def full_isomorphism(gra1, gra2): """ full graph isomorphism TODO: DEPRECATE """ assert gra1 == explicit(gra1) and gra2 == explicit(gra2) nxg1 = _networkx.from_graph(gra1) nxg2 = _networkx.from_graph(gra2) iso_dct = _networkx.isomorphism(nxg1, nxg2) return iso_dct
def full_subgraph_isomorphism(gra1, gra2): """ gra2 is fully isomorphic to a subgraph of gra1 TODO: DEPRECATE """ assert gra1 == explicit(gra1) and gra2 == explicit(gra2) nxg1 = _networkx.from_graph(gra1) nxg2 = _networkx.from_graph(gra2) iso_dct = _networkx.subgraph_isomorphism(nxg1, nxg2) return iso_dct
def full_isomorphism(gra1, gra2, igraph=False): """ full graph isomorphism TODO: DEPRECATE """ assert gra1 == explicit(gra1) and gra2 == explicit(gra2) if igraph: igr1 = _igraph.from_graph(gra1) igr2 = _igraph.from_graph(gra2) iso_dcts = _igraph.isomorphisms(igr1, igr2) iso_dct = iso_dcts[0] if iso_dcts else None else: nxg1 = _networkx.from_graph(gra1) nxg2 = _networkx.from_graph(gra2) iso_dct = _networkx.isomorphism(nxg1, nxg2) return iso_dct
def stereogenic_atom_keys(gra, assigned=False): """ Find stereogenic atoms in this graph. If the `assigned` flag is set to `False`, only unassigned stereogenic atoms will be detected. :param gra: the graph :param assigned: Include atoms that already have stereo assignments? :param assigned: bool :returns: the stereogenic atom keys :rtype: frozenset """ gra = without_bond_orders(gra) gra = explicit(gra) # for simplicity, add the explicit hydrogens back in atm_keys = dict_.keys_by_value(atom_bond_valences(gra), lambda x: x == 4) if not assigned: # Remove assigned stereo keys atm_keys -= atom_stereo_keys(gra) atm_ngb_keys_dct = atoms_neighbor_atom_keys(gra) def _is_stereogenic(atm_key): atm_ngb_keys = list(atm_ngb_keys_dct[atm_key]) pri_vecs = [ stereo_priority_vector(gra, atm_key, atm_ngb_key) for atm_ngb_key in atm_ngb_keys ] ret = not any(pv1 == pv2 for pv1, pv2 in itertools.combinations(pri_vecs, r=2)) return ret ste_gen_atm_keys = frozenset(filter(_is_stereogenic, atm_keys)) return ste_gen_atm_keys
def _set_bond_stereo_from_geometry(gra, bnd_keys, geo, geo_idx_dct): assert gra == explicit(gra) bnd_pars = [ bond_stereo_parity_from_geometry(gra, bnd_key, geo, geo_idx_dct) for bnd_key in bnd_keys ] gra = set_bond_stereo_parities(gra, dict(zip(bnd_keys, bnd_pars))) return gra
def _set_atom_stereo_from_geometry(gra, atm_keys, geo, geo_idx_dct): assert gra == explicit(gra) atm_pars = [ atom_stereo_parity_from_geometry(gra, atm_key, geo, geo_idx_dct) for atm_key in atm_keys ] gra = set_atom_stereo_parities(gra, dict(zip(atm_keys, atm_pars))) return gra
def rotational_bond_keys(gra, lin_keys=None, with_h_rotors=True): """ get all rotational bonds for a graph :param gra: the graph :param lin_keys: keys to linear atoms in the graph """ gra = explicit(gra) sym_dct = atom_symbols(gra) ngb_keys_dct = atoms_neighbor_atom_keys(gra) bnd_ord_dct = resonance_dominant_bond_orders(gra) rng_bnd_keys = list(itertools.chain(*rings_bond_keys(gra))) def _is_rotational_bond(bnd_key): ngb_keys_lst = [ngb_keys_dct[k] - bnd_key for k in bnd_key] is_single = max(bnd_ord_dct[bnd_key]) <= 1 has_neighbors = all(ngb_keys_lst) not_in_ring = bnd_key not in rng_bnd_keys is_h_rotor = any( set(map(sym_dct.