def union(gra1, gra2):
""" a union of two graphs
"""
assert not atom_keys(gra1) & atom_keys(gra2)
atm_dct = {}
atm_dct.update(atoms(gra1))
atm_dct.update(atoms(gra2))
bnd_dct = {}
bnd_dct.update(bonds(gra1))
bnd_dct.update(bonds(gra2))
return _create.from_atoms_and_bonds(atm_dct, bnd_dct)
def add_bonds(gra, keys, ord_dct=None, ste_par_dct=None, check=True):
""" add bonds to this molecular graph
"""
bnd_keys = set(bond_keys(gra))
bnd_ord_dct = bond_orders(gra)
bnd_ste_par_dct = bond_stereo_parities(gra)
keys = set(map(frozenset, keys))
ord_dct = {} if ord_dct is None else ord_dct
ste_par_dct = {} if ste_par_dct is None else ste_par_dct
if check:
assert not keys & bnd_keys, (
'{} and {} have a non-empty intersection'.format(keys, bnd_keys))
assert set(ord_dct.keys()) <= keys
assert set(ste_par_dct.keys()) <= keys
bnd_keys.update(keys)
bnd_ord_dct.update(ord_dct)
bnd_ste_par_dct.update(ste_par_dct)
atm_dct = atoms(gra)
bnd_dct = _create.bonds_from_data(bond_keys=bnd_keys,
bond_orders=bnd_ord_dct,
bond_stereo_parities=bnd_ste_par_dct)
gra = _create.from_atoms_and_bonds(atoms=atm_dct, bonds=bnd_dct)
return gra
def bond_induced_subgraph(gra, bnd_keys):
""" the subgraph induced by a subset of the bonds
"""
atm_keys = set(itertools.chain(*bnd_keys))
bnd_keys = set(bnd_keys)
assert atm_keys <= atom_keys(gra)
atm_dct = dict_.by_key(atoms(gra), atm_keys)
bnd_dct = dict_.by_key(bonds(gra), bnd_keys)
return _create.from_atoms_and_bonds(atm_dct, bnd_dct)
def subgraph(gra, atm_keys):
""" the subgraph induced by a subset of the atoms
"""
atm_keys = set(atm_keys)
assert atm_keys <= atom_keys(gra)
bnd_keys = set(filter(lambda x: x <= atm_keys, bond_keys(gra)))
atm_dct = dict_.by_key(atoms(gra), atm_keys)
bnd_dct = dict_.by_key(bonds(gra), bnd_keys)
return _create.from_atoms_and_bonds(atm_dct, bnd_dct)
def atom_count(gra, with_dummy=False, with_implicit=True):
""" count the number of atoms in this molecule
by default, this includes implicit hydrogens and excludes dummy atoms
"""
if not with_dummy:
gra = without_dummy_atoms(gra)
natms = len(atoms(gra))
if with_implicit:
atm_imp_hyd_vlc_dct = atom_implicit_hydrogen_valences(gra)
natms += sum(atm_imp_hyd_vlc_dct.values())
return natms
def remove_bonds(gra, bnd_keys, check=True):
""" remove bonds from the molecular graph
"""
all_bnd_keys = bond_keys(gra)
bnd_keys = set(map(frozenset, bnd_keys))
if check:
assert bnd_keys <= all_bnd_keys
bnd_keys = all_bnd_keys - bnd_keys
atm_dct = atoms(gra)
bnd_dct = dict_.by_key(bonds(gra), bnd_keys)
return _create.from_atoms_and_bonds(atm_dct, bnd_dct)
def frozen(gra):
""" hashable, sortable, immutable container of graph data
"""
atm_keys = sorted(atom_keys(gra))
bnd_keys = sorted(bond_keys(gra), key=sorted)
# make it sortable by replacing Nones with -infinity
atm_vals = numpy.array(dict_.values_by_key(atoms(gra), atm_keys))
bnd_vals = numpy.array(dict_.values_by_key(bonds(gra), bnd_keys))
atm_vals[numpy.equal(atm_vals, None)] = -numpy.inf
bnd_vals[numpy.equal(bnd_vals, None)] = -numpy.inf
frz_atms = tuple(zip(atm_keys, map(tuple, atm_vals)))
frz_bnds = tuple(zip(bnd_keys, map(tuple, bnd_vals)))
return (frz_atms, frz_bnds)