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

#os.putenv('LD_LIBRARY_PATH', '/raid1/people/xyz/dockenv /3rdparty/openeye/openeye/wrappers/libs/')
#os.putenv('PYTHONPATH', '/usr/local2/lib/python2.3:/raid1/people/xyz/dockenv/3rdparty/openeye/openeye/wrappers/python')
#p = os.getenv('PATH')+':/usr/local/bin:/raid1/people/xyz/dockenv/3rdparty/openeye/openeye/bin:/usr/local2/lib'
#p = ':/usr/local/bin:/raid1/people/xyz/dockenv/3rdparty/openeye/openeye/bin:/usr/local2/lib'
#os.putenv('PATH', p)

#print os.getenv('PATH')

ifs = oemolistream()
ifs.open(sys.argv[1])
ofs_1 = oemolostream()
ofs_1.open('temp.ism')

# Reaction 1: S- addition to halogenated acidic C-alpha-carbonyl atom

#Explicit hydrogens to avoid 5-bonded carbons and to prevent generation of identical copies in the case of attacked CH2
mol_sul = OEGraphMol()
OEParseSmiles(mol_sul, "[SH]")
libgen1 = OELibraryGen("[F,Cl,Br,I:1][C;!H0:2]([H:5])([*:7])[C:3](=[O,S:4]).[S:100][H:101]>>[*:1][C:2]([S-:100])([*:7])[*:3][*:4].[H:5][H:101]")
libgen1.SetExplicitHydrogens(True)
libgen1.SetValenceCorrection(False)

for mol in ifs.GetOEMols():
    libgen1.AddStartingMaterial(mol, 0)
    libgen1.AddStartingMaterial(mol_sul, 1)
    mol.Clear()
    mol_sul.Clear()

title_list = []
for products in libgen1.GetProducts():
    num = 1
    prot = 0
    title = products.GetTitle()+'cp_'+str(num)
    while title in title_list:
        num+=1
        title = products.GetTitle()+'cp_'+str(num)
    title_list.append(title)
    products.SetTitle(title)
    OEWriteMolecule(ofs_1, products)

ofs_1.close()
ifs.close()

#Remove doubles and H2
tempf = open('temp.ism', 'r')
ismf = open('cysprot_01rxn_alphahalogencarbonyls_'+sys.argv[1][:string.find(sys.argv[1], '.')]+'.ism', 'w')
smiles = {}
for line in tempf.readlines():
    newline1 = string.replace(line, '[HH].', '')
    newline2 = string.replace(newline1, '.[HH]', '')
    cols = string.split(newline2)
    if cols[1][:string.find(cols[1], '_')] not in smiles.keys():
        smiles[cols[1][:string.find(cols[1], '_')]] = [cols[0]]
    else:
        if cols[0] not in smiles[cols[1][:string.find(cols[1], '_')]]:
            smiles[cols[1][:string.find(cols[1], '_')]].append(cols[0])
        else:
            continue
    ismf.write(newline2)

ismf.close()
os.system('rm -f temp.ism')