def createInputWidgets(self, propertiesWidget):
inputsCategory = super(UIConstantNode,
self).createInputWidgets(propertiesWidget)
selector = QComboBox()
overrideType = QCheckBox()
for i in self._rawNode.pinTypes:
selector.addItem(i)
if self.input.dataType in self._rawNode.pinTypes:
selector.setCurrentIndex(
self._rawNode.pinTypes.index(self.input.dataType))
structSelector = QComboBox()
for i in [i.name for i in list(PinStructure)]:
structSelector.addItem(i)
overrideType.setChecked(self.input._rawPin.changeTypeOnConnection)
structSelector.setCurrentIndex(self.input._rawPin._currStructure)
selector.setEnabled(self.input._rawPin.changeTypeOnConnection)
overrideType.stateChanged.connect(selector.setEnabled)
overrideType.stateChanged.connect(self._rawNode.overrideTypeChanged)
selector.activated.connect(self._rawNode.updateType)
structSelector.activated.connect(self._rawNode.selectStructure)
structSelector.activated.connect(self.selectStructure)
inputsCategory.insertWidget(0, "DataType", selector)
inputsCategory.insertWidget(1, "Change Type On Connection",
overrideType)
inputsCategory.insertWidget(1, "Structure", structSelector)
def __init__(self, parent=None, **kwargs):
super(BoolEditor, self).__init__(parent=parent, **kwargs)
self._default_value = False
self.cbx = QCheckBox(self)
self.main_layout.addWidget(self.cbx)
self.cbx.toggled.connect(self.OnValueUpdated)
class BoolInputWidget(InputWidgetSingle):
"""Boolean data input widget"""
def __init__(self, parent=None, **kwds):
super(BoolInputWidget, self).__init__(parent=parent, **kwds)
self.cb = QCheckBox(self)
self.setWidget(self.cb)
self.cb.stateChanged.connect(
lambda val: self.dataSetCallback(bool(val)))
def setWidgetValue(self, val):
if bool(val):
self.cb.setCheckState(QtCore.Qt.Checked)
else:
self.cb.setCheckState(QtCore.Qt.Unchecked)
def _build_ui(self):
"""
ui should have:
* table with a list of available tests and show results after they are done
* way to filter tests
* button to run tests
"""
layout = QFormLayout()
# table to list test classes and the results
self.table = QTableWidget()
self.table.setColumnCount(2)
self.table.setHorizontalHeaderLabels(["test", "result"])
self.table.horizontalHeader().setSectionResizeMode(
0,
self.table.horizontalHeader().Interactive)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.table.horizontalHeader().setSectionResizeMode(
1,
self.table.horizontalHeader().Stretch)
self.table.setSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.MinimumExpanding)
self.table.setSelectionBehavior(self.table.SelectRows)
layout.addRow(self.table)
self.filter = QLineEdit()
self.filter.setPlaceholderText("filter test names")
self.filter.setClearButtonEnabled(True)
self.filter.textChanged.connect(self.apply_filter)
layout.addRow(self.filter)
self.profile = QCheckBox()
self.profile.setToolTip("profile functions called during testing "
"using cProfile")
layout.addRow("profile calls:", self.profile)
self.run_button = QPushButton("run tests")
self.run_button.clicked.connect(self.run_tests)
self.run_button.setToolTip(
"if no tests are selected on the table, run all tests\n" +
"otherwise, run selected tests")
layout.addRow(self.run_button)
self.fill_table()
self.table.resizeColumnToContents(0)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def __init__(self, session, isolde, main_frame, category_grid,
region_table, bottom_layout, update_button):
super().__init__(session, isolde, main_frame, sim_sensitive=True)
from Qt.QtCore import Qt
self._data_role = Qt.ItemDataRole.UserRole
cg = self.category_grid = category_grid
rt = self.region_table = region_table
rt.itemClicked.connect(self.item_clicked_cb)
self.update_button = update_button
update_button.clicked.connect(self.update)
from .problems import ProblemAggregator
pa = self.problem_aggregator = ProblemAggregator(session)
from Qt.QtWidgets import QCheckBox, QLabel, QSpinBox, QDoubleSpinBox, QLabel
cg.addWidget(QLabel("Unsatisfied restraints"), 0, 0)
cg.addWidget(QLabel("Validation issues"), 0, 1)
ocb = self.outliers_only_checkbox = QCheckBox("Outliers only")
cg.addWidget(ocb, 0, 2)
self.restraint_checkboxes = []
for i, name in enumerate(pa.registered_restraint_problem_types):
cb = QCheckBox(name)
cb.setChecked(True)
self.restraint_checkboxes.append(cb)
cg.addWidget(cb, i + 1, 0)
self.validation_checkboxes = []
for i, name in enumerate(pa.registered_validation_problem_types):
cb = QCheckBox(name)
cb.setChecked(True)
self.validation_checkboxes.append(cb)
cg.addWidget(cb, i + 1, 1)
csb = self.cutoff_spinbox = QDoubleSpinBox(main_frame)
csbl = QLabel("Dist cutoff")
csb.setRange(1.0, 10.0)
csb.setSingleStep(1.0)
csb.setValue(4.0)
bottom_layout.insertWidget(0, csb)
bottom_layout.insertWidget(1, csbl)
clsb = self.cluster_spinbox = QSpinBox(main_frame)
clsbl = QLabel("Min cluster size")
clsb.setRange(2, 20)
clsb.setValue(5)
bottom_layout.insertWidget(2, clsb)
bottom_layout.insertWidget(3, clsbl)
def __init__(self, settings, parent=None, description=None, pstvOnly=True):
super(ConfigDialog, self).__init__(parent)
self.setWindowTitle("Configure source")
self.layout = QGridLayout(self)
row = 0
self.widgets = {}
self.settings = settings
# Settings should be a dictionary
for name, val in settings.items():
label = QLabel(self)
label.setText(str(name))
self.layout.addWidget(label, row, 0, 1, 1)
# Check the type of each setting, and create widgets accordingly
if isinstance(val, str):
# A string of some kind
widget = QLineEdit(self)
widget.setText(val)
elif isinstance(val, list):
# A list of alternative values, first is selected
print("List: ", name)
continue
elif isinstance(val, bool):
widget = QCheckBox(self)
if val:
widget.setCheckState(Qt.CheckState.Checked)
else:
widget.setCheckState(Qt.CheckState.Unchecked)
elif isinstance(val, int):
widget = QLineEdit(self)
widget.setInputMask("9000000")
widget.setText(str(val).strip())
elif isinstance(val, float):
widget = QLineEdit(self)
if pstvOnly:
widget.setInputMask("0.000")
widget.setText(str(val).strip())
else:
print("Ignoring: " + name)
continue
widget.config = name
self.widgets[name] = widget
self.layout.addWidget(widget, row, 1, 1, 1)
row += 1
# Add OK and Cancel buttons
buttonbox = QDialogButtonBox(QDialogButtonBox.Ok
| QDialogButtonBox.Cancel)
buttonbox.accepted.connect(self.getValues)
buttonbox.rejected.connect(self.reject)
self.layout.addWidget(buttonbox, row, 1, 2, 1)
def addItem(self, item, selected=False):
checkBox = QCheckBox(item, self.menu)
checkBox.setTristate(self.triState)
if selected:
checkBox.setChecked(True)
checkableAction = QWidgetAction(self.menu)
checkableAction.setDefaultWidget(checkBox)
self.menu.addAction(checkableAction)
return checkBox
def test_resolution_clicked(self):
"""Test clicking on resolution checkboxes"""
def get_first_tree(stack):
