#
#  Copyright (c) 2016, Novartis Institutes for BioMedical Research Inc.
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#       nor the names of its contributors may be used to endorse or promote
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# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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# Created by Nadine Schneider, July 2016

import copy
from collections import defaultdict

from rdkit import Chem
from rdkit.Chem import AllChem


def transferAgentsToReactants(rxn):
  for a in range(rxn.GetNumAgentTemplates()):
    agent = rxn.GetAgentTemplate(a)
    rxn.AddReactantTemplate(agent)


def removeAgentsAndTransferToReactants(rxn):
  tmp = []
  rxn.RemoveAgentTemplates(tmp)
  for a in tmp:
    rxn.AddReactantTemplate(a)


def getNumPositiveCounts(fp):
  count = 0
  for k, v in fp.GetNonzeroElements().items():
    if v > 0:
      count += v
  return count


def getNumNegativeCounts(fp):
  count = 0
  for k, v in fp.GetNonzeroElements().items():
    if v < 0:
      count += abs(v)
  return count


def getNumPositiveBitCountsOfRadius0(fp, bitinfo):
  count = 0
  bitsUnmappedAtoms = []
  for k in bitinfo:
    if bitinfo[k][0][1] == 0:
      v = fp[k]
      if v > 0:
        count += 1
        bitsUnmappedAtoms.append((k, v))
  return count, bitsUnmappedAtoms


def getSumFps(fps):
  summedFP = copy.deepcopy(fps[0])
  for fp in fps[1:]:
    summedFP += fp
  return summedFP


def uniqueMolecules(mols):
  smiles = [Chem.MolToSmiles(mol) for mol in mols]
  uniqueMolecules = defaultdict(int)
  for n, smi in enumerate(smiles):
    uniqueMolecules[n] = smiles.index(smi)
  return uniqueMolecules, smiles