## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c

# $Id$
#
#  Copyright (C) 2000-2008  greg Landrum and Rational Discovery LLC
#
#   @@ All Rights Reserved @@
#  This file is part of the RDKit.
#  The contents are covered by the terms of the BSD license
#  which is included in the file license.txt, found at the root
#  of the RDKit source tree.
#
""" A module for molecules and stuff

 see Chem/index.html in the doc tree for documentation
 
"""
from rdkit import rdBase
from rdkit import RDConfig

from rdkit import DataStructs
from rdkit.Geometry import rdGeometry
import PeriodicTable as pyPeriodicTable
import rdchem
_HasSubstructMatchStr=rdchem._HasSubstructMatchStr
from rdchem import *
from rdmolfiles import *
from rdmolops import *
from inchi import *

def QuickSmartsMatch(smi,sma,unique=True,display=False):
  m = MolFromSmiles(smi)
  p = MolFromSmarts(sma)
  res = m.GetSubstructMatches(p,unique)
  if display:
    pass
  return res  

def CanonSmiles(smi,useChiral=1):
  m = MolFromSmiles(smi)
  return MolToSmiles(m,useChiral)

def SupplierFromFilename(fileN,delim='',**kwargs):
  ext = fileN.split('.')[-1].lower()
  if ext=='sdf':
    suppl = SDMolSupplier(fileN,**kwargs)
  elif ext=='csv':
    if not delim:
      delim = ','
    suppl = SmilesMolSupplier(fileN,delimiter=delim,**kwargs)
  elif ext=='txt':
    if not delim:
      delim='\t'
    suppl = SmilesMolSupplier(fileN,delimiter=delim,**kwargs)
  elif ext=='tdt':
    suppl = TDTMolSupplier(fileN,delimiter=delim,**kwargs)
  else:
    raise ValueError,"unrecognized extension: %s"%ext
    
  return suppl

def FindMolChiralCenters(mol,force=True,includeUnassigned=False):
  """
    >>> from rdkit import Chem
    >>> mol = Chem.MolFromSmiles('[C@H](Cl)(F)Br')
    >>> FindMolChiralCenters(mol)
    [(0, 'R')]
    >>> mol = Chem.MolFromSmiles('[C@@H](Cl)(F)Br')
    >>> FindMolChiralCenters(mol)
    [(0, 'S')]
  
    >>> FindMolChiralCenters(Chem.MolFromSmiles('CCC'))
    []

    By default unassigned stereo centers are not reported:
    >>> mol = Chem.MolFromSmiles('C[C@H](F)C(F)(Cl)Br')
    >>> FindMolChiralCenters(mol,force=True)
    [(1, 'S')]

    but this can be changed:
    >>> FindMolChiralCenters(mol,force=True,includeUnassigned=True)
    [(1, 'S'), (3, '?')]

    The handling of unassigned stereocenters for dependent stereochemistry is not correct:
    >>> Chem.FindMolChiralCenters(Chem.MolFromSmiles('C1CC(C)C(C)C(C)C1'),includeUnassigned=True)
    [(2, '?'), (6, '?')]
    >>> Chem.FindMolChiralCenters(Chem.MolFromSmiles('C1C[C@H](C)C(C)[C@H](C)C1'),includeUnassigned=True)
    [(2, 'S'), (4, '?'), (6, 'R')]
    
  """
  AssignStereochemistry(mol,force=force, flagPossibleStereoCenters=includeUnassigned)
  centers = []
  for atom in mol.GetAtoms():
    if atom.HasProp('_CIPCode'):
      centers.append((atom.GetIdx(),atom.GetProp('_CIPCode')))
    elif includeUnassigned and atom.HasProp('_ChiralityPossible'):
      centers.append((atom.GetIdx(),'?'))
  return centers

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


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