def compute_element_masses(self, inplace=False):
'''
Map element symbols to their corresponding (element) mass.
Args:
inplace (bool): Add as a column (default false - return series)
'''
elem_mass = symbol_to_element_mass()
mass = self['symbol'].astype('O').map(elem_mass)
if inplace:
self['mass'] = masses
else:
return masses
def compute_molecule(universe):
"""
Cluster atoms into molecules and create the :class:`~exatomic.molecule.Molecule`
table.
Args:
universe: Atomic universe
Returns:
molecule: Molecule table
Warning:
This function modifies the universe's atom (:class:`~exatomic.atom.Atom`)
table in place!
"""
nodes = universe.atom.index.values
bonded = universe.atom_two.ix[universe.atom_two["bond"] == True, ["atom0", "atom1"]]
edges = zip(bonded["atom0"].astype(np.int64), bonded["atom1"].astype(np.int64))
g = nx.Graph()
g.add_nodes_from(nodes)
g.add_edges_from(edges)
# generate molecule indices for the atom table
mapper = {}
i = 0
for k, v in g.degree().items(): # First handle single atom "molecules"
if v == 0:
mapper[k] = i
i += 1
for seht in connected_components(g): # Second handle multi atom molecules
for adx in seht:
mapper[adx] = i
i += 1
universe.atom["molecule"] = universe.atom.index.map(lambda x: mapper[x])
sym2mass = symbol_to_element_mass()
universe.atom["mass"] = universe.atom["symbol"].map(sym2mass)
grps = universe.atom.groupby("molecule")
molecule = grps["symbol"].value_counts().unstack().fillna(0).astype(np.int64)
molecule.columns.name = None
molecule["mass"] = grps["mass"].sum()
universe.atom["molecule"] = universe.atom["molecule"].astype("category")
del universe.atom["mass"]
return molecule
def get_element_masses(self):
"""Compute and return element masses from symbols."""
elem_mass = symbol_to_element_mass()
return self['symbol'].astype('O').map(elem_mass)
