#!/usr/local2/bin/python
import os, sys
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):
        #    libgen1 = OELibraryGen("[Na,K:2][*:1]>>[*-:1]")
         #   libgen2 = OELibraryGen("[*:2][Mg,Ca:3][*:1]>>[*-:1].[*-:2]")
          #  libgen1.SetExplicitHydrogens(True)
           # libgen1.SetValenceCorrection(False)
            #libgen2.SetExplicitHydrogens(True)
           # libgen2.SetValenceCorrection(False)
         #   for mol in ifs.GetOEMols():
          #      libgen1.AddStartingMaterial(mol, 0)
           #     libgen2.AddStartingMaterial(mol, 0)
            #    mol.Clear()

        #    for products in libgen1.GetProducts():
         #       title = products.GetTitle()[:-1]
          #      products.SetTitle(title)
           #     OEWriteMolecule(outf, products)
           # for products in libgen2.GetProducts():
            #    title = products.GetTitle()[:-1]
             #   products.SetTitle(title)
              #  OEWriteMolecule(outf, products)
            rxn_1 = OEUniMolecularRxn("[Na,K:2][*:1]>>[*-:1]")
# Have to do Zn, Mg, Ni by hand
            rxn_2 = OEUniMolecularRxn("[*:2][Ca:3][*:1]>>[*-:1].[*-:2]")
            #rxn_1 = OEUniMolecularRxn("[Na,K:2][*:1].[H:3]>>[*:1][H:3]")
            #rxn_2 = OEUniMolecularRxn("[*:2][Mg,Ca:3][*:1].[H:4][H:5]>>[*:1][H:4].[*:2][H:5]")
        #    prot = OEGraphMol()
        #    OEParseSmiles(prot, "H")
         #   hydr = OEGraphMol()
    #        OEParseSmiles(hydr, "HH")
            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()
#----------------------------------------------

remove_covalent_metals('ORIGINAL_MOLS/a2_kegg_012506.ism', 'ORIGINAL_MOLS/a3.1_kegg_012506.ism')
#will do a3.1_kegg_012506.ism by hand
#a3_f2f('ORIGINAL_MOLS/a3.1_kegg_012506.ism', 'ORIGINAL_MOLS/a3_kegg_012506.ism')