#!/usr/bin/python
import os, string, sys
from openeye.oechem import *

#-----------------------------------------------------------------------
# Check if wrong pattern (5-bonded Carbon from rxn 2) is found
def get_arom_right(mol, log, ofs1):
    pat = OESubSearch()
    pat.Init('[r][r]([N])([O-])[r]')
    if pat.SingleMatch(mol) == 1:
        for atom in mol.GetAtoms():
            if atom.IsCarbon() == 1:
                if atom.GetExplicitValence() == 5:
                    atom.SetAromatic(0)
                    idx_five_valent = atom.GetIdx()
                    for bond in mol.GetBonds():
                        begin = bond.GetBgn()
                        end = bond.GetEnd()
                        if begin.GetIdx() == idx_five_valent:
                            begin.SetAromatic(0)
                            end.SetAromatic(0)
                            bond.SetOrder(1)
                        elif end.GetIdx() == idx_five_valent:
                            begin.SetAromatic(0)
                            end.SetAromatic(0)
                            bond.SetOrder(1)
        OEWriteMolecule(ofs1, mol)
        log.write(mol.GetTitle()+' transformed!\n')
    else:
        OEWriteMolecule(ofs1, mol)
        log.write(mol.GetTitle()+' unchanged!\n')
#-------------------------------------------------------------------------

ifs = oemolistream()
ifs.open('b6.1'+sys.argv[1]+'_ln.ism')
ofs_1 = oemolostream()
ofs_1.open('b6.2'+sys.argv[1]+'_ln_out.ism')
logfile = open('b6.2'+sys.argv[1]+'_filter.log','w')


for molecule in ifs.GetOEMols():
    get_arom_right(molecule, logfile, ofs_1)
ofs_1.close()
ifs.close()
print '\nStarted b6.3_rxn_imin_aromatic.py\n'
os.system('b6.3_rxn_imin_aromatic.py '+sys.argv[1])