#! /usr/bin/env jython

# Copyright (c) 2013, GlaxoSmithKline Research & Development Ltd.
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#       copyright notice, this list of conditions and the following
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#       nor the names of its contributors may be used to endorse or promote
#       products derived from this software without specific prior written
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# Created by Jameed Hussain, July 2013


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))
