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

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

#-----------------------------------------------------------------------------
#Creates a list of already created names for mol2-files
def lookup_proc_codes():
    db = MySQLdb.connect(host='newelvis.ucsf.edu',passwd='secret',db='joha')
    c = db.cursor()
    c.execute('select Proc_Name from PROC_NAMES')
    mysql_proc_name_tupel = c.fetchall()
    c.close()
    db.close()
    proc_name_list = []
    for namet in mysql_proc_name_tupel:
        for pn in namet:
            proc_name_list.append(pn)
    print 'Got Existing File Names'
    return proc_name_list
#-----------------------------------------------------------------------------

#-----------------------------------------------------------------------------
#Creates a new title for a mol
def create_ntitle(ot, titles, en):
    db = MySQLdb.connect(host='newelvis.ucsf.edu',passwd='secret',db='joha')
    c = db.cursor()
    counter = 1
    nt = 'MFCDZ'+ot+'_p00'+str(counter)+en
    while nt in titles:
        counter+=1
        nt = 'MFCDZ'+ot+'_p00'+str(counter)+en
    print nt
    c.execute('insert into PROC_NAMES (Proc_Name) Values (%s)' , nt)
    c.close()
    db.close()
    return nt
#-----------------------------------------------------------------------------

try:
    file = sys.argv[1]
except IndexError:
    print 'usage: sdf2mol2_mysql_names.py sdf-file(from corina+ionizer) \'_\'suffix(for Folders after ring, e.g. SUBS)'
    raise SystemExit()
try:
    suffix = '_'+sys.argv[2]
except IndexError:
    suffix = ''

title_list = lookup_proc_codes()
ifs = oemolistream()
ofs = oemolostream()

if string.find(file, '_lp_') != -1: ti_path = 'LP'
elif string.find(file, '_ln_') != 1: ti_path = 'LN'
else:
    print 'something wrong with the pattern!'    
    raise SystemExit()

ifs.open(file)
for mol in ifs.GetOEMols():
    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
    title = create_ntitle(mol.GetTitle(), title_list, '_'+string.lower(ring_path)+'_'+string.lower(ti_path))
    title_list.append(title)
    mol.SetTitle(title)
    if os.path.exists('../MOLS/RING_'+ring_path+suffix+'/OH_'+ti_path+'/'+title+'.mol2'):
        print 'Error: title', title, 'not in title-list, but in mol folder ???!!!'
        raise SystemExit()

    # Are target folders existent ?
    if os.path.exists('../MOLS'):
        if os.path.exists('../MOLS/RING_'+ring_path+suffix):
            if os.path.exists('../MOLS/RING_'+ring_path+suffix+'/OH_'+ti_path):
                pass
            else:
                os.mkdir('../MOLS/RING_'+ring_path+suffix+'/OH_'+ti_path) 
        else:
            os.mkdir('MOLS/RING_'+ring_path+suffix) 
            os.mkdir('MOLS/RING_'+ring_path+suffix+'/OH_'+ti_path) 
    else:
        os.mkdir('MOLS') 
        os.mkdir('MOLS/RING_'+ring_path+suffix) 
        os.mkdir('MOLS/RING_'+ring_path+suffix+'/OH_'+ti_path) 

    ofs.open('../MOLS/RING_'+ring_path+suffix+'/OH_'+ti_path+'/'+title+'.mol2')
    OEWriteMol2File(ofs,mol)
    ofs.close()