def GetMorganFingerprint(mol, atomId=-1, radius=2, fpType='bv', nBits=2048, useFeatures=False):
"""
Calculates the Morgan fingerprint with the counts of atomId removed.
Parameters:
mol -- the molecule of interest
radius -- the maximum radius
fpType -- the type of Morgan fingerprint: 'count' or 'bv'
atomId -- the atom to remove the counts for (if -1, no count is removed)
nBits -- the size of the bit vector (only for fpType = 'bv')
useFeatures -- if false: ConnectivityMorgan, if true: FeatureMorgan
"""
if fpType not in ['bv', 'count']: raise ValueError("Unknown Morgan fingerprint type")
if not hasattr(mol, '_fpInfo'):
info = {}
# get the fingerprint
if fpType == 'bv': molFp = rdMD.GetMorganFingerprintAsBitVect(mol, radius, nBits=nBits, useFeatures=useFeatures, bitInfo=info)
else: molFp = rdMD.GetMorganFingerprint(mol, radius, useFeatures=useFeatures, bitInfo=info)
# construct the bit map
if fpType == 'bv': bitmap = [DataStructs.ExplicitBitVect(nBits) for x in range(mol.GetNumAtoms())]
else: bitmap = [[] for x in range(mol.GetNumAtoms())]
for bit, es in info.iteritems():
for at1, rad in es:
if rad == 0: # for radius 0
if fpType == 'bv': bitmap[at1][bit] = 1
else: bitmap[at1].append(bit)
else: # for radii > 0
env = Chem.FindAtomEnvironmentOfRadiusN(mol, rad, at1)
amap = {}
submol = Chem.PathToSubmol(mol, env, atomMap=amap)
for at2 in amap.keys():
if fpType == 'bv': bitmap[at2][bit] = 1
else: bitmap[at2].append(bit)
mol._fpInfo = (molFp, bitmap)
if atomId < 0:
return mol._fpInfo[0]
else: # remove the bits of atomId
if atomId >= mol.GetNumAtoms(): raise ValueError("atom index greater than number of atoms")
if len(mol._fpInfo) != 2: raise ValueError("_fpInfo not set")
if fpType == 'bv':
molFp = mol._fpInfo[0] ^ mol._fpInfo[1][atomId] # xor
else: # count
molFp = copy.deepcopy(mol._fpInfo[0])
# delete the bits with atomId
for bit in mol._fpInfo[1][atomId]:
molFp[bit] -= 1
return molFp
def test10BulkOps2(self):
nbits = 10000
bvs = []
for bvi in range(10):
bv = DataStructs.ExplicitBitVect(nbits)
for j in range(nbits):
x = random.randrange(0, nbits)
bv.SetBit(x)
bvs.append(bv)
bvs = tuple(bvs)
sims = DataStructs.BulkTanimotoSimilarity(bvs[0], bvs)
for i in range(len(bvs)):
sim = DataStructs.TanimotoSimilarity(bvs[0], bvs[i])
self.failUnless(feq(sim, sims[i]))
sims = DataStructs.BulkDiceSimilarity(bvs[0], bvs)
for i in range(len(bvs)):
sim = DataStructs.DiceSimilarity(bvs[0], bvs[i])
self.failUnless(feq(sim, sims[i]))
sims = DataStructs.BulkAllBitSimilarity(bvs[0], bvs)
for i in range(len(bvs)):
sim = DataStructs.AllBitSimilarity(bvs[0], bvs[i])
self.failUnless(feq(sim, sims[i]))
sims = DataStructs.BulkOnBitSimilarity(bvs[0], bvs)
for i in range(len(bvs)):
sim = DataStructs.OnBitSimilarity(bvs[0], bvs[i])
self.failUnless(feq(sim, sims[i]))
sims = DataStructs.BulkRogotGoldbergSimilarity(bvs[0], bvs)
for i in range(len(bvs)):
sim = DataStructs.RogotGoldbergSimilarity(bvs[0], bvs[i])
self.failUnless(feq(sim, sims[i]))
sims = DataStructs.BulkTverskySimilarity(bvs[0], bvs, 1, 1)
for i in range(len(bvs)):
sim = DataStructs.TverskySimilarity(bvs[0], bvs[i], 1, 1)
self.failUnless(feq(sim, sims[i]))
sim = DataStructs.TanimotoSimilarity(bvs[0], bvs[i])
self.failUnless(feq(sim, sims[i]))
sims = DataStructs.BulkTverskySimilarity(bvs[0], bvs, .5, .5)