__getitem__, ks)) == {'H'} for ks in ngb_keys_lst) return is_single and has_neighbors and not_in_ring and ( not is_h_rotor or with_h_rotors) rot_bnd_keys = frozenset(filter(_is_rotational_bond, bond_keys(gra))) lin_keys_lst = linear_segments_atom_keys(gra, lin_keys=lin_keys) dum_keys = tuple(atom_keys(gra, sym='X')) for keys in lin_keys_lst: bnd_keys = sorted((k for k in rot_bnd_keys if k & set(keys)), key=sorted) # Check whether there are neighboring atoms on either side of the # linear segment excl_keys = set(keys) | set(dum_keys) end_key1 = atom_neighbor_atom_key(gra, keys[0], excl_atm_keys=excl_keys) excl_keys |= {end_key1} end_key2 = atom_neighbor_atom_key(gra, keys[-1], excl_atm_keys=excl_keys) end_keys = {end_key1, end_key2} ngb_keys_lst = [ngb_keys_dct[k] - excl_keys for k in end_keys] has_neighbors = all(ngb_keys_lst) if not has_neighbors: rot_bnd_keys -= set(bnd_keys) else: rot_bnd_keys -= set(bnd_keys[:-1]) return rot_bnd_keys
def stereogenic_bond_keys(gra, assigned=False): """ Find stereogenic bonds in this graph. If the `assigned` flag is set to `False`, only unassigned stereogenic bonds will be detected. :param gra: the graph :param assigned: Include bonds that already have stereo assignments? :param assigned: bool :returns: the stereogenic bond keys :rtype: frozenset """ gra = without_bond_orders(gra) gra = explicit(gra) # for simplicity, add the explicit hydrogens back in # get candidates: planar bonds bnd_keys = sp2_bond_keys(gra) if not assigned: # remove bonds that already have stereo assignments bnd_keys -= bond_stereo_keys(gra) bnd_keys -= functools.reduce( # remove double bonds in small rings frozenset.union, filter(lambda x: len(x) < 8, rings_bond_keys(gra)), frozenset()) atm_ngb_keys_dct = atoms_neighbor_atom_keys(gra) def _is_stereogenic(bnd_key): atm1_key, atm2_key = bnd_key def _is_symmetric_on_bond(atm_key, atm_ngb_key): atm_ngb_keys = list(atm_ngb_keys_dct[atm_key] - {atm_ngb_key}) if not atm_ngb_keys: # C=:O: ret = True elif len(atm_ngb_keys) == 1: # C=N:-X ret = False else: assert len(atm_ngb_keys) == 2 # C=C(-X)-Y ret = (stereo_priority_vector( gra, atm_key, atm_ngb_keys[0]) == stereo_priority_vector( gra, atm_key, atm_ngb_keys[1])) return ret return not (_is_symmetric_on_bond(atm1_key, atm2_key) or _is_symmetric_on_bond(atm2_key, atm1_key)) ste_gen_bnd_keys = frozenset(filter(_is_stereogenic, bnd_keys)) return ste_gen_bnd_keys
def to_index_based_stereo(sgr): """ Convert a graph to index-based stereo assignments, where parities are defined relative to the ordering of indices rather than the absolute stereo priority. :param sgr: a graph with absolute stereo assignments :returns: a graph with index-based stereo assignments """ assert sgr == explicit(sgr), ( f"Not an explicit graph:\n{string(sgr, one_indexed=False)}") abs_srt_keys_dct = atoms_stereo_sorted_neighbor_atom_keys(sgr) atm_ste_keys = atom_stereo_keys(sgr) bnd_ste_keys = bond_stereo_keys(sgr) abs_atm_ste_par_dct = atom_stereo_parities(sgr) abs_bnd_ste_par_dct = bond_stereo_parities(sgr) idx_atm_ste_par_dct = {} idx_bnd_ste_par_dct = {} # Determine index-based stereo assignments for atoms for atm_key in atm_ste_keys: abs_srt_keys = abs_srt_keys_dct[atm_key] idx_srt_keys = sorted(abs_srt_keys) if util.is_even_permutation(idx_srt_keys, abs_srt_keys): idx_atm_ste_par_dct[atm_key] = abs_atm_ste_par_dct[atm_key] else: idx_atm_ste_par_dct[atm_key] = not abs_atm_ste_par_dct[atm_key] # Determine index-based stereo assignments for bonds for bnd_key in bnd_ste_keys: atm1_key, atm2_key = sorted(bnd_key) atm1_abs_srt_keys = abs_srt_keys_dct[atm1_key] atm2_abs_srt_keys = abs_srt_keys_dct[atm2_key] atm1_idx_srt_keys = sorted(atm1_abs_srt_keys) atm2_idx_srt_keys = sorted(atm2_abs_srt_keys) if not ((atm1_idx_srt_keys[0] != atm1_abs_srt_keys[0]) ^ (atm2_idx_srt_keys[0] != atm2_abs_srt_keys[0])): idx_bnd_ste_par_dct[bnd_key] = abs_bnd_ste_par_dct[bnd_key] else: idx_bnd_ste_par_dct[bnd_key] = not abs_bnd_ste_par_dct[bnd_key] sgr = set_atom_stereo_parities(sgr, idx_atm_ste_par_dct) sgr = set_bond_stereo_parities(sgr, idx_bnd_ste_par_dct) return sgr
