def is_bonded_to(self, other_atom, n_vdw_radii=1.2, default_vdw_radius=2.0*Angstroms):
#TODO deal with units
dist = magnitude(self.xyz - other_atom.xyz)
vdw_me = self.element.vdw_radius
if vdw_me is None:
vdw_me = default_vdw_radius
vdw_me = strip_units(vdw_me, convert_to=self.cartesian_units, assume_units=DistanceUnit.default)
vdw_other = self.element.vdw_radius
if vdw_other is None:
vdw_other = default_vdw_radius
vdw_other = strip_units(vdw_other, convert_to=self.cartesian_units, assume_units=DistanceUnit.default)
return dist < (vdw_me * n_vdw_radii/2 + vdw_other * n_vdw_radii/2)
def _is_valid_key_for(self, key, item):
if key is item:
return True
keysyms = tuple(a.full_symbol for a in key)
itsyms = tuple(a.full_symbol for a in item)
if keysyms != itsyms:
return False
kvals = strip_units(self.key_representation.values_for_molecule(key),
DistanceUnit.default,
assume_units=key.cartesian_units)
itvals = strip_units(self.key_representation.values_for_molecule(item),
DistanceUnit.default,
assume_units=item.cartesian_units)
cutoff = 10**(-self.equality_digits)
return np.all(abs(kvals - itvals) < abs(cutoff * kvals))
def _is_valid_key_for(self, key, item):
if key is item:
return True
keysyms = tuple(a.full_symbol for a in key)
itsyms = tuple(a.full_symbol for a in item)
if keysyms != itsyms:
return False
kvals = strip_units(self.key_representation.values_for_molecule(key),
DistanceUnit.default,
assume_units=key.cartesian_units)
itvals = strip_units(self.key_representation.values_for_molecule(item),
DistanceUnit.default,
assume_units=item.cartesian_units)
cutoff = 10**(-self.equality_digits)
return np.all(abs(kvals - itvals) < abs(cutoff*kvals))
def _key_chain_str(self, item):
itsyms = tuple(a.full_symbol for a in item)
items = self._heads[itsyms]
itvals = strip_units(self.key_representation.values_for_molecule(item),
DistanceUnit.default,
assume_units=item.cartesian_units)
itvals = [i * self._hash_mult for i in itvals]
return self._r_key_chain_str(items, itvals, "")
def _get_possibilities(self, item, create=True):
itsyms = tuple(a.full_symbol for a in item)
items = self._heads[itsyms]
itvals = strip_units(self.key_representation.values_for_molecule(item),
DistanceUnit.default,
assume_units=item.cartesian_units)
itvals = [i * self._hash_mult for i in itvals]
return self._r_get_possibilities(items, itvals, create)
def _key_chain_str(self, item):
itsyms = tuple(a.full_symbol for a in item)
items = self._heads[itsyms]
itvals = strip_units(self.key_representation.values_for_molecule(item),
DistanceUnit.default,
assume_units=item.cartesian_units)
itvals = [i * self._hash_mult for i in itvals]
return self._r_key_chain_str(items, itvals, "")
def _get_possibilities(self, item, create=True):
itsyms = tuple(a.full_symbol for a in item)
items = self._heads[itsyms]
itvals = strip_units(self.key_representation.values_for_molecule(item),
DistanceUnit.default,
assume_units=item.cartesian_units)
itvals = [i * self._hash_mult for i in itvals]
return self._r_get_possibilities(items, itvals, create)
def is_bonded_to(self,
other_atom,
n_vdw_radii=1.2,
default_vdw_radius=2.0 * Angstroms):
#TODO deal with units
dist = magnitude(self.xyz - other_atom.xyz)
vdw_me = self.element.vdw_radius
if vdw_me is None:
vdw_me = default_vdw_radius
vdw_me = strip_units(vdw_me,
convert_to=self.cartesian_units,
assume_units=DistanceUnit.default)
vdw_other = self.element.vdw_radius
if vdw_other is None:
vdw_other = default_vdw_radius
vdw_other = strip_units(vdw_other,
convert_to=self.cartesian_units,
assume_units=DistanceUnit.default)
return dist < (vdw_me * n_vdw_radii / 2 + vdw_other * n_vdw_radii / 2)