for i in range(len(bvs)):
sim = DataStructs.TverskySimilarity(bvs[0], bvs[i], .5, .5)
self.failUnless(feq(sim, sims[i]))
sim = DataStructs.DiceSimilarity(bvs[0], bvs[i])
self.failUnless(feq(sim, sims[i]))
def test7FPS(self):
bv = DataStructs.ExplicitBitVect(32)
bv.SetBit(0)
bv.SetBit(1)
bv.SetBit(17)
bv.SetBit(23)
bv.SetBit(31)
self.assertEqual(DataStructs.BitVectToFPSText(bv), "03008280")
bv2 = DataStructs.CreateFromFPSText("03008280")
self.assertEqual(bv, bv2)
self.assertRaises(ValueError, lambda: DataStructs.CreateFromFPSText("030082801"))
bv2 = DataStructs.CreateFromFPSText("")
self.assertEqual(bv2.GetNumBits(), 0)
def test10BulkOps3(self):
nbits = 10000
bvs = numpy.empty((10, ), DataStructs.ExplicitBitVect)
for bvi in range(10):
bv = DataStructs.ExplicitBitVect(nbits)
for j in range(nbits):
x = random.randrange(0, nbits)
bv.SetBit(x)
bvs[bvi] = bv
sims = DataStructs.BulkTanimotoSimilarity(bvs[0], bvs)
for i in range(len(bvs)):
sim = DataStructs.TanimotoSimilarity(bvs[0], bvs[i])
self.assertTrue(feq(sim, sims[i]))
sims = DataStructs.BulkDiceSimilarity(bvs[0], bvs)
for i in range(len(bvs)):
sim = DataStructs.DiceSimilarity(bvs[0], bvs[i])
self.assertTrue(feq(sim, sims[i]))
sims = DataStructs.BulkAllBitSimilarity(bvs[0], bvs)
for i in range(len(bvs)):
sim = DataStructs.AllBitSimilarity(bvs[0], bvs[i])
self.assertTrue(feq(sim, sims[i]))
sims = DataStructs.BulkOnBitSimilarity(bvs[0], bvs)
for i in range(len(bvs)):
sim = DataStructs.OnBitSimilarity(bvs[0], bvs[i])
self.assertTrue(feq(sim, sims[i]))
sims = DataStructs.BulkRogotGoldbergSimilarity(bvs[0], bvs)
for i in range(len(bvs)):
sim = DataStructs.RogotGoldbergSimilarity(bvs[0], bvs[i])
self.assertTrue(feq(sim, sims[i]))
sims = DataStructs.BulkTverskySimilarity(bvs[0], bvs, 1, 1)
for i in range(len(bvs)):
sim = DataStructs.TverskySimilarity(bvs[0], bvs[i], 1, 1)
self.assertTrue(feq(sim, sims[i]))
sim = DataStructs.TanimotoSimilarity(bvs[0], bvs[i])
self.assertTrue(feq(sim, sims[i]))
sims = DataStructs.BulkTverskySimilarity(bvs[0], bvs, .5, .5)
for i in range(len(bvs)):
sim = DataStructs.TverskySimilarity(bvs[0], bvs[i], .5, .5)
self.assertTrue(feq(sim, sims[i]))
sim = DataStructs.DiceSimilarity(bvs[0], bvs[i])
self.assertTrue(feq(sim, sims[i]))
def testNonUniqueCrash(self):
from rdkit import DataStructs
sz = 300
nbits = 40
nBitsToSet = int(nbits * .3)
N = 8
vs = []
for i in range(sz):
bv = DataStructs.ExplicitBitVect(nbits)
for j in range(nBitsToSet):
val = int(nbits * random.random())
bv.SetBit(val)
vs.append(bv)
vs.append(bv)
def taniFunc(i, j, bvs=vs):
d = 1 - DataStructs.FingerprintSimilarity(bvs[i], bvs[j])
return d
picker = rdSimDivPickers.MaxMinPicker()
mm1 = picker.LazyPick(taniFunc, len(vs), N)
self.assertEqual(len(mm1), N)
picker = None
picker = rdSimDivPickers.MaxMinPicker()
mm2 = picker.LazyBitVectorPick(vs, len(vs), N)
self.assertEqual(len(mm2), N)
picker = rdSimDivPickers.MaxMinPicker()
mm3 = picker.LazyBitVectorPick(vs, len(vs), N)
self.assertEqual(len(mm3), N)
# we get the occasional dupe randomly,
# make sure we don't get three dupes in a row
self.assertTrue(tuple(mm2) != tuple(mm1)) or (tuple(mm3) != tuple(mm1))
picker = None
ds = []
nvs = len(vs)
for i in range(nvs):
for j in range(i + 1, nvs):
d = taniFunc(i, j)
ds.append(d)
m = numpy.array(ds)
