RDKit的rdkit.Chem.Draw.SimilarityMaps模块中提供了相关方法。
from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import SimilarityMaps
mol = Chem.MolFromSmiles('COc1cccc2cc(C(=O)NCCCCN3CCN(c4cccc5nccnc54)CC3)oc21')
refmol = Chem.MolFromSmiles('CCCN(CCCCN1CCN(c2ccccc2OC)CC1)Cc1ccc2ccccc2c1')
fp = SimilarityMaps.GetAPFingerprint(mol, fpType='normal')
fp = SimilarityMaps.GetTTFingerprint(mol, fpType='normal')
fp = SimilarityMaps.GetMorganFingerprint(mol, fpType='bv')
fig, maxweight = SimilarityMaps.GetSimilarityMapForFingerprint(refmol, mol, SimilarityMaps.GetMorganFingerprint)
from rdkit import DataStructs
fig, maxweight = SimilarityMaps.GetSimilarityMapForFingerprint(refmol, mol, lambda m,idx: SimilarityMaps.GetMorganFingerprint(m, atomId=idx, radius=1, fpType='count'), metric=DataStructs.TanimotoSimilarity)
print(maxweight)
weights = SimilarityMaps.GetAtomicWeightsForFingerprint(refmol, mol, SimilarityMaps.GetMorganFingerprint)
print(["%.2f " % w for w in weights])
fig = SimilarityMaps.GetSimilarityMapFromWeights(mol, weights)
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