Spaces:
Sleeping
Sleeping
| import os | |
| from rdkit import Chem | |
| from rdkit.Chem import AllChem, rdShapeHelpers | |
| from rdkit.Chem.FeatMaps import FeatMaps | |
| from rdkit import RDConfig | |
| # Set up features to use in FeatureMap | |
| fdefName = os.path.join(RDConfig.RDDataDir, 'BaseFeatures.fdef') | |
| fdef = AllChem.BuildFeatureFactory(fdefName) | |
| fmParams = {} | |
| for k in fdef.GetFeatureFamilies(): | |
| fparams = FeatMaps.FeatMapParams() | |
| fmParams[k] = fparams | |
| keep = ('Donor', 'Acceptor', 'NegIonizable', 'PosIonizable', | |
| 'ZnBinder', 'Aromatic', 'Hydrophobe', 'LumpedHydrophobe') | |
| def get_FeatureMapScore(query_mol, ref_mol): | |
| featLists = [] | |
| for m in [query_mol, ref_mol]: | |
| rawFeats = fdef.GetFeaturesForMol(m) | |
| # filter that list down to only include the ones we're intereted in | |
| featLists.append([f for f in rawFeats if f.GetFamily() in keep]) | |
| fms = [FeatMaps.FeatMap(feats=x, weights=[1] * len(x), params=fmParams) for x in featLists] | |
| fms[0].scoreMode = FeatMaps.FeatMapScoreMode.Best | |
| fm_score = fms[0].ScoreFeats(featLists[1]) / min(fms[0].GetNumFeatures(), len(featLists[1])) | |
| return fm_score | |
| def calc_SC_RDKit_score(query_mol, ref_mol): | |
| fm_score = get_FeatureMapScore(query_mol, ref_mol) | |
| protrude_dist = rdShapeHelpers.ShapeProtrudeDist(query_mol, ref_mol, | |
| allowReordering=False) | |
| SC_RDKit_score = 0.5 * fm_score + 0.5 * (1 - protrude_dist) | |
| return SC_RDKit_score |