 | REF_LIGAND_FILE glide-dock_SP_CDK2.reflig.maegz 10 | USE_REF_LIGAND True 11 | -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_CDK2/glide-dock_SP_CDK2.reflig.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/docking/glide-dock_SP_CDK2/glide-dock_SP_CDK2.reflig.maegz -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_CDK2/glide-dock_SP_CDK2.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-dock_SP_CDK2.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_CDK8/glide-dock_SP_CDK8.in: -------------------------------------------------------------------------------- 1 | CORE_DEFINITION mcssmarts 2 | CORE_POS_MAX_RMSD 0.25 3 | CORE_RESTRAIN True 4 | FORCEFIELD OPLS_2005 5 | GRIDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/grids/glide-grid_CDK8-5HNB.zip 6 | LIGANDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/prepped_ligs/ligands/ligprep_cdk8-out.sdf 7 | POSE_OUTTYPE ligandlib 8 | PRECISION SP 9 | REF_LIGAND_FILE glide-dock_SP_CDK8.reflig.maegz 10 | USE_REF_LIGAND True 11 | -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_CDK8/glide-dock_SP_CDK8.reflig.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/docking/glide-dock_SP_CDK8/glide-dock_SP_CDK8.reflig.maegz -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_CDK8/glide-dock_SP_CDK8.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-dock_SP_CDK8.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_EG5/glide-dock_SP_EG5.in: -------------------------------------------------------------------------------- 1 | CORE_DEFINITION mcssmarts 2 | CORE_POS_MAX_RMSD 0.25 3 | CORE_RESTRAIN True 4 | FORCEFIELD OPLS_2005 5 | GRIDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/grids/glide-grid_EG5-3L9H.zip 6 | LIGANDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/prepped_ligs/ligands/ligprep_eg5-out.sdf 7 | POSE_OUTTYPE ligandlib 8 | PRECISION SP 9 | REF_LIGAND_FILE glide-dock_SP_EG5.reflig.maegz 10 | USE_REF_LIGAND True 11 | -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_EG5/glide-dock_SP_EG5.reflig.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/docking/glide-dock_SP_EG5/glide-dock_SP_EG5.reflig.maegz -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_EG5/glide-dock_SP_EG5.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-dock_SP_EG5.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_HIF2a/glide-dock_SP_HIF2a.in: -------------------------------------------------------------------------------- 1 | CORE_DEFINITION mcssmarts 2 | CORE_POS_MAX_RMSD 0.25 3 | CORE_RESTRAIN True 4 | FORCEFIELD OPLS_2005 5 | GRIDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/grids/glide-grid_HIF2a-5TBM.zip 6 | LIGANDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/prepped_ligs/ligands/ligprep_hif2a-out.sdf 7 | POSE_OUTTYPE ligandlib 8 | PRECISION SP 9 | REF_LIGAND_FILE glide-dock_SP_HIF2a.reflig.maegz 10 | USE_REF_LIGAND True 11 | -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_HIF2a/glide-dock_SP_HIF2a.reflig.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/docking/glide-dock_SP_HIF2a/glide-dock_SP_HIF2a.reflig.maegz -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_HIF2a/glide-dock_SP_HIF2a.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-dock_SP_HIF2a.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_MCL1/glide-dock_SP_MCL1.in: -------------------------------------------------------------------------------- 1 | CORE_DEFINITION mcssmarts 2 | CORE_POS_MAX_RMSD 0.25 3 | CORE_RESTRAIN True 4 | FORCEFIELD OPLS_2005 5 | GRIDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/grids/glide-grid_MCL1-4HW3.zip 6 | LIGANDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/prepped_ligs/ligands/ligprep_mcl1-out.sdf 7 | POSE_OUTTYPE ligandlib 8 | PRECISION SP 9 | REF_LIGAND_FILE glide-dock_SP_MCL1.reflig.maegz 10 | USE_REF_LIGAND True 11 | -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_MCL1/glide-dock_SP_MCL1.reflig.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/docking/glide-dock_SP_MCL1/glide-dock_SP_MCL1.reflig.maegz -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_MCL1/glide-dock_SP_MCL1.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-dock_SP_MCL1.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_P38/glide-dock_SP_P38.in: -------------------------------------------------------------------------------- 1 | CORE_DEFINITION mcssmarts 2 | CORE_POS_MAX_RMSD 0.25 3 | CORE_RESTRAIN True 4 | FORCEFIELD OPLS_2005 5 | GRIDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/grids/glide-grid_P38-3FLY.zip 6 | LIGANDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/prepped_ligs/ligands/ligprep_p38-out.sdf 7 | POSE_OUTTYPE ligandlib 8 | PRECISION SP 9 | REF_LIGAND_FILE glide-dock_SP_P38.reflig.maegz 10 | USE_REF_LIGAND True 11 | -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_P38/glide-dock_SP_P38.reflig.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/docking/glide-dock_SP_P38/glide-dock_SP_P38.reflig.maegz -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_P38/glide-dock_SP_P38.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-dock_SP_P38.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_PDE2/glide-dock_SP_PDE2.in: -------------------------------------------------------------------------------- 1 | CORE_DEFINITION mcssmarts 2 | CORE_POS_MAX_RMSD 0.25 3 | CORE_RESTRAIN True 4 | FORCEFIELD OPLS_2005 5 | GRIDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/grids/glide-grid_PDE2-4D08.zip 6 | LIGANDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/prepped_ligs/ligands/ligprep_pde2-out.sdf 7 | POSE_OUTTYPE ligandlib 8 | PRECISION SP 9 | REF_LIGAND_FILE glide-dock_SP_PDE2.reflig.maegz 10 | USE_REF_LIGAND True 11 | -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_PDE2/glide-dock_SP_PDE2.reflig.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/docking/glide-dock_SP_PDE2/glide-dock_SP_PDE2.reflig.maegz -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_PDE2/glide-dock_SP_PDE2.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-dock_SP_PDE2.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_PFKFB3/glide-dock_SP_PFKFB3.in: -------------------------------------------------------------------------------- 1 | CORE_DEFINITION mcssmarts 2 | CORE_POS_MAX_RMSD 0.25 3 | CORE_RESTRAIN True 4 | FORCEFIELD OPLS_2005 5 | GRIDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/grids/glide-grid_PFKFB3-6HVI.zip 6 | LIGANDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/prepped_ligs/ligands/ligprep_pfkfb3-out.sdf 7 | POSE_OUTTYPE ligandlib 8 | PRECISION SP 9 | REF_LIGAND_FILE glide-dock_SP_PFKFB3.reflig.maegz 10 | USE_REF_LIGAND True 11 | -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_PFKFB3/glide-dock_SP_PFKFB3.reflig.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/docking/glide-dock_SP_PFKFB3/glide-dock_SP_PFKFB3.reflig.maegz -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_PFKFB3/glide-dock_SP_PFKFB3.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-dock_SP_PFKFB3.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_PTP1B/glide-dock_SP_PTP1B.in: -------------------------------------------------------------------------------- 1 | CORE_DEFINITION mcssmarts 2 | CORE_POS_MAX_RMSD 0.25 3 | CORE_RESTRAIN True 4 | FORCEFIELD OPLS_2005 5 | GRIDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/grids/glide-grid_PTP1B-2QBS.zip 6 | LIGANDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/prepped_ligs/ligands/ligprep_ptp1b-out.sdf 7 | POSE_OUTTYPE ligandlib 8 | PRECISION SP 9 | REF_LIGAND_FILE glide-dock_SP_PTP1B.reflig.maegz 10 | USE_REF_LIGAND True 11 | -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_PTP1B/glide-dock_SP_PTP1B.reflig.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/docking/glide-dock_SP_PTP1B/glide-dock_SP_PTP1B.reflig.maegz -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_PTP1B/glide-dock_SP_PTP1B.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-dock_SP_PTP1B.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_SHP2/glide-dock_SP_SHP2.in: -------------------------------------------------------------------------------- 1 | CORE_DEFINITION mcssmarts 2 | CORE_POS_MAX_RMSD 0.25 3 | CORE_RESTRAIN True 4 | FORCEFIELD OPLS_2005 5 | GRIDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/grids/glide-grid_SHP2-5EHR.zip 6 | LIGANDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/prepped_ligs/ligands/ligprep_shp2-out.sdf 7 | POSE_OUTTYPE ligandlib 8 | PRECISION SP 9 | REF_LIGAND_FILE glide-dock_SP_SHP2.reflig.maegz 10 | USE_REF_LIGAND True 11 | -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_SHP2/glide-dock_SP_SHP2.reflig.