#!/usr/local2/bin/python2.3
# Creates artificial first thiophosphate, 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, sys

try:
    ifs = oemolistream()
    ifs.open('b_template_phosphate.sdf')
    phos = OEGraphMol()
    OEReadMolecule(ifs, phos)
    date = sys.argv[1]    
    dictsf1 = open('b7.2'+date+'_dicts1.txt', 'r')
    dictsf2 = open('b7.2'+date+'_dicts2.txt', 'r')
except IndexError:
    '\nUsage: b7.3_parts_connect_1.py _mol_32007(db+date)\n'
    raise SystemExit()

ofs_1 = oemolostream()
ofs_1.open('b7.3'+date+'_ln_nocorina.sdf')
     
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 = []
for title_file in os.listdir('.'):
    if title_file[-11:] == '_titles.txt':
        print 'Open & read '+title_file
        titlef = open(title_file, 'r')
        for line in titlef.readlines():
            title_list.append(line[:-1])
        titlef.close()

title_f = open('b7_titles.txt', 'w')

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
            prot = 0
            label = title[:string.find(title, '_')]+'_'+str(num)+'p'+str(prot)
            while label in title_list:
                num+=1
                label = title[:string.find(title, '_')]+'_'+str(num)+'p'+str(prot)
            title_list.append(label)
            products.SetTitle(label)
            OEWriteMolecule(ofs_1, products) 
            title_f.write(title+'\n')

# NO Protonation of Leaving Group ! (naming procedure wrong also)
#        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
                prot = 0
                label = title[:string.find(title, '_')]+'_'+str(num)+'p'+str(prot)
                while label in title_list:
                    num+=1
                    label = title[:string.find(title, '_')]+'_'+str(num)+'p'+str(prot)
                title_list.append(label)
                products.SetTitle(label)
                OEWriteMolecule(ofs_1, products) 
                title_f.write(title+'\n')
             
#            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 -d errorfile=b7.3'+date+'_ln_err.sdf,r2d,wh -t tracefile=b7.3'+date+'_ln_corina_trace.trc -i t=sdf -o t=sdf b7.3'+date+'_ln_nocorina.sdf b7.3'+date+'_ln.sdf')
#os.system('corina -d errorfile='+sys.argv[2]+'_parts_connect_1_ln_err.sdf,r2d,wh -t tracefile='+sys.argv[2]+'_parts_connect_1_ln_corina_trace.trc -i t=sdf -o t=sdf '+sys.argv[2]+'_parts_connect_1_lp.sdf '+sys.argv[2]+'_parts_connect_1_lp_corina.sdf')
os.system('b7.4_parts_connect_2.py '+date)