mmagnus / rna-tools

                #

                # fix missing U (the whole base at the moment)

                #

                if str(r.get_resname()).strip() == "U" and fix_missing_atoms:

                    for a in r:

                        if a.id == "N1":

                            break

                    else:

                        U_struc = PDB.PDBParser().get_structure('', path + '/data/U.pdb')

                        U = [U_atom for U_atom in U_struc[0].get_residues()][0]

                        r_atoms = [r["O4'"], r["C2'"], r["C1'"]]

                        U_atoms = [U["O4'"], U["C2'"], U["C1'"]]

                        sup = PDB.Superimposer()

                        sup.set_atoms(r_atoms, U_atoms)

                        rms = round(sup.rms, 3)

                        sup.apply(U_struc.get_atoms())  # to all atoms of U

                        r.add(U["N1"])

                        r.add(U["C2"])

                        r.add(U["O2"])

                        r.add(U["N3"])

                        r.add(U["C4"])

                        r.add(U["O4"])

                        r.add(U["C5"])

                        r.add(U["C6"])

                        fixed.append(['add the whole base U', chain.id, r, r.id[1]])

                #

                # fix missing G (the whole base at the moment)

                #

                #

                # fix missing C (the whole base at the moment)

                #

                if str(r.get_resname()).strip() == "C" and fix_missing_atoms:

                    for a in r:

                        if a.id == "N1":

                            break

                    else:

                        C_struc = PDB.PDBParser().get_structure('', path + '/data/C.pdb')

                        C = [C_atom for C_atom in C_struc[0].get_residues()][0]

                        r_atoms = [r["O4'"], r["C2'"], r["C1'"]]

                        C_atoms = [C["O4'"], C["C2'"], C["C1'"]]

                        sup = PDB.Superimposer()

                        sup.set_atoms(r_atoms, C_atoms)

                        rms = round(sup.rms, 3)

                        sup.apply(C_struc.get_atoms())  # to all atoms of C

                        r.add(C["N1"])

                        r.add(C["C2"])

                        r.add(C["O2"])

                        r.add(C["N3"])

                        r.add(C["C4"])

                        r.add(C["N4"])

                        r.add(C["C5"])

                        r.add(C["C6"])

                        fixed.append(['add the whole base C', chain.id, r, r.id[1]])

                #

                # fix missing U (the whole base at the moment)