#!/usr/bin/python
# Just replaces the marker atoms (one at a time, otherwise conformation gets screwed)
# for non-thio - phosphateesters
from openeye.oechem import *
import os, string, sys

try:
    ifs = oemolistream()
    ifs.open('b7.3'+sys.argv[1]+'_ln.sdf')

    ofs_1 = oemolostream()
    ofs_1.open('b7.4'+sys.argv[1]+'_ln_nocorina.sdf')
    #ofs_2 = oemolostream()
    #ofs_2.open('b8.4_parts_connect_2_lp.sdf')
except IndexError:
    print '\nUsage: b7.4_parts_connect_2.py file-identifier(e.g. _mol_32007)\n'
    raise SystemExit()


#leaving group
rxn_Mg = OEUniMolecularRxn("[*:41][Mg:1][P:2]([OH1:3])([Li:4])([Zn:5])[O-:6]>>[*:41][P:2]([OH1:3])([Li:4])([Zn:5])[O-:6]")
#non hydrolysed rest 1 (negatively charged)
rxn_Li_1 = OEUniMolecularRxn("[P:2]([OH1:3])([Li:4][O-,N-,S-:42])([Zn:5])[O-:6]>>[P:2]([OH1:3])([*-:42])([Zn:5])[O-:6]")
#non hydrolysed rest 1 (neutral)
rxn_Li_2 = OEUniMolecularRxn("[P:2]([OH1:3])([Li:4][Ov2,Nv3,Sv2,Cv4,F:42])([Zn:5])[O-:6]>>[P:2]([OH1:3])([*:42])([Zn:5])[O-:6]")
#non hydrolysed rest 2 (negatively charged)
rxn_Zn_1 = OEUniMolecularRxn("[P:2]([OH1:3])([Zn:5][O-,N-,S-:43])[O-:6]>>[P:2]([OH1:3])([*-:43])[O-:6]")
#non hydrolysed rest 2 (neutral)
rxn_Zn_2 = OEUniMolecularRxn("[P:2]([OH1:3])([Zn:5][Ov2,Nv3,Sv2,Cv4,F:43])[O-:6]>>[P:2]([OH1:3])([*:43])[O-:6]")


li_minus = OESubSearch()
li_minus.Init('[P][Li:4][N-,S-,O-]')
zn_minus = OESubSearch()
zn_minus.Init('[P][Zn:4][N-,S-,O-]')

for mol in ifs.GetOEMols():
    rxn_Mg(mol)
    if li_minus.SingleMatch(mol) == 1:
        rxn_Li_1(mol)
    else:
        rxn_Li_2(mol)
    if zn_minus.SingleMatch(mol) == 1:
       rxn_Zn_1(mol) 
    else: 
       rxn_Zn_2(mol) 
    OEWriteMolecule(ofs_1, mol)
ofs_1.close()
ifs.close()

#ifs.open('b8.3_parts_connect_1_lp_corina.sdf')
#for mol in ifs.GetOEMols():
#    rxn_Mg(mol)
#    if li_minus.SingleMatch(mol) == 1:
#        rxn_Li_1(mol)
#    else:
#        rxn_Li_2(mol)
#    if zn_minus.SingleMatch(mol) == 1:
#       rxn_Zn_1(mol)
#    else:
#       rxn_Zn_2(mol)
#    OEWriteMolecule(ofs_2, mol)
#ofs_2.close()
#ifs.close()

# corina for database (incl. ringconf + stereo)
os.system('corina -d errorfile=b7.4'+sys.argv[1]+'_ln_err.sdf,r2d,wh,stergen,msc=5,msi=13,names,preserve,rc,flapn,mc=10,sc -t tracefile=b7.4'+sys.argv[1]+'_ln_corina_trace.trc -i t=sdf -o t=sdf b7.4'+sys.argv[1]+'_ln_nocorina.sdf b7.4'+sys.argv[1]+'_ln_out.sdf')

print '\nNow run(on bjork)\nb7.5_ionizer.py '+sys.argv[1]+'\n'