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/docking/glide-dock_SP_SHP2/glide-dock_SP_SHP2.reflig.maegz -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_SHP2/glide-dock_SP_SHP2.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-dock_SP_SHP2.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_SYK/glide-dock_SP_SYK.in: -------------------------------------------------------------------------------- 1 | CORE_DEFINITION mcssmarts 2 | CORE_POS_MAX_RMSD 0.25 3 | CORE_RESTRAIN True 4 | FORCEFIELD OPLS_2005 5 | GRIDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/grids/glide-grid_SYK-4PV0.zip 6 | LIGANDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/prepped_ligs/ligands/ligprep_syk-out.sdf 7 | POSE_OUTTYPE ligandlib 8 | PRECISION SP 9 | REF_LIGAND_FILE glide-dock_SP_SYK.reflig.maegz 10 | USE_REF_LIGAND True 11 | -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_SYK/glide-dock_SP_SYK.reflig.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/docking/glide-dock_SP_SYK/glide-dock_SP_SYK.reflig.maegz -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_SYK/glide-dock_SP_SYK.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-dock_SP_SYK.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_TNKS2/glide-dock_SP_TNKS2.in: -------------------------------------------------------------------------------- 1 | CORE_DEFINITION mcssmarts 2 | CORE_POS_MAX_RMSD 0.25 3 | CORE_RESTRAIN True 4 | FORCEFIELD OPLS_2005 5 | GRIDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/grids/glide-grid_TNKS2-4UI5.zip 6 | LIGANDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/prepped_ligs/ligands/ligprep_tnks2-out.sdf 7 | POSE_OUTTYPE ligandlib 8 | PRECISION SP 9 | REF_LIGAND_FILE glide-dock_SP_TNKS2.reflig.maegz 10 | USE_REF_LIGAND True 11 | -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_TNKS2/glide-dock_SP_TNKS2.reflig.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/docking/glide-dock_SP_TNKS2/glide-dock_SP_TNKS2.reflig.maegz -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_TNKS2/glide-dock_SP_TNKS2.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-dock_SP_TNKS2.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_TYK2/glide-dock_SP_TYK2.in: -------------------------------------------------------------------------------- 1 | CORE_DEFINITION mcssmarts 2 | CORE_POS_MAX_RMSD 0.25 3 | CORE_RESTRAIN True 4 | FORCEFIELD OPLS_2005 5 | GRIDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/grids/glide-grid_TYK2-4GIH.zip 6 | LIGANDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/prepped_ligs/ligands/ligprep_tyk2-out.sdf 7 | POSE_OUTTYPE ligandlib 8 | PRECISION SP 9 | REF_LIGAND_FILE glide-dock_SP_TYK2.reflig.maegz 10 | USE_REF_LIGAND True 11 | -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_TYK2/glide-dock_SP_TYK2.reflig.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/docking/glide-dock_SP_TYK2/glide-dock_SP_TYK2.reflig.maegz -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_TYK2/glide-dock_SP_TYK2.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-dock_SP_TYK2.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_cMET/glide-dock_SP_cMET.in: -------------------------------------------------------------------------------- 1 | CORE_DEFINITION mcssmarts 2 | CORE_POS_MAX_RMSD 0.25 3 | CORE_RESTRAIN True 4 | FORCEFIELD OPLS_2005 5 | GRIDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/grids/glide-grid_cMET-4R1Y.zip 6 | LIGANDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/prepped_ligs/ligands/ligprep_cmet-out.sdf 7 | POSE_OUTTYPE ligandlib 8 | PRECISION SP 9 | REF_LIGAND_FILE glide-dock_SP_cMET.reflig.maegz 10 | USE_REF_LIGAND True 11 | -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_cMET/glide-dock_SP_cMET.reflig.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/docking/glide-dock_SP_cMET/glide-dock_SP_cMET.reflig.maegz -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_cMET/glide-dock_SP_cMET.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-dock_SP_cMET.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_thrombin/glide-dock_SP_thrombin.in: -------------------------------------------------------------------------------- 1 | CORE_DEFINITION mcssmarts 2 | CORE_POS_MAX_RMSD 0.25 3 | CORE_RESTRAIN True 4 | FORCEFIELD OPLS_2005 5 | GRIDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/grids/glide-grid_thrombin-2ZFF.zip 6 | LIGANDFILE /Users/bobym/Documents/Schrodinger/plbenchmark.prj/prepped_ligs/ligands/ligprep_thrombin_recurated-out.sdf 7 | POSE_OUTTYPE ligandlib 8 | PRECISION SP 9 | REF_LIGAND_FILE glide-dock_SP_thrombin.reflig.maegz 10 | USE_REF_LIGAND True 11 | -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_thrombin/glide-dock_SP_thrombin.reflig.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/docking/glide-dock_SP_thrombin/glide-dock_SP_thrombin.reflig.maegz -------------------------------------------------------------------------------- /preparation/docking/glide-dock_SP_thrombin/glide-dock_SP_thrombin.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-dock_SP_thrombin.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_CDK2-1H1Q/glide-grid_CDK2-1H1Q.in: -------------------------------------------------------------------------------- 1 | FORCEFIELD OPLS_2005 2 | GRID_CENTER 5.282894533333332, 44.22622391111112, 51.22174504444445 3 | GRIDFILE glide-grid_CDK2-1H1Q.zip 4 | INNERBOX 10, 10, 10 5 | OUTERBOX 23.324206419948453, 23.324206419948453, 23.324206419948453 6 | RECEP_FILE glide-grid_CDK2-1H1Q.maegz 7 | -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_CDK2-1H1Q/glide-grid_CDK2-1H1Q.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/glide-grids/glide-grid_CDK2-1H1Q/glide-grid_CDK2-1H1Q.maegz -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_CDK2-1H1Q/glide-grid_CDK2-1H1Q.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-grid_CDK2-1H1Q.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_CDK8-5HNB/glide-grid_CDK8-5HNB.in: -------------------------------------------------------------------------------- 1 | FORCEFIELD OPLS_2005 2 | GRID_CENTER -5.046645404255318, 12.01630429787234, -10.045419404255318 3 | GRIDFILE glide-grid_CDK8-5HNB.zip 4 | INNERBOX 10, 10, 10 5 | OUTERBOX 22.156444946365653, 22.156444946365653, 22.156444946365653 6 | RECEP_FILE glide-grid_CDK8-5HNB.maegz 7 | -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_CDK8-5HNB/glide-grid_CDK8-5HNB.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/glide-grids/glide-grid_CDK8-5HNB/glide-grid_CDK8-5HNB.maegz -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_CDK8-5HNB/glide-grid_CDK8-5HNB.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-grid_CDK8-5HNB.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_EG5-3L9H/glide-grid_EG5-3L9H.in: -------------------------------------------------------------------------------- 1 | FORCEFIELD OPLS_2005 2 | GRID_CENTER 28.184979242424248, 9.58830406060606, 17.318891969696974 3 | GRIDFILE glide-grid_EG5-3L9H.zip 4 | INNERBOX 10, 10, 10 5 | OUTERBOX 28.027414206327222, 28.027414206327222, 28.027414206327222 6 | RECEP_FILE glide-grid_EG5-3L9H.maegz 7 | -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_EG5-3L9H/glide-grid_EG5-3L9H.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/glide-grids/glide-grid_EG5-3L9H/glide-grid_EG5-3L9H.maegz -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_EG5-3L9H/glide-grid_EG5-3L9H.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-grid_EG5-3L9H.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_HIF2a-5TBM/glide-grid_HIF2a-5TBM.in: -------------------------------------------------------------------------------- 1 | FORCEFIELD OPLS_2005 2 | GRID_CENTER 24.22111610526316, -0.11141571052631577, -10.475763368421052 3 | GRIDFILE glide-grid_HIF2a-5TBM.zip 4 | INNERBOX 10, 10, 10 5 | OUTERBOX 23.244020963442296, 23.244020963442296, 23.244020963442296 6 | RECEP_FILE glide-grid_HIF2a-5TBM.maegz 7 | -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_HIF2a-5TBM/glide-grid_HIF2a-5TBM.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/glide-grids/glide-grid_HIF2a-5TBM/glide-grid_HIF2a-5TBM.maegz -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_HIF2a-5TBM/glide-grid_HIF2a-5TBM.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-grid_HIF2a-5TBM.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_MCL1-4HW3/glide-grid_MCL1-4HW3.in: -------------------------------------------------------------------------------- 1 | FORCEFIELD OPLS_2005 2 | GRID_CENTER 66.44574876744186, -32.85393388372093, 27.378120930232562 3 | GRIDFILE glide-grid_MCL1-4HW3.zip 4 | INNERBOX 10, 10, 10 5 | OUTERBOX 24.098357815943295, 24.098357815943295, 24.098357815943295 6 | RECEP_FILE glide-grid_MCL1-4HW3.maegz 7 | -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_MCL1-4HW3/glide-grid_MCL1-4HW3.