def name(session, name, text=None):
if name == "all":
raise UserError("\"all\" is reserved and cannot be redefined")
if text is None:
from chimerax.core.commands import get_selector
try:
sel = get_selector(name)
except KeyError:
raise UserError("\"%s\" is not defined" % name)
else:
value = _get_name_desc(sel, True)
session.logger.info('\t'.join([name, value]))
else:
try:
ast, used, unused = AtomSpecArg.parse(text, session)
if unused:
raise AnnotationError("contains extra trailing text")
except AnnotationError as e:
raise UserError("\"%s\": %s" % (text, str(e)))
def selector(session, models, results, spec=text):
objects, used, unused = ObjectsArg.parse(spec, session)
results.combine(objects)
selector.name_text = text
from chimerax.core.commands import register_selector
register_selector(name, selector, session.logger)
def name(session, name, text=None, skip_check=False):
if name == "all":
raise UserError("\"all\" is reserved and cannot be shown or defined")
if text is None:
from chimerax.core.commands import get_selector_description
try:
desc = get_selector_description(name, session)
except KeyError:
raise UserError("\"%s\" is not defined" % name)
else:
if desc:
session.logger.info('\t'.join([name, desc]))
else:
if _is_reserved(name):
raise UserError("\"%s\" is reserved and cannot be redefined" %
name)
if not skip_check:
try:
ast, used, unused = AtomSpecArg.parse(text, session)
if unused:
raise AnnotationError("contains extra trailing text")
except AnnotationError as e:
raise UserError("\"%s\": %s" % (text, str(e)))
def selector(session, models, results, spec=text):
objects, used, unused = ObjectsArg.parse(spec, session)
results.combine(objects)
from chimerax.core.commands import register_selector
register_selector(name, selector, session.logger, user=True, desc=text)
session.basic_actions.define(name, text)
def name_frozen(session, name, objects):
if _is_reserved(name):
raise UserError("\"%s\" is reserved and cannot be redefined" % name)
if objects.empty():
raise UserError("nothing is selected by specifier")
from chimerax.core.commands import register_selector
register_selector(name, objects, session.logger, user=True)
session.basic_actions.define(name, objects)
def register(selector_name, logger):
"""Register selector with ChimeraX.
"""
# Registration is simply telling ChimeraX which function
# to call when the selector is used. If an unexpected
# selector_name is given, the dictionary lookup will fail,
# and the resulting exception will be caught by ChimeraX.
from chimerax.core.commands import register_selector
register_selector(selector_name, _selector_func[selector_name], logger)
def create_selector(self, mol, logger):
if self._is_subassembly():
name = self.id
sel_name = ('A' + name) if is_integer(name) else name
def _selector(session, models, results, self=self, mol=mol):
atoms = self._subassembly_atoms(mol)
results.add_atoms(atoms)
from chimerax.core.commands import register_selector
register_selector(sel_name, _selector, logger)
def register_selectors(logger):
def select(results, models, group):
from .chem_group import find_group
atoms = find_group(group, models, return_collection=True)
for m in atoms.unique_structures:
results.add_model(m)
results.add_atoms(atoms)
from chimerax.core.commands import register_selector
for group_name in group_info.keys():
register_selector(group_name.replace(' ', '-'),
lambda ses, models, results, gn=group_name: select(
results, models, gn),
logger)
def register_selectors(logger, name):
if name == "tm":
register_selector("tm", tm_selector, logger, desc="transition metals")
elif any(name == sub for sub in Substituent.list()):
register_selector(
name,
lambda sess, models, results, sub_name=name: substituent_selection(
sess, sub_name, models, results),
logger,
desc="substituent %s" % name)
elif name == "connected":
register_selector("connected",
all_connected_selector,
logger,
desc="fragment connected to selected atoms")
def name_frozen(session, name, objects):
if name == "all":
raise UserError("\"all\" is reserved and cannot be redefined")
from chimerax.core.commands import register_selector
register_selector(name, objects, session.logger)
def register_selectors(logger):
from chimerax.core.commands import register_selector
register_selector("selAtoms", _sel_atoms_selector, logger)
register_selector("selMaps", _sel_maps_selector, logger, atomic=False)
register_selector("selModels", _sel_models_selector, logger, atomic=False)