def _stereo_corrected_geometry(sgr, geo, geo_idx_dct): """ correct the stereo parities of a geometry (works iterately to handle cases of higher-order stereo) """ assert sgr == explicit(sgr) gra = without_stereo_parities(sgr) if has_stereo(sgr): full_atm_ste_par_dct = atom_stereo_parities(sgr) full_bnd_ste_par_dct = bond_stereo_parities(sgr) atm_keys = set() bnd_keys = set() last_gra = None while last_gra != gra: last_gra = gra atm_keys.update(stereogenic_atom_keys(gra)) bnd_keys.update(stereogenic_bond_keys(gra)) atm_ste_par_dct = { atm_key: full_atm_ste_par_dct[atm_key] for atm_key in atm_keys } bnd_ste_par_dct = { bnd_key: full_bnd_ste_par_dct[bnd_key] for bnd_key in bnd_keys } geo, gra = _atom_stereo_corrected_geometry(gra, atm_ste_par_dct, geo, geo_idx_dct) geo, gra = _bond_stereo_corrected_geometry(gra, bnd_ste_par_dct, geo, geo_idx_dct) return geo
def from_index_based_stereo(sgr): """ Convert a graph from index-based stereo assignments back to absolute stereo assignments, where parities are independent of atom ordering. :param sgr: a graph with index-based stereo assignments :returns: a graph with absolute stereo assignments """ assert sgr == explicit(sgr), ( f"Not an explicit graph:\n{string(sgr, one_indexed=False)}") gra = without_stereo_parities(sgr) if has_stereo(sgr): atm_keys_pool = atom_stereo_keys(sgr) bnd_keys_pool = bond_stereo_keys(sgr) idx_atm_ste_par_dct = atom_stereo_parities(sgr) idx_bnd_ste_par_dct = bond_stereo_parities(sgr) atm_ngb_keys_dct = atoms_neighbor_atom_keys(sgr) atm_keys = set() bnd_keys = set() last_gra = None # Do the assignments iteratively to handle higher-order stereo while last_gra != gra: last_gra = gra abs_atm_ste_par_dct = {} abs_bnd_ste_par_dct = {} atm_keys.update(stereogenic_atom_keys(gra) & atm_keys_pool) bnd_keys.update(stereogenic_bond_keys(gra) & bnd_keys_pool) # Determine absolute stereo assignments for atoms for atm_key in atm_keys: abs_srt_keys = atom_stereo_sorted_neighbor_atom_keys( gra, atm_key, atm_ngb_keys_dct[atm_key]) idx_srt_keys = sorted(abs_srt_keys) if util.is_even_permutation(idx_srt_keys, abs_srt_keys): abs_atm_ste_par_dct[atm_key] = ( idx_atm_ste_par_dct[atm_key]) else: abs_atm_ste_par_dct[atm_key] = ( not idx_atm_ste_par_dct[atm_key]) # Determine absolute stereo assignments for bonds for bnd_key in bnd_keys: atm1_key, atm2_key = sorted(bnd_key) atm1_abs_srt_keys = atom_stereo_sorted_neighbor_atom_keys( gra, atm1_key, atm_ngb_keys_dct[atm1_key] - bnd_key) atm2_abs_srt_keys = atom_stereo_sorted_neighbor_atom_keys( gra, atm2_key, atm_ngb_keys_dct[atm2_key] - bnd_key) atm1_idx_srt_keys = sorted(atm1_abs_srt_keys) atm2_idx_srt_keys = sorted(atm2_abs_srt_keys) if not ((atm1_idx_srt_keys[0] != atm1_abs_srt_keys[0]) ^ (atm2_idx_srt_keys[0] != atm2_abs_srt_keys[0])): abs_bnd_ste_par_dct[bnd_key] = ( idx_bnd_ste_par_dct[bnd_key]) else: abs_bnd_ste_par_dct[bnd_key] = ( not idx_bnd_ste_par_dct[bnd_key]) gra = set_atom_stereo_parities(gra, abs_atm_ste_par_dct) gra = set_bond_stereo_parities(gra, abs_bnd_ste_par_dct) atm_ste_keys = atom_stereo_keys(gra) bnd_ste_keys = bond_stereo_keys(gra) assert atm_ste_keys == atm_keys_pool, ( "Index-based to absolute stereo conversion failed:\n" f"{str(atm_ste_keys)} != {str(atm_keys_pool)}") assert bnd_ste_keys == bnd_keys_pool, ( "Index-based to absolute stereo conversion failed:\n" f"{str(bnd_ste_keys)} != {str(bnd_keys_pool)}") return gra