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/glide-grids/glide-grid_MCL1-4HW3/glide-grid_MCL1-4HW3.maegz -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_MCL1-4HW3/glide-grid_MCL1-4HW3.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-grid_MCL1-4HW3.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_P38-3FLY/glide-grid_P38-3FLY.in: -------------------------------------------------------------------------------- 1 | FORCEFIELD OPLS_2005 2 | GRID_CENTER 21.947818975609763, 10.436158512195123, 31.109645219512192 3 | GRIDFILE glide-grid_P38-3FLY.zip 4 | INNERBOX 10, 10, 10 5 | OUTERBOX 25.74823458947555, 25.74823458947555, 25.74823458947555 6 | RECEP_FILE glide-grid_P38-3FLY.maegz 7 | -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_P38-3FLY/glide-grid_P38-3FLY.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/glide-grids/glide-grid_P38-3FLY/glide-grid_P38-3FLY.maegz -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_P38-3FLY/glide-grid_P38-3FLY.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-grid_P38-3FLY.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_PDE2-4D08/glide-grid_PDE2-4D08.in: -------------------------------------------------------------------------------- 1 | FORCEFIELD OPLS_2005 2 | GRID_CENTER 27.830484900000005, -10.716901, 23.050756783333323 3 | GRIDFILE glide-grid_PDE2-4D08.zip 4 | INNERBOX 10, 10, 10 5 | OUTERBOX 24.180662157644182, 24.180662157644182, 24.180662157644182 6 | RECEP_FILE glide-grid_PDE2-4D08.maegz 7 | -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_PDE2-4D08/glide-grid_PDE2-4D08.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/glide-grids/glide-grid_PDE2-4D08/glide-grid_PDE2-4D08.maegz -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_PDE2-4D08/glide-grid_PDE2-4D08.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-grid_PDE2-4D08.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_PFKFB3-6HVI/glide-grid_PFKFB3-6HVI.in: -------------------------------------------------------------------------------- 1 | FORCEFIELD OPLS_2005 2 | GRID_CENTER 91.87562425490195, 49.352734999999996, 267.83874372549025 3 | GRIDFILE glide-grid_PFKFB3-6HVI.zip 4 | INNERBOX 10, 10, 10 5 | OUTERBOX 25.627682527703097, 25.627682527703097, 25.627682527703097 6 | RECEP_FILE glide-grid_PFKFB3-6HVI.maegz 7 | -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_PFKFB3-6HVI/glide-grid_PFKFB3-6HVI.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/glide-grids/glide-grid_PFKFB3-6HVI/glide-grid_PFKFB3-6HVI.maegz -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_PFKFB3-6HVI/glide-grid_PFKFB3-6HVI.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-grid_PFKFB3-6HVI.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_PTP1B-2QBS/glide-grid_PTP1B-2QBS.in: -------------------------------------------------------------------------------- 1 | FORCEFIELD OPLS_2005 2 | GRID_CENTER 47.67892426666666, 10.873164977777776, 2.318312444444444 3 | GRIDFILE glide-grid_PTP1B-2QBS.zip 4 | INNERBOX 10, 10, 10 5 | OUTERBOX 25.464775153598723, 25.464775153598723, 25.464775153598723 6 | RECEP_FILE glide-grid_PTP1B-2QBS.maegz 7 | -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_PTP1B-2QBS/glide-grid_PTP1B-2QBS.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/glide-grids/glide-grid_PTP1B-2QBS/glide-grid_PTP1B-2QBS.maegz -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_PTP1B-2QBS/glide-grid_PTP1B-2QBS.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-grid_PTP1B-2QBS.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_SHP2-5EHR/glide-grid_SHP2-5EHR.in: -------------------------------------------------------------------------------- 1 | FORCEFIELD OPLS_2005 2 | GRID_CENTER 23.423770953488376, 41.32217697674419, 4.124977930232557 3 | GRIDFILE glide-grid_SHP2-5EHR.zip 4 | INNERBOX 10, 10, 10 5 | OUTERBOX 25.12206499127887, 25.12206499127887, 25.12206499127887 6 | RECEP_FILE glide-grid_SHP2-5EHR.maegz 7 | -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_SHP2-5EHR/glide-grid_SHP2-5EHR.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/glide-grids/glide-grid_SHP2-5EHR/glide-grid_SHP2-5EHR.maegz -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_SHP2-5EHR/glide-grid_SHP2-5EHR.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-grid_SHP2-5EHR.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_SYK-4PV0/glide-grid_SYK-4PV0.in: -------------------------------------------------------------------------------- 1 | FORCEFIELD OPLS_2005 2 | GRID_CENTER -0.3651927666666665, 1.397881583333333, 13.2271836 3 | GRIDFILE glide-grid_SYK-4PV0.zip 4 | INNERBOX 10, 10, 10 5 | OUTERBOX 26.751395269016925, 26.751395269016925, 26.751395269016925 6 | RECEP_FILE glide-grid_SYK-4PV0.maegz 7 | -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_SYK-4PV0/glide-grid_SYK-4PV0.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/glide-grids/glide-grid_SYK-4PV0/glide-grid_SYK-4PV0.maegz -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_SYK-4PV0/glide-grid_SYK-4PV0.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-grid_SYK-4PV0.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_TNKS2-4UI5/glide-grid_TNKS2-4UI5.in: -------------------------------------------------------------------------------- 1 | FORCEFIELD OPLS_2005 2 | GRID_CENTER -39.36747267647059, -12.448252882352943, 11.96837861764706 3 | GRIDFILE glide-grid_TNKS2-4UI5.zip 4 | INNERBOX 10, 10, 10 5 | OUTERBOX 23.874829406257508, 23.874829406257508, 23.874829406257508 6 | RECEP_FILE glide-grid_TNKS2-4UI5.maegz 7 | -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_TNKS2-4UI5/glide-grid_TNKS2-4UI5.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/glide-grids/glide-grid_TNKS2-4UI5/glide-grid_TNKS2-4UI5.maegz -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_TNKS2-4UI5/glide-grid_TNKS2-4UI5.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-grid_TNKS2-4UI5.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_TYK2-4GIH/glide-grid_TYK2-4GIH.in: -------------------------------------------------------------------------------- 1 | FORCEFIELD OPLS_2005 2 | GRID_CENTER -7.962335833333332, -9.11635713888889, -17.452904444444446 3 | GRIDFILE glide-grid_TYK2-4GIH.zip 4 | INNERBOX 10, 10, 10 5 | OUTERBOX 24.731089996419996, 24.731089996419996, 24.731089996419996 6 | RECEP_FILE glide-grid_TYK2-4GIH.maegz 7 | -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_TYK2-4GIH/glide-grid_TYK2-4GIH.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/glide-grids/glide-grid_TYK2-4GIH/glide-grid_TYK2-4GIH.maegz -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_TYK2-4GIH/glide-grid_TYK2-4GIH.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-grid_TYK2-4GIH.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_cMET-4R1Y/glide-grid_cMET-4R1Y.in: -------------------------------------------------------------------------------- 1 | FORCEFIELD OPLS_2005 2 | GRID_CENTER -22.341277380281692, 23.686690197183108, 97.83514353521129 3 | GRIDFILE glide-grid_cMET-4R1Y.zip 4 | INNERBOX 10, 10, 10 5 | OUTERBOX 25.19445536285471, 25.19445536285471, 25.19445536285471 6 | RECEP_FILE glide-grid_cMET-4R1Y.maegz 7 | -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_cMET-4R1Y/glide-grid_cMET-4R1Y.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/glide-grids/glide-grid_cMET-4R1Y/glide-grid_cMET-4R1Y.maegz -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_cMET-4R1Y/glide-grid_cMET-4R1Y.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-grid_cMET-4R1Y.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_galectin-5E89/glide-grid_galectin-5E89.in: -------------------------------------------------------------------------------- 1 | FORCEFIELD OPLS_2005 2 | GRID_CENTER 21.07448965333333, -9.457271280000004, 0.43933886666666666 3 | GRIDFILE glide-grid_galectin-5E89.zip 4 | INNERBOX 10, 10, 10 5 | OUTERBOX 30.847594599167113, 30.847594599167113, 30.847594599167113 6 | RECEP_FILE glide-grid_galectin-5E89.maegz 7 | -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_galectin-5E89/glide-grid_galectin-5E89.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/glide-grids/glide-grid_galectin-5E89/glide-grid_galectin-5E89.maegz -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_galectin-5E89/glide-grid_galectin-5E89.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-grid_galectin-5E89.