def compute_bonds(self, symbols, mapper=None, bond_extra=0.45):
"""
Update bonds based on radii and an extra factor (in atomic units).
.. code-block:: Python
symbols = universe.atom['symbol']
mapper = {'C': 2.0} # atomic units - Bohr
bond_extra = 0.2 # ditto
# updates universe.atom_two['bond']
universe.atom_two.compute_bonds(symbols, mapper, bond_extra)
Args:
symbols: Series of symbols from the atom table (e.g. uni.atom['symbol'])
mapper (dict): Dictionary of symbol, radii pairs (see note below)
bond_extra (float): Extra additive factor to include when computing bonds
Note:
If the mapper is none, or is missing data, the computation will use
default covalent radii available in :class:`~exa.relational.isotope`.
"""
if mapper is None:
mapper = symbol_to_radius()
elif not all(symbol in mapper for symbol in symbols.unique()):
sym2rad = symbol_to_radius()
for symbol in symbols.unique():
if symbol not in mapper:
mapper[symbol] = sym2rad[symbol]
# Note that the mapper is transformed here, but the same name is used...
mapper = symbols.astype(str).map(mapper)
radius0 = self['atom0'].map(mapper)
radius1 = self['atom1'].map(mapper)
mbl = radius0 + radius1 + bond_extra
self['bond'] = self['distance'] <= mbl
def _custom_traits(self):
'''
Create creates for the atomic size (using the covalent radius) and atom
colors (using the common `Jmol`_ color scheme). Note that that data is
present in the static data (see :mod:`~exa.relational.isotope`).
.. _Jmol: http://jmol.sourceforge.net/jscolors/
'''
self._set_categories()
grps = self.groupby('frame')
symbols = grps.apply(lambda g: g['symbol'].cat.codes.values) # Pass integers rather than string symbols
symbols = Unicode(symbols.to_json(orient='values')).tag(sync=True)
symmap = {i: v for i, v in enumerate(self['symbol'].cat.categories)}
sym2rad = symbol_to_radius()
radii = sym2rad[self['symbol'].unique()]
radii = Dict({i: radii[v] for i, v in symmap.items()}).tag(sync=True) # (Int) symbol radii
sym2col = symbol_to_color()
colors = sym2col[self['symbol'].unique()] # Same thing for colors
colors = Dict({i: colors[v] for i, v in symmap.items()}).tag(sync=True)
try:
atom_set = grps.apply(lambda g: g['set'].values).to_json(orient='values')
atom_set = Unicode(atom_set).tag(sync=True)
except KeyError:
atom_set = Unicode().tag(sync=True)
# Note that position traits (atom_x, atom_y, atom_z) are created automatically
# since we have defined _traits = ['x', 'y', 'z'] above.
return {'atom_symbols': symbols, 'atom_radii': radii, 'atom_colors': colors,
'atom_set': atom_set}
def _custom_traits(self):
"""
Create creates for the atomic size (using the covalent radius) and atom
colors (using the common `Jmol`_ color scheme). Note that that data is
present in the static data (see :mod:`~exa.relational.isotope`).
.. _Jmol: http://jmol.sourceforge.net/jscolors/
"""
self._set_categories()
kwargs = {}
grps = self.cardinal_groupby()
symbols = grps.apply(lambda g: g['symbol'].cat.codes.values) # Pass integers rather than string symbols
kwargs['atom_symbols'] = Unicode(symbols.to_json(orient='values')).tag(sync=True)
symmap = {i: v for i, v in enumerate(self['symbol'].cat.categories)}
sym2rad = symbol_to_radius()
radii = sym2rad[self['symbol'].unique()]
kwargs['atom_radii'] = Dict({i: radii[v] for i, v in symmap.items()}).tag(sync=True) # (Int) symbol radii
sym2col = symbol_to_color()
colors = sym2col[self['symbol'].unique()] # Same thing for colors
kwargs['atom_colors'] = Dict({i: colors[v] for i, v in symmap.items()}).tag(sync=True)
return kwargs
