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Create Bioinformatics_Drug_Discovery.py
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| import numpy as np | ||
| import pandas as pd | ||
| import rdkit | ||
| from rdkit import Chem | ||
| from rdkit.Chem import AllChem | ||
| from rdkit.Chem import rdFMCS | ||
| from rdkit.Chem import rdmolops | ||
| from rdkit.Chem import rdRDMolDescriptors | ||
| from rdkit.Chem import rdMolTransforms | ||
| from rdkit.Chem.Pharm2D import Pharm2D | ||
| from rdkit.Chem.Pharm2D import rdPharm2DUtils | ||
| from rdkit.Chem.Pharm2D import rdPharm2DSK | ||
| from rdkit.Chem.Pharm2D import rdPharm2DInterpreter | ||
| from rdkit.Chem.Pharm2D import rdPharm2DDraw | ||
| from rdkit.Chem.Pharm2D import rdPharm2DFilter | ||
| from rdkit.Chem.Pharm2D import rdPharm2DUtils | ||
| from rdkit.Chem.Pharm2D import rdPharm2DInterpreter | ||
| from rdkit.Chem.Pharm2D import rdPharm2DDraw | ||
| from rdkit.Chem.Pharm2D import rdPharm2DFilter | ||
| from rdkit.Chem.Pharm2D import rdPharm2DUtils | ||
| from rdkit.Chem.Pharm2D import rdPharm2DInterpreter | ||
| from rdkit.Chem.Pharm2D import rdPharm2DDraw | ||
| from rdkit.Chem.Pharm2D import rdPharm2DFilter | ||
| from rdkit.Chem.Scaffolds import MurckoScaffold | ||
| from rdkit.Chem.Scaffolds import rdMolDescriptors | ||
| from rdkit.Chem.rdMolDescriptors import GetAdjacencyMatrix | ||
| from rdkit.Chem.rdMolDescriptors import CalcMolFormula | ||
| from rdkit.Chem.rdMolDescriptors import GetMorganFingerprint | ||
| from rdkit.Chem.rdMolDescriptors import GetMACCSFingerprint | ||
| from rdkit.Chem.rdMolDescriptors import GetMolWt | ||
| from rdkit.Chem.rdMolDescriptors import GetTopologicalPolarity | ||
| from rdkit.Chem.rdMolDescriptors import GetHeavyAtomMolWt | ||
| from rdkit.Chem.rdMolDescriptors import GetChiralTag | ||
| from rdkit.Chem.rdMolDescriptors import GetExactMolWt | ||
| from rdkit.Chem.rdMolDescriptors import GetNumRotatableBonds | ||
| from rdkit.Chem.rdMolDescriptors import GetNumAromaticRings | ||
| from rdkit.Chem.rdMolDescriptors import GetNumHBA | ||
| from rdkit.Chem.rdMolDescriptors import GetNumHBD | ||
| from rdkit.Chem.rdMolDescriptors import GetNumExplicitHs | ||
| from rdkit.Chem.rdMolDescriptors import GetNumImplicitHs | ||
| from rdkit.Chem.rdMolDescriptors import GetNumLipinskiHBA | ||
| from rdkit.Chem.rdMolDescriptors import GetNumLipinskiHBD | ||
| from rdkit.Chem.rdMolDescriptors import GetNumRadicalElectrons | ||
| from rdkit.Chem.rdMolDescriptors import GetNumStereoCenters | ||
| from rdkit.Chem.rdMolDescriptors import GetNumValenceElectrons | ||
| from rdkit.Chem.rdMolDescriptors import GetRingCount | ||
| from rdkit.Chem.rdMolDescriptors import GetSSSR | ||
| from rdkit.Chem.rdMolDescriptors import GetSymmSSSR | ||
| from rdkit.Chem.rdMolDescriptors import GetSSSRDepict | ||
| from rdkit.Chem.rdMolDescriptors import GetMolBlocks | ||
| from rdkit.Chem.rdMolDescriptors import Get3DDistanceMatrix | ||
| from rdkit.Chem.rdMolDescriptors import GetMolFrags | ||
| from rdkit.Chem.rdMolDescriptors import Get3DDM | ||
| from rdkit.Chem.rdMolDescriptors import GetRingInfo | ||
| from rdkit.Chem.rdMolDescriptors import GetSymmSSSRIdx | ||
| from rdkit.Chem.rdMolDescriptors import GetFragmentableAtoms | ||
| from rdkit.Chem.rdMolDescriptors import GetAllPathsOfLengthN | ||
| from rdkit.Chem.rdMolDescriptors import GetAtomsWithUnsaturatedBonds | ||
| from rdkit.Chem.rdMolDescriptors import GetShortestPaths | ||