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_thrombin-2ZFF/glide-grid_thrombin-2ZFF.in: -------------------------------------------------------------------------------- 1 | FORCEFIELD OPLS_2005 2 | GRID_CENTER 17.23742396153846, -12.763850461538462, 22.472269326923083 3 | GRIDFILE glide-grid_thrombin-2ZFF.zip 4 | INNERBOX 10, 10, 10 5 | OUTERBOX 24.32785395709283, 24.32785395709283, 24.32785395709283 6 | RECEP_FILE glide-grid_thrombin-2ZFF.maegz 7 | -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_thrombin-2ZFF/glide-grid_thrombin-2ZFF.maegz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/glide-grids/glide-grid_thrombin-2ZFF/glide-grid_thrombin-2ZFF.maegz -------------------------------------------------------------------------------- /preparation/glide-grids/glide-grid_thrombin-2ZFF/glide-grid_thrombin-2ZFF.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/glide" glide-grid_thrombin-2ZFF.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_cdk2/ligprep_cdk2.inp: -------------------------------------------------------------------------------- 1 | INPUT_FILE_NAME ligprep_cdk2.smi 2 | OUT_SD ligprep_cdk2-out.sdf 3 | MAX_ATOMS 500 4 | FORCE_FIELD 16 5 | PH 7.4 6 | PH_THRESHOLD 0.0 7 | EPIK yes 8 | DETERMINE_CHIRALITIES no 9 | IGNORE_CHIRALITIES no 10 | NUM_STEREOISOMERS 32 11 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_cdk2/ligprep_cdk2.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/ligprep" -inp ligprep_cdk2.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_cdk2/ligprep_cdk2.smi: -------------------------------------------------------------------------------- 1 | [H][C]1=[N][C]2=[C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])[N]=[C]([N]([H])[C]3=[C]([H])[C]([H])=[C]([H])[C]([Br])=[C]3[H])[N]=[C]2[N]1[H],lig_17 2 | [H][C]1=[N][C]2=[C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])[N]=[C]([N]([H])[C]3=[C]([H])[C]([H])=[C]([H])[C]([H])=[C]3[H])[N]=[C]2[N]1[H],lig_1h1q 3 | [H]c1c(c(c(c(c1[H])Cl)[H])N([H])c2nc3c(c(n2)OC([H])([H])C4(C(C(C(C(C4([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])N=C(N3[H])[H])[H],lig_1h1r 4 | [H][C]1=[N][C]2=[C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])[N]=[C]([N]([H])[C]3=[C]([H])[C]([H])=[C]([S](=[O])(=[O])[N]([H])[H])[C]([H])=[C]3[H])[N]=[C]2[N]1[H],lig_1h1s 5 | [H][O][C]1=[C]([H])[C]([H])=[C]([N]([H])[C]2=[N][C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])=[C]3[N]=[C]([H])[N]([H])[C]3=[N]2)[C]([H])=[C]1[H],lig_1oi9 6 | [H][C]1=[N][C]2=[C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])[N]=[C]([N]([H])[C]3=[C]([H])[C]([S](=[O])(=[O])[N]([H])[H])=[C]([H])[C]([H])=[C]3[H])[N]=[C]2[N]1[H],lig_1oiu 7 | [H][C]1=[N][C]2=[C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])[N]=[C]([N]([H])[C]3=[C]([H])[C]([H])=[C]([C](=[O])[N]([H])[H])[C]([H])=[C]3[H])[N]=[C]2[N]1[H],lig_1oiy 8 | [H][O][C]([H])([H])[C]1=[C]([H])[C]([H])=[C]([H])[C]([N]([H])[C]2=[N][C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])=[C]3[N]=[C]([H])[N]([H])[C]3=[N]2)=[C]1[H],lig_20 9 | [H][C]1=[N][C]2=[C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])[N]=[C]([N]([H])[C]3=[C]([H])[C]([H])=[C]([H])[C]([O][C]([H])([H])[H])=[C]3[H])[N]=[C]2[N]1[H],lig_21 10 | [H][C]1=[N][C]2=[C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])[N]=[C]([N]([H])[C]3=[C]([H])[C]([H])=[C]([H])[C]([S][C]([H])([H])[H])=[C]3[H])[N]=[C]2[N]1[H],lig_22 11 | [H][C]1=[N][C]2=[C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])[N]=[C]([N]([H])[C]3=[C]([H])[C]([H])=[C]([O][C]([H])([H])[H])[C]([H])=[C]3[H])[N]=[C]2[N]1[H],lig_26 12 | [H][C]1=[N][C]2=[C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])[N]=[C]([N]([H])[C]3=[C]([H])[C]([H])=[C]([S](=[O])(=[O])[N]([H])[C]([H])([H])[H])[C]([H])=[C]3[H])[N]=[C]2[N]1[H],lig_28 13 | [H]c1c(c(c(c(c1N([H])c2nc3c(c(n2)OC([H])([H])C4(C(C(C(C(C4([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])N=C(N3[H])[H])[H])[H])S(=O)(=O)N(C([H])([H])[H])C([H])([H])[H])[H],lig_29 14 | [H]c1c(c(c(c(c1N([H])c2nc3c(c(n2)OC([H])([H])C4(C(C(C(C(C4([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])N=C(N3[H])[H])[H])[H])S(=O)(=O)C([H])([H])[H])[H],lig_30 15 | [H]c1c(c(c(c(c1N([H])c2nc3c(c(n2)OC([H])([H])C4(C(C(C(C(C4([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])N=C(N3[H])[H])[H])[H])[S@@](=O)C([H])([H])[H])[H],lig_31 16 | [H]c1c(c(c(c(c1N([H])c2nc3c(c(n2)OC([H])([H])C4(C(C(C(C(C4([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])N=C(N3[H])[H])[H])OC([H])([H])[H])S(=O)(=O)N([H])[H])[H],lig_32 17 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_cdk8/ligprep_cdk8.inp: -------------------------------------------------------------------------------- 1 | INPUT_FILE_NAME ligprep_cdk8.smi 2 | OUT_SD ligprep_cdk8-out.sdf 3 | MAX_ATOMS 500 4 | FORCE_FIELD 16 5 | PH 7.4 6 | PH_THRESHOLD 0.0 7 | EPIK yes 8 | DETERMINE_CHIRALITIES no 9 | IGNORE_CHIRALITIES no 10 | NUM_STEREOISOMERS 32 11 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_cdk8/ligprep_cdk8.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/ligprep" -inp ligprep_cdk8.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_cmet/ligprep_cmet.inp: -------------------------------------------------------------------------------- 1 | INPUT_FILE_NAME ligprep_cmet.smi 2 | OUT_SD ligprep_cmet-out.sdf 3 | MAX_ATOMS 500 4 | FORCE_FIELD 16 5 | PH 7.4 6 | PH_THRESHOLD 0.0 7 | EPIK yes 8 | DETERMINE_CHIRALITIES no 9 | IGNORE_CHIRALITIES no 10 | NUM_STEREOISOMERS 32 11 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_cmet/ligprep_cmet.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/ligprep" -inp ligprep_cmet.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_cmet/ligprep_cmet.smi: -------------------------------------------------------------------------------- 1 | [H][C]1=[C]([H])[C]([c]2[c]([H])[c]([F])[c]([H])[c]([F])[c]2[H])=[N][N]([C]([H])([H])[c]2[c]([H])[c]([H])[c]([H])[c]([N]([H])[C](=[O])[O][C]([H])([H])[H])[c]2[H])[C]1=[O],lig_CHEMBL3402744_300_4 2 | [H][C]1=[C]([H])[C]([c]2[c]([H])[c]([F])[c]([H])[c]([F])[c]2[H])=[N][N]([C]([H])([H])[c]2[c]([H])[c]([H])[c]([H])[c]([N]([H])[C](=[O])[O][C]([H])([H])[C]([H])([H])[H])[c]2[H])[C]1=[O],lig_CHEMBL3402745_200_5 3 | [H][C]1=[C]([H])[C]([c]2[c]([H])[c]([F])[c]([H])[c]([F])[c]2[H])=[N][N]([C]([H])([H])[c]2[c]([H])[c]([H])[c]([H])[c]([C]3=[N][C]([C]([H])([H])[H])=[N][O]3)[c]2[H])[C]1=[O],lig_CHEMBL3402747_3400_7 4 | [H][C]1=[C]([C]([H])([H])[H])[N]([H])[C]([c]2[c]([H])[c]([H])[c]([H])[c]([C]([H])([H])[N]3[N]=[C]([c]4[c]([H])[c]([F])[c]([H])[c]([F])[c]4[H])[C]([H])=[C]([H])[C]3=[O])[c]2[H])=[N]1,lig_CHEMBL3402748_5300_8 5 | [H][C]1=[C]([C]([H])([H])[H])[O][C]([c]2[c]([H])[c]([H])[c]([H])[c]([C]([H])([H])[N]3[N]=[C]([c]4[c]([H])[c]([F])[c]([H])[c]([F])[c]4[H])[C]([H])=[C]([H])[C]3=[O])[c]2[H])=[N]1,lig_CHEMBL3402749_500_9 6 | [H][C]1=[C]([C]([H])([H])[H])[S][C]([c]2[c]([H])[c]([H])[c]([H])[c]([C]([H])([H])[N]3[N]=[C]([c]4[c]([H])[c]([F])[c]([H])[c]([F])[c]4[H])[C]([H])=[C]([H])[C]3=[O])[c]2[H])=[N]1,lig_CHEMBL3402750_400_10 7 | [H][C]1=[C]([C]([H])([H])[H])[N]=[C]([c]2[c]([H])[c]([H])[c]([H])[c]([C]([H])([H])[N]3[N]=[C]([c]4[c]([H])[c]([F])[c]([H])[c]([F])[c]4[H])[C]([H])=[C]([H])[C]3=[O])[c]2[H])[S]1,lig_CHEMBL3402751_2100_11 8 | [H][C]1=[C]([c]2[c]([H])[c]([H])[c]([H])[c]([C]([H])([H])[N]3[N]=[C]([c]4[c]([H])[c]([F])[c]([H])[c]([F])[c]4[H])[C]([H])=[C]([H])[C]3=[O])[c]2[H])[N]=[C]([C]([H])([H])[H])[S]1,lig_CHEMBL3402752_30000_12 9 | [H][C]1=[C]([H])[C]([c]2[c]([H])[c]([F])[c]([H])[c]([F])[c]2[H])=[N][N]([C]([H])([H])[c]2[c]([H])[c]([H])[c]([H])[c](-[c]3[n][c]([H])[c]([C]([H])([H])[H])[c]([H])[c]3[H])[c]2[H])[C]1=[O],lig_CHEMBL3402753_200_13 10 | [H][C]1=[C]([H])[C]([c]2[c]([H])[c]([F])[c]([H])[c]([F])[c]2[H])=[N][N]([C]([H])([H])[c]2[c]([H])[c]([H])[c]([H])[c](-[c]3[n][c]([H])[c]([C]([H])([H])[H])[c]([H])[n]3)[c]2[H])[C]1=[O],lig_CHEMBL3402754_40_14 11 | [H][C]1=[C]([H])[C]([c]2[c]([H])[c]([F])[c]([H])[c]([F])[c]2[H])=[N][N]([C]([H])([H])[c]2[c]([H])[c]([H])[c]([H])[c](-[c]3[n][n][c]([C]([H])([H])[H])[c]([H])[c]3[H])[c]2[H])[C]1=[O],lig_CHEMBL3402755_4200_15 12 | [H][C]1=[C]([H])[C]([c]2[c]([H])[c]([H])[c]([H])[c]([C]#[N])[c]2[H])=[N][N]([C]([H])([H])[c]2[c]([H])[c]([H])[c]([H])[c](-[c]3[n][c]([H])[c]([O][C]([H])([H])[C]([H])([H])[N]4[C]([H])([H])[C]([H])([H])[O][C]([H])([H])[C]4([H])[H])[c]([H])[n]3)[c]2[H])[C]1=[O],lig_CHEMBL3402761_1_21 13 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_eg5/ligprep_eg5.inp: -------------------------------------------------------------------------------- 1 | INPUT_FILE_NAME ligprep_eg5.smi 2 | OUT_SD ligprep_eg5-out.sdf 3 | MAX_ATOMS 500 4 | FORCE_FIELD 16 5 | PH 7.4 6 | PH_THRESHOLD 0.0 7 | EPIK yes 8 | DETERMINE_CHIRALITIES no 9 | IGNORE_CHIRALITIES no 10 | NUM_STEREOISOMERS 32 11 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_eg5/ligprep_eg5.