def test3FPgenerator(self):
smiLines = open(self.smiName, 'r').readlines()
fparams = FragmentCatalog.FragCatParams(1, 6, self.fName)
fcat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
suppl = Chem.SmilesMolSupplier(self.smiName, " ", 0, 1, 0)
smiles = []
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, fcat)
smiles.append(Chem.MolToSmiles(mol))
assert fcat.GetNumEntries() == 21
assert fcat.GetFPLength() == 21, fcat.GetFPLength()
fpgen = FragmentCatalog.FragFPGenerator()
obits = [3, 2, 3, 3, 2, 3, 5, 5, 5, 4, 5, 6]
obls = [(0, 1, 2), (1, 3), (1, 4, 5), (1, 6, 7), (0, 8), (0, 6, 9),
(0, 1, 2, 3, 10), (0, 1, 2, 8, 11), (1, 3, 4, 5, 12),
(1, 4, 5, 13), (1, 3, 6, 7, 14), (0, 1, 6, 7, 9, 15)]
for i in range(len(smiles)):
smi = smiles[i]
mol = Chem.MolFromSmiles(smi)
fp = fpgen.GetFPForMol(mol, fcat)
if i < len(obits):
assert fp.GetNumOnBits() == obits[i], '%s: %s' % (
smi, str(fp.GetOnBits()))
obl = fp.GetOnBits()
if i < len(obls):
assert tuple(obl) == obls[i], '%s: %s' % (smi, obl)
def test4Serialize(self):
smiLines = open(self.smiName, 'r').readlines()
fparams = FragmentCatalog.FragCatParams(1, 6, self.fName)
fcat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
suppl = Chem.SmilesMolSupplier(self.smiName, " ", 0, 1, 0)
smiles = []
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, fcat)
smiles.append(Chem.MolToSmiles(mol))
assert fcat.GetNumEntries() == 21
assert fcat.GetFPLength() == 21, fcat.GetFPLength()
pkl = cPickle.dumps(fcat)
fcat2 = cPickle.loads(pkl)
assert fcat2.GetNumEntries() == 21
assert fcat2.GetFPLength() == 21, fcat2.GetFPLength()
fpgen = FragmentCatalog.FragFPGenerator()
for i in range(len(smiles)):
smi = smiles[i]
mol = Chem.MolFromSmiles(smi)
fp1 = fpgen.GetFPForMol(mol, fcat)
fp2 = fpgen.GetFPForMol(mol, fcat2)
assert fp1.GetNumOnBits() == fp2.GetNumOnBits()
obl1 = fp1.GetOnBits()
obl2 = fp2.GetOnBits()
assert tuple(obl1) == tuple(obl2)
def ScoreMolecules(suppl, catalog, maxPts=-1, actName='', acts=None, nActs=2, reportFreq=10):
""" scores the compounds in a supplier using a catalog
**Arguments**
- suppl: a mol supplier
- catalog: the FragmentCatalog
- maxPts: (optional) the maximum number of molecules to be
considered
- actName: (optional) the name of the molecule's activity property.
If this is not provided, the molecule's last property will be used.
- acts: (optional) a sequence of activity values (integers).
If not provided, the activities will be read from the molecules.
- nActs: (optional) number of possible activity values
- reportFreq: (optional) how often to display status information
**Returns**
a 2-tuple:
1) the results table (a 3D array of ints nBits x 2 x nActs)
2) a list containing the on bit lists for each molecule
"""
nBits = catalog.GetFPLength()
resTbl = numpy.zeros((nBits, 2, nActs), numpy.int)
obls = []
if not actName and not acts:
actName = suppl[0].GetPropNames()[-1]
fpgen = FragmentCatalog.FragFPGenerator()
suppl.reset()
i = 1
for mol in suppl:
if i and not i % reportFreq:
message('Done %d.\n' % (i))
if mol:
if not acts:
act = int(mol.GetProp(actName))
else:
act = acts[i - 1]
fp = fpgen.GetFPForMol(mol, catalog)
obls.append([x for x in fp.GetOnBits()])
for j in range(nBits):
resTbl[j, 0, act] += 1
for id_ in obls[i - 1]:
resTbl[id_ - 1, 0, act] -= 1
resTbl[id_ - 1, 1, act] += 1
else:
obls.append([])
i += 1
return resTbl, obls
def CalcGains(suppl,catalog,topN=-1,actName='',acts=None,
nActs=2,reportFreq=10,biasList=None,collectFps=0):
""" calculates info gains by constructing fingerprints
*DOC*
Returns a 2-tuple:
1) gains matrix
2) list of fingerprints
"""
nBits = catalog.GetFPLength()
if topN < 0:
topN = nBits
if not actName and not acts:
actName = suppl[0].GetPropNames()[-1]
gains = [0]*nBits
if hasattr(suppl,'__len__'):
nMols = len(suppl)
else:
nMols = -1