for w in stack.widget(1).children():
if isinstance(w, QTreeView):
self.assertIsInstance(w.model(),
src.tool._RMFHierarchyModel)
return w
raise ValueError("could not find tree")
def get_buttons(stack):
for w in stack.widget(1).children():
if isinstance(w, QCheckBox):
yield w
class TestChimeraObj:
pass
root = make_node("root", 0)
child1 = make_node("child1", 1, resolution=1)
child2 = make_node("child2", 2, resolution=10)
root.add_children((child1, child2))
mock_session = make_session()
m1 = Model(mock_session, 'test')
m1.rmf_hierarchy = root
m1.rmf_features = [make_node("f1", 4), make_node("f2", 5)]
m1.rmf_provenance = []
m1._rmf_resolutions = set((1, 10))
m1._selected_rmf_resolutions = set((1, None))
mock_session.models.add((m1, ))
r = src.tool.RMFViewer(mock_session, "RMF Viewer")
tree1 = get_first_tree(r.model_stack.widget(0))
res1b, res10b = list(get_buttons(r.model_stack.widget(0)))
# Call "clicked" methods directly
# Show/hide resolution 10
cb = QCheckBox('foo')
cb.setChecked(True)
r._resolution_button_clicked(cb, tree1, 10)
cb = QCheckBox('bar')
cb.setChecked(False)
r._resolution_button_clicked(cb, tree1, 10)
tree1.selectAll()
# Call indirectly via clicking each button
for b in res1b, res10b:
b.click()
class BoolEditor(BaseEditor, object):
attr_type = 'bool'
def __init__(self, parent=None, **kwargs):
super(BoolEditor, self).__init__(parent=parent, **kwargs)
self._default_value = False
self.cbx = QCheckBox(self)
self.main_layout.addWidget(self.cbx)
self.cbx.toggled.connect(self.OnValueUpdated)
def get_value(self):
return self.cbx.isChecked()
def initialize_editor(self):
editor_value = self.default_value
node_values = self.values
if node_values:
if len(node_values) > 1:
pass
elif len(node_values) == 1:
if node_values[0]:
editor_value = node_values[0]
self.cbx.blockSignals(True)
self.cbx.setChecked(editor_value)
self.cbx.blockSignals(False)
def set_connected(self, conn):
if conn != self._connection:
self._connection = conn
self.value_line.setText(conn)
self.cbx.setEnabled(False)
self.value_line.setProperty('class', 'Connected')
def add_ligand(tool):
rows = tool.ligand_table.rowCount()
if rows != 0:
rows -= 1
ligand_name = QTableWidgetItem()
name = "<click to choose>"
is_c2 = Qt.Unchecked
enabled = True
if rows > 0:
name = tool.ligand_table.item(rows - 1, 0).text()
is_c2 = tool.ligand_table.cellWidget(rows - 1, 1).layout().itemAt(0).widget().checkState()
enabled = tool.ligand_table.cellWidget(rows - 1, 1).layout().itemAt(0).widget().isEnabled()
ligand_name.setData(Qt.DisplayRole, name)
tool.ligand_table.setItem(rows, 0, ligand_name)
widget_that_lets_me_horizontally_align_a_checkbox = QWidget()
widget_layout = QHBoxLayout(widget_that_lets_me_horizontally_align_a_checkbox)
c2 = QCheckBox()
c2.setEnabled(enabled)
c2.setCheckState(is_c2)
widget_layout.addWidget(c2, 0, Qt.AlignHCenter)
widget_layout.setContentsMargins(0, 0, 0, 0)
tool.ligand_table.setCellWidget(
rows, 1, widget_that_lets_me_horizontally_align_a_checkbox
)
widget_that_lets_me_horizontally_align_an_icon = QWidget()
widget_layout = QHBoxLayout(widget_that_lets_me_horizontally_align_an_icon)
section_remove = QLabel()
dim = int(1.5 * section_remove.fontMetrics().boundingRect("Q").height())
section_remove.setPixmap(
QIcon(section_remove.style().standardIcon(
QStyle.SP_DialogDiscardButton)
).pixmap(dim, dim)
)
widget_layout.addWidget(section_remove, 0, Qt.AlignHCenter)
widget_layout.setContentsMargins(0, 0, 0, 0)
tool.ligand_table.setCellWidget(
rows, 2, widget_that_lets_me_horizontally_align_an_icon
)
rows += 1
tool.ligand_table.insertRow(rows)
widget_that_lets_me_horizontally_align_an_icon = QWidget()
widget_layout = QHBoxLayout(widget_that_lets_me_horizontally_align_an_icon)
ligand_add = QLabel("add ligand")
widget_layout.addWidget(ligand_add, 0, Qt.AlignHCenter)
widget_layout.setContentsMargins(0, 0, 0, 0)
tool.ligand_table.setCellWidget(rows, 1, widget_that_lets_me_horizontally_align_an_icon)
def _build_ui(self):
layout = QFormLayout()
self.substituent_table = SubstituentTable(singleSelect=True)
layout.addRow(self.substituent_table)
self.new_residue = QCheckBox()
self.new_residue.setCheckState(
Qt.Checked if SubstituteMouseMode.newRes else Qt.Unchecked)
layout.addRow("new residue:", self.new_residue)
self.res_name = QLineEdit()
self.res_name.setPlaceholderText("leave blank to keep current")
layout.addRow("set residue name:", self.res_name)
self.distance_names = QCheckBox()
self.distance_names.setCheckState(
Qt.Checked if SubstituteMouseMode.useRemoteness else Qt.Unchecked)
layout.addRow("distance atom names:", self.distance_names)
self.keep_open = QCheckBox()
layout.addRow("keep list open:", self.keep_open)
do_it = QPushButton("set substituent")
do_it.clicked.connect(self.set_sub)
layout.addRow(do_it)
self.keep_open.stateChanged.connect(
lambda state: do_it.setVisible(state != Qt.Checked))
self.keep_open.stateChanged.connect(self.sub_changed)
self.substituent_table.table.itemSelectionChanged.connect(
self.sub_changed)
self.new_residue.stateChanged.connect(self.sub_changed)
self.res_name.textChanged.connect(self.sub_changed)
self.distance_names.stateChanged.connect(self.sub_changed)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def _build_ui(self):
layout = QGridLayout()
tabs = QTabWidget()
calc_widget = QWidget()
calc_layout = QFormLayout(calc_widget)
settings_widget = QWidget()
settings_layout = QFormLayout(settings_widget)
steric_map_widget = QWidget()
steric_layout = QFormLayout(steric_map_widget)
cutout_widget = QWidget()
vol_cutout_layout = QFormLayout(cutout_widget)
layout.addWidget(tabs)
tabs.addTab(calc_widget, "calculation")
tabs.addTab(settings_widget, "settings")
tabs.addTab(steric_map_widget, "steric map")
tabs.addTab(cutout_widget, "volume cutout")
self.radii_option = QComboBox()
self.radii_option.addItems(["Bondi", "UMN"])
ndx = self.radii_option.findText(self.settings.radii, Qt.MatchExactly)
self.radii_option.setCurrentIndex(ndx)
settings_layout.addRow("radii:", self.radii_option)
self.scale = QDoubleSpinBox()
self.scale.setValue(self.settings.vdw_scale)
self.scale.setSingleStep(0.01)
self.scale.setRange(1., 1.5)
settings_layout.addRow("VDW scale:", self.scale)
set_ligand_atoms = QPushButton("set ligands to current selection")
set_ligand_atoms.clicked.connect(self.set_ligand_atoms)
set_ligand_atoms.setToolTip(
"specify atoms to use in calculation\n" +
"by default, all atoms will be used unless a single center is specified\n"
+
"in the case of a single center, all atoms except the center is used"
)
calc_layout.addRow(set_ligand_atoms)
self.set_ligand_atoms = set_ligand_atoms
self.radius = QDoubleSpinBox()
self.radius.setValue(self.settings.center_radius)
self.radius.setSuffix(" \u212B")
self.radius.setDecimals(1)
self.radius.setSingleStep(0.1)
self.radius.setRange(1., 15.)
