def _on_add_token(self, *args):
"""
Creates a new token and add it to the Naming Manager
:return: None
"""
load_token = True
if len(args) == 0:
load_token = False
token = None
if not load_token:
token = self._naming_lib.get_token_unique_name(name='New_Token')
elif load_token and len(args) == 1:
token = args[0].name
if token:
# Create a new item based on the token name and add it
item = QListWidgetItem(token)
item.setFlags(item.flags() | Qt.ItemIsEditable)
self.tokens_list.addItem(item)
# Add the data of the token to our JSON data file
if len(args) == 0:
self._naming_lib.add_token(token)
# Update necessary UI wigdets
if not load_token:
self.tokens_list.setCurrentItem(item)
def update_view(self):
"""
Updates file/folder view
:return:
"""
self.view.clear()
qdir = QDir(self.directory)
qdir.setNameFilters(self.get_filter_patterns())
filters = QDir.Dirs | QDir.AllDirs | QDir.Files | QDir.NoDot | QDir.NoDotDot
if self.show_hidden.isChecked():
filters = filters | QDir.Hidden
entries = qdir.entryInfoList(filters=filters,
sort=QDir.DirsFirst | QDir.Name)
file_path = self.get_file_path('..')
if os.path.exists(file_path) and file_path != self.directory:
icon = QFileIconProvider().icon(QFileInfo(self.directory))
QListWidgetItem(icon, '..', self.view, 0)
for info in entries:
icon = QFileIconProvider().icon(info)
suf = info.completeSuffix()
name, tp = (info.fileName(), 0) if info.isDir() else (
'%s%s' % (info.baseName(), '.%s' % suf if suf else ''), 1)
QListWidgetItem(icon, name, self.view, tp)
self.view.setFocus()
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 _on_add_rule(self, *args):
"""
Creates a new standard rule and add it to the Naming Manager
:return:
"""
load_rule = True
if len(args) == 0:
load_rule = False
self.description_rule_text.blockSignals(True)
rule = None
if not load_rule:
rule = self._naming_lib.get_rule_unique_name(name='New_Rule')
elif load_rule and len(args) == 1:
rule = args[0].name
if rule is not None:
# Create a new item based on the rule name and add it
item = QListWidgetItem(rule)
item.setFlags(item.flags() | Qt.ItemIsEditable)
self.rules_list.addItem(item)
# Add the data of the rule to our JSON data file
if len(args) == 0:
self._naming_lib.add_rule(rule)
# Update necessary UI Widgets
if not load_rule:
self.rules_list.setCurrentItem(item)
self.update_expression_menu()
self.update_rules_properties_state()
self.description_rule_text.blockSignals(False)
def _on_add_template_token(self, *args):
"""
Creates a new template token
:param args:
:return:
"""
load_template_token = True
if len(args) == 0:
load_template_token = False
template_token = None
if not load_template_token:
template_token = self._naming_lib.get_template_token_unique_name(
'New_Template_Token')
elif load_template_token and len(args) == 1:
template_token = args[0].name
if template_token is not None:
item = QListWidgetItem(template_token)
item.setFlags(item.flags() | Qt.ItemIsEditable)
self.template_tokens_list.addItem(item)
if len(args) == 0:
self._naming_lib.add_template_token(template_token)
if not load_template_token:
self.template_tokens_list.setCurrentItem(item)
def _on_add_template(self, *args):
"""
Creates a new template and add it to the Naming Manager
:return:
"""
load_template = True
if len(args) == 0:
load_template = False
template = None
if not load_template:
template = self._naming_lib.get_template_unique_name(
'New_Template')
elif load_template and len(args) == 1:
template = args[0].name
if template is not None:
item = QListWidgetItem(template)
item.setFlags(item.flags() | Qt.ItemIsEditable)
self.templates_list.addItem(item)
if len(args) == 0:
self._naming_lib.add_template(template)
if not load_template:
self.templates_list.setCurrentItem(item)
def createVariable(self, uid=None):
if uid == False:
uid = uuid4()
var = VariableBase(self.graph.getUniqVarName('NewVar'), 0, self.graph, self, DataTypes.Float, uid=uid)
item = QListWidgetItem(self.listWidget)
item.setSizeHint(QtCore.QSize(60, 38))
self.listWidget.setItemWidget(item, var)
return var
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)
def refresh(self, directories):
directories = python.force_list(directories)
self.clear()
for diretory_found in directories:
name = diretory_found
if not path_utils.is_dir(diretory_found):
name = 'Directory Not Valid! {}'.format(diretory_found)
item = QListWidgetItem()
item.setText(name)
item.setSizeHint(QSize(20, 25))
self.addItem(item)
def appendOutput(self, pw):
item = QListWidgetItem(self.lwOutputs)
item.setSizeHint(QtCore.QSize(pw.sizeHint().width(), 80))
self.lwOutputs.addItem(item)
self.lwOutputs.setItemWidget(item, pw)
del item
def createVariableWrapperAndAddToList(self, rawVariable):
uiVariable = UIVariable(rawVariable, self)
item = QListWidgetItem(self.listWidget)
item.setSizeHint(QtCore.QSize(60, 20))
self.listWidget.setItemWidget(item, uiVariable)
return uiVariable
def addWidget(self, widget):
item = QListWidgetItem(self)
item.setSizeHint(widget.sizeHint())
super(ItemWidgetsList, self).addItem(item)