#!/usr/local2/bin/python2.3
# Just replaces the marker atoms (one at a time, otherwise conformation will be screwed up
from openeye.oechem import *
import os, string, sys

ifs = oemolistream()

ofs_1 = oemolostream()
ofs_1.open(sys.argv[1]+'_ln.sdf')
ofs_2 = oemolostream()
ofs_2.open(sys.argv[1]+'_lp.sdf')

rxn_Mg = OEUniMolecularRxn("[*:41][Mg:1][P:2]([SH1:3])([Li:4])([Zn:5])[O-:6]>>[*:41][P:2]([SH1:3])([Li:4])([Zn:5])[O-:6]")
rxn_Li_1 = OEUniMolecularRxn("[P:2]([SH1:3])([Li:4][O-,N-,S-:42])([Zn:5])[O-:6]>>[P:2]([SH1:3])([*-:42])([Zn:5])[O-:6]")
rxn_Li_2 = OEUniMolecularRxn("[P:2]([SH1:3])([Li:4][Ov2,Nv3,Sv2,Cv4:42])([Zn:5])[O-:6]>>[P:2]([SH1:3])([*:42])([Zn:5])[O-:6]")
rxn_Zn_1 = OEUniMolecularRxn("[P:2]([SH1:3])([Zn:5][O-,N-,S-:43])[O-:6]>>[P:2]([SH1:3])([*-:43])[O-:6]")
rxn_Zn_2 = OEUniMolecularRxn("[P:2]([SH1:3])([Zn:5][Ov2,Nv3,Sv2,Cv4:43])[O-:6]>>[P:2]([SH1:3])([*: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-]')

ifs.open(sys.argv[1]+'_parts_connect_1_ln_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_1, mol)
ofs_1.close()
ifs.close()

ifs.open(sys.argv[1]+'_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()

# Test - corina (quick)
#os.system('corina.nirvana -d errorfile='sys.argv[1]+'_parts_connect_2_err.sdf,r2d,wh -t tracefile='sys.argv[1]+'_parts_connect_2_corina_trace.trc -i t=sdf -o t=sdf 'sys.argv[1]+'_parts_connect_2.sdf 'sys.argv[1]+'_parts_connect_2_corina.sdf')

# corina for database (incl. ringconf + stereo)
#os.system('corina.nirvana -d errorfile='sys.argv[1]+'_parts_connect_2_err.sdf,r2d,wh,stergen,msc=5,msi=13,names,preserve,rc,flapn,mc=15,sc -t tracefile='sys.argv[1]+'_parts_connect_2_corina_trace.trc -i t=sdf -o t=sdf 'sys.argv[1]+'_parts_connect_2.sdf 'sys.argv[1]+'_parts_connect_2_corina.sdf')