settings_layout.addRow("radius around center:", self.radius)
self.method = QComboBox()
self.method.addItems(["Lebedev", "Monte-Carlo"])
self.method.setToolTip("Lebedev: deterministic method\n" +
"Monte-Carlo: non-deterministic method")
ndx = self.method.findText(self.settings.method, Qt.MatchExactly)
self.method.setCurrentIndex(ndx)
settings_layout.addRow("integration method:", self.method)
leb_widget = QWidget()
leb_layout = QFormLayout(leb_widget)
leb_layout.setContentsMargins(0, 0, 0, 0)
self.radial_points = QComboBox()
self.radial_points.addItems(["20", "32", "64", "75", "99", "127"])
self.radial_points.setToolTip(
"more radial points will give more accurate results, but integration will take longer"
)
ndx = self.radial_points.findText(self.settings.radial_points,
Qt.MatchExactly)
self.radial_points.setCurrentIndex(ndx)
leb_layout.addRow("radial points:", self.radial_points)
self.angular_points = QComboBox()
self.angular_points.addItems([
"110", "194", "302", "590", "974", "1454", "2030", "2702", "5810"
])
self.angular_points.setToolTip(
"more angular points will give more accurate results, but integration will take longer"
)
ndx = self.angular_points.findText(self.settings.angular_points,
Qt.MatchExactly)
self.angular_points.setCurrentIndex(ndx)
leb_layout.addRow("angular points:", self.angular_points)
settings_layout.addRow(leb_widget)
mc_widget = QWidget()
mc_layout = QFormLayout(mc_widget)
mc_layout.setContentsMargins(0, 0, 0, 0)
self.min_iter = QSpinBox()
self.min_iter.setValue(self.settings.minimum_iterations)
self.min_iter.setRange(0, 10000)
self.min_iter.setToolTip(
"each iteration is 3000 points\n" +
"iterations continue until convergence criteria are met")
mc_layout.addRow("minimum interations:", self.min_iter)
settings_layout.addRow(mc_widget)
if self.settings.method == "Lebedev":
mc_widget.setVisible(False)
elif self.settings.method == "Monte-Carlo":
leb_widget.setVisible(False)
self.report_component = QComboBox()
self.report_component.addItems(["total", "quadrants", "octants"])
ndx = self.report_component.findText(self.settings.report_component,
Qt.MatchExactly)
self.report_component.setCurrentIndex(ndx)
settings_layout.addRow("report volume:", self.report_component)
self.use_scene = QCheckBox()
self.use_scene.setChecked(self.settings.use_scene)
self.use_scene.setToolTip(
"quadrants/octants will use the orientation the molecule is displayed in"
)
settings_layout.addRow("use display orientation:", self.use_scene)
self.method.currentTextChanged.connect(
lambda text, widget=leb_widget: widget.setVisible(text == "Lebedev"
))
self.method.currentTextChanged.connect(
lambda text, widget=mc_widget: widget.setVisible(text ==
"Monte-Carlo"))
self.use_centroid = QCheckBox()
self.use_centroid.setChecked(self.settings.use_centroid)
self.use_centroid.setToolTip(
"place the center between selected atoms\n" +
"might be useful for polydentate ligands")
calc_layout.addRow("use centroid of centers:", self.use_centroid)
self.steric_map = QCheckBox()
self.steric_map.setChecked(self.settings.steric_map)
self.steric_map.setToolTip(
"produce a 2D projection of steric bulk\ncauses buried volume to be reported for individual quadrants"
)
steric_layout.addRow("create steric map:", self.steric_map)
self.num_pts = QSpinBox()
self.num_pts.setRange(25, 250)
self.num_pts.setValue(self.settings.num_pts)
self.num_pts.setToolTip("number of points along x and y axes")
steric_layout.addRow("number of points:", self.num_pts)
self.include_vbur = QCheckBox()
self.include_vbur.setChecked(self.settings.include_vbur)
steric_layout.addRow("label quadrants with %V<sub>bur</sub>",
self.include_vbur)
self.map_shape = QComboBox()
self.map_shape.addItems(["circle", "square"])
ndx = self.map_shape.findText(self.settings.map_shape, Qt.MatchExactly)
self.map_shape.setCurrentIndex(ndx)
steric_layout.addRow("map shape:", self.map_shape)
self.auto_minmax = QCheckBox()
self.auto_minmax.setChecked(self.settings.auto_minmax)
steric_layout.addRow("automatic min. and max.:", self.auto_minmax)
self.map_min = QDoubleSpinBox()
self.map_min.setRange(-15., 0.)
self.map_min.setSuffix(" \u212B")
self.map_min.setSingleStep(0.1)
self.map_min.setValue(self.settings.map_min)
steric_layout.addRow("minimum value:", self.map_min)
self.map_max = QDoubleSpinBox()
self.map_max.setRange(0., 15.)
self.map_max.setSuffix(" \u212B")
self.map_max.setSingleStep(0.1)
self.map_max.setValue(self.settings.map_max)
steric_layout.addRow("maximum value:", self.map_max)
self.num_pts.setEnabled(self.settings.steric_map)
self.steric_map.stateChanged.connect(
lambda state, widget=self.num_pts: widget.setEnabled(state == Qt.
Checked))
self.include_vbur.setEnabled(self.settings.steric_map)
self.steric_map.stateChanged.connect(
lambda state, widget=self.include_vbur: widget.setEnabled(
state == Qt.Checked))
self.map_shape.setEnabled(self.settings.steric_map)
self.steric_map.stateChanged.connect(
lambda state, widget=self.map_shape: widget.setEnabled(state == Qt.
Checked))
self.auto_minmax.setEnabled(self.settings.steric_map)
self.steric_map.stateChanged.connect(
lambda state, widget=self.auto_minmax: widget.setEnabled(
state == Qt.Checked))
self.map_min.setEnabled(not self.settings.auto_minmax
and self.settings.steric_map)
self.steric_map.stateChanged.connect(
lambda state, widget=self.map_min, widget2=self.auto_minmax: widget
.setEnabled(state == Qt.Checked and not widget2.isChecked()))
self.auto_minmax.stateChanged.connect(
lambda state, widget=self.map_min, widget2=self.steric_map: widget.
setEnabled(not state == Qt.Checked and widget2.isChecked()))
self.map_max.setEnabled(not self.settings.auto_minmax
and self.settings.steric_map)
self.steric_map.stateChanged.connect(
lambda state, widget=self.map_max, widget2=self.auto_minmax: widget
.setEnabled(state == Qt.Checked and not widget2.isChecked()))
self.auto_minmax.stateChanged.connect(
lambda state, widget=self.map_max, widget2=self.steric_map: widget.
setEnabled(not state == Qt.Checked and widget2.isChecked()))
self.display_cutout = QComboBox()
self.display_cutout.addItems(["no", "free", "buried"])
ndx = self.display_cutout.findText(self.settings.display_cutout,
Qt.MatchExactly)
self.display_cutout.setCurrentIndex(ndx)
self.display_cutout.setToolTip("show free or buried volume")
vol_cutout_layout.addRow("display volume:", self.display_cutout)
self.point_spacing = QDoubleSpinBox()
self.point_spacing.setDecimals(3)
self.point_spacing.setRange(0.01, 0.5)
self.point_spacing.setSingleStep(0.005)
self.point_spacing.setSuffix(" \u212B")
self.point_spacing.setValue(self.settings.point_spacing)
self.point_spacing.setToolTip(
"distance between points on cutout\n" +
"smaller spacing will narrow gaps, but increase time to create the cutout"
)
vol_cutout_layout.addRow("point spacing:", self.point_spacing)
self.intersection_scale = QDoubleSpinBox()
self.intersection_scale.setDecimals(2)
self.intersection_scale.setRange(1., 10.)
self.intersection_scale.setSingleStep(0.5)
self.intersection_scale.setSuffix("x")
self.intersection_scale.setToolTip(
"relative density of points where VDW radii intersect\n" +
"higher density will narrow gaps, but increase time to create cutout"
)
self.intersection_scale.setValue(self.settings.intersection_scale)
vol_cutout_layout.addRow("intersection density:",
self.intersection_scale)
self.cutout_labels = QComboBox()
self.cutout_labels.addItems(["none", "quadrants", "octants"])
ndx = self.cutout_labels.findText(self.settings.cutout_labels,
Qt.MatchExactly)
self.cutout_labels.setCurrentIndex(ndx)
vol_cutout_layout.addRow("label sections:", self.cutout_labels)
self.point_spacing.setEnabled(self.settings.display_cutout != "no")
self.intersection_scale.setEnabled(
self.settings.display_cutout != "no")
self.cutout_labels.setEnabled(self.settings.display_cutout != "no")
self.display_cutout.currentTextChanged.connect(
lambda text, widget=self.point_spacing: widget.setEnabled(text !=
"no"))
self.display_cutout.currentTextChanged.connect(
lambda text, widget=self.intersection_scale: widget.setEnabled(
text != "no"))
self.display_cutout.currentTextChanged.connect(
lambda text, widget=self.cutout_labels: widget.setEnabled(text !=
"no"))
calc_vbur_button = QPushButton(
"calculate % buried volume for selected centers")
calc_vbur_button.clicked.connect(self.calc_vbur)
calc_layout.addRow(calc_vbur_button)
self.calc_vbur_button = calc_vbur_button
remove_vbur_button = QPushButton(
"remove % buried volume visualizations")
remove_vbur_button.clicked.connect(self.del_vbur)
vol_cutout_layout.addRow(remove_vbur_button)
self.table = QTableWidget()
self.table.setColumnCount(3)
self.table.setHorizontalHeaderLabels(['model', 'center', '%Vbur'])
self.table.setSelectionBehavior(QTableWidget.SelectRows)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.table.resizeColumnToContents(0)
self.table.resizeColumnToContents(1)
self.table.resizeColumnToContents(2)
self.table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.Interactive)
self.table.horizontalHeader().setSectionResizeMode(
1, QHeaderView.Interactive)
self.table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.Stretch)
calc_layout.addRow(self.table)
menu = QMenuBar()
export = menu.addMenu("&Export")
clear = QAction("Clear data table", self.tool_window.ui_area)
clear.triggered.connect(self.clear_table)
export.addAction(clear)
copy = QAction("&Copy CSV to clipboard", self.tool_window.ui_area)
copy.triggered.connect(self.copy_csv)
shortcut = QKeySequence(Qt.CTRL + Qt.Key_C)
copy.setShortcut(shortcut)
export.addAction(copy)
self.copy = copy
save = QAction("&Save CSV...", self.tool_window.ui_area)
save.triggered.connect(self.save_csv)
#this shortcut interferes with main window's save shortcut
#I've tried different shortcut contexts to no avail
#thanks Qt...
