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

#----------------------------------------------
def remove_covalent_metals(inf, outf):
    ifs = oemolistream(inf)
    ofs = oemolostream(outf)
    pat = OESubSearch()
    pat.Init('[K,Na,Ca]')
    for mol in ifs.GetOEMols():
        if pat.SingleMatch(mol):
            # Monovalent Cations
            rxn_1 = OEUniMolecularRxn("[Na,K:2][*:1]>>[*-:1]")
            # Divalent cations
            rxn_2 = OEUniMolecularRxn("[*:2][Ca:3][*:1]>>[*-:1].[*-:2]")
            rxn_1(mol)
            rxn_2(mol)
            OEWriteMolecule(ofs, mol)
        else:
            OEWriteMolecule(ofs, mol)
    ofs.close()

#----------------------------------------------
def a3_f2f(inf, outf):
    ifs = oemolistream(inf)
    ofs = oemolostream(outf)
    ofs.SetFormat(OEFormat_ISM)
    for mol in ifs.GetOEMols():
        heavy_atom = 0
        for atom in mol.GetAtoms():
            if atom.IsHydrogen() != 1:
                heavy_atom+=1
        if heavy_atom <= 48 and heavy_atom > 4:
            OEWriteMolecule(ofs, mol)
        else:
            pass
    ifs.close()
    ofs.close()
#----------------------------------------------

try:
    inputfile = sys.argv[1]
    outputfile = 'a3.1'+sys.argv[1][string.find(sys.argv[1], '_'):string.find(sys.argv[1], '_out')]+'_out.ism'
except IndexError:
    print '\Usage: a3.1_sdf2ism_filter.py Molfile(sdf) -> will remove Cations !\n'
    raise SystemExit()

remove_covalent_metals(inputfile, outputfile)