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/ligprep" -inp ligprep_eg5.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_hif2a/ligprep_hif2a.inp: -------------------------------------------------------------------------------- 1 | INPUT_FILE_NAME ligprep_hif2a.smi 2 | OUT_SD ligprep_hif2a-out.sdf 3 | MAX_ATOMS 500 4 | FORCE_FIELD 16 5 | PH 7.4 6 | PH_THRESHOLD 0.0 7 | EPIK yes 8 | DETERMINE_CHIRALITIES no 9 | IGNORE_CHIRALITIES no 10 | NUM_STEREOISOMERS 32 11 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_hif2a/ligprep_hif2a.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/ligprep" -inp ligprep_hif2a.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_jnk1/ligprep_jnk1.inp: -------------------------------------------------------------------------------- 1 | INPUT_FILE_NAME ligprep_jnk1.smi 2 | OUT_SD ligprep_jnk1-out.sdf 3 | MAX_ATOMS 500 4 | FORCE_FIELD 16 5 | PH 7.4 6 | PH_THRESHOLD 0.0 7 | EPIK yes 8 | DETERMINE_CHIRALITIES no 9 | IGNORE_CHIRALITIES no 10 | NUM_STEREOISOMERS 32 11 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_jnk1/ligprep_jnk1.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/ligprep" -inp ligprep_jnk1.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_jnk1/ligprep_jnk1.smi: -------------------------------------------------------------------------------- 1 | CCOc1c(c(cc(n1)NC(=O)Cc2cc(c(cc2OC)Br)OC)N)C#N,lig_17124-1 2 | CCOc1c(c(cc(n1)NC(=O)Cc2ccccc2)N)C#N,lig_18624-1 3 | CCOc1c(c(cc(n1)NC(=O)Cc2ccccc2Cl)N)C#N,lig_18625-1 4 | CCOc1c(c(cc(n1)NC(=O)Cc2cccc(c2)Cl)N)C#N,lig_18626-1 5 | CCOc1c(c(cc(n1)NC(=O)Cc2ccc(cc2)Cl)N)C#N,lig_18627-1 6 | CCOc1c(c(cc(n1)NC(=O)Cc2ccccc2C)N)C#N,lig_18628-1 7 | CCOc1c(c(cc(n1)NC(=O)Cc2cccc(c2)C)N)C#N,lig_18629-1 8 | CCOc1c(c(cc(n1)NC(=O)Cc2ccc(cc2)C)N)C#N,lig_18630-1 9 | CCOc1c(c(cc(n1)NC(=O)Cc2ccccc2OC)N)C#N,lig_18631-1 10 | CCOc1c(c(cc(n1)NC(=O)Cc2cccc(c2)OC)N)C#N,lig_18632-1 11 | CCOc1c(c(cc(n1)NC(=O)Cc2ccc(cc2)OC)N)C#N,lig_18633-1 12 | CCOc1c(c(cc(n1)NC(=O)Cc2cc(ccc2OC)OC)N)C#N,lig_18634-1 13 | CCOc1c(c(cc(n1)NC(=O)Cc2cc(ccc2C)C)N)C#N,lig_18635-1 14 | CCOc1c(c(cc(n1)NC(=O)Cc2cc(ccc2Br)Br)N)C#N,lig_18636-1 15 | CCOc1c(c(cc(n1)NC(=O)Cc2cc(c(cc2OC)NC(=O)C)OC)N)C#N,lig_18637-1 16 | CCOc1c(c(cc(n1)NC(=O)Cc2cc(c(cc2OC)S(=O)(=O)C)OC)N)C#N,lig_18638-1 17 | CCOc1c(c(cc(n1)NC(=O)Cc2cc(c(cc2OC)[N+](=O)[O-])OC)N)C#N,lig_18639-1 18 | CC(C)Oc1c(c(cc(n1)NC(=O)Cc2cc(c(cc2OC)S(=O)(=O)C)OC)N)C#N,lig_18652-1 19 | COc1ccc(c(c1)CC(=O)Nc2cc(c(c(n2)OCCO)C#N)N)OC,lig_18658-1 20 | COCCOc1c(c(cc(n1)NC(=O)Cc2cc(ccc2OC)OC)N)C#N,lig_18659-1 21 | COc1ccc(c(c1)CC(=O)Nc2cc(c(c(n2)OCCS(=O)(=O)C)C#N)N)OC,lig_18660-1 22 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_mcl1/ligprep_mcl1.inp: -------------------------------------------------------------------------------- 1 | INPUT_FILE_NAME ligprep_mcl1.smi 2 | OUT_SD ligprep_mcl1-out.sdf 3 | MAX_ATOMS 500 4 | FORCE_FIELD 16 5 | PH 7.4 6 | PH_THRESHOLD 0.0 7 | EPIK yes 8 | DETERMINE_CHIRALITIES no 9 | IGNORE_CHIRALITIES no 10 | NUM_STEREOISOMERS 32 11 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_mcl1/ligprep_mcl1.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/ligprep" -inp ligprep_mcl1.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_p38/ligprep_p38.inp: -------------------------------------------------------------------------------- 1 | INPUT_FILE_NAME ligprep_p38.smi 2 | OUT_SD ligprep_p38-out.sdf 3 | MAX_ATOMS 500 4 | FORCE_FIELD 16 5 | PH 7.4 6 | PH_THRESHOLD 0.0 7 | EPIK yes 8 | DETERMINE_CHIRALITIES no 9 | IGNORE_CHIRALITIES no 10 | NUM_STEREOISOMERS 32 11 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_p38/ligprep_p38.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/ligprep" -inp ligprep_p38.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_pde2/ligprep_pde2.inp: -------------------------------------------------------------------------------- 1 | INPUT_FILE_NAME ligprep_pde2.smi 2 | OUT_SD ligprep_pde2-out.sdf 3 | MAX_ATOMS 500 4 | FORCE_FIELD 16 5 | PH 7.4 6 | PH_THRESHOLD 0.0 7 | EPIK yes 8 | DETERMINE_CHIRALITIES no 9 | IGNORE_CHIRALITIES no 10 | NUM_STEREOISOMERS 32 11 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_pde2/ligprep_pde2.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/ligprep" -inp ligprep_pde2.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_pde2/ligprep_pde2.smi: -------------------------------------------------------------------------------- 1 | Cc1c2nnc(n2c3cc(ccc3n1)CN4CCOCC4)c5ccccc5Cl,lig_43249674 2 | Cc1c2nnc(n2c3cc(ccc3n1)CN4CCOCC4)c5ccc(cc5Cl)F,lig_48009208 3 | Cc1c2nnc(n2c3cc(ccc3n1)CN4CCOCC4)c5c(cccc5Cl)F,lig_48022468 4 | Cc1c(cccn1)c2nnc3n2c4cc(ccc4nc3C)CN5CCOCC5,lig_48168913 5 | Cc1c2nnc(n2c3cc(ccc3n1)CN4CCOCC4)c5cc(cnc5)OC,lig_48271249 6 | Cc1c2nnc(n2c3cc(ccc3n1)CN4CCOCC4)c5cc(cnc5)OC(C)C,lig_49072088 7 | Cc1c2nnc(n2c3cc(ccc3n1)CN4CCOCC4)c5cc(ccc5Cl)OC,lig_49137374 8 | CCCCOc1cc(cnc1)c2nnc3n2c4cc(ccc4nc3C)CN5CCOCC5,lig_49137530 9 | CCCCOc1ccc(c(c1)c2nnc3n2c4cc(ccc4nc3C)CN5CCOCC5)Cl,lig_49175789 10 | Cc1c2nnc(n2c3cc(ccc3n1)CN4CCOCC4)c5cc(ccc5Cl)OC(C)C,lig_49175828 11 | CCOc1ccc(c(c1)c2nnc3n2c4cc(ccc4nc3C)CN5CCOCC5)Cl,lig_49220392 12 | CCCOc1ccc(c(c1)c2nnc3n2c4cc(ccc4nc3C)CN5CCOCC5)Cl,lig_49220548 13 | CCCOc1cc(cnc1)c2nnc3n2c4cc(ccc4nc3C)CN5CCOCC5,lig_49396360 14 | Cc1c2nnc(n2c3cc(ccc3n1)CN4CCOCC4)c5cc(cnc5)OCCF,lig_49580115 15 | Cc1c2nnc(n2c3cc(ccc3n1)CN4CCOCC4)c5cc(cnc5)OCC6CC6,lig_49582390 16 | CCOCc1cc(cnc1)c2nnc3n2c4cc(ccc4nc3C)CN5CCOCC5,lig_49582468 17 | Cc1c2nnc(n2c3cc(ccc3n1)CN4CCOCC4)c5cc(cnc5)OCCOC,lig_49585367 18 | Cc1c2nnc(n2c3cc(ccc3n1)CN4CCOCC4)c5cc(cnc5)CCOC,lig_49932129 19 | Cc1c2nnc(n2c3cc(ccc3n1)CN4CCOCC4)c5cc(cnc5)OCCCF,lig_49932714 20 | Cc1c2nnc(n2c3cc(ccc3n1)CN4CCOCC4)c5cc(cnc5)CCCOC,lig_50107616 21 | CCCCOc1cc(cnc1Cl)c2nnc3n2c4cc(ccc4nc3C)CN5CCOCC5,lig_50181001 22 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_pfkfb3/ligprep_pfkfb3.inp: -------------------------------------------------------------------------------- 1 | INPUT_FILE_NAME ligprep_pfkfb3.smi 2 | OUT_SD ligprep_pfkfb3-out.sdf 3 | MAX_ATOMS 500 4 | FORCE_FIELD 16 5 | PH 7.4 6 | PH_THRESHOLD 0.0 7 | EPIK yes 8 | DETERMINE_CHIRALITIES no 9 | IGNORE_CHIRALITIES no 10 | NUM_STEREOISOMERS 32 11 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_pfkfb3/ligprep_pfkfb3.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/ligprep" -inp ligprep_pfkfb3.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_ptp1b/ligprep_ptp1b.inp: -------------------------------------------------------------------------------- 1 | INPUT_FILE_NAME ligprep_ptp1b.smi 2 | OUT_SD ligprep_ptp1b-out.sdf 3 | MAX_ATOMS 500 4 | FORCE_FIELD 16 5 | PH 7.4 6 | PH_THRESHOLD 0.0 7 | EPIK yes 8 | DETERMINE_CHIRALITIES no 9 | IGNORE_CHIRALITIES no 10 | NUM_STEREOISOMERS 32 11 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_ptp1b/ligprep_ptp1b.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/ligprep" -inp ligprep_ptp1b.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_ptp1b/ligprep_ptp1b.smi: -------------------------------------------------------------------------------- 1 | [H]c1c(c(c(c(c1[H])[H])C([H])([H])S(=O)(=O)N2C(C(C(C(C2([H])[H])([H])[H])([H])N([H])c3c(c(c(c(c3[H])C4=C(C(=C(S4)C(=O)[O-])OC([H])([H])C(=O)[O-])Br)[H])[H])[H])([H])[H])([H])[H])[H])[H],lig_20667_2qbp 2 | [H]c1c(c(c(c(c1[H])[H])C([H])([H])N([H])c2c(c(c(c(c2[H])C3=C(C(=C(S3)C(=O)[O-])OC([H])([H])C(=O)[O-])Br)[H])[H])[H])[H])[H],lig_20669_2qbr 3 | [H]c1c(c(c(c(c1[H])N([H])C2(C(C(C(C(C2([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])[H])C3=C(C(=C(S3)C(=O)[O-])OC([H])([H])C(=O)[O-])Br)[H],lig_20670_2qbs 4 | [H]c1c(c(c(c(c1[H])N([H])C2(C(C(C(C(C2([H])[H])(C([H])([H])[H])C([H])([H])[H])([H])[H])(C([H])([H])[H])C([H])([H])[H])([H])[H])[H])[H])C3=C(C(=C(S3)C(=O)[O-])OC([H])([H])C(=O)[O-])Br)[H],lig_23330_2qbq 5 | [H]c1c(c(c(c(c1[H])N([H])[H])[H])C2=C(C(=C(S2)C(=O)[O-])OC([H])([H])C(=O)[O-])Br)[H],lig_23466 6 | [H]c1c(c(c(c(c1[H])OC([H])([H])[H])[H])C2=C(C(=C(S2)C(=O)[O-])OC([H])([H])C(=O)[O-])Br)[H],lig_23467 7 | [H]c1c(c(c(c(c1[H])N([H])C(=O)C([H])([H])C([H])([H])[H])[H])C2=C(C(=C(S2)C(=O)[O-])OC([H])([H])C(=O)[O-])Br)[H],lig_23468 8 | [H]c1c(c(c(c(c1[H])[H])C(=O)N([H])c2c(c(c(c(c2[H])C3=C(C(=C(S3)C(=O)[O-])OC([H])([H])C(=O)[O-])Br)[H])[H])[H])[H])[H],lig_23469 9 | [H]c1c(c(c(c(c1[H])N([H])C(=O)N([H])C([H])(C([H])([H])[H])C([H])([H])[H])[H])C2=C(C(=C(S2)C(=O)[O-])OC([H])([H])C(=O)[O-])Br)[H],lig_23470 