#shortcut = QKeySequence(Qt.CTRL + Qt.Key_S)
#save.setShortcut(shortcut)
#save.setShortcutContext(Qt.WidgetShortcut)
export.addAction(save)
delimiter = export.addMenu("Delimiter")
comma = QAction("comma", self.tool_window.ui_area, checkable=True)
comma.setChecked(self.settings.delimiter == "comma")
comma.triggered.connect(lambda *args, delim="comma": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(comma)
tab = QAction("tab", self.tool_window.ui_area, checkable=True)
tab.setChecked(self.settings.delimiter == "tab")
tab.triggered.connect(lambda *args, delim="tab": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(tab)
space = QAction("space", self.tool_window.ui_area, checkable=True)
space.setChecked(self.settings.delimiter == "space")
space.triggered.connect(lambda *args, delim="space": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(space)
semicolon = QAction("semicolon",
self.tool_window.ui_area,
checkable=True)
semicolon.setChecked(self.settings.delimiter == "semicolon")
semicolon.triggered.connect(lambda *args, delim="semicolon": self.
settings.__setattr__("delimiter", delim))
delimiter.addAction(semicolon)
add_header = QAction("&Include CSV header",
self.tool_window.ui_area,
checkable=True)
add_header.setChecked(self.settings.include_header)
add_header.triggered.connect(self.header_check)
export.addAction(add_header)
comma.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
comma.triggered.connect(
lambda *args, action=space: action.setChecked(False))
comma.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=space: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
space.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
space.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
space.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=space: action.setChecked(False))
menu.setNativeMenuBar(False)
self._menu = menu
layout.setMenuBar(menu)
menu.setVisible(True)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
class BondEditor(ToolInstance):
help = "https://github.com/QChASM/SEQCROW/wiki/Bond-Editor-Tool"
SESSION_ENDURING = False
SESSION_SAVE = False
def __init__(self, session, name):
super().__init__(session, name)
self.tool_window = MainToolWindow(self)
self.settings = _BondEditorSettings(session, name)
self._build_ui()
def _build_ui(self):
layout = QGridLayout()
tabs = QTabWidget()
layout.addWidget(tabs)
ts_bond_tab = QWidget()
ts_options = QFormLayout(ts_bond_tab)
self.tsbond_color = ColorButton(has_alpha_channel=False,
max_size=(16, 16))
self.tsbond_color.set_color(self.settings.tsbond_color)
ts_options.addRow("color:", self.tsbond_color)
self.tsbond_transparency = QSpinBox()
self.tsbond_transparency.setRange(1, 99)
self.tsbond_transparency.setValue(self.settings.tsbond_transparency)
self.tsbond_transparency.setSuffix("%")
ts_options.addRow("transparency:", self.tsbond_transparency)
self.tsbond_radius = QDoubleSpinBox()
self.tsbond_radius.setRange(0.01, 1)
self.tsbond_radius.setDecimals(3)
self.tsbond_radius.setSingleStep(0.005)
self.tsbond_radius.setSuffix(" \u212B")
self.tsbond_radius.setValue(self.settings.tsbond_radius)
ts_options.addRow("radius:", self.tsbond_radius)
draw_tsbonds = QPushButton("draw TS bonds on selected atoms/bonds")
draw_tsbonds.clicked.connect(self.run_tsbond)
ts_options.addRow(draw_tsbonds)
self.draw_tsbonds = draw_tsbonds
erase_tsbonds = QPushButton("erase selected TS bonds")
erase_tsbonds.clicked.connect(self.run_erase_tsbond)
ts_options.addRow(erase_tsbonds)
self.erase_tsbonds = erase_tsbonds
bond_tab = QWidget()
bond_options = QFormLayout(bond_tab)
self.bond_halfbond = QCheckBox()
self.bond_halfbond.setChecked(self.settings.bond_halfbond)
self.bond_halfbond.setToolTip(
"each half of the bond will be colored according to the atom's color"
)
bond_options.addRow("half-bond:", self.bond_halfbond)
self.bond_color = ColorButton(has_alpha_channel=True,
max_size=(16, 16))
self.bond_color.set_color(self.settings.bond_color)
self.bond_color.setEnabled(
self.bond_halfbond.checkState() != Qt.Checked)
self.bond_halfbond.stateChanged.connect(
lambda state, widget=self.bond_color: self.bond_color.setEnabled(
state != Qt.Checked))
bond_options.addRow("color:", self.bond_color)
self.bond_radius = QDoubleSpinBox()
self.bond_radius.setRange(0.01, 1)
self.bond_radius.setDecimals(3)
self.bond_radius.setSingleStep(0.005)
self.bond_radius.setSuffix(" \u212B")
self.bond_radius.setValue(self.settings.bond_radius)
bond_options.addRow("radius:", self.bond_radius)
draw_tsbonds = QPushButton("draw bond between selected atoms")
draw_tsbonds.clicked.connect(self.run_bond)
bond_options.addRow(draw_tsbonds)
self.draw_tsbonds = draw_tsbonds
erase_bonds = QPushButton("erase selected bonds")
erase_bonds.clicked.connect(
lambda *, ses=self.session: run(ses, "delete bonds sel"))
bond_options.addRow(erase_bonds)
self.erase_bonds = erase_bonds
hbond_tab = QWidget()
hbond_options = QFormLayout(hbond_tab)
self.hbond_color = ColorButton(has_alpha_channel=True,
max_size=(16, 16))
self.hbond_color.set_color(self.settings.hbond_color)
hbond_options.addRow("color:", self.hbond_color)
self.hbond_radius = QDoubleSpinBox()
self.hbond_radius.setDecimals(3)
self.hbond_radius.setSuffix(" \u212B")
self.hbond_radius.setValue(self.settings.hbond_radius)
hbond_options.addRow("radius:", self.hbond_radius)
self.hbond_dashes = QSpinBox()
self.hbond_dashes.setRange(0, 28)
self.hbond_dashes.setSingleStep(2)
self.hbond_radius.setSingleStep(0.005)
self.hbond_dashes.setValue(self.settings.hbond_dashes)
hbond_options.addRow("dashes:", self.hbond_dashes)
draw_hbonds = QPushButton("draw H-bonds")
draw_hbonds.clicked.connect(self.run_hbond)
hbond_options.addRow(draw_hbonds)
self.draw_hbonds = draw_hbonds
erase_hbonds = QPushButton("erase all H-bonds")
erase_hbonds.clicked.connect(
lambda *, ses=self.session: run(ses, "~hbonds"))
hbond_options.addRow(erase_hbonds)
self.erase_hbonds = erase_hbonds
tm_bond_tab = QWidget()
tm_bond_options = QFormLayout(tm_bond_tab)
self.tm_bond_color = ColorButton(has_alpha_channel=True,
max_size=(16, 16))
self.tm_bond_color.set_color(self.settings.tm_bond_color)
tm_bond_options.addRow("color:", self.tm_bond_color)
self.tm_bond_radius = QDoubleSpinBox()
self.tm_bond_radius.setDecimals(3)
self.tm_bond_radius.setSuffix(" \u212B")
self.tm_bond_radius.setValue(self.settings.tm_bond_radius)
tm_bond_options.addRow("radius:", self.tm_bond_radius)
self.tm_bond_dashes = QSpinBox()
self.tm_bond_dashes.setRange(0, 28)
self.tm_bond_dashes.setSingleStep(2)
self.tm_bond_radius.setSingleStep(0.005)
self.tm_bond_dashes.setValue(self.settings.tm_bond_dashes)
tm_bond_options.addRow("dashes:", self.tm_bond_dashes)
draw_tm_bonds = QPushButton("draw metal coordination bonds")
draw_tm_bonds.clicked.connect(self.run_tm_bond)
tm_bond_options.addRow(draw_tm_bonds)
self.draw_tm_bonds = draw_tm_bonds
erase_tm_bonds = QPushButton("erase all metal coordination bonds")
erase_tm_bonds.clicked.connect(self.del_tm_bond)
tm_bond_options.addRow(erase_tm_bonds)
self.erase_tm_bonds = erase_tm_bonds
bond_length_tab = QWidget()
bond_length_layout = QFormLayout(bond_length_tab)
self.bond_distance = QDoubleSpinBox()
self.bond_distance.setRange(0.5, 10.0)
self.bond_distance.setSingleStep(0.05)
self.bond_distance.setValue(1.51)
self.bond_distance.setSuffix(" \u212B")
bond_length_layout.addRow("bond length:", self.bond_distance)
self.move_fragment = QComboBox()
self.move_fragment.addItems(["both", "smaller", "larger"])
bond_length_layout.addRow("move side:", self.move_fragment)
bond_lookup = QGroupBox("bond length lookup:")
bond_lookup_layout = QGridLayout(bond_lookup)
bond_lookup_layout.addWidget(
QLabel("elements:"),
0,
0,
)
self.ele1 = ElementButton("C", single_state=True)
self.ele1.clicked.connect(
lambda *args, button=self.ele1: self.open_ptable(button))
bond_lookup_layout.addWidget(self.ele1, 0, 1,
Qt.AlignRight | Qt.AlignTop)
bond_lookup_layout.addWidget(QLabel("-"), 0, 2,
Qt.AlignHCenter | Qt.AlignVCenter)
self.ele2 = ElementButton("C", single_state=True)
self.ele2.clicked.connect(
lambda *args, button=self.ele2: self.open_ptable(button))
bond_lookup_layout.addWidget(self.ele2, 0, 3,
Qt.AlignLeft | Qt.AlignTop)
bond_lookup_layout.addWidget(QLabel("bond order:"), 1, 0)
self.bond_order = BondOrderSpinBox()
self.bond_order.setRange(1., 3.)
