[Biopython] How to pull out the coordinates for het groups?

[Jing Lu]

Hi,

I want to pull out ligand from pdb file, then for each ligand(or het group)
save it as pdb, and keep the header. I have try the following code, but it
didn't return the result I want. Could you please give me some suggestion?

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for filename in os.listdir(workdir):
        print filename
        if '.bio' in filename:
            parser = PDBParser(PERMISSIVE=1)
            structure = parser.get_structure(filename[:4], filename)
            structure_copy = copy.deepcopy(structure) # for each ligand
renew the structure

            het_id_all = get_het_id(structure_copy) # only return the
ligands of structure

            for het_id in het_id_all:
                for model in structure_copy:
                    for chain in model:
                        for residue in chain:
                            id = residue.id
                            if id[0] is not het_id:
                                chain.detach_child(id)
                        if len(chain) == 0:
                            model.detach_child(chain.id)

                name = './ligand/' + filename[:9] + '_' + het_id[2:] + '_' +
str(id[1]).zfill(4) + chain.id + '.pdb'
                save_structure(structure_copy, name)
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