10 | [H]c1c(c(c(c(c1[H])N([H])C(=O)OC([H])([H])[H])[H])C2=C(C(=C(S2)C(=O)[O-])OC([H])([H])C(=O)[O-])Br)[H],lig_23471 11 | [H]c1c(c(c(c(c1[H])N([H])S(=O)(=O)c2c(c(c(c(c2[H])[H])F)[H])[H])[H])C3=C(C(=C(S3)C(=O)[O-])OC([H])([H])C(=O)[O-])Br)[H],lig_23472 12 | [H]c1c(c(c(c(c1[H])[H])C([H])([H])Oc2c(c(c(c(c2[H])C3=C(C(=C(S3)C(=O)[O-])OC([H])([H])C(=O)[O-])Br)[H])[H])[H])[H])[H],lig_23473 13 | [H]c1c(c(c(c(c1[H])N([H])C([H])([H])C2(C(C(C(C(C2([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])[H])C3=C(C(=C(S3)C(=O)[O-])OC([H])([H])C(=O)[O-])Br)[H],lig_23474 14 | [H]c1c(c(c(c(c1[H])N([H])C2(C(C(C(C2([H])[H])([H])[H])([H])[H])([H])[H])[H])[H])C3=C(C(=C(S3)C(=O)[O-])OC([H])([H])C(=O)[O-])Br)[H],lig_23475 15 | [H]c1c(c(c(c(c1[H])N([H])C2(C(C(C(C(C(C2([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])[H])C3=C(C(=C(S3)C(=O)[O-])OC([H])([H])C(=O)[O-])Br)[H],lig_23476 16 | [H]c1c(c(c(c(c1[H])N([H])C2(C(C(OC(C2([H])[H])([H])[H])([H])[H])([H])[H])[H])[H])C3=C(C(=C(S3)C(=O)[O-])OC([H])([H])C(=O)[O-])Br)[H],lig_23477 17 | [H]c1c(c(c(c(c1[H])N([H])C2(C(C(N(C(C2([H])[H])([H])[H])C(=O)C([H])([H])[H])([H])[H])([H])[H])[H])[H])C3=C(C(=C(S3)C(=O)[O-])OC([H])([H])C(=O)[O-])Br)[H],lig_23479 18 | [H]c1c(c(c(c(c1[H])N([H])C([H])([H])C2(C(C(N(C(C2([H])[H])([H])[H])C(=O)OC([H])([H])[H])([H])[H])([H])[H])[H])[H])C3=C(C(=C(S3)C(=O)[O-])OC([H])([H])C(=O)[O-])Br)[H],lig_23480 19 | [H]c1c(c(c(c(c1[H])N([H])C2(C(C(N(C(C2([H])[H])([H])[H])S(=O)(=O)C([H])([H])[H])([H])[H])([H])[H])[H])[H])C3=C(C(=C(S3)C(=O)[O-])OC([H])([H])C(=O)[O-])Br)[H],lig_23482 20 | [H]c1c(c(c(c(c1[H])[H])S(=O)(=O)N2C(C(C(C(C2([H])[H])([H])[H])([H])N([H])c3c(c(c(c(c3[H])C4=C(C(=C(S4)C(=O)[O-])OC([H])([H])C(=O)[O-])Br)[H])[H])[H])([H])[H])([H])[H])[H])[H],lig_23483 21 | [H]c1c(c(c(c(c1[H])[H])C([H])([H])S(=O)(=O)N2C(C(C(C(C2([H])[H])([H])[H])([H])N([H])c3c(c(c(c(c3[H])C4=C(C(=C(S4)C(=O)[O-])OC([H])([H])C(=O)[O-])[H])[H])[H])[H])([H])[H])([H])[H])[H])[H],lig_23484 22 | [H]c1c(c(c(c(c1[H])[H])C([H])([H])S(=O)(=O)N2C(C(C(C(C2([H])[H])([H])[H])([H])N([H])c3c(c(c(c(c3[H])C4=C(C(=C(S4)C(=O)[O-])OC([H])([H])C(=O)[O-])C([H])([H])[H])[H])[H])[H])([H])[H])([H])[H])[H])[H],lig_23485 23 | [H]c1c(c(c(c(c1[H])[H])C([H])([H])S(=O)(=O)N2C(C(C(C(C2([H])[H])([H])[H])([H])N([H])c3c(c(c(c(c3[H])C4=C(C(=C(S4)C(=O)[O-])OC([H])([H])C(=O)[O-])Cl)[H])[H])[H])([H])[H])([H])[H])[H])[H],lig_23486 24 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_shp2/ligprep_shp2.inp: -------------------------------------------------------------------------------- 1 | INPUT_FILE_NAME ligprep_shp2.smi 2 | OUT_SD ligprep_shp2-out.sdf 3 | MAX_ATOMS 500 4 | FORCE_FIELD 16 5 | PH 7.4 6 | PH_THRESHOLD 0.0 7 | EPIK yes 8 | DETERMINE_CHIRALITIES no 9 | IGNORE_CHIRALITIES no 10 | NUM_STEREOISOMERS 32 11 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_shp2/ligprep_shp2.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/ligprep" -inp ligprep_shp2.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_shp2/ligprep_shp2.smi: -------------------------------------------------------------------------------- 1 | [H][c]1[n][c]([N]2[C]([H])([H])[C]([H])([H])[C]([C]([H])([H])[H])([N+]([H])([H])[H])[C]([H])([H])[C]2([H])[H])[c]([H])[n][c]1-[c]1[c]([H])[c]([H])[c]([H])[c]([Cl])[c]1[Cl],lig_10 2 | [H][c]1[n][c](-[c]2[c]([H])[c]([H])[c]([H])[c]([Cl])[c]2[Cl])[c]([N]([H])[C]([H])([H])[H])[n][c]1[N]1[C]([H])([H])[C]([H])([H])[C]([C]([H])([H])[H])([N+]([H])([H])[H])[C]([H])([H])[C]1([H])[H],lig_11 3 | [H][c]1[n][c]([N]2[C]([H])([H])[C@]([H])([C]([H])([H])[H])[N+]([H])([H])[C@]([H])([C]([H])([H])[H])[C]2([H])[H])[n][c]([N]([H])[H])[c]1-[c]1[c]([H])[c]([H])[c]([H])[c]([Cl])[c]1[H],lig_3 4 | [H][c]1[n][c]([N]2[C]([H])([H])[C@]([H])([C]([H])([H])[H])[N+]([H])([H])[C@]([H])([C]([H])([H])[H])[C]2([H])[H])[n][c]([N]([H])[H])[c]1-[c]1[c]([H])[c]([H])[c]([Cl])[c]([Cl])[c]1[H],lig_4 5 | [H][c]1[n][c]([N]2[C]([H])([H])[C]([H])([H])[C]([H])([N+]([H])([H])[H])[C]([H])([H])[C]2([H])[H])[n][c]([N]([H])[H])[c]1-[c]1[c]([H])[c]([H])[c]([H])[c]([Cl])[c]1[Cl],lig_6 6 | [H][c]1[n][c]([N]2[C]([H])([H])[C]([H])([H])[C]([H])([N+]([H])([C]([H])([H])[H])[C]([H])([H])[H])[C]([H])([H])[C]2([H])[H])[n][c]([N]([H])[H])[c]1-[c]1[c]([H])[c]([H])[c]([H])[c]([Cl])[c]1[Cl],lig_7 7 | [H][c]1[n][c]([N]2[C]([H])([H])[C]([H])([H])[C]([C]([H])([H])[H])([N+]([H])([H])[H])[C]([H])([H])[C]2([H])[H])[n][c]([N]([H])[H])[c]1-[c]1[c]([H])[c]([H])[c]([H])[c]([Cl])[c]1[Cl],lig_E1 8 | [H][c]1[n][c](-[c]2[c]([H])[c]([H])[c]([H])[c]([Cl])[c]2[Cl])[c]([N]([H])[H])[n][c]1[N]1[C]([H])([H])[C]([H])([H])[C@@]([H])([C]([H])([H])[N+]([H])([H])[H])[C]1([H])[H],lig_E14 9 | [H][c]1[n][c]([N]2[C]([H])([H])[C]([H])([H])[C]([C]([H])([H])[H])([N+]([H])([H])[H])[C]([H])([H])[C]2([H])[H])[n][c]([N]([H])[H])[c]1-[c]1[c]([H])[c]([H])[c]([H])[c]([C]([H])([H])[H])[c]1[Cl],lig_E2 10 | [H][c]1[c]([H])[c]([Cl])[c]([Cl])[c](-[c]2[n][c]([Br])[c]([N]3[C]([H])([H])[C]([H])([H])[C]([C]([H])([H])[H])([N+]([H])([H])[H])[C]([H])([H])[C]3([H])[H])[n][c]2[N]([H])[H])[c]1[H],lig_E22 11 | [H][c]1[c]([H])[c]([Cl])[c]([Cl])[c](-[c]2[n][c]([Cl])[c]([N]3[C]([H])([H])[C]([H])([H])[C]([C]([H])([H])[H])([N+]([H])([H])[H])[C]([H])([H])[C]3([H])[H])[n][c]2[N]([H])[H])[c]1[H],lig_E23 12 | [H][c]1[c]([H])[c]([Cl])[c]([Cl])[c](-[c]2[n][c]([C]([H])([H])[H])[c]([N]3[C]([H])([H])[C]([H])([H])[C]([C]([H])([H])[H])([N+]([H])([H])[H])[C]([H])([H])[C]3([H])[H])[n][c]2[N]([H])[H])[c]1[H],lig_E24 13 | [H][c]1[c]([H])[c]([Cl])[c]([Cl])[c](-[c]2[n][c]([C]#[N])[c]([N]3[C]([H])([H])[C]([H])([H])[C]([C]([H])([H])[H])([N+]([H])([H])[H])[C]([H])([H])[C]3([H])[H])[n][c]2[N]([H])[H])[c]1[H],lig_E25 14 | [H][c]1[c]([H])[c]([Cl])[c]([Cl])[c](-[c]2[n][c]([C](=[O])[N]([H])[H])[c]([N]3[C]([H])([H])[C]([H])([H])[C]([C]([H])([H])[H])([N+]([H])([H])[H])[C]([H])([H])[C]3([H])[H])[n][c]2[N]([H])[H])[c]1[H],lig_E26 15 | [H][c]1[n][c](-[c]2[c]([H])[c]([H])[c]([H])[c]([Cl])[c]2[Cl])[c]([N]([H])[H])[n][c]1[N]1[C]([H])([H])[C@]([H])([C]([H])([H])[H])[N+]([H])([H])[C@]([H])([C]([H])([H])[H])[C]1([H])[H],lig_E27 16 | [H][C]1=[C]([H])[N]([H])[c]2[c]1[c]([H])[c]([H])[c]([H])[c]2-[c]1[n][c]([H])[c]([N]2[C]([H])([H])[C]([H])([H])[C]([C]([H])([H])[H])([N+]([H])([H])[H])[C]([H])([H])[C]2([H])[H])[n][c]1[N]([H])[H],lig_E28 17 | [H][C]1=[C]([c]2[n][c]([H])[c]([N]3[C]([H])([H])[C]([H])([H])[C]([C]([H])([H])[H])([N+]([H])([H])[H])[C]([H])([H])[C]3([H])[H])[n][c]2[N]([H])[H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]1([H])[H],lig_E29 18 | [H][C]1=[C]([Cl])[S][C]([c]2[c]([H])[n][c]([N]3[C]([H])([H])[C]([H])([H])[C]([C]([H])([H])[H])([N+]([H])([H])[H])[C]([H])([H])[C]3([H])[H])[n][c]2[N]([H])[H])=[C]1[H],lig_E3 19 | [H][c]1[c]([H])[c]([Cl])[c]([Cl])[c](-[c]2[n][n][c]([N]3[C]([H])([H])[C]([H])([H])[C]([C]([H])([H])[H])([N+]([H])([H])[H])[C]([H])([H])[C]3([H])[H])[n][c]2[N]([H])[H])[c]1[H],lig_E30 20 | [H][C]1=[C]([c]2[c]([H])[n][c]([N]3[C]([H])([H])[C]([H])([H])[C]([C]([H])([H])[H])([N+]([H])([H])[H])[C]([H])([H])[C]3([H])[H])[n][c]2[N]([H])[H])[S][C]([C]([H])([H])[H])=[C]1[H],lig_E4 21 | [H][c]1[n][c]([N]2[C]([H])([H])[C]([H])([H])[C]([C]([H])([H])[H])([N+]([H])([H])[H])[C]([H])([H])[C]2([H])[H])[n][c]([N]([H])[H])[c]1-[c]1[c]([H])[c]([O][C]([H])([H])[H])[c]([H])[c]([Cl])[c]1[Cl],lig_E5 22 | [H][O][c]1[c]([H])[c]([Cl])[c]([Cl])[c](-[c]2[c]([H])[n][c]([N]3[C]([H])([H])[C]([H])([H])[C]([C]([H])([H])[H])([N+]([H])([H])[H])[C]([H])([H])[C]3([H])[H])[n][c]2[N]([H])[H])[c]1[H],lig_E6 23 | [H][c]1[n][c](-[c]2[c]([H])[c]([H])[c]([H])[c]([Cl])[c]2[Cl])[c]([N]([H])[H])[n][c]1[N]1[C]([H])([H])[C]([H])([H])[C]([C]([H])([H])[H])([C]([H])([H])[N+]([H])([H])[H])[C]([H])([H])[C]1([H])[H],lig_E8 24 | [H][c]1[n][c](-[c]2[c]([H])[c]([H])[c]([H])[c]([Cl])[c]2[Cl])[c]([N]([H])[H])[n][c]1[N]1[C]([H])([H])[C]([H])([H])[C]([H])([C]([H])([H])[N+]([H])([H])[H])[C]([H])([H])[C]1([H])[H],lig_E9 25 | [H][c]1[n][c](-[c]2[c]([H])[c]([H])[c]([H])[c]([Cl])[c]2[Cl])[c]([N]([H])[H])[n][c]1[N]1[C]([H])([H])[C]([H])([H])[C]([C]([H])([H])[H])([N+]([H])([H])[H])[C]([H])([H])[C]1([H])[H],lig_SHP099-1 26 | [H][c]1[n][c]([N]2[C]([H])([H])[C@]([H])([C]([H])([H])[H])[N+]([H])([H])[C@]([H])([C]([H])([H])[H])[C]2([H])[H])[n][c]([N]([H])[H])[c]1-[c]1[c]([H])[c]([H])[c]([H])[c]([Cl])[c]1[Cl],lig_SHP836-2 27 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_syk/ligprep_syk.inp: -------------------------------------------------------------------------------- 1 | INPUT_FILE_NAME ligprep_syk.smi 2 | OUT_SD ligprep_syk-out.sdf 3 | MAX_ATOMS 500 4 | FORCE_FIELD 16 5 | PH 7.4 6 | PH_THRESHOLD 0.0 7 | EPIK yes 8 | DETERMINE_CHIRALITIES no 9 | IGNORE_CHIRALITIES no 10 | NUM_STEREOISOMERS 32 11 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_syk/ligprep_syk.