self.bond_order.setValue(1)
self.bond_order.setSingleStep(0.5)
self.bond_order.setDecimals(1)
self.bond_order.valueChanged.connect(self.check_bond_lengths)
bond_lookup_layout.addWidget(self.bond_order, 1, 1, 1, 3)
bond_lookup_layout.setColumnStretch(0, 0)
bond_lookup_layout.setColumnStretch(1, 0)
bond_lookup_layout.setColumnStretch(2, 0)
bond_lookup_layout.setColumnStretch(3, 1)
bond_length_layout.addRow(bond_lookup)
self.status = QStatusBar()
self.status.setSizeGripEnabled(False)
bond_lookup_layout.addWidget(self.status, 2, 0, 1, 4)
self.do_bond_change = QPushButton("change selected bond lengths")
self.do_bond_change.clicked.connect(self.change_bond_length)
bond_length_layout.addRow(self.do_bond_change)
tabs.addTab(bond_tab, "covalent bonds")
tabs.addTab(ts_bond_tab, "TS bonds")
tabs.addTab(hbond_tab, "H-bonds")
tabs.addTab(tm_bond_tab, "coordination bonds")
tabs.addTab(bond_length_tab, "bond length")
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def run_tsbond(self, *args):
args = ["tsbond", "sel"]
color = self.tsbond_color.get_color()
args.extend(["color", "rgb(%i, %i, %i)" % tuple(color[:-1])])
self.settings.tsbond_color = tuple([c / 255. for c in color])
radius = self.tsbond_radius.value()
args.extend(["radius", "%.3f" % radius])
self.settings.tsbond_radius = radius
transparency = self.tsbond_transparency.value()
args.extend(["transparency", "%i" % transparency])
self.settings.tsbond_transparency = transparency
run(self.session, " ".join(args))
def run_erase_tsbond(self, *args):
run(self.session, "~tsbond sel")
def run_bond(self, *args):
# TODO: switch to `bond sel` in 1.2
sel = selected_atoms(self.session)
halfbond = self.bond_halfbond.checkState() == Qt.Checked
self.settings.bond_halfbond = halfbond
if not halfbond:
color = self.bond_color.get_color()
color = tuple(x / 255. for x in color)
self.settings.bond_color = color
radius = self.bond_radius.value()
self.settings.bond_radius = radius
for b in selected_bonds(self.session):
b.halfbond = halfbond
if not halfbond:
b.color = np.array([int(x * 255) for x in color])
b.radius = radius
for i, a1 in enumerate(sel):
for a2 in sel[:i]:
if a1.structure is a2.structure and a2 not in a1.neighbors:
new_bond = a1.structure.new_bond(a1, a2)
new_bond.halfbond = halfbond
if not halfbond:
new_bond.color = np.array(
[int(x * 255) for x in color])
new_bond.radius = radius
def run_hbond(self, *args):
args = ["hbonds", "reveal", "true"]
color = self.hbond_color.get_color()
args.extend(["color", "rgb(%i, %i, %i)" % tuple(color[:-1])])
self.settings.hbond_color = tuple([c / 255. for c in color])
radius = self.hbond_radius.value()
args.extend(["radius", "%.3f" % radius])
self.settings.hbond_radius = radius
dashes = self.hbond_dashes.value()
args.extend(["dashes", "%i" % dashes])
self.settings.hbond_dashes = dashes
run(self.session, " ".join(args))
def run_tm_bond(self, *args):
color = self.tm_bond_color.get_color()
self.settings.tm_bond_color = tuple([c / 255. for c in color])
radius = self.tm_bond_radius.value()
self.settings.tm_bond_radius = radius
dashes = self.tm_bond_dashes.value()
self.settings.tm_bond_dashes = dashes
models = self.session.models.list(type=AtomicStructure)
for model in models:
rescol = ResidueCollection(model, bonds_matter=False)
try:
tm_list = rescol.find([
AnyTransitionMetal(), "Na", "K", "Rb", "Cs", "Fr", "Mg",
"Ca", "Sr", "Ba", "Ra"
])
for tm in tm_list:
for atom in rescol.atoms:
if atom is tm:
continue
if atom.is_connected(tm):
pbg = model.pseudobond_group(
model.PBG_METAL_COORDINATION,
create_type="normal")
pbg.new_pseudobond(tm.chix_atom, atom.chix_atom)
pbg.dashes = dashes
pbg.color = color
pbg.radius = radius
except LookupError:
pass
def del_tm_bond(self, *args):
models = self.session.models.list(type=AtomicStructure)
for model in models:
pbg = model.pseudobond_group(model.PBG_METAL_COORDINATION,
create_type=None)
if pbg is not None:
pbg.delete()
def open_ptable(self, button):
self.tool_window.create_child_window("select element",
window_class=PTable2,
button=button,
callback=self.check_bond_lengths)
def check_bond_lengths(self, *args):
ele1 = self.ele1.text()
ele2 = self.ele2.text()
key = ORDER_BOND_ORDER.key(ele1, ele2)
order = "%.1f" % self.bond_order.value()
if key in ORDER_BOND_ORDER.bonds and order in ORDER_BOND_ORDER.bonds[
key]:
self.bond_distance.setValue(ORDER_BOND_ORDER.bonds[key][order])
self.status.showMessage("")
else:
self.status.showMessage("no bond data for %s-%s %sx bonds" %
(ele1, ele2, order))
def change_bond_length(self, *args):
dist = self.bond_distance.value()
atom_pairs = []
sel = selected_atoms(self.session)
if len(sel) == 2 and sel[0].structure is sel[1].structure:
atom_pairs.append(sel)
for bond in selected_bonds(self.session):
if not all(atom in sel for atom in bond.atoms):
atom_pairs.append(bond.atoms)
for bond in selected_pseudobonds(self.session):
if not all(atom in sel for atom in bond.atoms):
atom_pairs.append(bond.atoms)
for pair in atom_pairs:
atom1, atom2 = pair
frag1 = get_fragment(atom1,
stop=atom2,
max_len=atom1.structure.num_atoms)
frag2 = get_fragment(atom2,
stop=atom1,
max_len=atom1.structure.num_atoms)
v = atom2.coord - atom1.coord
cur_dist = np.linalg.norm(v)
change = dist - cur_dist
if self.move_fragment.currentText() == "both":
change = 0.5 * change
frag1.coords -= change * v / cur_dist
frag2.coords += change * v / cur_dist
elif self.move_fragment.currentText() == "smaller":
if len(frag1) < len(frag2) or (len(frag1) == len(frag2)
and sum(frag1.elements.masses) <
sum(frag2.elements.masses)):
frag1.coords -= change * v / cur_dist
else:
frag2.coords += change * v / cur_dist
elif self.move_fragment.currentText() == "larger":
if len(frag1) > len(frag2) or (len(frag1) == len(frag2)
and sum(frag1.elements.masses) >
sum(frag2.elements.masses)):
frag1.coords -= change * v / cur_dist
else:
frag2.coords += change * v / cur_dist
def _build_ui(self):
layout = QGridLayout()
tabs = QTabWidget()
