def run(pluginManager):
"""
Entry point for the plugin manager
:param configx: plugin manager instance
:return: None
"""
printer = pluginManager.setup()
molecule = quickLoad(pluginManager, pluginManager.arg('load'))
printer('Filtering Atoms:')
for atom in iter_atoms(molecule):
if filter_atom(pluginManager, atom, 'atomfilter'):
printer(atom)
printer.spacer()
printer('\nFiltering Atom Pairs:')
for atom1, atom2 in iter_atom_pairs(molecule, bound=False, unique=False):
if filter_atom_pair(pluginManager, atom1, atom2, 'atomfilter', 'secondfilter'):
printer('{} {}'.format(atom1.get_name(), atom2.get_name()))
printer.spacer()
printer('\nUsing Custom Filter Function:')
filter.register_custom_fuction('firstOf', firstOfElement)
for atom in iter_atoms(molecule):
if filter_atom(pluginManager, atom, 'customfilter'):
printer(atom)
def run(pluginManager):
"""
Entry point for the plugin manager
:param pluginManager: plugin manager instance
:return: None
"""
printer = pluginManager.setup()
molecule = quickLoad(pluginManager, pluginManager.arg("load"))
printer("Filtering Atoms:")
for atom in iter_atoms(molecule):
if filter_atom(pluginManager, atom, "atomfilter"):
printer(atom)
printer.spacer()
printer("\nFiltering Atom Pairs:")
for atom1, atom2 in iter_atom_pairs(molecule, bound=False, unique=False):
if filter_atom_pair(pluginManager, atom1, atom2, "atomfilter", "secondfilter"):
printer("{} {}".format(atom1.get_name(), atom2.get_name()))
printer.spacer()
printer("\nUsing Custom Filter Function:")
filter.register_custom_fuction("firstOf", firstOfElement)
for atom in iter_atoms(molecule):
if filter_atom(pluginManager, atom, "customfilter"):
printer(atom)
def expand(self, pluginManager):
printer = pluginManager.get_active_printer()
loader = pluginManager.get_variable('loader')
active_id = loader.get_active_id()
if not active_id.startswith('shelx'):
printer.highlight('Error: Wrong input file ID: {}.'.format(active_id))
printer('Molecule expansion currently only works with \'Shelxl\' type files.')
printer('Note: CIFs written by \'Shelxl\' will be supported soon.')
return
symmetry_elements = loader.get_symmetry()
lattice = float(loader.get_lattice())
if lattice > 0:
centric = True
else:
centric = False
symms = []
for symm in symmetry_elements:
symm = SymmetryElement(symm, centric=False)
symms.append(symm)
if centric:
symms.append(SymmetryElement(['-X', '-Y', '-Z']))
for symm in symmetry_elements:
symm = SymmetryElement(symm, centric=True)
symms.append(symm)
newatoms = []
asymunits = {str(symm): [] for symm in symms}
for atom in iter_atoms(self):
atom.normalize()
for symm in symms:
newatom = symm + atom
newatom.normalize()
if not atom - newatom < 0.1:
newatoms.append(newatom)
else:
atom.set_special(True)
asymunits[str(symm)].append(newatom)
for atom in newatoms:
self += atom