def update_complete_list(self, lines=None, extra=None):
self.clear()
if lines or extra:
self.show_me()
if lines:
for i in [x for x in lines if not x.name == 'mro']:
item = QListWidgetItem(i.name)
item.setData(32, i)
self.addItem(item)
if extra:
font = self.font()
font.setItalic(True)
font.setPointSize(font.pointSize() * 0.8)
for e in extra:
item = QListWidgetItem(e.name)
item.setData(32, e)
item.setFont(font)
self.addItem(item)
font = QFont('monospace', self.line_height, False)
fm = QFontMetrics(font)
width = fm.width(' ') * max([len(x.name)
for x in lines or extra]) + 40
self.resize(max(250, width), 250)
self.setCurrentRow(0)
else:
self.hide_me()
def _show_selected_unparameterised_residue(self, item):
residue, by_name, by_comp = item.data(USER_ROLE)
tlist = self._template_list
tlist.clear()
self._do_for_all.setCheckState(False)
from Qt.QtWidgets import QListWidgetItem
tlist.addItem(QListWidgetItem("Matches by residue name"))
def get_ccd_template_and_name(session, tname):
from ..openmm.amberff.template_utils import template_name_to_ccd_name
from chimerax import mmcif
ccd_name, extra_info = template_name_to_ccd_name(tname)
if ccd_name is None:
return (None, '')
try:
tmpl = mmcif.find_template_residue(session, ccd_name)
except ValueError:
return (None, "No CCD template found")
description = tmpl.description
if extra_info is not None:
description += ', ' + extra_info
return (tmpl, description)
for (tname, score) in by_name:
ccd_template, description = get_ccd_template_and_name(
self.session, tname)
entry_text = tname
entry_text += " (Score: {:.3f})".format(score)
if len(description):
entry_text += " " + description
entry = QListWidgetItem(entry_text)
entry.setData(USER_ROLE, (residue, tname, ccd_template))
tlist.addItem(entry)
tlist.addItem(QListWidgetItem("Matches by similar topology"))
for (tname, score) in by_comp:
ccd_template, description = get_ccd_template_and_name(
self.session, tname)
entry_text = tname
entry_text += " (Score: {:.3f})".format(score)
if len(description):
entry_text += " " + description
entry = QListWidgetItem(entry_text)
entry.setData(USER_ROLE, (residue, tname, ccd_template))
tlist.addItem(entry)
tlist.repaint()
from ..view import focus_on_selection
# show all atoms in the residue and its bonded neighbors, to help
# diagnose bonding errors
residue.atoms.displays = True
for r in residue.neighbors:
r.atoms.displays = True
focus_on_selection(self.session, residue.atoms)