def _add_surface(surface):
session = surface.session
models = session.models
if models.have_model(surface):
# Reusing existing model.
return
# Check if request model id is already being used.
model_id = surface.id
if model_id:
if models.have_id(model_id):
from chimerax.core.errors import UserError
id_string = '.'.join('%d'%i for i in model_id)
raise UserError('Model id #%s already in use' % id_string)
# If parent models don't exist create grouping models.
p = None
for i in range(1,len(model_id)):
if not models.have_id(model_id[:i]):
from chimerax.core.models import Model
m = Model('shape', session)
m.id = model_id[:i]
models.add([m], parent = p)
p = m
# Add surface.
models.add([surface])
def split(session, structures = None, chains = None, ligands = False, connected = False, atoms = None):
'''
Partition atoms into separate structures. If only the first argument is given then those
structures are split into a separate structure for each chain. If chains, ligands, connected,
or atoms keywords are given then additional partitioning into smaller subsets is performed.
Parameters
----------
Structures : Structures or None
Structures to split. If no structures specified then all are used.
chains : bool
Split each chain into into a separate atomic structure.
ligands : bool
Split each connected ligand into a separate atomic structure.
connected : bool
Split each connected subset of atoms into a separate atomic structure.
atoms : list of Atoms
Split specified atoms into separate atomic structures. This option
can be specified multiple times.
'''
if structures is None:
from chimerax import atomic
structures = atomic.all_atomic_structures(session)
if chains is None and not ligands and not connected and atoms is None:
chains = True
slist = []
olist = []
log = session.logger
from chimerax.core.models import Model
for m in structures:
clist = split_molecule(m, chains, ligands, connected, atoms)
if clist:
parent = Model(m.name, session)
parent.id = m.id
for i, c in enumerate(clist):
c.id = parent.id + (i+1,)
c.position = m.position
parent.add(clist)
slist.append(m)
olist.append(parent)
msg = 'Split %s (#%s) into %d models' % (m.name, m.id_string, len(clist))
else:
msg = 'Did not split %s, has only one piece' % m.name
log.status(msg)
log.info(msg)
models = session.models
models.close(slist)
models.add(olist)
def _find_model(session, id, create=False, new_name='group'):
if len(id) == 0:
return None
ml = session.models
pl = ml.list(model_id=id)
if pl:
p = pl[0]
elif create:
from chimerax.core.models import Model
p = Model(new_name, session)
p.id = id
pp = _find_model(session, id[:-1], True, new_name)
ml.add([p], parent=pp)
else:
p = None
return p
