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 = bonds_from_data(bnd_keys=bnd_keys,
bnd_ord_dct=bnd_ord_dct,
bnd_ste_par_dct=bnd_ste_par_dct)
gra = from_atoms_and_bonds(atm_dct=atm_dct, bnd_dct=bnd_dct)
return gra
def yaml_dictionary(gra, one_indexed=True):
""" generate a YAML dictionary representing a given graph
"""
if one_indexed:
# shift to one-indexing when we print
atm_key_dct = {atm_key: atm_key + 1 for atm_key in atom_keys(gra)}
gra = relabel(gra, atm_key_dct)
yaml_atm_dct = atoms(gra)
yaml_bnd_dct = bonds(gra)
# prepare the atom dictionary
yaml_atm_dct = dict(sorted(yaml_atm_dct.items()))
yaml_atm_dct = dict_.transform_values(
yaml_atm_dct, lambda x: dict(zip(ATM_PROP_NAMES, x)))
# perpare the bond dictionary
yaml_bnd_dct = dict_.transform_keys(yaml_bnd_dct,
lambda x: tuple(sorted(x)))
yaml_bnd_dct = dict(sorted(yaml_bnd_dct.items()))
yaml_bnd_dct = dict_.transform_keys(yaml_bnd_dct,
lambda x: '-'.join(map(str, x)))
yaml_bnd_dct = dict_.transform_values(
yaml_bnd_dct, lambda x: dict(zip(BND_PROP_NAMES, x)))
yaml_gra_dct = {'atoms': yaml_atm_dct, 'bonds': yaml_bnd_dct}
return yaml_gra_dct
def relabel(gra, atm_key_dct):
""" relabel the graph with new atom keys
"""
orig_atm_keys = atom_keys(gra)
assert set(atm_key_dct.keys()) <= orig_atm_keys, ('{}\n{}'.format(
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(gra), _relabel_atom_key)
bnd_dct = dict_.transform_keys(bonds(gra), _relabel_bond_key)
return 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 distance_ranges_from_coordinates(gra, dist_dct, ang_dct=None, dih_dct=None,
angstrom=True, degree=True,
rings_keys=(), keys=None, check=False):
""" generate a set of distance ranges from coordinate values
:param gra: molecular graph
atom keys specifying the order of indices in the matrix
:param dist_dct: a dictionary of desired distances for certain atoms; the
keys are pairs of atoms, the values are distances in angstroms
:type dist_dct: dict[(int, int): float]
:param ang_dct: a dictionary of desired angles for certain atoms; the keys
are triples of atoms; if the first or last element in a triple is None,
an appopriate neighboring atom will be found
:param dih_dct: a dictionary of desired angles for certain atoms; the keys
are quadruples of atoms; if the first or last element in a triple is
None, an appopriate neighboring atom will be found
:type dist_dct: dict[(int, int, int): float]
:param rings_keys: keys for rings in the graph; angle ranges will
automatically be set to allow ring formation
:param keys: set of keys that can be used to fill in the angle keys; if
None, all graph keys will be considered available for use
:param check: check the angle keys to make sure they can all be filled in?
"""
keys = atom_keys(gra) if keys is None else keys
ang_dct = {} if ang_dct is None else ang_dct
dih_dct = {} if dih_dct is None else dih_dct
# Fill in angle keys
ang_key_filler_ = angle_key_filler_(gra, keys, check=check)
ang_dct = dict_.transform_keys(ang_dct, ang_key_filler_)
if None in ang_dct:
ang_dct.pop(None)
# Fill in dihedral keys
dih_dct = dict_.transform_keys(dih_dct, ang_key_filler_)
if None in dih_dct:
dih_dct.pop(None)
# Convert angles into distances
dist_dct = dict_.transform_keys(dist_dct, frozenset)
for (key1, key2, key3), a123 in ang_dct.items():
a123 *= phycon.DEG2RAD if degree else 1.
