def add_atoms(gra, sym_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_sym_dct = atom_symbols(gra)
atm_imp_hyd_vlc_dct = atom_implicit_hydrogen_valences(gra)
atm_ste_par_dct = atom_stereo_parities(gra)
keys = set(sym_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_sym_dct.update(sym_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_sym_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 bond_symmetry_numbers(gra, frm_bnd_key=None, brk_bnd_key=None):
""" symmetry numbers, by bond
the (approximate) symmetry number of the torsional potential for this bond,
based on the hydrogen counts for each atom
It is reduced to 1 if one of the H atoms in the torsional bond is a
neighbor to the special bonding atom (the atom that is being transferred)
"""
imp_gra = implicit(gra)
atm_imp_hyd_vlc_dct = atom_implicit_hydrogen_valences(imp_gra)
bnd_keys = bond_keys(imp_gra)
tfr_atm = None
if frm_bnd_key and brk_bnd_key:
for atm_f in list(frm_bnd_key):
for atm_b in list(brk_bnd_key):
if atm_f == atm_b:
tfr_atm = atm_f
if tfr_atm:
neighbor_dct = atom_neighbor_keys(gra)
nei_tfr = neighbor_dct[tfr_atm]
atms = gra[0]
all_hyds = []
for atm in atms:
if atms[atm][0] == 'H':
all_hyds.append(atm)
else:
nei_tfr = {}
bnd_sym_num_dct = {}
bnd_sym_nums = []
for bnd_key in bnd_keys:
bnd_sym = 1
vlc = max(map(atm_imp_hyd_vlc_dct.__getitem__, bnd_key))
if vlc == 3:
bnd_sym = 3
if tfr_atm:
for atm in nei_tfr:
nei_s = neighbor_dct[atm]
h_nei = 0
for nei in nei_s:
if nei in all_hyds:
h_nei += 1
if h_nei == 3:
bnd_sym = 1
bnd_sym_nums.append(bnd_sym)
bnd_sym_num_dct = dict(zip(bnd_keys, bnd_sym_nums))
# fill in the rest of the bonds for completeness
bnd_sym_num_dct = dict_.by_key(bnd_sym_num_dct, bond_keys(gra), fill_val=1)
return bnd_sym_num_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 add_atom_implicit_hydrogen_valences(gra, inc_atm_imp_hyd_vlc_dct):
""" add atom imlicit hydrogen valences
(increments can be positive or negative)
"""
atm_keys = list(inc_atm_imp_hyd_vlc_dct.keys())
atm_imp_hyd_vlcs = numpy.add(
dict_.values_by_key(atom_implicit_hydrogen_valences(gra), atm_keys),
dict_.values_by_key(inc_atm_imp_hyd_vlc_dct, atm_keys))
assert all(atm_imp_hyd_vlc >= 0 for atm_imp_hyd_vlc in atm_imp_hyd_vlcs)
atm_imp_hyd_vlc_dct = dict_.transform_values(
dict(zip(atm_keys, atm_imp_hyd_vlcs)), int)
return set_atom_implicit_hydrogen_valences(gra, atm_imp_hyd_vlc_dct)
def from_graph(gra):
""" networkx graph object from a molecular graph
"""
nxg = networkx.Graph()
nxg.add_nodes_from(atom_keys(gra))
nxg.add_edges_from(bond_keys(gra))
networkx.set_node_attributes(nxg, atom_symbols(gra), 'symbol')
networkx.set_node_attributes(nxg, atom_implicit_hydrogen_valences(gra),
'implicit_hydrogen_valence')
networkx.set_node_attributes(nxg, atom_stereo_parities(gra),
'stereo_parity')
networkx.set_edge_attributes(nxg, bond_orders(gra), 'order')
networkx.set_edge_attributes(nxg, bond_stereo_parities(gra),
'stereo_parity')
return nxg
def explicit(gra, atm_keys=None):
""" make the hydrogens at these atoms explicit
"""
atm_keys = backbone_keys(gra) if atm_keys is None else atm_keys
atm_keys = sorted(atm_keys)
atm_imp_hyd_vlc_dct = dict_.by_key(atom_implicit_hydrogen_valences(gra),
atm_keys)
atm_exp_hyd_keys_dct = {}
next_atm_key = max(atom_keys(gra)) + 1
for atm_key in atm_keys:
imp_hyd_vlc = atm_imp_hyd_vlc_dct[atm_key]
atm_exp_hyd_keys_dct[atm_key] = set(
range(next_atm_key, next_atm_key + imp_hyd_vlc))
next_atm_key += imp_hyd_vlc
gra = set_atom_implicit_hydrogen_valences(
gra, dict_.by_key({}, atm_keys, fill_val=0))
gra = add_atom_explicit_hydrogen_keys(gra, atm_exp_hyd_keys_dct)
return gra