from __future__ import absolute_import, division, print_function from scitbx.math import dihedral_angle from mmtbx.ligands.ready_set_basics import construct_xyz from mmtbx.ligands.ready_set_basics import generate_atom_group_atom_names from mmtbx.ligands.hierarchy_utils import new_atom_with_inheritance from mmtbx.ligands.hierarchy_utils import add_hydrogens_to_atom_group_using_bad from cctbx.geometry_restraints.linking_class import linking_class origin_ids = linking_class() def get_proton_info(ag): proton_name=proton_element='H' if is_perdeuterated(ag): proton_name=proton_element='D' return proton_element, proton_name def _generate_bonds_with_origin_ids_in_list(bond_proxies, specific_origin_ids=None): assert specific_origin_ids for specific_origin_id in specific_origin_ids: for p in bond_proxies.get_proxies_with_origin_id(specific_origin_id): yield p def add_side_chain_acid_hydrogens_to_atom_group(atom_group, anchors=None, configuration_index=0, bond_length=0.95, element='H', ): """Add hydrogen atoms to side-chain acid in place Args: atom_group (TYPE): Atom group anchors (None, optional): Atoms that specify the acids moeity configuration_index (int, optional): Configuration to return """ assert element in ['H', 'D'] c, o1, o2 = anchors if configuration_index>=2: tmp = o1.name o1.name = o2.name o2.name = tmp tmp = o1 o1 = o2 o2 = tmp configuration_index=configuration_index%2 if o2.name==' OD2': name = ' HD2' atom = atom_group.get_atom('CB') elif o2.name==' OE2': name = ' HE2' atom = atom_group.get_atom('CG') else: assert 0 if element=='D': name = name.replace('H', 'D') dihedral = dihedral_angle(sites=[atom.xyz, c.xyz, o1.xyz, o2.xyz, ], deg=True) ro2 = construct_xyz(o2, bond_length, c, 120., o1, dihedral, period=2, ) i = configuration_index atom = atom_group.get_atom(name.strip()) if atom: pass #atom.xyz = ro2[i] else: atom = new_atom_with_inheritance(name, element, ro2[i], o2) atom_group.append_atom(atom) def add_side_chain_acid_hydrogens_to_residue_group(residue_group, configuration_index=0, element='H', ): """Adds hydrogen atoms to side-chain acid. Args: residue_group (TYPE): Specific residue group """ def _get_atom_names(residue_group): assert len(residue_group.atom_groups())==1 atom_group = residue_group.atom_groups()[0] lookup = {'ASP' : ['CG', 'OD1', 'OD2'], 'GLU' : ['CD', 'OE1', 'OE2'], } return lookup.get(atom_group.resname, []) # if element=='H': bond_length=0.95 elif element=='D': bond_length=1.00 else: assert 0 atoms = _get_atom_names(residue_group) for atom_group, atoms in generate_atom_group_atom_names(residue_group, atoms, ): if atom_group is None: continue tmp = add_side_chain_acid_hydrogens_to_atom_group( atom_group, # append_to_end_of_model=append_to_end_of_model, anchors = atoms, configuration_index=configuration_index, bond_length=bond_length, element=element, ) def add_side_chain_acid_hydrogens(hierarchy, configuration_index=0, element='H', ): """Add hydrogen atoms to every side-chain acid (ASP and GLU). Not very useful as adding to a single residue group (below) would be more prectical. Args: hierarchy (TYPE): Model hierarchy configuration_index (int, optional): Defaults to zero. Determines which of the four configurations the added hydrogen will be: 0 - Current Ox2 gets Hx2 (x=D,E) pointing out 1 - Current Ox2 gets Hx2 (x=D,E) pointing in 2 - Current Ox1 gets swapped with Ox2, gets Hx2 (x=D,E) pointing out 3 - Current Ox1 gets swapped with Ox2, gets Hx2 (x=D,E) pointing in """ for residue_group in hierarchy.residue_groups(): for atom_group in residue_group.atom_groups(): if atom_group.resname in ['ASP', 'GLU']: add_side_chain_acid_hydrogens_to_residue_group( residue_group, configuration_index=configuration_index, element=element, ) # # isolated CYS need HG # def add_cys_hg_to_atom_group(atom_group, append_to_end_of_model=False, element='H', ): """Adds hydrogen to CYS Args: atom_group (TYPE): atom_group in hirarchy append_to_end_of_model (bool, optional): Some programs like the additional atoms added at end of PDB Returns: TYPE: New chains, if any """ assert element in ['H', 'D'] rc = add_hydrogens_to_atom_group_using_bad( atom_group, ' HG '.replace('H', element), element, 'SG', 'CB', 'CA', 1.2, 120., 160., append_to_end_of_model=append_to_end_of_model, ) return rc def add_cys_hg_to_residue_group(residue_group, append_to_end_of_model=False, element='H', ): rc=[] for atom_group in residue_group.atom_groups(): if atom_group.resname not in ['CYS']: continue rc += add_cys_hg_to_atom_group( atom_group, append_to_end_of_model=append_to_end_of_model, element=element, ) return rc def conditional_add_cys_hg_to_atom_group(geometry_restraints_manager, residue_group, element='H', append_to_end_of_model=False, ): """Adds HG atom to CYS if no disulfur bridge Args: geometry_restraints_manager (TYPE): GRM residue_group (TYPE): CYS residue group """ # could be more general to include other disulphide amino acids resnames = [] for atom_group in residue_group.atom_groups(): resnames.append(atom_group.resname) if 'CYS' not in resnames: return None sgs = [] for atom in residue_group.atoms(): if atom.name.strip()=='SG' and atom.parent().resname=='CYS': sgs.append(atom.i_seq) assert len(sgs) in [0, 1] sg_bonds = [] if sgs: specific_origin_ids = [origin_ids.get_origin_id('SS BOND'), origin_ids.get_origin_id('metal coordination'), ] for bond in geometry_restraints_manager.get_all_bond_proxies(): if not hasattr(bond, 'get_proxies_with_origin_id'): continue for p in _generate_bonds_with_origin_ids_in_list(bond, specific_origin_ids): assert p.origin_id in specific_origin_ids if sgs[0] in p.i_seqs: sg_bonds.append(p.i_seqs) rc = [] if len(sg_bonds)==0: rc += add_cys_hg_to_residue_group(residue_group, element=element, append_to_end_of_model=append_to_end_of_model, ) return rc def add_disulfur_hydrogen_atoms(geometry_restraints_manager, hierarchy, element='H', ): """Example of usage """ for residue_group in hierarchy.residue_groups(): resnames=[] for atom_group in residue_group.atom_groups(): resnames.append(atom_group.resname) if 'CYS' in resnames: rc = conditional_add_cys_hg_to_atom_group(geometry_restraints_manager, residue_group, element=element, ) def remove_cys_hg_from_residue_group(rg): proton_element, proton_name = get_proton_info(rg) for ag in rg.atom_groups(): if ag.resname not in ['CYS']: continue for atom in ag.atoms(): if atom.name==' %sG ' % proton_element: ag.remove_atom(atom) break def generate_bonded_i_seqs(geometry_restraints_manager, rg, j_seq): def _not_j_seq(j_seq, i_seqs): i_seqs.remove(j_seq) return i_seqs[0] bonds = [] for bond in geometry_restraints_manager.pair_proxies().bond_proxies.simple: if j_seq in bond.i_seqs: bonds.append(_not_j_seq(j_seq, list(bond.i_seqs))) for bond in geometry_restraints_manager.pair_proxies().bond_proxies.asu: if j_seq in [bond.i_seq, bond.j_seq]: bonds.append(_not_j_seq(j_seq, [bond.i_seq, bond.j_seq])) return bonds def conditional_remove_cys_hg_to_atom_group(geometry_restraints_manager, rg, ): sgs = None for atom in rg.atoms(): if atom.name.strip()=='SG' and atom.parent().resname=='CYS': sgs = atom.i_seq break if sgs: sg_bonds = generate_bonded_i_seqs(geometry_restraints_manager, rg, sgs) if len(sg_bonds)>2: remove_cys_hg_from_residue_group(rg)