def testDetails2(self): Crippen._Init() inF = open(self.detailName2, 'rb') if 0: outF = open('tmp.pkl', 'wb+') self._writeDetailFile(inF, outF) self._doDetailFile(inF)
def pySlogP_VSA_(mol, bins=None, force=1): """ *Internal Use Only* """ if not force: try: res = mol._slogpVSA except AttributeError: pass else: if res.all(): return res if bins is None: bins = logpBins Crippen._Init() propContribs = Crippen._GetAtomContribs(mol, force=force) volContribs = _LabuteHelper(mol) ans = numpy.zeros(len(bins) + 1, 'd') for i in range(len(propContribs)): prop = propContribs[i] vol = volContribs[i + 1] if prop is not None: bin = bisect.bisect_right(bins, prop[0]) ans[bin] += vol mol._slogpVSA = ans return ans
def testDetails2(self): Crippen._Init() inF = open(self.detailName2,'rb') if 0: outF = open('tmp.pkl','wb+') self._writeDetailFile(inF,outF) self._doDetailFile(inF)
def pySlogP_VSA_(mol,bins=None,force=1): """ *Internal Use Only* """ if not force: try: res = mol._slogpVSA except AttributeError: pass else: if res.all(): return res if bins is None: bins = logpBins Crippen._Init() propContribs = Crippen._GetAtomContribs(mol,force=force) volContribs = _LabuteHelper(mol) ans = numpy.zeros(len(bins)+1,'d') for i in range(len(propContribs)): prop = propContribs[i] vol = volContribs[i+1] if prop is not None: bin = bisect.bisect_right(bins,prop[0]) ans[bin] += vol mol._slogpVSA=ans return ans
def testDetails(self): Crippen._Init() with open(self.detailName, 'rb') as inF: if 0: outF = open('tmp.pkl', 'wb+') self._writeDetailFile(inF, outF) self._doDetailFile(inF)
def testDetails(self): Crippen._Init() with open(self.detailName,'rb') as inF: if 0: outF = open('tmp.pkl','wb+') self._writeDetailFile(inF,outF) self._doDetailFile(inF)
def testDetails2(self): Crippen._Init() with open(self.detailName2,'r') as inTF: buf = inTF.read().replace('\r\n', '\n').encode('utf-8') inTF.close() with io.BytesIO(buf) as inF: if 0: outF = open('tmp.pkl','wb+') self._writeDetailFile(inF,outF) self._doDetailFile(inF)
def testDetails2(self): Crippen._Init() with open(self.detailName2, 'r') as inTF: buf = inTF.read().replace('\r\n', '\n').encode('utf-8') inTF.close() with io.BytesIO(buf) as inF: if 0: outF = open('tmp.pkl', 'wb+') self._writeDetailFile(inF, outF) self._doDetailFile(inF)
def pyPEOE_VSA_(mol, bins=None, force=1): """ *Internal Use Only* """ if not force: try: res = mol._peoeVSA except AttributeError: pass else: if res.all(): return res if bins is None: bins = chgBins Crippen._Init() #print('\ts:',repr(mol.GetMol())) #print('\t\t:',len(mol.GetAtoms())) rdPartialCharges.ComputeGasteigerCharges(mol) #propContribs = [float(x.GetProp('_GasteigerCharge')) for x in mol.GetAtoms()] propContribs = [] for at in mol.GetAtoms(): p = at.GetProp('_GasteigerCharge') try: v = float(p) except ValueError: v = 0.0 propContribs.append(v) #print '\tp',propContribs volContribs = _LabuteHelper(mol) #print '\tv',volContribs ans = numpy.zeros(len(bins) + 1, 'd') for i in range(len(propContribs)): prop = propContribs[i] vol = volContribs[i + 1] if prop is not None: bin = bisect.bisect_right(bins, prop) ans[bin] += vol mol._peoeVSA = ans return ans
from __future__ import print_function from rdkit import RDConfig import gzip import os.path from rdkit.six.moves import cPickle from rdkit import Chem from rdkit.Chem import Crippen Crippen._Init() def runIt(inFileName, outFileName, smiCol=0, maxMols=-1, delim=','): inF = gzip.open(inFileName, 'r') outF = open(outFileName, 'wb+') mols = [] nDone = 0 for line in inF.readlines(): if line[0] != '#': splitL = line.strip().split(delim) smi = splitL[smiCol].strip() print(smi) mol = Chem.MolFromSmiles(smi) if mol: contribs = Crippen._GetAtomContribs(mol) cPickle.dump((smi, contribs), outF) nDone += 1 if maxMols > 0 and nDone >= maxMols: break outF.close() if __name__ == '__main__':