fpgen = FragmentCatalog.FragFPGenerator()
#ranker = InfoTheory.InfoBitRanker(nBits,nActs,InfoTheory.InfoType.ENTROPY)
if biasList:
ranker = InfoTheory.InfoBitRanker(nBits,nActs,InfoTheory.InfoType.BIASENTROPY)
ranker.SetBiasList(biasList)
else:
ranker = InfoTheory.InfoBitRanker(nBits,nActs,InfoTheory.InfoType.ENTROPY)
i = 0
fps = []
for mol in suppl:
if not acts:
try:
act = int(mol.GetProp(actName))
except KeyError:
message('ERROR: Molecule has no property: %s\n'%(actName))
message('\tAvailable properties are: %s\n'%(str(mol.GetPropNames())))
raise KeyError(actName)
else:
act = acts[i]
if i and not i%reportFreq:
if nMols>0:
message('Done %d of %d.\n'%(i,nMols))
else:
message('Done %d.\n'%(i))
fp = fpgen.GetFPForMol(mol,catalog)
ranker.AccumulateVotes(fp,act)
i+=1;
if collectFps:
fps.append(fp)
gains = ranker.GetTopN(topN)
return gains,fps
def _test5MoreComplex(self):
lastIdx = 0
ranges = {}
suppl = Chem.SmilesMolSupplierFromText('\n'.join(self.smiList), ',', 0, -1, 0)
for i, mol in enumerate(suppl):
nEnt = self.fgen.AddFragsFromMol(mol, self.fragCat)
ranges[i] = range(lastIdx, lastIdx + nEnt)
lastIdx += nEnt
# now make sure that those bits are contained in the signatures:
fpgen = FragmentCatalog.FragFPGenerator()
for i, mol in enumerate(suppl):
fp = fpgen.GetFPForMol(mol, self.fragCat)
for bit in ranges[i]:
assert fp[bit], '%s: %s' % (Chem.MolToSmiles(mol), str(bit))
def _testBits(self, fragCat):
fpgen = FragmentCatalog.FragFPGenerator()
obits = [3, 2, 3, 3, 2, 3, 5, 5, 5, 4, 5, 6]
obls = self.list2Obls
suppl = Chem.SmilesMolSupplierFromText('\n'.join(self.smiList2), ',', 0, -1, 0)
i = 0
for mol in suppl:
fp = fpgen.GetFPForMol(mol, fragCat)
if i < len(obits):
smi = Chem.MolToSmiles(mol)
assert fp.GetNumOnBits() == obits[i], '%s: %s' % (smi, str(fp.GetOnBits()))
obl = fp.GetOnBits()
if i < len(obls):
assert tuple(obl) == obls[i], '%s: %s' % (smi, obl)
i += 1
def test9Issue116(self):
smiList = ['Cc1ccccc1']
suppl = Chem.SmilesMolSupplierFromText('\n'.join(smiList), ',', 0, -1, 0)
cat = BuildFragmentCatalog.BuildCatalog(suppl, minPath=2, maxPath=2)
assert cat.GetFPLength() == 2
assert cat.GetBitDescription(0) == 'ccC'
fpgen = FragmentCatalog.FragFPGenerator()
mol = Chem.MolFromSmiles('Cc1ccccc1')
fp = fpgen.GetFPForMol(mol, cat)
assert fp[0]
assert fp[1]
mol = Chem.MolFromSmiles('c1ccccc1-c1ccccc1')
fp = fpgen.GetFPForMol(mol, cat)
assert not fp[0]
assert fp[1]
def test7Issue116(self):
smiList = ['Cc1ccccc1']
suppl = Chem.SmilesMolSupplierFromText('\n'.join(smiList), ',', 0, -1, 0)
fparams = FragmentCatalog.FragCatParams(2, 2, self.fName, 1.0e-8)
cat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, cat)
self.assertEqual(cat.GetFPLength(), 2)
self.assertEqual(cat.GetBitDescription(0), 'ccC')
fpgen = FragmentCatalog.FragFPGenerator()
mol = Chem.MolFromSmiles('Cc1ccccc1')
fp = fpgen.GetFPForMol(mol, cat)
self.assertEqual(fp[0], 1)
self.assertEqual(fp[1], 1)
mol = Chem.MolFromSmiles('c1ccccc1-c1ccccc1')
fp = fpgen.GetFPForMol(mol, cat)
self.assertEqual(fp[0], 0)
self.assertEqual(fp[1], 1)
ms = [Chem.MolFromSmiles('OCC(NC1CC1)CCC'), Chem.MolFromSmiles('OCC=CC(=O)O')]
# 片段存储器
fcat = FragmentCatalog.FragCatalog(fparams)
# 片段生成器
for m in ms:
fcgen.AddFragsFromMol(m, fcat)
# 查看分子片段数量
num_entries = fcat.GetNumEntries()
print(num_entries) # 17
# 存储器收集完所有片段后 ， 再用它来生成分子指纹
# 创建一个片段指纹生成器：FragFPGenerator()
fpgen = FragmentCatalog.FragFPGenerator()
# 传入分子和存储器用于生成指纹:GetFPForMol(mol,fcat)
fp1 = fpgen.GetFPForMol(ms[1], fcat)
# 以字符串形式查看指纹:ToBitString()
print(fp1.ToBitString()) # 10000000000000011
# 查看指纹中哪些位是有效的:GetOnBits()
print(list(fp1.GetOnBits())) # [0, 15, 16]
# 可以用处理一般分子指纹的方法来处理片段分子指纹，例如寻找相同的片段
# 先对分子指纹做“&”位运算，两个指纹结果都为1时，结果为1，否则为0
# 获取两个指纹中都出现的片段：GetOnBits()
# 查看片段信息：GetEnteyDescription()
fp0 = fpgen.GetFPForMol(ms[0], fcat)