| from rdkit.Chem.rdMolDescriptors import GetAdjacencyMatrixWithDoubleBondsAsOne | ||
| from rdkit.Chem.rdMolDescriptors import GetAtomsAndBonds | ||
| from rdkit.Chem.rdMolDescriptors import GetFragmentNumbers | ||
| from rdkit.Chem.rdMolDescriptors import GetHarmonicAtomBondsDistances | ||
| from rdkit.Chem.rdMolDescriptors import GetPathToSubmol | ||
| from rdkit.Chem.rdMolDescriptors import GetTopologicalAtomNumbers | ||
| from rdkit.Chem.rdMolDescriptors import GetTopologicalAtomGroups | ||
| from rdkit.Chem.rdMolDescriptors import GetTopologicalDistanceMatrix | ||
| from rdkit.Chem.rdMolDescriptors import GetAtomsWithRings | ||
| from rdkit.Chem.rdMolDescriptors import GetAllRingsOfSizeN | ||
| from rdkit.Chem.rdMolDescriptors import GetTopologicalPharmacophoreAtomPairs | ||
| from rdkit.Chem.rdMolDescriptors import GetAllAtomEnvironmentSubgraphs | ||
| from rdkit.Chem.rdMolDescriptors import GetMolChemicalSymbols | ||
| from rdkit.Chem.rdMolDescriptors import GetAromaticAtomsAndBonds | ||
| from rdkit.Chem.rdMolDescriptors import GetTopologicalCharge | ||
| from rdkit.Chem.rdMolDescriptors import GetAllAtomAndBondPairs | ||
| from rdkit.Chem.rdMolDescriptors import GetAtomsAndBondsInSmallestSetOfSmallestRings | ||
| from rdkit.Chem.rdMolDescriptors import GetNumBridgeheadAtoms | ||
| from rdkit.Chem.rdMolDescriptors import GetTopologicalPharmacophore | ||
| from rdkit.Chem.rdMolDescriptors import GetAtomBondsAndAngles | ||
| from rdkit.Chem.rdMolDescriptors import GetPathToSubmolHistograms | ||
| from rdkit.Chem.rdMolDescriptors import GetDistanceMatrixForPath | ||
| from rdkit.Chem.rdMolDescriptors import GetSubgraphForPath | ||
| from rdkit.Chem.rdMolDescriptors import GetHarmonicRingBondsDistances | ||
| from rdkit.Chem.rdMolDescriptors import GetMorganFingerprintForPath | ||
| from rdkit.Chem.rdMolDescriptors import GetDistanceMatrixForSubmolHistograms | ||
| from rdkit.Chem.rdMolDescriptors import GetAllAtomAndBondPaths | ||
| from rdkit.Chem.rdMolDescriptors import GetPathsToSubmols | ||
| from rdkit.Chem.rdMolDescriptors import GetTopologicalAtomPaths | ||
| from rdkit.Chem.rdMolDescriptors import GetAllPathsToSubmolHistograms | ||
| from rdkit.Chem.rdMolDescriptors import GetMolSaltFormula | ||
| from rdkit.Chem.rdMolDescriptors import GetNumRotatableRings | ||
| from rdkit.Chem.rdMolDescriptors import GetMorganFingerprint | ||
| from rdkit.Chem.rdMolDescriptors import GetAtomEnvironment | ||
| from rdkit.Chem.rdMolDescriptors import GetAdjacencyMatrixForSubmolHistograms | ||
| from rdkit.Chem.rdMolDescriptors import GetNumLipinskiRo5Violations | ||
| from rdkit.Chem.rdMolDescriptors import GetAdjacencyMatrixSmartsPattern | ||
| from rdkit.Chem.rdMolDescriptors import GetAdjacencyMatrixMorganFingerprint | ||
| from rdkit.Chem.rdMolDescriptors import GetAtomPairFingerprint | ||
| from rdkit.Chem.rdMolDescriptors import GetAtomPairTorsionFingerprint | ||
| def virtual_screening(ligand_library, target_ protein): | ||
| """ | ||
| Perform virtual screening of a ligand library against a target protein. | ||
| """ | ||
| # Prepare ligand library and target protein | ||
| ligand_smiles = [Chem.MolToSmiles(ligand) for ligand in ligand_library] | ||
| target_mol = Chem.MolFromPDBFile(target_protein) | ||
| target_fp = AllChem.GetMorganFingerprint(target_mol, 2) | ||
|
|
||
| # Calculate fingerprints and similarity scores for each ligand | ||
| fingerprints = [AllChem |