def test_bond_assignment():
# Check that if the pair isn't found then a length is still returned
assert 1.4 < bonds.get_avg_bond_length(atom_i_label='X',
atom_j_label='X') < 1.6
# Check that if the pair isn't found but the VdW radii are defined then
# return something sensible
assert 2.0 < bonds.get_avg_bond_length(atom_i_label='Ir',
atom_j_label='As') < 3.0
# CH bond should be ~1.1 Å
assert 0.8 < bonds.get_avg_bond_length(atom_i_label='C',
atom_j_label='H') < 1.2
def set_attack_r0(self, species, shift_factor):
"""Set the ideal distance between a and c atoms in a substitution
centre"""
r0 = get_avg_bond_length(atom_i_label=species.atoms[self.a_atom].label,
atom_j_label=species.atoms[self.c_atom].label)
self.r0_ac = shift_factor * r0
return None
def add_capping_atom(atom_index, n_atom_index, graph, s_molecule):
"""
Add a capping atom. Example::
H
/
C_a---C_b - H -> C_a--H where C_a is numbered atom_index,
\ C_b is numbered n_atom_index
\
H
Arguments:
atom_index (int):
n_atom_index (int):
graph (nx.Graph): Current molecular graph of the stripped/truncated
molecule
s_molecule (autode.species.Species): Stripped molecule
"""
logger.info(f'Swapping saturated carbon {n_atom_index} next to atom '
f'{atom_index} for hydrogen')
graph.add_node(n_atom_index, atom_label='H', stereo=False)
# Relabel the atom in the stripped molecule
s_molecule.atoms[n_atom_index].label = 'H'
# Shift the added capping hydrogen to the 'ideal' E-H bond length
curr_dist = s_molecule.distance(atom_index, n_atom_index)
ideal_dist = get_avg_bond_length(s_molecule.atoms[atom_index].label, 'H')
shift_vec = (s_molecule.atoms[n_atom_index].coord -
s_molecule.atoms[atom_index].coord)
shift_vec *= (ideal_dist - curr_dist) / curr_dist
s_molecule.atoms[n_atom_index].translate(vec=shift_vec)
return None
def add_stereochem(self, central_atom):
"""
Adds stereochemistry around an atom, by placing atoms are the correct
coordinates for the stereochemistry. For tetrahedral centres, '@'
means looking along the bond from the first atom bonded to the centre,
the other atoms go anticlockwise in their index order in the atoms
list. For alkene centres, '@' means the atoms go anticlockwise in their
index order in the atoms list (this works as the same thing is applied
to every centre)
Arguments:
central_atom (int): index of the atom having stereochemistry added
around it
"""
vectors_dict = {
'@td':
np.array(([0, 0, 1], [0, 2 * np.sqrt(2) / 3, -1 / 3],
[-np.sqrt(2 / 3), -np.sqrt(2) / 3,
-1 / 3], [np.sqrt(2 / 3), -np.sqrt(2) / 3, -1 / 3])),
'@@td':
np.array(([0, 0, 1], [0, 2 * np.sqrt(2) / 3, -1 / 3],
[np.sqrt(2 / 3), -np.sqrt(2) / 3,
-1 / 3], [-np.sqrt(2 / 3), -np.sqrt(2) / 3, -1 / 3])),
'@al':
np.array(([1.0, 0.0, 0.0], [-0.5, np.sqrt(3) / 2,
0], [-0.5, -np.sqrt(3) / 2, 0])),
'@@al':
np.array(([1.0, 0.0, 0.0], [-0.5, -np.sqrt(3) / 2,
0], [-0.5, np.sqrt(3) / 2, 0]))
}
vectors = vectors_dict[self.stereochem_dict[central_atom]]
self.stereocentres.append(central_atom)
central_translation = -1 * self.atoms[central_atom].coord
# centre the central atom
self.shift_atom(central_atom, central_translation)
bonded_atoms = []
for i, bond in enumerate(self.bonds):
# get the bonded atom in the order meant for the stereochemistry
if bond[0] == central_atom:
bonded_atom = bond[1]
elif bond[1] == central_atom:
bonded_atom = bond[0]
else:
continue
if self.stereochem_dict[central_atom] in ['@td', '@@td']:
# for tetrahedral centres, this is how the ordering is defined
if self.atoms[bonded_atom].label == 'H':
if bonded_atoms[0] < central_atom:
bonded_atoms.insert(1, bonded_atom)
else:
bonded_atoms.insert(0, bonded_atom)
elif i in self.ring_closing_bond_list:
bonded_atoms.insert(0, bonded_atom)
else:
bonded_atoms.append(bonded_atom)
else:
bonded_atoms.append(bonded_atom)
for i, bonded_atom in enumerate(bonded_atoms):
if bonded_atom in self.stereocentres:
# don't want to lose the orientation around the old
# stereocentres, so rotate it into the right position
self.rotate_stereocluster(central_atom, bonded_atom,
vectors[i])
bond_length = get_avg_bond_length(self.atoms[central_atom].label,
self.atoms[bonded_atom].label)
bonded_translation = (bond_length * vectors[i] -
self.atoms[bonded_atom].coord)
self.shift_atom(bonded_atom, bonded_translation, central_atom)
self.add_cluster([central_atom] + bonded_atoms)
def make_graph(species,
rel_tolerance=0.25,
bond_list=None,
allow_invalid_valancies=False):
"""
Make the molecular graph from the 'bonds' determined on a distance criteria
or a smiles parser object. All attributes default to false::
Nodes attributes;
(0) atom_label: Atomic symbol of this atom
(1) stereo: Is this atom part of some stereochemistry e.g. R/S or
E/Z
Edge attributes;
(1) pi: Is this bond a pi bond. If it is then there should be no
rotation the bond axis in conformer generation
(2) active: Is this bond being made/broken
(applies only to TransitionState objects)
Arguments:
species (autode.species.Species):
Keyword Arguments:
rel_tolerance (float):
bond_list (list(tuple)):
allow_invalid_valancies (bool):
"""
logger.info('Generating molecular graph with NetworkX')
graph = nx.Graph()
# Add the atoms to the graph all are initially assumed not to be
# stereocenters
for i in range(species.n_atoms):
graph.add_node(i, atom_label=species.atoms[i].label, stereo=False)
# If bonds are specified then add edges to the graph and return
if bond_list is not None:
for bond in bond_list:
graph.add_edge(bond[0], bond[1], pi=False, active=False)
species.graph = graph
return None
else:
# Loop over the unique pairs of atoms and add 'bonds'
coords = species.coordinates
dist_mat = distance_matrix(coords, coords)
for i in get_atom_ids_sorted_type(species):
# Iterate through the closest atoms to atom i
for j in np.argsort(dist_mat[i]):
if i == j:
# Don't bond atoms to themselves
continue
# Get r_avg for this X-Y bond e.g. C-C -> 1.5
avg_bond_length = get_avg_bond_length(species.atoms[i].label,
species.atoms[j].label)
# If the distance between atoms i and j are less or equal to
# 1.25x average length add a 'bond'
if (dist_mat[i, j] <= avg_bond_length * (1.0 + rel_tolerance)
and (i, j) not in graph.edges):
graph.add_edge(i, j, pi=False, active=False)
species.graph = graph
set_graph_attributes(species)
if not allow_invalid_valancies:
remove_bonds_invalid_valancies(species)
return None