def set_atom_implicit_hydrogen_valences(gra, atm_imp_hyd_vlc_dct):
""" set atom implicit hydrogen valences
"""
atm_dct = mdict.set_by_key_by_position(atoms(gra), atm_imp_hyd_vlc_dct,
ATM_IMP_HYD_VLC_POS)
bnd_dct = bonds(gra)
return _create.from_atoms_and_bonds(atm_dct, bnd_dct)
def add_atoms(gra, symb_dct, imp_hyd_vlc_dct=None, ste_par_dct=None):
""" add atoms to this molecular graph, setting their keys
"""
atm_keys = atom_keys(gra)
atm_symb_dct = atom_symbols(gra)
atm_imp_hyd_vlc_dct = atom_implicit_hydrogen_valences(gra)
atm_ste_par_dct = atom_stereo_parities(gra)
keys = set(symb_dct.keys())
imp_hyd_vlc_dct = {} if imp_hyd_vlc_dct is None else imp_hyd_vlc_dct
ste_par_dct = {} if ste_par_dct is None else ste_par_dct
assert not keys & atm_keys
assert set(imp_hyd_vlc_dct.keys()) <= keys
assert set(ste_par_dct.keys()) <= keys
atm_symb_dct.update(symb_dct)
atm_imp_hyd_vlc_dct.update(imp_hyd_vlc_dct)
atm_ste_par_dct.update(ste_par_dct)
atm_dct = _create.atoms_from_data(
atom_symbols=atm_symb_dct,
atom_implicit_hydrogen_valences=atm_imp_hyd_vlc_dct,
atom_stereo_parities=atm_ste_par_dct)
bnd_dct = bonds(gra)
gra = _create.from_atoms_and_bonds(atoms=atm_dct, bonds=bnd_dct)
return gra
def add_bonds(xgr, keys, ord_dct=None, ste_par_dct=None):
""" add bonds to this molecular graph
"""
bnd_keys = set(bond_keys(xgr))
bnd_ord_dct = bond_orders(xgr)
bnd_ste_par_dct = bond_stereo_parities(xgr)
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
assert not 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(xgr)
bnd_dct = _create.bonds_from_data(bond_keys=bnd_keys,
bond_orders=bnd_ord_dct,
bond_stereo_parities=bnd_ste_par_dct)
xgr = _create.from_atoms_and_bonds(atoms=atm_dct, bonds=bnd_dct)
return xgr
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
ord_dct = dict_.transform_keys(ord_dct, frozenset)
ste_par_dct = dict_.transform_keys(ste_par_dct, frozenset)
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 subgraph(xgr, atm_keys):
""" the subgraph induced by a subset of the atoms
"""
atm_keys = set(atm_keys)
assert atm_keys <= atom_keys(xgr)
bnd_keys = set(filter(lambda x: x <= atm_keys, bond_keys(xgr)))
atm_dct = dict_.by_key(atoms(xgr), atm_keys)
bnd_dct = dict_.by_key(bonds(xgr), bnd_keys)
return _create.from_atoms_and_bonds(atm_dct, bnd_dct)
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 remove_bonds(xgr, bnd_keys):
""" remove bonds from the molecular graph
"""
all_bnd_keys = bond_keys(xgr)
bnd_keys = set(bnd_keys)
assert bnd_keys <= all_bnd_keys
bnd_keys = all_bnd_keys - bnd_keys
atm_dct = atoms(xgr)
bnd_dct = dict_.by_key(bonds(xgr), bnd_keys)
return _create.from_atoms_and_bonds(atm_dct, bnd_dct)
def bond_induced_subgraph(xgr, bnd_keys, saddle=False):
""" 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(xgr)
if not saddle:
assert bnd_keys <= bond_keys(xgr)
atm_dct = dict_.by_key(atoms(xgr), atm_keys)
bnd_dct = dict_.by_key(bonds(xgr), bnd_keys)
return _create.from_atoms_and_bonds(atm_dct, bnd_dct)
def union(xgr1, xgr2):
""" a union of two graphs
"""
assert not atom_keys(xgr1) & atom_keys(xgr2)
atm_dct = {}
atm_dct.update(atoms(xgr1))
atm_dct.update(atoms(xgr2))
bnd_dct = {}
bnd_dct.update(bonds(xgr1))
bnd_dct.update(bonds(xgr2))
return _create.from_atoms_and_bonds(atm_dct, bnd_dct)
