rdkit.Chem.SaltRemover

Package rdkit :: Package Chem :: Module SaltRemover |
[hide private]
[frames] | no frames]

# Source Code for Module rdkit.Chem.SaltRemover

      1  # $Id$
      2  #
      3  #  Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
      4  #  All rights reserved.
      5  #
      6  # Redistribution and use in source and binary forms, with or without
      7  # modification, are permitted provided that the following conditions are
      8  # met:
      9  #
     10  #     * Redistributions of source code must retain the above copyright
     11  #       notice, this list of conditions and the following disclaimer.
     12  #     * Redistributions in binary form must reproduce the above
     13  #       copyright notice, this list of conditions and the following
     14  #       disclaimer in the documentation and/or other materials provided
     15  #       with the distribution.
     16  #     * Neither the name of Novartis Institutes for BioMedical Research Inc.
     17  #       nor the names of its contributors may be used to endorse or promote
     18  #       products derived from this software without specific prior written permission.
     19  #
     20  # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
     21  # "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
     22  # LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
     23  # A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
     24  # OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
     25  # SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
     26  # LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
     27  # DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
     28  # THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
     29  # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
     30  # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
     31  #
     32  # Created by Greg Landrum, Dec 2006
     33  #
     34
     35  from rdkit import Chem
     36  import os,re
     37
     38  from rdkit import RDConfig
     39
     40 -class SaltRemover(object):
     41    defnFilename=os.path.join(RDConfig.RDDataDir,'Salts.txt')
     42    defnData = None
     43    salts = None
     44 -  def __init__(self,defnFilename=None,defnData=None):
     45      if defnFilename:
     46        self.defnFilename = defnFilename
     47      self.defnData = defnData
     48      self._initPatterns()
     49
     50 -  def _initPatterns(self):
     51      """
     52
     53      >>> remover = SaltRemover()
     54      >>> len(remover.salts)>0
     55      True
     56
     57      >>> remover = SaltRemover(defnData="[Cl,Br]")
     58      >>> len(remover.salts)
     59      1
     60
     61      >>> remover = SaltRemover(defnData="[Cl,fail]")
     62      Traceback (most recent call last):
     63        ...
     64      ValueError: [Cl,fail]
     65
     66      """
     67      whitespace = re.compile(r'[\t ]+')
     68      if self.defnData:
     69        from rdkit.six.moves import cStringIO as StringIO
     70        inF = StringIO(self.defnData)
     71      else:
     72        inF = open(self.defnFilename,'r')
     73      self.salts = []
     74      for line in inF:
     75        line = line.strip().split('//')[0]
     76        if line:
     77          splitL = whitespace.split(line)
     78          salt = Chem.MolFromSmarts(splitL[0])
     79          if salt is None:
     80            raise ValueError(line)
     81          self.salts.append(salt)
     82
     83 -  def StripMol(self,mol,dontRemoveEverything=False):
     84      """
     85
     86      >>> remover = SaltRemover(defnData="[Cl,Br]")
     87      >>> len(remover.salts)
     88      1
     89
     90      >>> mol = Chem.MolFromSmiles('CN(C)C.Cl')
     91      >>> res = remover.StripMol(mol)
     92      >>> res is not None
     93      True
     94      >>> res.GetNumAtoms()
     95      4
     96
     97      Notice that all salts are removed:
     98      >>> mol = Chem.MolFromSmiles('CN(C)C.Cl.Cl.Br')
     99      >>> res = remover.StripMol(mol)
    100      >>> res.GetNumAtoms()
    101      4
    102
    103      Matching (e.g. "salt-like") atoms in the molecule are unchanged:
    104      >>> mol = Chem.MolFromSmiles('CN(Br)Cl')
    105      >>> res = remover.StripMol(mol)
    106      >>> res.GetNumAtoms()
    107      4
    108
    109      >>> mol = Chem.MolFromSmiles('CN(Br)Cl.Cl')
    110      >>> res = remover.StripMol(mol)
    111      >>> res.GetNumAtoms()
    112      4
    113
    114      Charged salts are handled reasonably:
    115      >>> mol = Chem.MolFromSmiles('C[NH+](C)(C).[Cl-]')
    116      >>> res = remover.StripMol(mol)
    117      >>> res.GetNumAtoms()
    118      4
    119
    120
    121      Watch out for this case (everything removed):
    122      >>> remover = SaltRemover()
    123      >>> len(remover.salts)>1
    124      True
    125      >>> mol = Chem.MolFromSmiles('CC(=O)O.[Na]')
    126      >>> res = remover.StripMol(mol)
    127      >>> res.GetNumAtoms()
    128      0
    129
    130      dontRemoveEverything helps with this by leaving the last salt:
    131      >>> res = remover.StripMol(mol,dontRemoveEverything=True)
    132      >>> res.GetNumAtoms()
    133      4
    134
    135      but in cases where the last salts are the same, it can't choose
    136      between them, so it returns all of them:
    137      >>> mol = Chem.MolFromSmiles('Cl.Cl')
    138      >>> res = remover.StripMol(mol,dontRemoveEverything=True)
    139      >>> res.GetNumAtoms()
    140      2
    141
    142      """
    143      def _applyPattern(m,salt,notEverything):
    144        nAts = m.GetNumAtoms()
    145        if not nAts:
    146          return m
    147        res = m
    148
    149        t = Chem.DeleteSubstructs(res,salt,True)
    150        if not t or (notEverything and t.GetNumAtoms()==0):
    151          return res;
    152        else:
    153          res = t
    154        while res.GetNumAtoms() and nAts>res.GetNumAtoms():
    155          nAts = res.GetNumAtoms()
    156          t = Chem.DeleteSubstructs(res,salt,True)
    157          if notEverything and t.GetNumAtoms()==0:
    158            break
    159          else:
    160            res = t
    161        return res
    162
    163      if dontRemoveEverything and len(Chem.GetMolFrags(mol))<=1:
    164        return mol
    165      modified=False
    166      for i,salt in enumerate(self.salts):
    167        tMol = _applyPattern(mol,salt,dontRemoveEverything)
    168        if tMol is not mol:
    169          mol = tMol
    170          modified=True
    171          if dontRemoveEverything and len(Chem.GetMolFrags(mol))<=1:
    172            break
    173      if modified and mol.GetNumAtoms()>0:
    174        Chem.SanitizeMol(mol)
    175      return mol
    176
    177 -  def __call__(self,mol,dontRemoveEverything=False):
    178      """
    179
    180      >>> remover = SaltRemover(defnData="[Cl,Br]")
    181      >>> len(remover.salts)
    182      1
    183
    184      >>> mol = Chem.MolFromSmiles('CN(C)C.Cl')
    185      >>> res = remover(mol)
    186      >>> res is not None
    187      True
    188      >>> res.GetNumAtoms()
    189      4
    190
    191      """
    192      return self.StripMol(mol,dontRemoveEverything=dontRemoveEverything)
    193
    194
    195  #------------------------------------
    196  #
    197  #  doctest boilerplate
    198  #
    199 -def _test():
    200    import doctest,sys
    201    return doctest.testmod(sys.modules["__main__"])
    202
    203
    204  if __name__ == '__main__':
    205    import sys
    206    failed,tried = _test()
    207    sys.exit(failed)
    208