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/ligprep" -inp ligprep_syk.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_thrombin_recurated/ligprep_thrombin_recurated.csv: -------------------------------------------------------------------------------- 1 | SMILES,Title,Ki (uM),Error 2 | c1ccc(cc1)C[C@H](C(=O)N2CCC[C@H]2C(=O)NCc3cccc(c3)F)[NH3+],lig_1a,3.99,2.12 3 | c1ccc(cc1)C[C@H](C(=O)N2CCC[C@H]2C(=O)NCc3cccc(c3)Cl)[NH3+],lig_1b,0.18,0.14 4 | c1ccc(cc1)C[C@H](C(=O)N2CCC[C@H]2C(=O)NCc3cccc(c3)Br)[NH3+],lig_1c,0.56,0.147 5 | c1ccc(cc1)C[C@H](C(=O)N2CCC[C@H]2C(=O)NCc3cccc(c3)I)[NH3+],lig_1d,0.54,0.23 6 | O=C(N1CCC[C@H]1C(NCc2cc(C(F)(F)F)ccc2)=O)[C@H]([NH3+])Cc3ccccc3,lig_2a,15.09,3.28 7 | O=C(N1CCC[C@H]1C(NCc2cc(OC)ccc2)=O)[C@H]([NH3+])Cc3ccccc3,lig_2b,4.83,0.52 8 | O=C(N1CCC[C@H]1C(NCc2cc(O)ccc2)=O)[C@H]([NH3+])Cc3ccccc3,lig_2c,4.91,0.35 9 | O=C(N1CCC[C@H]1C(NCc2cc(N)ccc2)=O)[C@H]([NH3+])Cc3ccccc3,lig_2d,14.73,1.95 10 | O=C(N1CCC[C@H]1C(NCc2cc([N+]([O-])=O)ccc2)=O)[C@H]([NH3+])Cc3ccccc3,lig_2e,8.7,1.88 11 | Cc1cccc(c1)CNC(=O)[C@@H]2CCCN2C(=O)[C@@H](Cc3ccccc3)[NH3+],lig_3a,1.21,0.21 12 | CCc1cccc(c1)CNC(=O)[C@@H]2CCCN2C(=O)[C@@H](Cc3ccccc3)[NH3+],lig_3b,5.17,0.96 13 | CC(C)c1cc(CNC([C@@H]2CCCN2C([C@H]([NH3+])Cc3ccccc3)=O)=O)ccc1,lig_3c,185,69 14 | CC(C)(C)c1cc(CNC([C@@H]2CCCN2C([C@H]([NH3+])Cc3ccccc3)=O)=O)ccc1,lig_3d,> 1000, 15 | O=C([C@@H]1CCCN1C([C@H]([NH3+])Cc2ccccc2)=O)NCc3ccc(C(N)=N)cc3,lig_4,0.004,0.0012 16 | c1ccc(cc1)C[C@H](C(=O)N2CCC[C@H]2C(=O)NCc3ccccc3)[NH3+],lig_5,11.21,6.7 17 | c1ccc(cc1)C[C@H](C(=O)N2CCC[C@H]2C(=O)NCc3cc(ccc3Cl)Cl)[NH3+],lig_6a,0.06,0.02 18 | Cc1ccc(cc1CNC(=O)[C@@H]2CCCN2C(=O)[C@@H](Cc3ccccc3)[NH3+])Cl,lig_6b,0.26,0.09 19 | O=C([C@@H]1CCCN1C([C@H]([NH3+])Cc2ccccc2)=O)NCc3c(OC)ccc(Cl)c3,lig_6c,0.27,0.08 20 | Oc1c(CNC([C@@H]2CCCN2C([C@H]([NH3+])Cc3ccccc3)=O)=O)cc(Cl)cc1,lig_6d,0.433,0.206 21 | c1ccc(cc1)C[C@H](C(=O)N2CCC[C@H]2C(=O)NCc3cc(ccc3F)Cl)[NH3+],lig_6e,0.5,0.028 22 | Cc1ccc(c(c1)CNC(=O)[C@@H]2CCCN2C(=O)[C@@H](Cc3ccccc3)[NH3+])C,lig_7a,2.78,0.17 23 | O=C([C@@H]1CCCN1C([C@H]([NH3+])Cc2ccccc2)=O)NCc3ccc(Cl)cc3,lig_7b,3.99,1.75 24 | O=C([C@@H]1CCCN1C([C@H]([NH3+])Cc2ccccc2)=O)NCc3c(Cl)cccc3,lig_7c,1.46,0.33 25 | O=C(N1CCC[C@H]1C(NCC2CCCC(N)C2)=O)[C@H]([NH3+])Cc3ccccc3,lig_7d,7.6,1.35 26 | O=C([C@@H]1CCCN1C([C@H]([NH3+])Cc2ccccc2)=O)NCc3cc(CO)ccc3,lig_7e,75.77,36 27 | O=C([C@@H]1CCCN1C([C@H]([NH3+])Cc2ccccc2)=O)NCc3ccc(CO)cc3,lig_7f,34.55,15 -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_thrombin_recurated/ligprep_thrombin_recurated.inp: -------------------------------------------------------------------------------- 1 | INPUT_FILE_NAME ligprep_thrombin_recurated.csv 2 | OUT_SD ligprep_thrombin_recurated-out.sdf 3 | MAX_ATOMS 500 4 | FORCE_FIELD 16 5 | PH 7.8 6 | PH_THRESHOLD 0.0 7 | EPIK yes 8 | DETERMINE_CHIRALITIES no 9 | IGNORE_CHIRALITIES no 10 | NUM_STEREOISOMERS 32 11 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_thrombin_recurated/ligprep_thrombin_recurated.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/ligprep" -inp ligprep_thrombin_recurated.inp -HOST localhost:10 -NJOBS 1 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_tnks2/ligprep_tnks2.inp: -------------------------------------------------------------------------------- 1 | INPUT_FILE_NAME ligprep_tnks2.smi 2 | OUT_SD ligprep_tnks2-out.sdf 3 | MAX_ATOMS 500 4 | FORCE_FIELD 16 5 | PH 7.4 6 | PH_THRESHOLD 0.0 7 | EPIK yes 8 | DETERMINE_CHIRALITIES no 9 | IGNORE_CHIRALITIES no 10 | NUM_STEREOISOMERS 32 11 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_tnks2/ligprep_tnks2.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/ligprep" -inp ligprep_tnks2.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_tnks2/ligprep_tnks2.smi: -------------------------------------------------------------------------------- 1 | [H][c]1[c]([H])[c]([H])[c]([C]2=[N][c]3[c]([H])[c]([H])[c]([H])[c]([H])[c]3[C](=[O])[N]2[H])[c]([H])[c]1[H],lig_1a 2 | [H][c]1[c]([H])[c]([H])[c]2[c]([c]1[H])[N]=[C]([c]1[c]([H])[c]([H])[c]([O][C]([H])([H])[H])[c]([H])[c]1[H])[N]([H])[C]2=[O],lig_1b 3 | [H][c]1[c]([H])[c]([H])[c]2[c]([c]1[H])[N]=[C]([c]1[c]([H])[c]([H])[c]([C]([C]([H])([H])[H])([C]([H])([H])[H])[C]([H])([H])[H])[c]([H])[c]1[H])[N]([H])[C]2=[O],lig_3a 4 | [H][c]1[c]([H])[c]2[c]([c]([H])[c]1[F])[C](=[O])[N]([H])[C]([c]1[c]([H])[c]([H])[c]([C]([C]([H])([H])[H])([C]([H])([H])[H])[C]([H])([H])[H])[c]([H])[c]1[H])=[N]2,lig_3b 5 | [H][O][C]([c]1[c]([H])[c]([H])[c]([C]2=[N][c]3[c]([H])[c]([H])[c]([H])[c]([H])[c]3[C](=[O])[N]2[H])[c]([H])[c]1[H])([C]([H])([H])[H])[C]([H])([H])[H],lig_5a 6 | [H][O][C]([c]1[c]([H])[c]([H])[c]([C]2=[N][c]3[c]([H])[c]([H])[c]([H])[c]([F])[c]3[C](=[O])[N]2[H])[c]([H])[c]1[H])([C]([H])([H])[H])[C]([H])([H])[H],lig_5b 7 | [H][O][C]([c]1[c]([H])[c]([H])[c]([C]2=[N][c]3[c]([H])[c]([H])[c]([H])[c]([Cl])[c]3[C](=[O])[N]2[H])[c]([H])[c]1[H])([C]([H])([H])[H])[C]([H])([H])[H],lig_5c 8 | [H][O][C]([c]1[c]([H])[c]([H])[c]([C]2=[N][c]3[c]([H])[c]([H])[c]([F])[c]([H])[c]3[C](=[O])[N]2[H])[c]([H])[c]1[H])([C]([H])([H])[H])[C]([H])([H])[H],lig_5d 9 | [H][O][C]([c]1[c]([H])[c]([H])[c]([C]2=[N][c]3[c]([H])[c]([H])[c]([Cl])[c]([H])[c]3[C](=[O])[N]2[H])[c]([H])[c]1[H])([C]([H])([H])[H])[C]([H])([H])[H],lig_5e 10 | [H][O][C]([c]1[c]([H])[c]([H])[c]([C]2=[N][c]3[c]([F])[c]([H])[c]([H])[c]([H])[c]3[C](=[O])[N]2[H])[c]([H])[c]1[H])([C]([H])([H])[H])[C]([H])([H])[H],lig_5f 11 | [H][O][C]([c]1[c]([H])[c]([H])[c]([C]2=[N][c]3[c]([Cl])[c]([H])[c]([H])[c]([H])[c]3[C](=[O])[N]2[H])[c]([H])[c]1[H])([C]([H])([H])[H])[C]([H])([H])[H],lig_5g 12 | [H][O][C]([c]1[c]([H])[c]([H])[c]([C]2=[N][c]3[c]([O][C]([H])([H])[H])[c]([H])[c]([H])[c]([H])[c]3[C](=[O])[N]2[H])[c]([H])[c]1[H])([C]([H])([H])[H])[C]([H])([H])[H],lig_5h 13 | [H][O][C]([c]1[c]([H])[c]([H])[c]([C]2=[N][c]3[c]([c]([H])[c]([H])[c]([H])[c]3[C]([H])([H])[H])[C](=[O])[N]2[H])[c]([H])[c]1[H])([C]([H])([H])[H])[C]([H])([H])[H],lig_5i 14 | [H][O][C]([c]1[c]([H])[c]([H])[c]([C]2=[N][c]3[c]([H])[c]([H])[c]([F])[c]([F])[c]3[C](=[O])[N]2[H])[c]([H])[c]1[H])([C]([H])([H])[H])[C]([H])([H])[H],lig_5j 15 | [H][O][C]([c]1[c]([H])[c]([H])[c]([C]2=[N][c]3[c]([F])[c]([H])[c]([F])[c]([H])[c]3[C](=[O])[N]2[H])[c]([H])[c]1[H])([C]([H])([H])[H])[C]([H])([H])[H],lig_5k 16 | [H][O][C]([c]1[c]([H])[c]([H])[c]([C]2=[N][c]3[c]([F])[c]([H])[c]([H])[c]([F])[c]3[C](=[O])[N]2[H])[c]([H])[c]1[H])([C]([H])([H])[H])[C]([H])([H])[H],lig_5l 17 | [H][O][C]([c]1[c]([H])[c]([H])[c]([C]2=[N][c]3[c]([c]([H])[c]([F])[c]([H])[c]3[C]([H])([H])[H])[C](=[O])[N]2[H])[c]([H])[c]1[H])([C]([H])([H])[H])[C]([H])([H])[H],lig_5m 18 | [H][O][C]([H])([H])[C]([H])([H])[O][C]([c]1[c]([H])[c]([H])[c]([C]2=[N][c]3[c]([H])[c]([H])[c]([F])[c]([H])[c]3[C](=[O])[N]2[H])[c]([H])[c]1[H])([C]([H])([H])[H])[C]([H])([H])[H],lig_5n 19 | [H][O][C]([H])([H])[C]([H])([H])[O][C]([c]1[c]([H])[c]([H])[c]([C]2=[N][c]3[c]([c]([H])[c]([F])[c]([H])[c]3[C]([H])([H])[H])[C](=[O])[N]2[H])[c]([H])[c]1[H])([C]([H])([H])[H])[C]([H])([H])[H],lig_5o 20 | [H][c]1[c]([H])[c]2[c]([c]([H])[c]1[F])[C](=[O])[N]([H])[C]([c]1[c]([H])[c]([H])[c]([C]([O][C]([H])([H])[C]([H])([H])[O][C]([H])([H])[H])([C]([H])([H])[H])[C]([H])([H])[H])[c]([H])[c]1[H])=[N]2,lig_5p 21 | [H][O][C]([c]1[c]([H])[n][c]([C]2=[N][c]3[c]([H])[c]([H])[c]([F])[c]([H])[c]3[C](=[O])[N]2[H])[c]([H])[c]1[H])([C]([H])([H])[H])[C]([H])([H])[H],lig_7 22 | [H][c]1[c]([H])[c]2[c]([c]([H])[c]1[F])[C](=[O])[N]([H])[C]([c]1[c]([H])[c]([H])[c]([N]3[C]([H])([H])[C]([H])([H])[N+]([H])([C]([H])([H])[H])[C]([H])([H])[C]3([H])[H])[c]([H])[c]1[H])=[N]2,lig_8a 23 | [H][c]1[c]([H])[c]([N]2[C]([H])([H])[C]([H])([H])[N+]([H])([C]([H])([H])[H])[C]([H])([H])[C]2([H])[H])[c]([H])[c]([H])[c]1[C]1=[N][c]2[c]([c]([H])[c]([F])[c]([H])[c]2[C]([H])([H])[H])[C](=[O])[N]1[H],lig_8b 24 | [H][c]1[c]([F])[c]([H])[c]2[c]([c]1[F])[N]=[C]([c]1[c]([H])[c]([H])[c]([C]3([H])[C]([H])([H])[C]([H])([H])[N+]([H])([H])[C]([H])([H])[C]3([H])[H])[c]([H])[c]1[H])[N]([H])[C]2=[O],lig_8c 25 | [H][c]1[c]([H])[c]([C]2([H])[C]([H])([H])[C]([H])([H])[N+]([H])([H])[C]([H])([H])[C]2([H])[H])[c]([H])[c]([H])[c]1[C]1=[N][c]2[c]([c]([H])[c]([F])[c]([H])[c]2[C]([H])([H])[H])[C](=[O])[N]1[H],lig_8d 26 | [H][c]1[c]([F])[c]([H])[c]2[c]([c]1[F])[N]=[C]([c]1[c]([H])[c]([H])[c]([C]3([H])[C]([H])([H])[C]([H])([H])[N+]([H])([C]([H])([H])[H])[C]([H])([H])[C]3([H])[H])[c]([H])[c]1[H])[N]([H])[C]2=[O],lig_8e 27 | [H][c]1[c]([H])[c]([C]2([H])[C]([H])([H])[C]([H])([H])[N+]([H])([C]([H])([H])[H])[C]([H])([H])[C]2([H])[H])[c]([H])[c]([H])[c]1[C]1=[N][c]2[c]([c]([H])[c]([F])[c]([H])[c]2[C]([H])([H])[H])[C](=[O])[N]1[H],lig_8f 28 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_tyk2/ligprep_tyk2.inp: -------------------------------------------------------------------------------- 1 | INPUT_FILE_NAME ligprep_tyk2.smi 2 | OUT_SD ligprep_tyk2-out.sdf 3 | MAX_ATOMS 500 4 | FORCE_FIELD 16 5 | PH 7.4 6 | PH_THRESHOLD 0.0 7 | EPIK yes 8 | DETERMINE_CHIRALITIES no 9 | IGNORE_CHIRALITIES no 10 | NUM_STEREOISOMERS 32 11 | -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_tyk2/ligprep_tyk2.sh: -------------------------------------------------------------------------------- 1 | "${SCHRODINGER}/ligprep" -inp ligprep_tyk2.