def bond_induced_subgraph(gra, bnd_keys, stereo=False):
""" 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)
sub = _create.from_atoms_and_bonds(atm_dct, bnd_dct)
if not stereo:
sub = without_stereo_parities(sub)
return sub
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 subgraph(gra, atm_keys, stereo=False):
""" the subgraph induced by a subset of the atoms
:param gra: the graph
:param atm_keys: the atom keys to be included in the subgraph
:param stereo: whether or not to include stereo in the subgraph
:returns: the subgraph
"""
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)
sub = _create.from_atoms_and_bonds(atm_dct, bnd_dct)
if not stereo:
sub = without_stereo_parities(sub)
return sub
def relabel(xgr, atm_key_dct):
""" relabel the graph with new atom keys
"""
orig_atm_keys = atom_keys(xgr)
assert set(atm_key_dct.keys()) <= orig_atm_keys
new_atm_key_dct = dict(zip(orig_atm_keys, orig_atm_keys))
new_atm_key_dct.update(atm_key_dct)
_relabel_atom_key = new_atm_key_dct.__getitem__
def _relabel_bond_key(bnd_key):
return frozenset(map(_relabel_atom_key, bnd_key))
atm_dct = dict_.transform_keys(atoms(xgr), _relabel_atom_key)
bnd_dct = dict_.transform_keys(bonds(xgr), _relabel_bond_key)
return _create.from_atoms_and_bonds(atm_dct, bnd_dct)
def from_yaml_dictionary(yaml_gra_dct, one_indexed=True):
""" read the graph from a yaml dictionary
"""
atm_dct = yaml_gra_dct['atoms']
bnd_dct = yaml_gra_dct['bonds']
atm_dct = dict_.transform_values(
atm_dct, lambda x: tuple(map(x.__getitem__, ATM_PROP_NAMES)))
bnd_dct = dict_.transform_keys(bnd_dct,
lambda x: frozenset(map(int, x.split('-'))))
bnd_dct = dict_.transform_values(
bnd_dct, lambda x: tuple(map(x.__getitem__, BND_PROP_NAMES)))
gra = _create.from_atoms_and_bonds(atm_dct, bnd_dct)
if one_indexed:
# revert one-indexing if the input is one-indexed
atm_key_dct = {atm_key: atm_key - 1 for atm_key in atom_keys(gra)}
gra = relabel(gra, atm_key_dct)
return gra
def from_string(gra_str):
""" read the graph from a string
"""
yaml_gra_dct = yaml.load(gra_str, Loader=yaml.FullLoader)
atm_dct = yaml_gra_dct['atoms']
bnd_dct = yaml_gra_dct['bonds']
atm_dct = dict_.transform_values(
atm_dct, lambda x: tuple(map(x.__getitem__, ATM_PROP_NAMES)))
bnd_dct = dict_.transform_keys(
bnd_dct, lambda x: frozenset(map(int, x.split('-'))))
bnd_dct = dict_.transform_values(
bnd_dct, lambda x: tuple(map(x.__getitem__, BND_PROP_NAMES)))
gra = _create.from_atoms_and_bonds(atm_dct, bnd_dct)
# shift back to zero-indexing when we read it in
atm_key_dct = {atm_key: atm_key-1 for atm_key in atom_keys(gra)}
gra = relabel(gra, atm_key_dct)
return gra
def set_bond_stereo_parities(sgr, bnd_par_dct):
""" set bond parities
"""
bnd_dct = mdict.set_by_key_by_position(bonds(sgr), bnd_par_dct,
BND_STE_PAR_POS)
return _create.from_atoms_and_bonds(atoms(sgr), bnd_dct)
def set_atom_stereo_parities(sgr, atm_par_dct):
""" set atom parities
"""
atm_dct = mdict.set_by_key_by_position(atoms(sgr), atm_par_dct,
ATM_STE_PAR_POS)
return _create.from_atoms_and_bonds(atm_dct, bonds(sgr))
def set_bond_orders(rgr, bnd_ord_dct):
""" set bond orders
"""
bnd_dct = mdict.set_by_key_by_position(bonds(rgr), bnd_ord_dct,
BND_ORD_POS)
return _create.from_atoms_and_bonds(atoms(rgr), bnd_dct)
