measure = 'tanimoto'
morganradius = 2
dmetric = None
fpcode = None
# old OE codes:
#fpcodes={'lingo':OEFPType_Lingo,
# 'maccs':OEFPType_MACCS166,
# 'path':OEFPType_Path}
fpcodes = {
'rdkit': FingerprintMols.GetRDKFingerprint,
'maccs': MACCSkeys.GenMACCSKeys,
'morgan':
lambda mol: AllChem.GetMorganFingerprintAsBitVect(mol, morganradius),
'atompairs': lambda mol: Chem.GetAtomPairFingerPrint(mol, 2)
}
# tversky(F1, F2)= F1@F2 / ( a*sum(F1) + b*sum(F2) - (1-a-b)* F1@F2 )
dmetrics = {
'tanimoto': DataStructs.TanimotoSimilarity, # a, b = 1, 1
'dice': DataStructs.DiceSimilarity, # a, b = 0.5, 0.5
'cosine': DataStructs.CosineSimilarity,
'tversky': lambda m1, m2: DataStructs.TverskySimilarity(m1, m2, 0.5, 0.5),
'sokal': DataStructs.SokalSimilarity
}
#########################
# Module initialization #
#########################
