#!/usr/local2/bin/python
import os, sys, string
from openeye.oechem import *



#----------------------------------------------
def a3_f2f(inf, outf):
    metal_list = []
    ifs = oemolistream(inf)
    ofs = oemolostream(outf)
    ofs.SetFormat(OEFormat_ISM)
    for mol in ifs.GetOEMols():
        metal = 0
        carbon = 0
        heavy_atom = 0
        for atom in mol.GetAtoms():
            if not atom.IsHydrogen():
                heavy_atom+=1
                if atom.IsMetal():
                   metal = 1
        #    elif not atom.IsHydrogen() and not atom.IsNitrogen() and not atom.IsCarbon and not atom.IsHalogen() and not atom.IsOxygen() and not atom.IsPhosphorus() and not atom.IsSulfur():
                if atom.IsCarbon():
                    carbon = 1
        if heavy_atom <= 48 and heavy_atom > 4 and carbon == 1 and string.find(OECreateAbsSmiString(mol), '*') == -1:
            OEWriteMolecule(ofs, mol)
            if metal == 1:
                print OECreateAbsSmiString(mol), mol.GetTitle()
                metal_list.append(mol.GetTitle())
        else:
            pass
    print metal_list
    ifs.close()
    ofs.close()
#----------------------------------------------

a3_f2f('ORIGINAL_MOLS/a3.2_kegg_012506.ism', 'ORIGINAL_MOLS/a3.3_kegg_012506.ism')
#a3_f2f(sys.argv[1], sys.argv[2])