def libadd_ring(self):
"""add ring to library or open it in a new model"""
selection = self.session.seqcrow_ordered_selection_manager.selection
if not selection.single_structure:
raise RuntimeError("selected atoms must be on the same model")
rescol = ResidueCollection(selection[0].structure)
walk_atoms = rescol.find(
[AtomSpec(atom.atomspec) for atom in selection])
if len(walk_atoms) < 1:
raise RuntimeError("no walk direction could be determined")
ring_name = self.ring_name.text()
ring = Ring(rescol, name=ring_name, end=walk_atoms)
ring.comment = "E:%s" % ",".join(
[str(rescol.atoms.index(atom) + 1) for atom in walk_atoms])
if len(ring_name) == 0:
chimerax_ring = ResidueCollection(ring).get_chimera(self.session)
chimerax_ring.name = "ring preview"
self.session.models.add([chimerax_ring])
bild_obj = show_walk_highlight(ring, chimerax_ring,
[0.9, 0.4, 0.3, 0.9], self.session)
self.session.models.add(bild_obj, parent=chimerax_ring)
else:
check_aaronlib_dir()
filename = os.path.join(AARONLIB, "Rings", ring_name + ".xyz")
if os.path.exists(filename):
exists_warning = QMessageBox()
exists_warning.setIcon(QMessageBox.Warning)
exists_warning.setText(
"%s already exists.\nWould you like to overwrite?" %
filename)
exists_warning.setStandardButtons(QMessageBox.Yes
| QMessageBox.No)
rv = exists_warning.exec_()
if rv == QMessageBox.Yes:
ring.write(outfile=filename)
self.tool_window.status("%s added to ring library" %
ring_name)
else:
self.tool_window.status(
"%s has not been added to ring library" % ring_name)
else:
ring.write(outfile=filename)
self.tool_window.status("%s added to ring library" % ring_name)
type=str,
nargs=1,
required=True,
dest='walk',
help="comma-separated list of atoms to define" +
"the direction the ring is traversed (1-indexed)"
)
args = libaddring_parser.parse_args()
ring = Ring(args.infile)
walk_atoms = args.walk.split(',')
ring.find_end(len(walk_atoms), walk_atoms)
ring.comment = "E:%s" % args.walk
if args.name is None:
print(ring.write(outfile=False))
else:
ring_lib = Ring.AARON_LIBS
ring_file = os.path.join(os.path.dirname(Ring.AARON_LIBS), args.name + '.xyz')
if os.path.exists(ring_file):
overwrite = input(
"%s already exists.\nWould you like to overwrite it? (YES/no)\n" % ring_file
)
if overwrite != "YES":
print("%s to overwrite, not overwriting" % overwrite)
sys.exit(0)
ring.write(outfile=ring_file)