# $Id$
#
#  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.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Created by Greg Landrum, October 2006
#
import os,weakref,re
from rdkit.six.moves import cStringIO as StringIO
from rdkit import RDConfig

class FGHierarchyNode(object):
  children=None
  name=""
  label=""
  pattern=None
  smarts=""
  rxnSmarts=""
  parent=None
  removalReaction=None
  def __init__(self,name,patt,smarts="",label="",rxnSmarts="",parent=None):
    self.name=name
    self.pattern=patt
    if parent:
      self.parent=weakref.ref(parent)
    self.label=label
    self.smarts=smarts
    self.children = []
    self.rxnSmarts=rxnSmarts

  def __len__(self):
    res = 1
    for child in self.children:
      res += len(child)
    return res

class FuncGroupFileParseError(ValueError):
  pass

groupDefns = {}
hierarchy=None
lastData=None
lastFilename=None
def BuildFuncGroupHierarchy(fileNm=None,data=None,force=False):
  global groupDefns,hierarchy,lastData,lastFilename
  if not force and hierarchy and (not data or data==lastData) and \
        (not fileNm or fileNm==lastFilename): 
    return hierarchy[:]
  lastData=data
  splitter = re.compile('\t+')
  from rdkit import Chem

  if not fileNm and not data:
    fileNm = os.path.join(RDConfig.RDDataDir,'Functional_Group_Hierarchy.txt')

  if fileNm:
    inF = open(fileNm,'r')
    lastFilename = fileNm
  elif data:
    inF = StringIO(data)
  else:
    raise ValueError("need data or filename")

  groupDefns={}
  res = []
  lineNo=0
  for line in inF.readlines():
    lineNo+=1
    line=line.strip()
    line = line.split('//')[0]
    if not line:
      continue
    splitL = splitter.split(line)
    if len(splitL)<3:
      raise FuncGroupFileParseError("Input line %d (%s) is not long enough."%(lineNo,repr(line)))
    label = splitL[0].strip()
    if label in groupDefns:
      raise FuncGroupFileParseError("Duplicate label on line %d."%lineNo)
    labelHierarchy = label.split('.')
    if len(labelHierarchy)>1:
      for i in range(len(labelHierarchy)-1):
        tmp = '.'.join(labelHierarchy[:i+1])
        if not tmp in groupDefns:
          raise FuncGroupFileParseError("Hierarchy member %s (line %d) not found."%(tmp,lineNo))
      parent = groupDefns['.'.join(labelHierarchy[:-1])]
    else:
      parent = None
    smarts = splitL[1]
    patt = Chem.MolFromSmarts(smarts)
    if not patt:
      raise FuncGroupFileParseError('Smarts "%s" (line %d) could not be parsed.'%(smarts,lineNo))
      
    name = splitL[2].strip()
    
    rxnSmarts=''
    if len(splitL)>3:
      rxnSmarts=splitL[3]

    node = FGHierarchyNode(name,patt,smarts=smarts,label=label,parent=parent,rxnSmarts=rxnSmarts)
    if parent:
      parent.children.append(node)
    else:
      res.append(node)
    groupDefns[label] = node
  hierarchy=res[:]
  return res

def _SetNodeBits(mol,node,res,idx):
  ms = mol.GetSubstructMatches(node.pattern)
  count = 0
  seen = {}
  for m in ms:
    if m[0] not in seen:
      count+=1
      seen[m[0]] = 1
  if count:
    res[idx] = count
    idx += 1
    for child in node.children:
      idx=_SetNodeBits(mol,child,res,idx)
  else:
    idx += len(node)
  return idx

def CreateMolFingerprint(mol,hierarchy):
  totL = 0
  for entry in hierarchy:
    totL += len(entry)
  res = [0]*totL
  idx = 0
  for entry in hierarchy:
    idx = _SetNodeBits(mol,entry,res,idx)
  return res