layout.addWidget(tabs)
ts_bond_tab = QWidget()
ts_options = QFormLayout(ts_bond_tab)
self.tsbond_color = ColorButton(has_alpha_channel=False,
max_size=(16, 16))
self.tsbond_color.set_color(self.settings.tsbond_color)
ts_options.addRow("color:", self.tsbond_color)
self.tsbond_transparency = QSpinBox()
self.tsbond_transparency.setRange(1, 99)
self.tsbond_transparency.setValue(self.settings.tsbond_transparency)
self.tsbond_transparency.setSuffix("%")
ts_options.addRow("transparency:", self.tsbond_transparency)
self.tsbond_radius = QDoubleSpinBox()
self.tsbond_radius.setRange(0.01, 1)
self.tsbond_radius.setDecimals(3)
self.tsbond_radius.setSingleStep(0.005)
self.tsbond_radius.setSuffix(" \u212B")
self.tsbond_radius.setValue(self.settings.tsbond_radius)
ts_options.addRow("radius:", self.tsbond_radius)
draw_tsbonds = QPushButton("draw TS bonds on selected atoms/bonds")
draw_tsbonds.clicked.connect(self.run_tsbond)
ts_options.addRow(draw_tsbonds)
self.draw_tsbonds = draw_tsbonds
erase_tsbonds = QPushButton("erase selected TS bonds")
erase_tsbonds.clicked.connect(self.run_erase_tsbond)
ts_options.addRow(erase_tsbonds)
self.erase_tsbonds = erase_tsbonds
bond_tab = QWidget()
bond_options = QFormLayout(bond_tab)
self.bond_halfbond = QCheckBox()
self.bond_halfbond.setChecked(self.settings.bond_halfbond)
self.bond_halfbond.setToolTip(
"each half of the bond will be colored according to the atom's color"
)
bond_options.addRow("half-bond:", self.bond_halfbond)
self.bond_color = ColorButton(has_alpha_channel=True,
max_size=(16, 16))
self.bond_color.set_color(self.settings.bond_color)
self.bond_color.setEnabled(
self.bond_halfbond.checkState() != Qt.Checked)
self.bond_halfbond.stateChanged.connect(
lambda state, widget=self.bond_color: self.bond_color.setEnabled(
state != Qt.Checked))
bond_options.addRow("color:", self.bond_color)
self.bond_radius = QDoubleSpinBox()
self.bond_radius.setRange(0.01, 1)
self.bond_radius.setDecimals(3)
self.bond_radius.setSingleStep(0.005)
self.bond_radius.setSuffix(" \u212B")
self.bond_radius.setValue(self.settings.bond_radius)
bond_options.addRow("radius:", self.bond_radius)
draw_tsbonds = QPushButton("draw bond between selected atoms")
draw_tsbonds.clicked.connect(self.run_bond)
bond_options.addRow(draw_tsbonds)
self.draw_tsbonds = draw_tsbonds
erase_bonds = QPushButton("erase selected bonds")
erase_bonds.clicked.connect(
lambda *, ses=self.session: run(ses, "delete bonds sel"))
bond_options.addRow(erase_bonds)
self.erase_bonds = erase_bonds
hbond_tab = QWidget()
hbond_options = QFormLayout(hbond_tab)
self.hbond_color = ColorButton(has_alpha_channel=True,
max_size=(16, 16))
self.hbond_color.set_color(self.settings.hbond_color)
hbond_options.addRow("color:", self.hbond_color)
self.hbond_radius = QDoubleSpinBox()
self.hbond_radius.setDecimals(3)
self.hbond_radius.setSuffix(" \u212B")
self.hbond_radius.setValue(self.settings.hbond_radius)
hbond_options.addRow("radius:", self.hbond_radius)
self.hbond_dashes = QSpinBox()
self.hbond_dashes.setRange(0, 28)
self.hbond_dashes.setSingleStep(2)
self.hbond_radius.setSingleStep(0.005)
self.hbond_dashes.setValue(self.settings.hbond_dashes)
hbond_options.addRow("dashes:", self.hbond_dashes)
draw_hbonds = QPushButton("draw H-bonds")
draw_hbonds.clicked.connect(self.run_hbond)
hbond_options.addRow(draw_hbonds)
self.draw_hbonds = draw_hbonds
erase_hbonds = QPushButton("erase all H-bonds")
erase_hbonds.clicked.connect(
lambda *, ses=self.session: run(ses, "~hbonds"))
hbond_options.addRow(erase_hbonds)
self.erase_hbonds = erase_hbonds
tm_bond_tab = QWidget()
tm_bond_options = QFormLayout(tm_bond_tab)
self.tm_bond_color = ColorButton(has_alpha_channel=True,
max_size=(16, 16))
self.tm_bond_color.set_color(self.settings.tm_bond_color)
tm_bond_options.addRow("color:", self.tm_bond_color)
self.tm_bond_radius = QDoubleSpinBox()
self.tm_bond_radius.setDecimals(3)
self.tm_bond_radius.setSuffix(" \u212B")
self.tm_bond_radius.setValue(self.settings.tm_bond_radius)
tm_bond_options.addRow("radius:", self.tm_bond_radius)
self.tm_bond_dashes = QSpinBox()
self.tm_bond_dashes.setRange(0, 28)
self.tm_bond_dashes.setSingleStep(2)
self.tm_bond_radius.setSingleStep(0.005)
self.tm_bond_dashes.setValue(self.settings.tm_bond_dashes)
tm_bond_options.addRow("dashes:", self.tm_bond_dashes)
draw_tm_bonds = QPushButton("draw metal coordination bonds")
draw_tm_bonds.clicked.connect(self.run_tm_bond)
tm_bond_options.addRow(draw_tm_bonds)
self.draw_tm_bonds = draw_tm_bonds
erase_tm_bonds = QPushButton("erase all metal coordination bonds")
erase_tm_bonds.clicked.connect(self.del_tm_bond)
tm_bond_options.addRow(erase_tm_bonds)
self.erase_tm_bonds = erase_tm_bonds
bond_length_tab = QWidget()
bond_length_layout = QFormLayout(bond_length_tab)
self.bond_distance = QDoubleSpinBox()
self.bond_distance.setRange(0.5, 10.0)
self.bond_distance.setSingleStep(0.05)
self.bond_distance.setValue(1.51)
self.bond_distance.setSuffix(" \u212B")
bond_length_layout.addRow("bond length:", self.bond_distance)
self.move_fragment = QComboBox()
self.move_fragment.addItems(["both", "smaller", "larger"])
bond_length_layout.addRow("move side:", self.move_fragment)
bond_lookup = QGroupBox("bond length lookup:")
bond_lookup_layout = QGridLayout(bond_lookup)
bond_lookup_layout.addWidget(
QLabel("elements:"),
0,
0,
)
self.ele1 = ElementButton("C", single_state=True)
self.ele1.clicked.connect(
lambda *args, button=self.ele1: self.open_ptable(button))
bond_lookup_layout.addWidget(self.ele1, 0, 1,
Qt.AlignRight | Qt.AlignTop)
bond_lookup_layout.addWidget(QLabel("-"), 0, 2,
Qt.AlignHCenter | Qt.AlignVCenter)
self.ele2 = ElementButton("C", single_state=True)
self.ele2.clicked.connect(
lambda *args, button=self.ele2: self.open_ptable(button))
bond_lookup_layout.addWidget(self.ele2, 0, 3,
Qt.AlignLeft | Qt.AlignTop)
bond_lookup_layout.addWidget(QLabel("bond order:"), 1, 0)
self.bond_order = BondOrderSpinBox()
self.bond_order.setRange(1., 3.)
