#!/usr/bin/python
# for THIOphosphate-esters
# 1) Create dictionaries; per possible leaving group with its ligands
# {title_1:{leaving_group1: [ligands in triangular plane...], leaving_group2 (if existent): [ligands in triangular plane...]...}
# 2) Dicitonary for chirality of the three ligands in plane (per leaving group) => are at least two of them identical => no chirality
from openeye.oechem import *
import os, string, sys

try:
    date = sys.argv[1]
    ifs = oemolistream()
    ifs.open('b8.1'+date+'_ln.ism')
    outf1 = open('b8.2'+date+'_dicts1_temp.txt', 'w')
    outf2 = open('b8.2'+date+'_dicts2.txt', 'w')
except IndexError:
    print '\nUsage: b8.2_parts_split_2.py file-identifier(e.g. mol_32007)\n'    
    raise SystemExit()

leaving_group = OESubSearch()
leaving_group.Init('[Cu][O&X2&!H1&!-,N&X3&!-,S&X2&!H1&!-,F,C&X2]')

phos_pat = OESubSearch()
phos_pat.Init('[PX1]=[S]')

leavings = {}
for mol in ifs.GetOEMols():
    title = mol.GetTitle()
    leavings[title] = {}
    count,parts = OEDetermineComponents(mol)
    pred = OEPartPred(parts)

    for i in xrange(1,count+1):
        pred.SelectPart(i)
        newlig = OEGraphMol()
        OESubsetMol(newlig, mol, pred)
        smiles = OECreateIsoSmiString(newlig)
        if phos_pat.SingleMatch(newlig) != 1 and leaving_group.SingleMatch(newlig) == 1:
            if smiles not in leavings[title].values():
                leavings[title][smiles] = []
                for j in xrange(i+1, count+1):
                    pred.SelectPart(j)
                    potlig = OEGraphMol()
                    OESubsetMol(potlig, mol, pred)
                    smiles2 = OECreateIsoSmiString(potlig)
                    if phos_pat.SingleMatch(potlig) != 1:
                        leavings[title][smiles].append(smiles2)
                for j in xrange(1, i):
                    pred.SelectPart(j)
                    potlig = OEGraphMol()
                    OESubsetMol(potlig, mol, pred)
                    smiles2 = OECreateIsoSmiString(potlig)
                    if phos_pat.SingleMatch(newlig) != 1:
                        leavings[title][smiles].append(smiles2)
ifs.close()

#print leavings

ox_cop = OESubSearch()
ox_cop.Init('[O-X1][Cu]') # refers to the attacking OH!

# have to write files for dicts, since command OEPartPred needs different OEchem-version than the rxn-commands (might be fixed in v1.3.3)
title_list = []
for title in leavings.keys():
    for key in leavings[title].keys():
        num = 1 
        newtitle = title+'_1'
        while newtitle in title_list:
            num+=1
            newtitle = title+'_'+str(num)
        title_list.append(newtitle)
        outf1.write(newtitle+' '+key+' '+leavings[title][key][0]+' '+leavings[title][key][1]+'\n')

        old_chiral = 0
        for lig in leavings[title][key]:
            chiral = 0
            for lig2 in leavings[title][key]:
                lig2_smi = OEGraphMol()
                OEParseSmiles(lig2_smi, lig2) 
#                if ox_cop.SingleMatch(lig2_smi) == 1:
#                    print OECreateIsoSmiString(lig2_smi)
                if lig2 == lig or ox_cop.SingleMatch(lig2_smi) == 1:
                    chiral+=1
#                print chiral, old_chiral
                if chiral > old_chiral:
                    old_chiral = chiral
        outf2.write(newtitle+' '+key+' '+str(old_chiral)+'\n')

outf1.close()
outf2.close()

os.system('mv b8.2'+date+'_dicts1_temp.txt b8.2'+date+'_dicts1.txt')
print '\nNOW:\nsource ~/login_OE_RXN_CHP\nthen invoke\nb8.3_thio_parts_connect_1.py '+date+'\n'
raise SystemExit()

# Ensure correct protonation
inf1 = open('b8.2'+date+'_dicts1_temp.txt', 'r')
outf1 = open('b8.2'+date+'_dicts1.txt', 'w')

for line in inf1.readlines():
    newline1 = string.replace(line, ' O[Cu] ','  [O-][Cu] ')
    newline2 = string.replace(newline1, ' O[Cu]\n','  [O-][Cu]\n')
    outf1.write(newline2)

outf1.close()
inf1.close()
os.system('rm -f b8.2'+date+'_dicts1_temp.txt')
print '\nNOW:\nsource ~/login_OE_RXN_CHP\nthen invoke\nb8.3_thio_parts_connect_1.py '+date+'\n'