#
#  Copyright (c) 2016, Novartis Institutes for BioMedical Research Inc.
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# Created by Nadine Schneider, July 2016


from rdkit import Chem
from rdkit.Chem import AllChem
from collections import defaultdict
import copy


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