def getligs(self):
        """Get all ligands from a PDB file and prepare them for analysis.
        Returns all non-empty ligands.
        """

        if config.PEPTIDES == [] and config.INTRA is None:
            # Extract small molecule ligands (default)
            ligands = []

            # Filter for ligands using lists
            ligand_residues, self.lignames_all, self.water = self.filter_for_ligands()

            all_res_dict = {(a.GetName(), a.GetChain(), a.GetNum()): a for a in ligand_residues}
            self.lignames_kept = list(set([a.GetName() for a in ligand_residues]))

            if not config.BREAKCOMPOSITE:
                #  Update register of covalent links with those between DNA/RNA subunits
                self.covalent += nucleotide_linkage(all_res_dict)
                #  Find fragment linked by covalent bonds
                res_kmers = self.identify_kmers(all_res_dict)
            else:
                res_kmers = [[a, ] for a in ligand_residues]
            write_message("{} ligand kmer(s) detected for closer inspection.\n".format(len(res_kmers)), mtype='debug')
            for kmer in res_kmers:  # iterate over all ligands and extract molecules + information
                if len(kmer) > config.MAX_COMPOSITE_LENGTH:
                    write_message("Ligand kmer(s) filtered out with a length of {} fragments ({} allowed).\n".format(
                        len(kmer), config.MAX_COMPOSITE_LENGTH), mtype='debug')
                else:
                    ligands.append(self.extract_ligand(kmer))

        else:
            # Extract peptides from given chains
            self.water = [o for o in pybel.ob.OBResidueIter(self.proteincomplex.OBMol) if o.GetResidueProperty(9)]
            if config.PEPTIDES != []:
                peptide_ligands = [self.getpeptides(chain) for chain in config.PEPTIDES]
            elif config.INTRA is not None:
                peptide_ligands = [self.getpeptides(config.INTRA), ]

            ligands = [p for p in peptide_ligands if p is not None]
            self.covalent, self.lignames_kept, self.lignames_all = [], [], set()

        return [lig for lig in ligands if len(lig.mol.atoms) != 0]
Get all ligands from a PDB file and prepare them for analysis.
        Returns all non-empty ligands.