self.bond_order.setValue(1)
self.bond_order.setSingleStep(0.5)
self.bond_order.setDecimals(1)
self.bond_order.valueChanged.connect(self.check_bond_lengths)
bond_lookup_layout.addWidget(self.bond_order, 1, 1, 1, 3)
bond_lookup_layout.setColumnStretch(0, 0)
bond_lookup_layout.setColumnStretch(1, 0)
bond_lookup_layout.setColumnStretch(2, 0)
bond_lookup_layout.setColumnStretch(3, 1)
bond_length_layout.addRow(bond_lookup)
self.status = QStatusBar()
self.status.setSizeGripEnabled(False)
bond_lookup_layout.addWidget(self.status, 2, 0, 1, 4)
self.do_bond_change = QPushButton("change selected bond lengths")
self.do_bond_change.clicked.connect(self.change_bond_length)
bond_length_layout.addRow(self.do_bond_change)
tabs.addTab(bond_tab, "covalent bonds")
tabs.addTab(ts_bond_tab, "TS bonds")
tabs.addTab(hbond_tab, "H-bonds")
tabs.addTab(tm_bond_tab, "coordination bonds")
tabs.addTab(bond_length_tab, "bond length")
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
class BaseFileFolderDialog(BaseDialog,
abstract_dialog.AbstractFileFolderDialog):
"""
Base dialog classes for folders and files
"""
def_title = 'Select File'
def_size = (200, 125)
def_use_app_browser = False
def __init__(self, name='BaseFileFolder', parent=None, **kwargs):
super(BaseFileFolderDialog, self).__init__(name=name, parent=parent)
self.directory = None
self.filters = None
self._use_app_browser = kwargs.pop('use_app_browser',
self.def_use_app_browser)
self.set_filters('All Files (*.*)')
# By default, we set the directory to the user folder
self.set_directory(os.path.expanduser('~'))
self.center()
def open_app_browser(self):
return
def ui(self):
super(BaseFileFolderDialog, self).ui()
from tpDcc.libs.qt.widgets import directory
self.places = dict()
self.grid = layouts.GridLayout()
sub_grid = layouts.GridLayout()
self.grid.addWidget(QLabel('Path:'), 0, 0, Qt.AlignRight)
self.path_edit = QLineEdit(self)
self.path_edit.setReadOnly(True)
self.filter_box = QComboBox(self)
self.file_edit = QLineEdit(self)
self.view = directory.FileListWidget(self)
self.view.setWrapping(True)
self.view.setFocusPolicy(Qt.StrongFocus)
self.open_button = QPushButton('Select', self)
self.cancel_button = QPushButton('Cancel', self)
size = QSize(32, 24)
self.up_button = QPushButton('Up')
self.up_button.setToolTip('Go up')
self.up_button.setMinimumSize(size)
self.up_button.setMaximumSize(size)
size = QSize(56, 24)
self.refresh_button = QPushButton('Reload')
self.refresh_button.setToolTip('Reload file list')
self.refresh_button.setMinimumSize(size)
self.refresh_button.setMaximumSize(size)
self.show_hidden = QCheckBox('Hidden')
self.show_hidden.setChecked(False)
self.show_hidden.setToolTip('Toggle show hidden files')
sub_grid.addWidget(self.up_button, 0, 1)
sub_grid.addWidget(self.path_edit, 0, 2)
sub_grid.addWidget(self.refresh_button, 0, 3)
sub_grid.addWidget(self.show_hidden, 0, 4)
self.grid.addLayout(sub_grid, 0, 1)
self.grid.addWidget(self.get_drives_widget(), 1, 0)
self.grid.addWidget(self.view, 1, 1)
self.grid.addWidget(QLabel('File name:'), 7, 0, Qt.AlignRight)
self.grid.addWidget(self.file_edit, 7, 1)
self.filter_label = QLabel('Filter:')
self.grid.addWidget(self.filter_label, 8, 0, Qt.AlignRight)
self.grid.addWidget(self.filter_box, 8, 1)
hbox = layouts.GridLayout()
hbox.addWidget(self.open_button, 0, 0, Qt.AlignRight)
hbox.addWidget(self.cancel_button, 0, 1, Qt.AlignRight)
self.grid.addLayout(hbox, 9, 1, Qt.AlignRight)
self.main_layout.addLayout(self.grid)
self.setGeometry(200, 100, 600, 400)
self.open_button.clicked.connect(self.accept)
self.cancel_button.clicked.connect(self.reject)
self.up_button.clicked.connect(self.go_up)
self.refresh_button.clicked.connect(self.update_view)
self.show_hidden.stateChanged.connect(self.update_view)
self.view.directory_activated.connect(
self.activate_directory_from_view)
self.view.file_activated.connect(self.activate_file_from_view)
self.view.file_selected.connect(self.select_file_item)
self.view.folder_selected.connect(self.select_folder_item)
self.view.up_requested.connect(self.go_up)
self.view.update_requested.connect(self.update_view)
def exec_(self, *args, **kwargs):
if self._use_app_browser:
return self.open_app_browser()
else:
self.update_view()
self.filter_box.currentIndexChanged.connect(self.update_view)
accepted = super(BaseFileFolderDialog, self).exec_()
self.filter_box.currentIndexChanged.disconnect(self.update_view)
return self.get_result() if accepted == 1 else None
def set_filters(self, filters, selected=0):
self.filter_box.clear()
filter_types = filters.split(';;')
for ft in filter_types:
extensions = string.extract(ft, '(', ')')
filter_name = string.rstrips(ft, '({})'.format(extensions))
extensions = extensions.split(' ')
self.filter_box.addItem(
'{} ({})'.format(filter_name, ','.join(extensions)),
extensions)
if 0 <= selected < self.filter_box.count():
self.filter_box.setCurrentIndex(selected)
self.filters = filters
def get_drives_widget(self):
"""
Returns a QGroupBox widget that contains all disk drivers of the PC in a vertical layout
:return: QGroupBox
"""
w = QGroupBox('')
w.setParent(self)
box = layouts.VerticalLayout()
box.setAlignment(Qt.AlignTop)
places = [(getpass.getuser(),
os.path.realpath(os.path.expanduser('~')))]
places += [
(q, q) for q in
[os.path.realpath(x.absolutePath()) for x in QDir().drives()]
]
for label, loc in places:
icon = QFileIconProvider().icon(QFileInfo(loc))
drive_btn = QRadioButton(label)
drive_btn.setIcon(icon)
drive_btn.setToolTip(loc)
drive_btn.setProperty('path', loc)
drive_btn.clicked.connect(self.go_to_drive)
self.places[loc] = drive_btn
box.addWidget(drive_btn)
w.setLayout(box)
return w
def go_to_drive(self):
"""
Updates widget to show the content of the selected disk drive
"""
sender = self.sender()
self.set_directory(sender.property('path'), False)
def get_result(self):
tf = self.file_edit.text()
sf = self.get_file_path(tf)
return sf, os.path.dirname(sf), tf.split(os.pathsep)
def get_filter_patterns(self):
"""
Get list of filter patterns that are being used by the widget
:return: list<str>
"""
idx = self.filter_box.currentIndex()
if idx >= 0:
return self.filter_box.itemData(idx)
else:
return []
def get_file_path(self, file_name):
"""
Returns file path of the given file name taking account the selected directory
:param file_name: str, name of the file without path
:return: str
"""
sname = file_name.split(os.pathsep)[0]
return os.path.realpath(
os.path.join(os.path.abspath(self.directory), sname))
# def accept(self):
# self._overlay.close()
# super(BaseFileFolderDialog, self).accept()
#
#
# def reject(self):
# self._overlay.close()
# super(BaseFileFolderDialog, self).reject()
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 set_directory(self, path, check_drive=True):
"""
Sets the directory that you want to explore
:param path: str, valid path
:param check_drive: bool,
:return:
"""
self.directory = os.path.realpath(path)
self.path_edit.setText(self.directory)
self.file_edit.setText('')
# If necessary, update selected disk driver
if check_drive:
for loc in self.places:
rb = self.places[loc]
rb.setAutoExclusive(False)
rb.setChecked(loc.lower() == self.directory.lower())
rb.setAutoExclusive(True)
self.update_view()
self.up_button.setEnabled(not self.cant_go_up())
def go_up(self):
"""
Updates the current directory to go to its parent directory
"""
self.set_directory(os.path.dirname(self.directory))
def cant_go_up(self):
"""
Checks whether we can naviage to current selected parent directory or not
:return: bool
"""
return os.path.dirname(self.directory) == self.directory
def activate_directory_from_view(self, name):
"""
Updates selected directory
:param name: str, name of the directory
"""
self.set_directory(os.path.join(self.directory, name))
def activate_file_from_view(self, name):
"""
Updates selected file text and returns its info by accepting it
:param name: str, name of the file
"""
self.select_file_item(name=name)
self.accept()
def select_file_item(self, name):
"""
Updates selected file text and returns its info by accepting it
:param name: str, name of the file
"""
self.file_edit.setText(name)
def select_folder_item(self, name):
"""
Updates selected folder text and returns its info by accepting it
:param name: str, name of the folder
"""
self.file_edit.setText(name)
def ui(self):
super(BaseFileFolderDialog, self).ui()
from tpDcc.libs.qt.widgets import directory
self.places = dict()
self.grid = layouts.GridLayout()
sub_grid = layouts.GridLayout()
self.grid.addWidget(QLabel('Path:'), 0, 0, Qt.AlignRight)
self.path_edit = QLineEdit(self)
self.path_edit.setReadOnly(True)
self.filter_box = QComboBox(self)
self.file_edit = QLineEdit(self)
self.view = directory.FileListWidget(self)
self.view.setWrapping(True)
self.view.setFocusPolicy(Qt.StrongFocus)
self.open_button = QPushButton('Select', self)
self.cancel_button = QPushButton('Cancel', self)
size = QSize(32, 24)
self.up_button = QPushButton('Up')
self.up_button.setToolTip('Go up')
self.up_button.setMinimumSize(size)
self.up_button.setMaximumSize(size)
size = QSize(56, 24)
self.refresh_button = QPushButton('Reload')
self.refresh_button.setToolTip('Reload file list')
self.refresh_button.setMinimumSize(size)
self.refresh_button.setMaximumSize(size)
self.show_hidden = QCheckBox('Hidden')
self.show_hidden.setChecked(False)
self.show_hidden.setToolTip('Toggle show hidden files')
sub_grid.addWidget(self.up_button, 0, 1)
sub_grid.addWidget(self.path_edit, 0, 2)
sub_grid.addWidget(self.refresh_button, 0, 3)
sub_grid.addWidget(self.show_hidden, 0, 4)
self.grid.addLayout(sub_grid, 0, 1)
self.grid.addWidget(self.get_drives_widget(), 1, 0)
self.grid.addWidget(self.view, 1, 1)
self.grid.addWidget(QLabel('File name:'), 7, 0, Qt.AlignRight)
self.grid.addWidget(self.file_edit, 7, 1)
self.filter_label = QLabel('Filter:')
self.grid.addWidget(self.filter_label, 8, 0, Qt.AlignRight)
self.grid.addWidget(self.filter_box, 8, 1)
hbox = layouts.GridLayout()
hbox.addWidget(self.open_button, 0, 0, Qt.AlignRight)
hbox.addWidget(self.cancel_button, 0, 1, Qt.AlignRight)
self.grid.addLayout(hbox, 9, 1, Qt.AlignRight)
self.main_layout.addLayout(self.grid)
self.setGeometry(200, 100, 600, 400)
self.open_button.clicked.connect(self.accept)
self.cancel_button.clicked.connect(self.reject)
self.up_button.clicked.connect(self.go_up)
self.refresh_button.clicked.connect(self.update_view)
self.show_hidden.stateChanged.connect(self.update_view)
self.view.directory_activated.connect(
self.activate_directory_from_view)
self.view.file_activated.connect(self.activate_file_from_view)
self.view.file_selected.connect(self.select_file_item)
self.view.folder_selected.connect(self.select_folder_item)
self.view.up_requested.connect(self.go_up)
self.view.update_requested.connect(self.update_view)
class Second(QMainWindow):
def __init__(self):
super(Second, self).__init__()
self.setWindowTitle("Add new device")
self.nameLabel = QLabel(self)
self.nameLabel.move(10, 10)
self.nameLabel.setText("Device name")
self.nameEntry = QLineEdit(self)
self.nameEntry.move(10, 40)
self.nameEntry.resize(100, 30)
self.colorLabel = QLabel(self)
self.colorLabel.move(120, 10)
self.colorLabel.setText("Color cameras")
self.colorEntry = QLineEdit(self)
self.colorEntry.move(140, 40)
self.colorEntry.resize(70, 30)
self.colorEntry.setValidator(QtGui.QIntValidator())
self.monoLabel = QLabel(self)
self.monoLabel.move(230, 10)
self.monoLabel.setText("Mono cameras")
self.monoEntry = QLineEdit(self)
self.monoEntry.move(250, 40)
self.monoEntry.resize(70, 30)
self.monoEntry.setValidator(QtGui.QIntValidator())
self.depthPresent = QCheckBox("Include depth", self)
self.depthPresent.move(10, 80)
self.depthPresent.resize(150, 30)
self.depthPresent.stateChanged.connect(self.toggle_depth)
self.leftfovLabel = QLabel(self)
self.leftfovLabel.move(10, 120)
self.leftfovLabel.setText("Left FOV deg.")