k12 = frozenset({key1, key2})
k23 = frozenset({key2, key3})
k13 = frozenset({key1, key3})
d12 = (dist_dct[k12] if k12 in dist_dct else
heuristic_bond_distance(gra, key1, key2, angstrom=angstrom))
d23 = (dist_dct[k23] if k23 in dist_dct else
heuristic_bond_distance(gra, key2, key3, angstrom=angstrom))
d13 = numpy.sqrt(d12**2 + d23**2 - 2*d12*d23*numpy.cos(a123))
dist_dct[k13] = d13
# Convert convert fixed distances into ranges
dist_range_dct = {k: (d, d) for k, d in dist_dct.items()}
# Convert dihedrals into distances
for (key1, key2, key3, key4), val in dih_dct.items():
# Allow user to leave dihedrals open-ended, as a lower or upper bound
if isinstance(val, numbers.Number):
d1234 = val
else:
assert hasattr(val, '__len__') and len(val) == 2
d1234 = next(v for v in val if v is not None)
d1234 *= phycon.DEG2RAD if degree else 1.
k12 = frozenset({key1, key2})
k23 = frozenset({key2, key3})
k34 = frozenset({key3, key4})
k13 = frozenset({key1, key3})
k24 = frozenset({key2, key4})
k14 = frozenset({key1, key4})
d12 = (dist_dct[k12] if k12 in dist_dct else
heuristic_bond_distance(gra, key1, key2, angstrom=angstrom))
d23 = (dist_dct[k23] if k23 in dist_dct else
heuristic_bond_distance(gra, key2, key3, angstrom=angstrom))
d34 = (dist_dct[k34] if k34 in dist_dct else
heuristic_bond_distance(gra, key3, key4, angstrom=angstrom))
d13 = (dist_dct[k13] if k13 in dist_dct else
heuristic_bond_distance(gra, key1, key3, angstrom=angstrom))
d24 = (dist_dct[k24] if k24 in dist_dct else
heuristic_bond_distance(gra, key2, key4, angstrom=angstrom))
term1 = (d12**2 + d23**2 - d13**2)*(d23**2 + d34**2 - d24**2)
term2 = 2*d23**2 * (d13**2 + d24**2 - d23**2)
denom = numpy.sqrt(
(4*d12**2 * d23**2 - (d12**2 + d23**2 - d13**2)**2) *
(4*d23**2 * d34**2 - (d23**2 + d34**2 - d24**2)**2))
d14 = numpy.sqrt((term1 + term2 - numpy.cos(d1234) * denom) /
(2 * d23**2))
if isinstance(val, numbers.Number) or val[0] == val[1]:
dist_range_dct[k14] = (d14, d14)
elif val[0] is None:
ld14 = closest_approach(gra, key1, key4)
dist_range_dct[k14] = (ld14, d14)
elif val[1] is None:
ud14 = 999.
dist_range_dct[k14] = (d14, ud14)
else:
raise ValueError("Invalid dih_dict: {}".format(str(dih_dct)))
for rng_keys in rings_keys:
assert hasattr(keys, '__iter__'), (
"Please pass in rings keys as a list of lists")
rsz = len(rng_keys)
a123 = (rsz - 2.) * 180. / rsz
la123 = (a123 - 10.) * phycon.DEG2RAD
ua123 = (a123 + 10.) * phycon.DEG2RAD
for key1, key2, key3 in mit.windowed(rng_keys + rng_keys[:2], 3):
k12 = frozenset({key1, key2})
k23 = frozenset({key2, key3})
k13 = frozenset({key1, key3})
d12 = (dist_dct[k12] if k12 in dist_dct else
heuristic_bond_distance(gra, key1, key2, angstrom=angstrom))
d23 = (dist_dct[k23] if k23 in dist_dct else
heuristic_bond_distance(gra, key2, key3, angstrom=angstrom))
ld13 = numpy.sqrt(d12**2 + d23**2 - 2*d12*d23*numpy.cos(la123))
ud13 = numpy.sqrt(d12**2 + d23**2 - 2*d12*d23*numpy.cos(ua123))
dist_range_dct[k13] = (ld13, ud13)
return dist_range_dct