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Python Crippen._GetAtomContribs方法代码示例

本文整理汇总了Python中rdkit.Chem.Crippen._GetAtomContribs方法的典型用法代码示例。如果您正苦于以下问题:Python Crippen._GetAtomContribs方法的具体用法?Python Crippen._GetAtomContribs怎么用?Python Crippen._GetAtomContribs使用的例子?那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在rdkit.Chem.Crippen的用法示例。


在下文中一共展示了Crippen._GetAtomContribs方法的5个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Python代码示例。

示例1: pySlogP_VSA_

# 需要导入模块: from rdkit.Chem import Crippen [as 别名]
# 或者: from rdkit.Chem.Crippen import _GetAtomContribs [as 别名]
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
开发者ID:abradle,项目名称:rdkit,代码行数:30,代码来源:MolSurf.py

示例2: _doDetailFile

# 需要导入模块: from rdkit.Chem import Crippen [as 别名]
# 或者: from rdkit.Chem.Crippen import _GetAtomContribs [as 别名]
  def _doDetailFile(self,inF,nFailsAllowed=1):
    done = 0
    verbose=0
    nFails=0
    while not done:
      if verbose: print('---------------')
      try:
        smi,refContribs = cPickle.load(inF)
      except EOFError:
        done = 1
      else:
        refContribs = [x[0] for x in refContribs]
        refOrder= numpy.argsort(refContribs)
        try:
          mol = Chem.MolFromSmiles(smi)
        except:
          import traceback
          traceback.print_exc()
          mol = None
        if mol:
          mol=Chem.AddHs(mol,1)
          smi2 = Chem.MolToSmiles(mol)
          contribs = Crippen._GetAtomContribs(mol)
          contribs = [x[0] for x in contribs]
          #
          #  we're comparing to the old results using the oelib code.
          #  Since we have some disagreements with them as to what is
          #  aromatic and what isn't, we may have different numbers of
          #  Hs. For the sake of comparison, just pop those off our
          #  new results.
          #
          while len(contribs)>len(refContribs):
            del contribs[-1]
          order = numpy.argsort(contribs)

          for i in range(len(refContribs)):
            refL = refContribs[refOrder[i]]
            l = contribs[order[i]]
            if not feq(refL,l):
              print('%s (%s): %d %6.5f != %6.5f'%(smi,smi2,order[i],refL,l))
              Crippen._GetAtomContribs(mol,force=1)
              print('-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*')
              nFails +=1
              break;
        else:
          print('Problems with SMILES:',smi)
    self.assertTrue(nFails<nFailsAllowed)
开发者ID:BielitzLabs,项目名称:rdkit,代码行数:49,代码来源:UnitTestCrippen.py

示例3: _writeDetailFile

# 需要导入模块: from rdkit.Chem import Crippen [as 别名]
# 或者: from rdkit.Chem.Crippen import _GetAtomContribs [as 别名]
 def _writeDetailFile(self, inF, outF):
   while 1:
     try:
       smi, refContribs = pickle.load(inF)
     except EOFError:
       break
     else:
       mol = Chem.MolFromSmiles(smi)
       if mol:
         mol = Chem.AddHs(mol, 1)
         smi2 = Chem.MolToSmiles(mol)
         contribs = Crippen._GetAtomContribs(mol)
         pickle.dump((smi, contribs), outF)
       else:
         print('Problems with SMILES:', smi)
开发者ID:rdkit,项目名称:rdkit,代码行数:17,代码来源:UnitTestCrippen.py

示例4: runIt

# 需要导入模块: from rdkit.Chem import Crippen [as 别名]
# 或者: from rdkit.Chem.Crippen import _GetAtomContribs [as 别名]
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()
开发者ID:abradle,项目名称:rdkit,代码行数:20,代码来源:BuildCrippenTestSet.py

示例5: _writeDetailFile

# 需要导入模块: from rdkit.Chem import Crippen [as 别名]
# 或者: from rdkit.Chem.Crippen import _GetAtomContribs [as 别名]
 def _writeDetailFile(self,inF,outF):
   while 1:
     try:
       smi,refContribs = cPickle.load(inF)
     except EOFError:
       break
     else:
       try:
         mol = Chem.MolFromSmiles(smi)
       except:
         import traceback
         traceback.print_exc()
         mol = None
       if mol:
         mol=Chem.AddHs(mol,1)
         smi2 = Chem.MolToSmiles(mol)
         contribs = Crippen._GetAtomContribs(mol)
         cPickle.dump((smi,contribs),outF)
       else:
         print 'Problems with SMILES:',smi
开发者ID:CKannas,项目名称:rdkit,代码行数:22,代码来源:UnitTestCrippen.py


注:本文中的rdkit.Chem.Crippen._GetAtomContribs方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。