#!/usr/local2/bin/python2.3
# Creates artificial first phosphate, where every substituent is marked by a unique metal (Mg is leaving group and is axial to the
# O--group = former ihydroxide nucelophile)
from openeye.oechem import *
import os, string

rxn = 11

ifs = oemolistream()
ifs.open('b_react_ti_10_template_phosphate.sdf')
phos = OEGraphMol()
OEReadMolecule(ifs, phos)

ofs_1 = oemolostream()
ofs_1.open('b_react_ti_11_parts_connect_1_ln.sdf')
ofs_2 = oemolostream()
ofs_2.open('b_react_ti_11_parts_connect_1_lp.sdf')

dictsf1 = open('b_react_ti_11_parts_split_2_dicts1.txt', 'r')
dictsf2 = open('b_react_ti_11_parts_split_2_dicts2.txt', 'r')
leavings = {}
chiral_dict = {}

for line in dictsf1.readlines():
    leavings[string.split(line)[0]] = {}
    leavings[string.split(line)[0]][string.split(line)[1]] = [string.split(line)[2], string.split(line)[3]]
for line in dictsf2.readlines():
    chiral_dict[string.split(line)[0]] = {}
    chiral_dict[string.split(line)[0]][string.split(line)[1]] = int(string.split(line)[2])

libgen1 = OELibraryGen("[Mg:1][P:2]([OH1:3])([Li:4])([Zn:5])[O-:6].[Cu:11][*:12].[Cu:21][*:22].[Cu:31][*:32]>>[*:12][Mg:1][P:2]([OH1:3])([Li:4][*:22])([Zn:5][*:32])[O-:6]")
libgen2 = OELibraryGen("[Mg:1][P:2]([OH1:3])([Li:4])([Zn:5])[O-:6].[Cu:11][*:12].[Cu:21][*:22].[Cu:31][*:32].[H:100]>>[H:100][*+:12][Mg:1][P:2]([OH1:3])([Li:4][*:22])([Zn:5][*:32])[O-:6]")

lgs = OEGraphMol()
lig1 = OEGraphMol()
lig2 = OEGraphMol()
hyd = OEGraphMol()

title_list = []
rxn_n = 1
while rxn_n < rxn:
  try:
    old_title_file = open('b_react_ti_'+str(rxn_n)+'_ln.ism','r')
    for title in old_title_file.readlines():
        title_list.append(string.split(title)[1])
    old_title_file.close()
  except IOError:
    pass
  try:
    old_title_file = open('b_react_ti_'+str(rxn_n)+'_lp.ism','r')
    for title in old_title_file.readlines():
        title_list.append(string.split(title)[1])
    old_title_file.close()
  except IOError:
    pass
  rxn_n+=1

ti_count = 0
for title in leavings.keys():
    for lg in leavings[title].keys():
        OEParseSmiles(lgs, lg) 
        OEParseSmiles(lig1, leavings[title][lg][0])
        OEParseSmiles(lig2, leavings[title][lg][1])
        libgen1.SetStartingMaterial(phos, 0)
        libgen1.SetStartingMaterial(lgs, 1)
        libgen1.SetStartingMaterial(lig1, 2)
        libgen1.SetStartingMaterial(lig2, 3)
        OEParseSmiles(hyd, '[H]')
        libgen2.SetStartingMaterial(phos, 0)
        libgen2.SetStartingMaterial(lgs, 1)
        libgen2.SetStartingMaterial(lig1, 2)
        libgen2.SetStartingMaterial(lig2, 3)
        libgen2.SetStartingMaterial(hyd, 4)
        lgs.Clear()
        lig1.Clear()
        lig2.Clear()
        hyd.Clear()

        for products in libgen1.GetProducts():
            num = 1
            label = title[:string.find(title, '_')]+'_'+str(num)
            while label in title_list:
                num+=1
                label = title[:string.find(title, '_')]+'_'+str(num)
            title_list.append(label)
            products.SetTitle(label)
            OEWriteMolecule(ofs_1, products) 
        for products in libgen2.GetProducts():
            num = 1
            label = title[:string.find(title, '_')]+'_'+str(num)
            while label in title_list:
                num+=1
                label = title[:string.find(title, '_')]+'_'+str(num)
            title_list.append(label)
            products.SetTitle(label)
            OEWriteMolecule(ofs_2, products) 
 
    # if P is chiral => create the enantiomer too
    for lg in leavings[title].keys():
        if chiral_dict[title][lg] == 1:
            OEParseSmiles(lgs, lg)
            OEParseSmiles(lig1, leavings[title][lg][0])
            OEParseSmiles(lig2, leavings[title][lg][1])
            libgen1.SetStartingMaterial(phos, 0)
            libgen1.SetStartingMaterial(lgs, 1)
            libgen1.SetStartingMaterial(lig2, 2)
            libgen1.SetStartingMaterial(lig1, 3)
            OEParseSmiles(hyd, '[H]')
            libgen2.SetStartingMaterial(phos, 0)
            libgen2.SetStartingMaterial(lgs, 1)
            libgen2.SetStartingMaterial(lig1, 2)
            libgen2.SetStartingMaterial(lig2, 3)
            libgen2.SetStartingMaterial(hyd, 4)
            lgs.Clear()
            lig1.Clear()
            lig2.Clear()
            hyd.Clear()

            for products in libgen1.GetProducts():
                num = 1
                label = title[:string.find(title, '_')]+'_'+str(num)
                while label in title_list:
                    num+=1
                    label = title[:string.find(title, '_')]+'_'+str(num)
                title_list.append(label)
                products.SetTitle(label)
                OEWriteMolecule(ofs_1, products) 
            for products in libgen2.GetProducts():
                num = 1
                label = title[:string.find(title, '_')]+'_'+str(num)
                while label in title_list:
                    num+=1
                    label = title[:string.find(title, '_')]+'_'+str(num)
                title_list.append(label)
                products.SetTitle(label)
                OEWriteMolecule(ofs_2, products) 

ofs_1.close()
ofs_2.close()
os.system('corina.nirvana -d errorfile=b_react_ti_11_parts_connect_1_ln_err.sdf,r2d,wh -t tracefile=b_react_ti_11_parts_connect_1_ln_corina_trace.trc -i t=sdf -o t=sdf b_react_ti_11_parts_connect_1_ln.sdf b_react_ti_11_parts_connect_1_ln_corina.sdf')
os.system('corina.nirvana -d errorfile=b_react_ti_11_parts_connect_1_ln_err.sdf,r2d,wh -t tracefile=b_react_ti_11_parts_connect_1_ln_corina_trace.trc -i t=sdf -o t=sdf b_react_ti_11_parts_connect_1_lp.sdf b_react_ti_11_parts_connect_1_lp_corina.sdf')
print '************** DONE WITH b_react_ti_11_parts_connect_1.py invoking invoking b_react_ti_11_parts_connect_2.py *******************'

#os.system('b_react_ti_11_parts_connect_2.py')