picker = rdSimDivPickers.HierarchicalClusterPicker(
rdSimDivPickers.ClusterMethod.WARD)
p1 = list(picker.Pick(m, nvs, N))
def process_one_target(file, targets, top_n_matches, outfile=None):
import rdkit
import base64
from rdkit import RDLogger
from rdkit import DataStructs
from pstats import SortKey
import pickle
from operator import itemgetter
import csv
target_results = {}
read = pickle.load(open(file, 'rb'))
fingerprint_set = []
for sm, identifier, fp in read:
# Next TRY here as some do not convert
try:
bv = DataStructs.ExplicitBitVect(base64.b64decode(fp))
except:
bv = None
fingerprint_set += [(sm, bv, identifier)]
for smile_target in targets:
best_so_far = [('', 0.0) for index in range(top_n_matches)]
bit_target = targets[smile_target]
# Find scores for non-None fingerprints in fingerprint set
scores = []
for (smile, fingerprint, identifier) in fingerprint_set:
try:
score = DataStructs.TanimotoSimilarity(fingerprint, bit_target)
scores += [(smile, score, identifier)]
except:
pass
sorted_scores = sorted(scores, key=itemgetter(1))
new_list = sorted_scores[-top_n_matches:]
target_results[smile_target] = new_list
if outfile:
with open(outfile, 'wb') as f:
pickle.dump(target_results, f)
return outfile
else:
return (target_results)
def generateIFP(self, ligand, protein):
"""Generates the complete IFP from each residue's bitstring"""
IFPvector = DataStructs.ExplicitBitVect(
len(self.interactions) * len(protein.residues))
i = 0
IFP = ''
for residue in sorted(protein.residues, key=get_resnumber):
bitstring = self.generateBitstring(ligand,
protein.residues[residue])
for bit in bitstring:
if bit == '1':
IFPvector.SetBit(i)
i += 1
IFP += bitstring
ligand.setIFP(IFP, IFPvector)
return IFPvector
def MapToClusterFP(self, fp):
""" Map the fingerprint to a smaller sized (= number of clusters) fingerprint
Each cluster get a bit in the new fingerprint and is turned on if any of the bits in
the cluster are turned on in the original fingerprint"""
ebv = DataStructs.ExplicitBitVect(self._nClusters)
i = 0
for cls in self._clusters:
for bid in cls:
if fp[bid]:
ebv.SetBit(i)
break
i += 1
return ebv
def _BuildFp(self,data):
data = list(data)
pkl = str(data[self.fpCol])
del data[self.fpCol]
self._numProcessed+=1;
try:
if self._usePickles:
newFp = cPickle.loads(pkl)
else:
newFp = DataStructs.ExplicitBitVect(pkl)
except:
import traceback
traceback.print_exc()
newFp = None
if newFp:
newFp._fieldsFromDb = data
return newFp
def _BuildFp(self, data):
data = list(data)
pkl = bytes(data[self.fpCol], encoding='Latin1')
del data[self.fpCol]
self._numProcessed += 1
try:
if self._usePickles:
newFp = pickle.loads(pkl, encoding='bytes')
else:
newFp = DataStructs.ExplicitBitVect(pkl)
except Exception:
import traceback
traceback.print_exc()
newFp = None
if newFp:
newFp._fieldsFromDb = data
return newFp
def test4ebv(self):
n = 30
m = 2048
dm = 800
lst = []
for i in range(n):
v = DataStructs.ExplicitBitVect(m)
for j in range(dm):
v.SetBit(random.randrange(0, m))
lst.append(v)
dMat = rdmmc.GetTanimotoDistMat(lst)
sMat = rdmmc.GetTanimotoSimMat(lst)
for i in range(n * (n - 1) // 2):
assert feq(sMat[i] + dMat[i], 1.0)
def CalculateFP3Fingerprint(mol: Chem.Mol,
rtype: str = 'bitstring') -> Tuple[str, dict, Any]:
"""Calculate FP3 fingerprints (55 bits).