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR -------------------------------------------------------------------------------- /preparation/ligand-prep/ligprep_tyk2/ligprep_tyk2.smi: -------------------------------------------------------------------------------- 1 | [H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)C([H])([H])[H])[H])[H])Cl)[H],lig_ejm_31 2 | [H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)C([H])([H])C([H])([H])[H])[H])[H])Cl)[H],lig_ejm_42 3 | [H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)C([H])(C([H])([H])[H])C([H])([H])[H])[H])[H])Cl)[H],lig_ejm_43 4 | [H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)C(C([H])([H])[H])(C([H])([H])[H])C([H])([H])[H])[H])[H])Cl)[H],lig_ejm_44 5 | [H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)C([H])([H])C3(C(C3([H])[H])([H])[H])[H])[H])[H])Cl)[H],lig_ejm_45 6 | [H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)C3(C(C3([H])[H])([H])[H])[H])[H])[H])Cl)[H],lig_ejm_46 7 | [H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)C3(C(C(C3([H])[H])([H])[H])([H])[H])[H])[H])[H])Cl)[H],lig_ejm_47 8 | [H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)C3(C(C(C(C3([H])[H])([H])[H])([H])[H])([H])[H])[H])[H])[H])Cl)[H],lig_ejm_48 9 | [H]c1c(c(c(c(c1[H])[H])C(=O)N([H])c2c(c(c(c(n2)[H])[H])N([H])C(=O)c3c(c(c(c(c3Cl)[H])[H])[H])Cl)[H])[H])[H],lig_ejm_49 10 | [H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)C([H])([H])O[H])[H])[H])Cl)[H],lig_ejm_50 11 | [H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)N([H])C([H])([H])C([H])([H])[H])[H])[H])Cl)[H],lig_ejm_54 12 | [H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)OC([H])([H])[H])[H])[H])Cl)[H],lig_ejm_55 13 | [H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)[C@@]3([C@](C3([H])[H])([H])F)[H])[H])[H])Cl)[H],lig_jmc_23 14 | [H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)[C@@]3([C@](C3([H])[H])([H])Cl)[H])[H])[H])Cl)[H],lig_jmc_27 15 | [H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)[C@@]3([C@](C3([H])[H])([H])C([H])([H])[H])[H])[H])[H])Cl)[H],lig_jmc_28 16 | [H]c1c(c(c(c(c1[H])Cl)C(=O)N([H])c2c(c(nc(c2[H])N([H])C(=O)[C@@]3([C@](C3([H])[H])([H])C#N)[H])[H])[H])Cl)[H],lig_jmc_30 17 | -------------------------------------------------------------------------------- /preparation/mappers/perses-mapper.py: -------------------------------------------------------------------------------- 1 | import yaml 2 | import numpy as np 3 | from rdkit import Chem 4 | from openfe.setup import SmallMoleculeComponent 5 | from openfe.setup.ligand_network_planning import minimal_spanning_graph 6 | from openfe.setup.atom_mapping.perses_mapper import PersesAtomMapper 7 | from openfe.setup.atom_mapping.perses_scorers import default_perses_scorer 8 | from openmm import unit 9 | from collections import OrderedDict 10 | 11 | # load ligands 12 | ligands_supp = Chem.SDMolSupplier('../02_ligands/ligands.sdf', removeHs=False) 13 | ligand_mols = [SmallMoleculeComponent(m) for m in ligands_supp] 14 | 15 | # create minimum spanning graph 16 | mapper = PersesAtomMapper(allow_ring_breaking=False, preserve_chirality=True, 17 | use_positions=True, coordinate_tolerance=0.2*unit.angstrom) 18 | 19 | network = minimal_spanning_graph(ligand_mols, [mapper,], default_perses_scorer) 20 | 21 | # Get edges 22 | edges = [edge for edge in network.edges] 23 | 24 | # Analyze distance overlap for manual validation 25 | for i, edge in enumerate(edges): 26 | if np.any(edge.get_distances() > 1): 27 | name = f"{edge.componentA.name}_{edge.componentB.name}" 28 | print(f"{name} exceeds 1 A pairwise distance") 29 | 30 | output = {} 31 | output['mapper'] = "Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, coordinate_tolerance=0.2), default non geometric scorer" 32 | output['planner'] = "openfe v0.5 minimal_spanning_graph" 33 | 34 | edges_dict = dict() 35 | 36 | for edge in network.edges: 37 | edge_name = f'edge_{edge.componentA.name}_{edge.componentB.name}' 38 | mapping = [list(i) for i in edge.componentA_to_componentB.items()] 39 | edges_dict[edge_name] = { 40 | 'ligand_a': edge.componentA.name, 41 | 'ligand_b': edge.componentB.name, 42 | 'atom mapping': edge.componentA_to_componentB, 43 | 'score': f"{edge.annotations['score']:.3f}",} 44 | 45 | output['edges'] = edges_dict 46 | 47 | with open('01_perses_openfe.yml', 'w') as yaml_file: 48 | yaml.dump(output, yaml_file, default_flow_style=None, sort_keys=False) 49 | -------------------------------------------------------------------------------- /preparation/prep-methods.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openforcefield/protein-ligand-benchmark/fd88824f9114244f95a14b485e6d6c96c1de716d/preparation/prep-methods.pdf -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | # Helper file to handle all configs 2 | 3 | [coverage:run] 4 | # .coveragerc to control coverage.py and pytest-cov 5 | omit = 6 | # Omit the tests 7 | */tests/* 8 | # Omit generated versioneer 9 | plbenchmark/_version.py 10 | 11 | [yapf] 12 | # YAPF, in .style.yapf files this shows up as "[style]" header 13 | COLUMN_LIMIT = 119 14 | INDENT_WIDTH = 4 15 | USE_TABS = False 16 | 17 | [flake8] 18 | # Flake8, PyFlakes, etc 19 | max-line-length = 119 20 | 21 | [versioneer] 22 | # Automatic version numbering scheme 23 | VCS = git 24 | style = pep440 25 | versionfile_source = plbenchmark/_version.py 26 | versionfile_build = plbenchmark/_version.py 27 | tag_prefix = '' 28 | 29 | [aliases] 30 | test = pytest 31 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | """ 2 | protein-ligand-benchmark 3 | Protein-Ligand Benchmark Dataset for testing Parameters and Methods of Free Energy Calculations. 4 | """ 5 | import sys 6 | from setuptools import setup, find_packages 7 | import versioneer 8 | 9 | short_description = __doc__.split("\n") 10 | 11 | # from https://github.com/pytest-dev/pytest-runner#conditional-requirement 12 | needs_pytest = {'pytest', 'test', 'ptr'}.intersection(sys.argv) 13 | pytest_runner = ['pytest-runner'] if needs_pytest else [] 14 | 15 | try: 16 | with open("README.md", "r") as handle: 17 | long_description = handle.read() 18 | except IOError: 19 | long_description = "\n".join(short_description[2:]) 20 | 21 | 22 | setup( 23 | # Self-descriptive entries which should always be present 24 | name='plbenchmark', 25 | author='David F. Hahn', 26 | author_email='davidfriedrichhahn@gmail.com', 27 | description=short_description[0], 28 | long_description=long_description, 29 | long_description_content_type="text/markdown", 30 | version=versioneer.get_version(), 31 | cmdclass=versioneer.get_cmdclass(), 32 | license='MIT', 33 | 34 | # Which Python importable modules should be included when your package is installed 35 | # Handled automatically by setuptools. Use 'exclude' to prevent some specific 36 | # subpackage(s) from being added, if needed 37 | packages=find_packages(), 38 | package_data={'': ['*.yml', '*.pdb', '*.sdf']}, 39 | 40 | # Optional include package data to ship with your package 41 | # Customize MANIFEST.in if the general case does not suit your needs 42 | # Comment out this line to prevent the files from being packaged with your software 43 | include_package_data=True, 44 | 45 | # Allows `setup.py test` to work correctly with pytest 46 | setup_requires=[] + pytest_runner, 47 | 48 | # Additional entries you may want simply uncomment the lines you want and fill in the data 49 | # url='http://www.my_package.com', # Website 50 | # install_requires=[], # Required packages, pulls from pip if needed; do not use for Conda deployment 51 | # platforms=['Linux', 52 | # 'Mac OS-X', 53 | # 'Unix', 54 | # 'Windows'], # Valid platforms your code works on, adjust to your flavor 55 | # python_requires=">=3.5", # Python version restrictions 56 | 57 | # Manual control if final package is compressible or not, set False to prevent the .egg from being made 58 | # zip_safe=False, 59 | 60 | ) 61 | --------------------------------------------------------------------------------