#!/usr/local2/bin/python2.3
# transform sdfs to mol2 and give new titles

import sys, string, os
from openeye.oechem import *

title_list = []
dir = os.listdir('.')
for file in dir:
    if string.find(file, 'sdf2mol2') != -1 and file[-4:] == '.txt':
        title_listf = open(file, 'r')
        for line in title_listf.readlines():
            title_list.append(line[:-1])
        title_listf.close()
    else:
        pass


ifs = oemolistream()
ofs = oemolostream()

molecule = None

try:
    if sys.argv[2] == 'stereo':
        stereo = 1
        print 'only chiral compounds are processed'
    else:
        stereo = 0
    if sys.argv[3] == 'GS':
        gsorhe = '_GS'
    else:
        gsorhe = ''
except IndexError:
    print '\nusage:\nf_sdf2mol2_singles_phopsphates.py sdf-file stereo (or xxx -> no only stereo) GS (or xxx -> no GS)\n'
    raise SystemExit()

try:
    title_listf = open(sys.argv[1][:string.find(sys.argv[1], '_corina_')]+'_titles_sdf2mol2.txt', 'a')
    file_list = [sys.argv[1]]
except IndexError:
    print 'usage: f_sdf2mol2_singles_phopsphates.py molfilename stereo(not mandatory)'
for file in file_list:
    if string.find(sys.argv[1], '_p1') != -1:
        p1 = '1'
    else:
        p1 = '0'
    if string.find(file, '_lp_') != -1: ti_path = 'LP'
    elif string.find(file, '_ln_') != 1: ti_path = 'LN'
    else: ti_path = 'LN'
    if stereo == 1:
        chiral_list = []
        if ti_path == 'LP':
            sfile = open(file[:string.find(file, '_lp')]+'_parts_split_2_dicts2.txt', 'r')       
        elif ti_path == 'LN':
            sfile = open(file[:string.find(file, '_ln')]+'_parts_split_2_dicts2.txt', 'r')       
        for line in sfile.readlines():
            if string.split(line)[-1] == '1':
                chiral_list.append(string.split(line)[0][4:12])

    ifs.open(file)
    for mol in ifs.GetOEMols():
        if mol.NumAtoms() < 71:
            if stereo == 1:
                temp_title = mol.GetTitle()
                if temp_title[4:string.find(temp_title, '_')] in chiral_list:
                    pass
                else:
                    continue
            else:
                pass
            OEPerceiveChiral(mol)
            OEFindRingAtomsAndBonds(mol)
            OETriposAtomTypes(mol)
            OETriposAtomTypeNames(mol)
            OETriposBondTypeNames(mol)
            OETriposAtomNames(mol)
            OEAssignAromaticFlags(mol)
            OEGasteigerPartialCharges(mol)
            count, parts = OEDetermineRingSystems(mol)
            if count == 0: ring_path = 'NO'
            elif count == 1: ring_path = 'ONE'
            elif count > 1: ring_path = 'MORE'
            else:
                print 'something wrong with the rings!'
                raise SystemExit()
            # Generate title, evtl new ionization state out of ionizer
            if string.find(mol.GetTitle(), 'ZINC') != -1:
                pretitle = string.replace(mol.GetTitle(), 'ZINC', 'MFCD')
            else:
                pretitle =('MFCD'+mol.GetTitle())
            title = pretitle+'_p'+p1+'01_'+string.lower(ring_path)+'_'+string.lower(ti_path)
            num = 1
##  #        while title in 'titles_RING_'+ring_path+'_'+ti_path:
            while title in title_list:
                num+=1
                title = pretitle+'_p'+p1+'0'+str(num)+'_'+string.lower(ring_path)+'_'+string.lower(ti_path)
      #      'titles_RING_'+ring_path+'_'+ti_path.append(title)
            mol.SetTitle(title)
            title_list.append(title)
            if os.path.exists('MOLS/RING_'+ring_path+'_SUBS_PHOS'+gsorhe+'/OH_'+ti_path+'/'+title+'.mol2') or os.path.exists('MOLS/RING_'+ring_path+'_SUBS_PHOS/OH_'+ti_path+'/'+title+'.mol2.gz'):
                print title, 'exists already ..... skipping !'
                continue
            else:
                pass
            ofs.open('MOLS/RING_'+ring_path+'_SUBS_PHOS'+gsorhe+'/OH_'+ti_path+'/'+title+'.mol2')
            OEWriteMol2File(ofs,mol)
            ofs.close()
        else:
            continue

        title_listf.write(title+'\n')

title_listf.close()