:param rtype: Type of output, may either be:
bitstring (default), returns a binary string
rdkit, return the native rdkit DataStructs
dict, for a dict of bits turned on
"""
m = pybel.readstring('smi', Chem.MolToSmiles(mol))
temp = m.calcfp('FP3').bits
if rtype == 'dict':
return {f'FP3_{i}': 1 for i in temp}
bv = DataStructs.ExplicitBitVect(55)
bv.SetBitsFromList([x - 1 for x in temp])
if rtype == 'rdkit':
return bv
return bv.ToBitString()
def __setstate__(self, pkl):
self.__vects = {}
self.__orVect = None
self.__numBits = -1
self.__needReset = True
szI = struct.calcsize('I')
offset = 0
nToRead = struct.unpack('<I', pkl[offset:offset + szI])[0]
offset += szI
for i in range(nToRead):
k = struct.unpack('<I', pkl[offset:offset + szI])[0]
offset += szI
l = struct.unpack('<I', pkl[offset:offset + szI])[0]
offset += szI
sz = struct.calcsize('%ds' % l)
bv = DataStructs.ExplicitBitVect(
struct.unpack('%ds' % l, pkl[offset:offset + sz])[0])
offset += sz
self.AddVect(k, bv)
def __setstate__(self, pkl):
if six.PY3 and isinstance(pkl, str):
pkl = bytes(pkl, encoding='Latin1')
self.__vects = {}
self.__orVect = None
self.__numBits = -1
self.__needReset = True
szI = struct.calcsize('I')
offset = 0
nToRead = struct.unpack('<I', pkl[offset:offset + szI])[0]
offset += szI
for _ in range(nToRead):
k = struct.unpack('<I', pkl[offset:offset + szI])[0]
offset += szI
l = struct.unpack('<I', pkl[offset:offset + szI])[0]
offset += szI
sz = struct.calcsize('%ds' % l)
bv = DataStructs.ExplicitBitVect(struct.unpack('%ds' % l, pkl[offset:offset + sz])[0])
offset += sz
self.AddVect(k, bv)
def testNonUniqueCrash(self):
from rdkit import DataStructs
sz = 10
nbits = 20
nBitsToSet = int(nbits * .3)
N = 12
vs = []
for i in range(sz):
bv = DataStructs.ExplicitBitVect(nbits)
for j in range(nBitsToSet):
val = int(nbits * random.random())
bv.SetBit(val)
vs.append(bv)
vs.append(bv)
def taniFunc(i, j, bvs=vs):
d = 1 - DataStructs.FingerprintSimilarity(bvs[i], bvs[j])
return d
picker = rdSimDivPickers.MaxMinPicker()
try:
mm = picker.LazyPick(taniFunc, len(vs), N)
except:
ok = False
else:
ok = True
self.failUnless(ok)
self.failUnless(len(mm) == N)
picker = None
ds = []
nvs = len(vs)
for i in range(nvs):
for j in range(i + 1, nvs):
d = taniFunc(i, j)
ds.append(d)
m = numpy.array(ds)
picker = rdSimDivPickers.HierarchicalClusterPicker(
rdSimDivPickers.ClusterMethod.WARD)
p1 = list(picker.Pick(m, nvs, N))
def test11BulkNeighbors(self):
nbits = 2048
bvs = []
for bvi in range(1000):
bv = DataStructs.ExplicitBitVect(nbits)
for j in range(nbits):
x = random.randrange(0, nbits)
bv.SetBit(x)
bvs.append(bv)
qs = bvs[:10]
db = bvs[10:]
for metric in ['Tanimoto','Cosine', 'Kulczynski', 'Dice', 'Sokal',
'McConnaughey', 'Asymmetric', 'BraunBlanquet', 'Russel',
'RogotGoldberg']:
bulkSim = getattr(DataStructs,f'Bulk{metric}Similarity')
nbrSim = getattr(DataStructs,f'{metric}SimilarityNeighbors')
tgts = []
for q in qs:
sims = bulkSim(q,db)
sim, idx = max((sim, -idx) for idx, sim in enumerate(sims))
tgts.append((-idx,sim))
nbrs = nbrSim(qs,db)
self.assertEqual(tgts,nbrs)
def test1Cluster(self):
if BitClusterer is None:
return
cmg = rdInfoTheory.BitCorrMatGenerator()
cmg.SetBitList(self.blist)
for fp in self.fps:
cmg.CollectVotes(fp)
corrMat = cmg.GetCorrMatrix()
bcl = BitClusterer.BitClusterer(self.blist, self.nbits / 2)
bcl.ClusterBits(corrMat)
cls = bcl.GetClusters()
for cl in cls:
assert len(cl) == 2
assert (cl[0] + self.nbits / 2) == cl[1]
tfp = DataStructs.ExplicitBitVect(self.nbits)
obits = range(0, self.nbits / 4) + range(self.nbits / 2,
3 * self.nbits / 4)
tfp.SetBitsFromList(obits)
rvc = bcl.MapToClusterScores(tfp)
assert len(rvc) == self.nbits / 2
for i in range(self.nbits / 2):
if i < self.nbits / 4:
assert rvc[i] == 2
else:
assert rvc[i] == 0
nfp = bcl.MapToClusterFP(tfp)
assert len(nfp) == self.nbits / 2
for i in range(self.nbits / 2):
if i < self.nbits / 4:
assert nfp[i]
else:
assert not nfp[i]
def test1Cluster(self):
cmg = rdInfoTheory.BitCorrMatGenerator()
cmg.SetBitList(self.blist)
for fp in self.fps:
cmg.CollectVotes(fp)
corrMat = cmg.GetCorrMatrix()
bcl = BitClusterer.BitClusterer(self.blist, self.nbits // 2)
bcl.ClusterBits(corrMat)
cls = bcl.GetClusters()
for cl in cls:
self.assertEqual(len(cl), 2)
self.assertEqual((cl[0] + self.nbits // 2), cl[1])
bcl.SetClusters(cls)
self.assertRaises(AssertionError, bcl.SetClusters, cls[:-1])
tfp = DataStructs.ExplicitBitVect(self.nbits)
obits = list(range(0, self.nbits // 4)) + list(
range(self.nbits // 2, 3 * self.nbits // 4))
tfp.SetBitsFromList(obits)
rvc = bcl.MapToClusterScores(tfp)
self.assertEqual(len(rvc), self.nbits // 2)
for i in range(self.nbits // 2):
if i < self.nbits // 4:
self.assertEqual(rvc[i], 2)
else:
self.assertEqual(rvc[i], 0)
nfp = bcl.MapToClusterFP(tfp)
self.assertEqual(len(nfp), self.nbits // 2)
for i in range(self.nbits // 2):
if i < self.nbits // 4:
self.assertTrue(nfp[i])
else:
self.assertFalse(nfp[i])
def partialSimilarity(atomID):
""" Determine similarity for the atoms set by atomID """
# create empty fp
modifiedFP = DataStructs.ExplicitBitVect(1024)
modifiedFP.SetBitsFromList(aBits[atomID])
return DataStructs.TverskySimilarity(subsFp, modifiedFP, 0, 1)
fpq = [
Chem.RDKFingerprint(x,
fpSize=2048,
minPath=7,
useBondOrder=False,
nBitsPerHash=1,
minSize=2048,
useHs=False) for x in MyMolList
]
#fpq = [Chem.PatternFingerprint(x,fpSize=2048) for x in MyMolList]
AllQBits = [list(fpqe.GetOnBits()) for fpqe in fpq]
AllQBits = list(set([j for i in AllQBits for j in i]))
if len(AllQBits) == 0:
AllQBits = [2047]
bv = DataStructs.ExplicitBitVect(2048)
bv.SetBitsFromList(AllQBits)
print " the number of compounds generated from the compound used to query: ", len(
MyMolList)
print len(AllQBits)
print Chem.MolToSmiles(MyMol)
print len(MyMolFp.GetOnBits())
################################ End Query Ensemble Creation ################################################################
############################ Find the AntiSmash compounds with the most overlap with the query ensemble fingerprint #########
print " Culling the AntiSmash compounds "
print " examining fingerprints : ", len(fps)
MySearchList = []
similarity = 0.17
def test3Bounds(self):
nbits = 10
bv1 = DataStructs.ExplicitBitVect(nbits)
bv1[0]
with self.assertRaisesRegex(IndexError, ""):
bv1[11]
def test01BVWithAllOnes(self):
bv1 = DataStructs.ExplicitBitVect(10, True)
for i in range(10):
assert bv1.GetBit(i) == 1