# $Id$
#
#  Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
#  All rights reserved.
# 
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met: 
#
#     * Redistributions of source code must retain the above copyright 
#       notice, this list of conditions and the following disclaimer.
#     * Redistributions in binary form must reproduce the above
#       copyright notice, this list of conditions and the following 
#       disclaimer in the documentation and/or other materials provided 
#       with the distribution.
#     * Neither the name of Novartis Institutes for BioMedical Research Inc. 
#       nor the names of its contributors may be used to endorse or promote 
#       products derived from this software without specific prior written permission.
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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# Created by Greg Landrum, Dec 2006
#

from rdkit import Chem
import os,re

from rdkit import RDConfig

class SaltRemover(object):
  defnFilename=os.path.join(RDConfig.RDDataDir,'Salts.txt')
  defnData = None
  salts = None
  def __init__(self,defnFilename=None,defnData=None):
    if defnFilename:
      self.defnFilename = defnFilename
    self.defnData = defnData
    self._initPatterns()

  def _initPatterns(self):
    """

    >>> remover = SaltRemover()
    >>> len(remover.salts)>0
    True

    >>> remover = SaltRemover(defnData="[Cl,Br]")
    >>> len(remover.salts)
    1
    
    """
    whitespace = re.compile(r'[\t ]+')
    if self.defnData:
      from rdkit.six.moves import cStringIO as StringIO
      inF = StringIO(self.defnData)
    else:
      inF = open(self.defnFilename,'r')
    self.salts = []
    for line in inF:
      line = line.strip().split('//')[0]
      if line:
        splitL = whitespace.split(line)
        try:
          salt = Chem.MolFromSmarts(splitL[0])
        except:
          import traceback
          traceback.print_exc()
          raise ValueError(line)
        self.salts.append(salt)

  def StripMol(self,mol,dontRemoveEverything=False):
    """

    >>> remover = SaltRemover(defnData="[Cl,Br]")
    >>> len(remover.salts)
    1

    >>> mol = Chem.MolFromSmiles('CN(C)C.Cl')
    >>> res = remover.StripMol(mol)
    >>> res is not None
    True
    >>> res.GetNumAtoms()
    4

    Notice that all salts are removed:
    >>> mol = Chem.MolFromSmiles('CN(C)C.Cl.Cl.Br')
    >>> res = remover.StripMol(mol)
    >>> res.GetNumAtoms()
    4

    Matching (e.g. "salt-like") atoms in the molecule are unchanged:
    >>> mol = Chem.MolFromSmiles('CN(Br)Cl')
    >>> res = remover.StripMol(mol)
    >>> res.GetNumAtoms()
    4

    >>> mol = Chem.MolFromSmiles('CN(Br)Cl.Cl')
    >>> res = remover.StripMol(mol)
    >>> res.GetNumAtoms()
    4

    Charged salts are handled reasonably:
    >>> mol = Chem.MolFromSmiles('C[NH+](C)(C).[Cl-]')
    >>> res = remover.StripMol(mol)
    >>> res.GetNumAtoms()
    4


    Watch out for this case (everything removed):
    >>> remover = SaltRemover()
    >>> len(remover.salts)>1
    True
    >>> mol = Chem.MolFromSmiles('CC(=O)O.[Na]')
    >>> res = remover.StripMol(mol)
    >>> res.GetNumAtoms()
    0

    dontRemoveEverything helps with this by leaving the last salt:
    >>> res = remover.StripMol(mol,dontRemoveEverything=True)
    >>> res.GetNumAtoms()
    4

    but in cases where the last salts are the same, it can't choose
    between them, so it returns all of them:
    >>> mol = Chem.MolFromSmiles('Cl.Cl')
    >>> res = remover.StripMol(mol,dontRemoveEverything=True)
    >>> res.GetNumAtoms()
    2

    """
    def _applyPattern(m,salt,notEverything):
      nAts = m.GetNumAtoms()
      if not nAts:
        return m
      res = m

      t = Chem.DeleteSubstructs(res,salt,True)
      if not t or (notEverything and t.GetNumAtoms()==0):
        return res;
      else:
        res = t
      while res.GetNumAtoms() and nAts>res.GetNumAtoms():
        nAts = res.GetNumAtoms()
        t = Chem.DeleteSubstructs(res,salt,True)
        if notEverything and t.GetNumAtoms()==0:
          break
        else:
          res = t
      return res

    if dontRemoveEverything and len(Chem.GetMolFrags(mol))<=1:
      return mol
    modified=False
    for i,salt in enumerate(self.salts):
      tMol = _applyPattern(mol,salt,dontRemoveEverything)
      if tMol is not mol:
        mol = tMol
        modified=True
        if dontRemoveEverything and len(Chem.GetMolFrags(mol))<=1:
          break
    if modified and mol.GetNumAtoms()>0:
      Chem.SanitizeMol(mol)
    return mol

  def __call__(self,mol,dontRemoveEverything=False):
    """

    >>> remover = SaltRemover(defnData="[Cl,Br]")
    >>> len(remover.salts)
    1

    >>> mol = Chem.MolFromSmiles('CN(C)C.Cl')
    >>> res = remover(mol)
    >>> res is not None
    True
    >>> res.GetNumAtoms()
    4

    """
    return self.StripMol(mol,dontRemoveEverything=dontRemoveEverything)

  
#------------------------------------
#
#  doctest boilerplate
#
def _test():
  import doctest,sys
  return doctest.testmod(sys.modules["__main__"])


if __name__ == '__main__':
  import sys
  failed,tried = _test()
  sys.exit(failed)
