def numpy_pp_fps(mols):
""" Calculate Gobbi and Poppinger pharmacophore fingerprints and return them as numpy.ndarrays
:param mols: {list} list of molecules (RDKit mols)
:return: numpy array containing row-wise fingerprints for every molecule
"""
feat_fact = ChemicalFeatures.BuildFeatureFactory()
sig_fact = SigFactory(feat_fact, useCounts=False, minPointCount=2, maxPointCount=3)
sig_fact.SetBins([(0, 2), (2, 4), (4, 6), (6, 8), (8, 100)])
sig_fact.Init()
return _rdk2numpy([Generate.Gen2DFingerprint(m, sig_fact) for m in mols if m])
def getFactory(self):
factory = SigFactory.SigFactory()
factory.SetPatternsFromSmarts(['O', 'N'])
factory.SetBins([(0, 2), (2, 5), (5, 8)])
factory.SetMinCount(2)
factory.SetMaxCount(3)
return factory
def setUp(self):
fdefFile = os.path.join(RDConfig.RDCodeDir, 'Chem', 'Pharm2D',
'test_data', 'BaseFeatures.fdef')
featFactory = ChemicalFeatures.BuildFeatureFactory(fdefFile)
self.factory = SigFactory.SigFactory(featFactory, minPointCount=2, maxPointCount=3)
self.factory.SetBins([(0, 2), (2, 5), (5, 8)])
self.factory.Init()
def BuildSigFactory(options=None, fdefFile=None,
bins=[(2, 3), (3, 4), (4, 5), (5, 6), (6, 7), (7, 8), (8, 100)],
skipFeats=('LumpedHydrophobe', 'ZnBinder')):
if options:
fdefFile = options.fdefFile
if not fdefFile:
raise ValueError('bad fdef file')
from rdkit.Chem import ChemicalFeatures
from rdkit.Chem.Pharm2D import SigFactory
featFactory = ChemicalFeatures.BuildFeatureFactory(fdefFile)
sigFactory = SigFactory.SigFactory(featFactory, skipFeats=skipFeats, trianglePruneBins=False)
sigFactory.SetBins(bins)
return sigFactory
def get_cats_factory(features='cats', names=False):
""" Get the feature combinations paired to all possible distances
:param features: {str} which pharmacophore features to consider; available: ["cats", "rdkit"]
:param names: {bool} whether to return an array describing the bits with names of features and distances
:return: RDKit signature factory to be used for 2D pharmacophore fingerprint calculation
"""
if features == 'cats':
fdef = fdef_cats
else:
fdef = fdef_rdkit
factory = ChemicalFeatures.BuildFeatureFactoryFromString(fdef)
sigfactory = SigFactory.SigFactory(factory, useCounts=True, minPointCount=2, maxPointCount=2)
sigfactory.SetBins([(0, 1), (1, 2), (2, 3), (3, 4), (4, 5), (5, 6), (6, 7), (7, 8), (8, 9), (9, 10)])
sigfactory.Init()
if names:
descs = [sigfactory.GetBitDescription(i) for i in range(sigfactory.GetSigSize())]
return sigfactory, descs
else:
return sigfactory
def DefaultSigFactory(fdefFile=None,
minPointCount=2,
maxPointCount=3,
bins=[(2, 3), (3, 4), (4, 5), (5, 6), (6, 7), (7, 8),
(8, 100)]):
from rdkit.Chem.Pharm2D import SigFactory
from rdkit.Chem import ChemicalFeatures
if fdefFile is None:
from rdkit import RDConfig
import os.path
fdefFile = os.path.join(RDConfig.RDDataDir, 'BaseFeatures.fdef')
featFactory = ChemicalFeatures.BuildFeatureFactory(fdefFile, )
factory = SigFactory.SigFactory(featFactory,
skipFeats=('ZnBinder', 'LumpedHydrophobe'),
minPointCount=minPointCount,
maxPointCount=maxPointCount,
trianglePruneBins=False)
factory.SetBins(tuple(bins))
factory.Init()
return factory
def _exampleCode():
import os
from rdkit import RDConfig
from rdkit.Chem import ChemicalFeatures
from rdkit.Chem.Pharm2D import SigFactory, Generate
fdefFile = os.path.join(RDConfig.RDCodeDir, 'Chem', 'Pharm2D', 'test_data',
'BaseFeatures.fdef')
featFactory = ChemicalFeatures.BuildFeatureFactory(fdefFile)
factory = SigFactory.SigFactory(featFactory)
factory.SetBins([(1, 2), (2, 5), (5, 8)])
factory.Init()
mol = Chem.MolFromSmiles('OCC(=O)CCCN')
sig = Generate.Gen2DFingerprint(mol, factory)
print('onbits:', list(sig.GetOnBits()))
_verbose = 0
for bit in sig.GetOnBits():
atoms = GetAtomsMatchingBit(factory, bit, mol)
print('\tBit %d: ' % (bit), atoms)
print('finished')
break
else:
if _verbose: print 'Found one'
# we found it
protoPharm.sort()
protoPharm = tuple(protoPharm)
if protoPharm not in res:
res.append(protoPharm)
if justOne: break
return res
if __name__ == '__main__':
from rdkit import Chem
from rdkit.Chem.Pharm2D import SigFactory,Generate
factory = SigFactory.SigFactory()
factory.SetBins([(1,2),(2,5),(5,8)])
factory.SetPatternsFromSmarts(['O','N'])
factory.SetMinCount(2)
factory.SetMaxCount(3)
sig = factory.GetSignature()
mol = Chem.MolFromSmiles('OCC(=O)CCCN')
Generate.Gen2DFingerprint(mol,sig)
print 'onbits:',list(sig.GetOnBits())
_verbose=0
for bit in sig.GetOnBits():
atoms = GetAtomsMatchingBit(sig,bit,mol)
print '\tBit %d: '%(bit),atoms
from rdkit import Chem
from rdkit.Chem import ChemicalFeatures # 2D PharmacoPhore FingerPrints
from rdkit.Chem import Pharm2D
from rdkit.Chem.Pharm2D import Generate
from rdkit.Chem.Pharm2D import SigFactory
from rdkit.Chem.Pharm2D import DefaultSigFactory
from rdkit import RDConfig
from rdkit import DataStructs
import os, sys
dataDir = os.path.join(RDConfig.RDCodeDir, 'Chem/Pharm2D/test_data')
featFact = ChemicalFeatures.BuildFeatureFactory(
os.path.join(dataDir, 'BaseFeatures.fdef'))
print "########"
sigFact = SigFactory.SigFactory(featFact)
bins = tuple([(2, 3), (3, 4), (4, 5), (5, 6), (6, 7), (7, 8), (8, 100)])
sigFact.SetBins(bins)
sigFact.Init()
def calc_p4_fp(mol):
fp = Generate.Gen2DFingerprint(mol, sigFact)
return fp
def calc_tanimoto(fp1, fp2):
tc = DataStructs.TanimotoSimilarity(fp1, fp2)
return tc
if __name__ == "__main__":
def setUp(self):
self.factory = SigFactory.SigFactory()
self.factory.SetPatternsFromSmarts(['O', 'N'])
self.factory.SetBins([(0, 2), (2, 5), (5, 8)])
self.factory.SetMinCount(2)
self.factory.SetMaxCount(3)
