#! /usr/bin/env jython

# Copyright (c) 2013, GlaxoSmithKline Research & Development Ltd.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
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#     * 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
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#       with the distribution.
#     * Neither the name of GlaxoSmithKline Research & Development Ltd.
#       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
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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# Created by Jameed Hussain, July 2013
from __future__ import print_function

import sys
import re
import array

from chemaxon.util import MolHandler
from chemaxon.struc import Molecule
from chemaxon.descriptors import ChemicalFingerprint
from chemaxon.descriptors import CFParameters
from chemaxon.descriptors import SimilarityCalculatorFactory

def desalt(mol):
  parmol=mol
  smi=mol.toFormat("smiles")
  parcount=0;
  msmi=smi.split('.')
  for smi in msmi:
      mol=MolHandler(smi).getMolecule()
      count=mol.getAtomCount()
      if count > parcount:
         parcount =count
         parmol = mol
  return parmol


cfp = CFParameters("<?xml version=\"1.0\" encoding=\"UTF-8\"?><ChemicalFingerprintConfiguration Version =\"0.3\" schemaLocation=\"cfp.xsd\">    <Parameters Length=\"1024\" BondCount=\"7\" BitCount=\"4\"/>    <StandardizerConfiguration Version =\"0.1\"><Actions><Action ID=\"aromatize\" Act=\"aromatize\"/> </Actions> </StandardizerConfiguration><ScreeningConfiguration><ParametrizedMetrics><ParametrizedMetric Name=\"Tversky\" ActiveFamily=\"Generic\" Metric=\"Tversky\" Threshold=\"0.5\" TverskyAlpha=\"0.1\" TverskyBeta=\"0.9\"/></ParametrizedMetrics></ScreeningConfiguration></ChemicalFingerprintConfiguration>")
cfp.setLength(1024)
cfp.setBondCount(7)
cfp.setBitCount(4)

#output needs to look like this:
#qSubs,qSmi,qID,inSmi,id,tversky

#first read in queries
q_split_input=open("frag_q_split_out", 'r')

queries=[]
for line in q_split_input:
    info = line.rstrip().split(",")
    #print info

    #generate fp for query
    #print info[2]
    mol = MolHandler(info[2]).getMolecule()
    mol.aromatize(Molecule.AROM_GENERAL)

    qfp = ChemicalFingerprint(cfp)
    qfp.generate(mol)
    qintfp = array.array('i',list(map(int,qfp.toFloatArray())))

    queries.append( (qintfp,info[0],info[1],info[2]) )

#print queries

for line in sys.stdin:
	
    line_fields = re.split('\s|,',line)
    dbsmi = line_fields[0]
    dbid = line_fields[1]

    mol = MolHandler(dbsmi).getMolecule()
    mol_desalted = desalt(mol)
    mol_desalted.aromatize(Molecule.AROM_GENERAL)
    #print mol_desalted.toFormat("smiles")

    fp = ChemicalFingerprint(cfp)
    fp.generate(mol)
    intfp = array.array('i',list(map(int,fp.toFloatArray())))

    for q in queries:
        qsmi = q[1]
        qid = q[2]
        qsub = q[3]

        sc = SimilarityCalculatorFactory.create("Tversky;0.95;0.05")
        sc.setQueryFingerprint(q[0])

        tversky = sc.getSimilarity(intfp)

        if(tversky >= 0.9):
            print("%s,%s,%s,%s,%s,%s" % (qsub,qsmi,qid,dbsmi,dbid,tversky))


