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

ifs = oemolistream()
ifs.open('b4.1'+sys.argv[1]+'_ln.ism')
ofs_1 = oemolostream()
ofs_1.open('b4.2'+sys.argv[1]+'_ln.ism')
logfile = open('b4.2'+sys.argv[1]+'_filter.log','w')

# Check if pattern (5-bonded Carbon from rxn 1) is found
for mol in ifs.GetOEMols():
    pat = OESubSearch()
#    pat.Init('[r*][r#6]([N])([OH])=[r!#8&!#6]') << don't know why, but is not recognized reliably! >>
    pat.Init('[r]([N])([O-])')
    if pat.SingleMatch(mol) == 1:
        for atom in mol.GetAtoms():
            if atom.IsCarbon() == 1:
                if atom.GetExplicitValence() == 5:
                    atom.SetAromatic(0)
#                    degree = atom.GetExplicitDegree()
#                    print 'degree', degree
#                    valence = atom.GetExplicitValence()
#                    print 'valence', valence
                    idx_five_valent = atom.GetIdx()
#                    print 'index', idx_five_valent
        # every bond, which connects an atom to the identified C, is reduced (or kept) to the order of 1
        # the involved atoms are all set non-aromatic (also the C itself several times)
                    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)
#                print 'set begin', end.GetIdx(), begin.GetIdx()
                        elif end.GetIdx() == idx_five_valent:
                            begin.SetAromatic(0)
                            end.SetAromatic(0)
                            bond.SetOrder(1)
#                print 'set end', end.GetIdx(), begin.GetIdx()
        OEWriteMolecule(ofs_1, mol)
        logfile.write(mol.GetTitle()+' transformed!\n')
# for Debugging
#        count_total = 0
#        count = 0
#        for atom in mol.GetAtoms():
#            count_total+=1 
#            if atom.IsAromatic() == 1:
#                print 'aromatic'
#                degree = atom.GetExplicitDegree()
#                print 'degree', degree
#                valence = atom.GetExplicitValence()
#                print 'valence', valence
#                idx_five_valent = atom.GetIdx()
#                print 'index', idx_five_valent
#            elif atom.IsAromatic() == 0 and atom.IsInRing() == 1:
#                count+=1
#                print 'non aromatic'
#                degree = atom.GetExplicitDegree()
#                print 'degree', degree
#                valence = atom.GetExplicitValence()
#                print 'valence', valence
#                idx_five_valent = atom.GetIdx()
#                print 'index', idx_five_valent
#        print count, count_total
    else:
        OEWriteMolecule(ofs_1, mol)
        logfile.write(mol.GetTitle()+' unchanged!\n')
logfile.close() 
ofs_1.close()
ifs.close()

print '\nb4.3_rxn_amidine_aromatic.py\n'
os.system('b4.3_rxn_amidine_aromatic.py '+sys.argv[1])