def added_atoms(session, atoms, to_atoms):
amap = {(a.residue.chain_id, a.residue.number, a.name): a for a in atoms}
from chimerax.atomic import Atoms
added = Atoms([
a for a in to_atoms
if (a.residue.chain_id, a.residue.number, a.name) not in amap
])
session.selection.clear()
added.selected = True
session.logger.status('Added %d atoms' % len(added), log=True)
return added
def replace_residue(session, residue, new_residue_name):
block_if_sim_running(session)
from chimerax.core.errors import UserError
from chimerax.isolde.cmd import isolde_start
isolde_start(session)
from chimerax.atomic import Residues
if isinstance(residue, Residues):
if len(residue) != 1:
raise UserError('Must have a single residue selected!')
residue = residue[0]
if len(residue.neighbors):
raise UserError(
'Replacement by graph matching is currently only '
'supported for ligands with no covalent bonds to other residues!')
from ..template_utils import (fix_residue_from_template,
fix_residue_to_match_md_template)
from chimerax import mmcif
try:
cif_template = mmcif.find_template_residue(session, new_residue_name)
except:
err_str = (
'Could not find a mmCIF template for residue name {}. '
'For novel residues not in the Chemical Components Dictionary, '
'you will need to provide this first.').format(new_residue_name)
raise UserError(err_str)
fix_residue_from_template(residue,
cif_template,
rename_residue=True,
match_by='element')
ff = session.isolde.forcefield_mgr[session.isolde.sim_params.forcefield]
ligand_db = session.isolde.forcefield_mgr.ligand_db(
session.isolde.sim_params.forcefield)
from chimerax.isolde.openmm.openmm_interface import find_residue_templates
from chimerax.atomic import Residues
tdict = find_residue_templates(Residues([residue]),
ff,
ligand_db=ligand_db,
logger=session.logger)
md_template_name = tdict.get(0)
if md_template_name is not None:
fix_residue_to_match_md_template(session,
residue,
ff._templates[md_template_name],
cif_template=cif_template)
from chimerax.atomic import Atoms, Atom
chiral_centers = Atoms(
[a for a in residue.atoms if residue.ideal_chirality(a.name) != 'N'])
if len(chiral_centers):
warn_str = (
'Rebuilt ligand {} has chiral centres at atoms {} '
'(highlighted). Since the current algorithm used to match topologies '
'is not chirality aware, you should check these sites carefully to '
'ensure they are sensible. If in doubt, it is best to delete with '
'"del #{}/{}:{}{}" and replace with "isolde add ligand {}".'
).format(residue.name, ','.join(chiral_centers.names),
residue.structure.id_string, residue.chain_id, residue.number,
residue.insertion_code, residue.name)
session.selection.clear()
chiral_centers.selected = True
chiral_centers.draw_modes = Atom.BALL_STYLE
from chimerax.isolde.view import focus_on_selection
focus_on_selection(session, chiral_centers)
session.logger.warning(warn_str)
def select_pick(self, pick, set_sel):
if set_sel:
self.session.selection.clear()
if pick:
atoms = Atoms()
bonds = Bonds()
if not hasattr(pick, "__iter__"):
pick = [pick]
first_selected = None
for p in pick:
if isinstance(p, PickedAtoms):
for atom in p.atoms:
if atom in atoms:
continue
connected_atoms = get_fragment(
atom, max_len=atom.structure.num_atoms)
atoms = atoms.merge(connected_atoms)
if first_selected is None:
first_selected = atoms[0].selected
elif isinstance(p, PickedAtom):
if p.atom in atoms:
continue
connected_atoms = get_fragment(
p.atom, max_len=p.atom.structure.num_atoms)
atoms = atoms.merge(connected_atoms)
if first_selected is None:
first_selected = atoms[0].selected
elif isinstance(p, PickedBonds):
for bond in p.bonds:
if bond.atoms[0] in atoms:
continue
connected_atoms = get_fragment(
bond.atoms[0], max_len=bond.structure.num_atoms)
atoms = atoms.merge(connected_atoms)
if first_selected is None:
first_selected = atoms[0].selected
elif isinstance(p, PickedBond):
if p.bond.atoms[0] in atoms:
continue
connected_atoms = get_fragment(
p.bond.atoms[0], max_len=p.bond.structure.num_atoms)
atoms = atoms.merge(connected_atoms)
if first_selected is None:
first_selected = atoms[0].selected
elif isinstance(p, PickedResidues):
for res in p.residues:
for atom in res:
if atom in atoms:
continue
connected_atoms = get_fragment(
atom, max_len=res.structure.num_atoms)
atoms = atoms.merge(connected_atoms)
if first_selected is None:
first_selected = atoms[0].selected
elif isinstance(p, PickedResidue):
for atom in p.residue.atoms:
if atoms in atoms:
continue
connected_atoms = get_fragment(
atom, max_len=p.residue.structure.num_atoms)
atoms = atoms.merge(connected_atoms)
if first_selected is None:
first_selected = atoms[0].selected
for atom in atoms:
for neighbor, bond in zip(atom.neighbors, atom.bonds):
bonds = bonds.merge(Bonds([bond]))
if first_selected is not None:
atoms.selected = not first_selected
bonds.selected = not first_selected
else:
run(self.session, "select clear")