def run(pluginManager):
"""
This is the entry point for the plugin manager.
The plugin manager will pass a reference to itself
to the function.
Use the APD_Printer instance returned by
pluginManager.setup() instead of the 'print'
statement to generate autoformated cmd line output.
:param pluginManager: Reference to the plugin manager
instance.
"""
global printer
printer = pluginManager.setup()
data = pluginManager.get_variable('data')
molecule = data['exp']
printer.table(['Atom 1', 'Atom 2', 'Type', 'Distance'], head=True)
restraints = RestraintManager()
for atom1, atom2 in iter_atom_pairs(molecule, bound=False):
if atom1.get_element() == 'H' or atom2.get_element() == 'H':
continue
value = getBondNumber(atom1, atom2)
if value:
r = Restraint(value, atom1-atom2, atom1, atom2, 'exp')
printer.table('{:7>},{:7<},1-{},{:5.3f}'.format(atom1.get_name(),
atom2.get_name(),
value+1,
atom1-atom2).split(','))
restraints.add(atom1, atom2, r)
printer.table(done=True)
restraints = RestraintManager()
for molecule in data.values():
for atom1, atom2 in iter_atom_pairs(molecule, bound=False):
if atom1.get_element() == 'H' or atom2.get_element() == 'H':
continue
value = getBondNumber(atom1, atom2)
if value:
restraints.add(atom1, atom2, Restraint(value,
atom1.cartDistance(atom2),
atom1,
atom2,
modelCompound=molecule.name))
restraintList = restraints.harvestRestraints()
restraints.selfSum()
bondMap = restraints.mapBonds(restraintList)
with open(pluginManager.arg('write'), 'w') as fp:
fp.write('REM Invariom based geometry restraints:')
fp.write(''.join([str(r) for r in sorted(bondMap.keys(), key=lambda string: string[17:])]))
printer()
printer.spacer()
printer('\n{} written.'.format(pluginManager.arg('write')))
printer('\nAdd \'+{}\' to your shelxl instruction file\'s header.'.format(pluginManager.arg('write')))
def find_rings(atoms, bonds=None):
graph = Graph()
# bonds = None
class DummyMolecule(object):
pass
mol = DummyMolecule()
mol.atoms = atoms
if bonds is None:
for atom1, atom2 in iter_atom_pairs():
graph.add_edge(atom1.name, atom2.name)
else:
blacklist = []
for b in bonds:
for atom2i in b[1:10]:
string = ' : '.join(sorted([atoms[b[0]].name, atoms[atom2i].name]))
if not string in blacklist:
if is_bound(atoms[b[0]].cart, atoms[b[0]].element, atoms[atom2i].cart, atoms[atom2i].element):
graph.add_edge(atoms[b[0]].name, atoms[atom2i].name)
blacklist.append(string)
ring_list = cycle_basis(graph)
return ring_list
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)