def move_models_and_atoms(tf, models, atoms, move_whole_molecules, base_model):
if move_whole_molecules and atoms is not None and len(atoms) > 0:
models = list(models) + list(atoms.unique_structures)
from chimerax.atomic import Atoms
atoms = Atoms()
if atoms is None:
from chimerax.atomic import Atoms
atoms = Atoms()
global position_history
position_history.record_position(models, atoms, base_model)
for m in models:
# TODO: Handle case where parent of volume has non-identity position. tf is in scene coords.
m.position = tf * m.position
if len(atoms) > 0:
atoms.coords = tf * atoms.coords
position_history.record_position(models, atoms, base_model)
def apply_strict_ncs(template_atoms, ncs_map):
'''
Copy the transformed coordinates of the template atoms to the given NCS
atoms.
Args:
* template_atoms: a :class:`Atoms` instance
* ncs_map: a list of (:class:`Place`, :class:`Atoms`) pairs. Each
array of atoms must have a 1:1 correspondence to the template_atoms.
Atoms will be sorted according to (chain, residue number, insertion
code, atom name) before applying the NCS operators.
'''
from chimerax.atomic import Atoms
template_atoms = Atoms(
sorted(template_atoms,
key=lambda a: (a.residue.chain_id, a.residue.number, a.residue.
insertion_code, a.name)))
for (place, ncs_atoms) in ncs_map:
ncs_atoms = Atoms(
sorted(ncs_atoms,
key=lambda a: (a.residue.chain_id, a.residue.number, a.
residue.insertion_code, a.name)))
ncs_atoms.coords = place * template_atoms.coords