self.leftfovEntry = QLineEdit(self)
self.leftfovEntry.move(180, 120)
self.leftfovEntry.resize(140, 30)
self.leftfovEntry.setValidator(QtGui.QDoubleValidator())
self.rightfovLabel = QLabel(self)
self.rightfovLabel.move(10, 160)
self.rightfovLabel.setText("Right FOV deg.")
self.rightfovEntry = QLineEdit(self)
self.rightfovEntry.move(180, 160)
self.rightfovEntry.resize(140, 30)
self.rightfovEntry.setValidator(QtGui.QDoubleValidator())
self.rgbfovLabel = QLabel(self)
self.rgbfovLabel.move(10, 200)
self.rgbfovLabel.setText("RGB FOV deg.")
self.rgbfovEntry = QLineEdit(self)
self.rgbfovEntry.move(180, 200)
self.rgbfovEntry.resize(140, 30)
self.rgbfovEntry.setValidator(QtGui.QDoubleValidator())
self.lrdistanceLabel = QLabel(self)
self.lrdistanceLabel.move(10, 240)
self.lrdistanceLabel.resize(200, 30)
self.lrdistanceLabel.setText("Left - Right distance cm.")
self.lrdistanceEntry = QLineEdit(self)
self.lrdistanceEntry.move(180, 240)
self.lrdistanceEntry.resize(140, 30)
self.lrdistanceEntry.setValidator(QtGui.QDoubleValidator())
self.lrgbdistanceLabel = QLabel(self)
self.lrgbdistanceLabel.move(10, 280)
self.lrgbdistanceLabel.resize(200, 30)
self.lrgbdistanceLabel.setText("Left - RGB distance cm.")
self.lrgbdistanceEntry = QLineEdit(self)
self.lrgbdistanceEntry.move(180, 280)
self.lrgbdistanceEntry.resize(140, 30)
self.lrgbdistanceEntry.setValidator(QtGui.QDoubleValidator())
self.saveButton = QPushButton("Save", self)
self.saveButton.resize(100, 30)
self.saveButton.clicked.connect(self.save)
self.cancelButton = QPushButton("Cancel", self)
self.cancelButton.resize(100, 30)
self.cancelButton.clicked.connect(self.cancel)
self.toggle_depth(False)
def toggle_depth(self, checked):
if checked:
self.leftfovLabel.setVisible(True)
self.leftfovEntry.setVisible(True)
self.rightfovLabel.setVisible(True)
self.rightfovEntry.setVisible(True)
self.rgbfovLabel.setVisible(True)
self.rgbfovEntry.setVisible(True)
self.lrdistanceLabel.setVisible(True)
self.lrdistanceEntry.setVisible(True)
self.lrgbdistanceLabel.setVisible(True)
self.lrgbdistanceEntry.setVisible(True)
self.saveButton.move(200, 330)
self.cancelButton.move(30, 330)
self.resize(330, 380)
else:
self.leftfovLabel.setVisible(False)
self.leftfovEntry.setVisible(False)
self.rightfovLabel.setVisible(False)
self.rightfovEntry.setVisible(False)
self.rgbfovLabel.setVisible(False)
self.rgbfovEntry.setVisible(False)
self.lrdistanceLabel.setVisible(False)
self.lrdistanceEntry.setVisible(False)
self.lrgbdistanceLabel.setVisible(False)
self.lrgbdistanceEntry.setVisible(False)
self.saveButton.move(200, 120)
self.cancelButton.move(30, 120)
self.resize(330, 170)
def save(self, *args, **kwargs):
try:
data = {
"name": self.nameEntry.text(),
"color_count": int(self.colorEntry.text()),
"mono_count": int(self.monoEntry.text()),
}
if self.depthPresent.isChecked():
data.update({
"depth":
True,
"left_fov_deg":
float(self.leftfovEntry.text()),
"right_fov_deg":
float(self.rightfovEntry.text()),
"rgb_fov_deg":
float(self.rgbfovEntry.text()),
"left_to_right_distance_cm":
float(self.lrdistanceEntry.text()),
"left_to_rgb_distance_cm":
float(self.lrgbdistanceEntry.text()),
})
append_to_json(
data,
Path(__file__).parent.parent / Path('custom_devices.json'))
self.close()
INITIALIZE()
self.instance.getRegisteredTools(['NodeBoxTool'])[0].refresh()
except Exception as e:
QMessageBox.warning(self, "Warning", str(e))
def cancel(self):
self.close()
def _build_ui(self):
layout = QFormLayout()
self.radii_option = QComboBox()
self.radii_option.addItems(["Bondi", "UMN"])
ndx = self.radii_option.findText(self.settings.radii, Qt.MatchExactly)
self.radii_option.setCurrentIndex(ndx)
layout.addRow("radii:", self.radii_option)
self.L_option = QComboBox()
self.L_option.addItems([
"to centroid of coordinating atoms",
"bisect angle between coordinating atoms"
])
ndx = self.L_option.findText(self.settings.L_option, Qt.MatchExactly)
self.L_option.setCurrentIndex(ndx)
layout.addRow("L axis:", self.L_option)
self.sterimol2vec = QGroupBox("Sterimol2Vec")
sterimol2vec_layout = QFormLayout(self.sterimol2vec)
self.at_L = QDoubleSpinBox()
self.at_L.setRange(-10, 30)
self.at_L.setDecimals(2)
self.at_L.setSingleStep(0.25)
self.at_L.setValue(self.settings.at_L)
sterimol2vec_layout.addRow("L value:", self.at_L)
layout.addRow(self.sterimol2vec)
self.sterimol2vec.setCheckable(True)
self.sterimol2vec.toggled.connect(lambda x: self.at_L.setEnabled(x))
self.sterimol2vec.setChecked(self.settings.sterimol2vec)
self.display_vectors = QCheckBox()
self.display_vectors.setChecked(self.settings.display_vectors)
layout.addRow("show vectors:", self.display_vectors)
self.display_radii = QCheckBox()
self.display_radii.setChecked(self.settings.display_radii)
layout.addRow("show radii:", self.display_radii)
calc_sterimol_button = QPushButton(
"calculate parameters for selected ligands")
calc_sterimol_button.clicked.connect(self.calc_sterimol)
layout.addRow(calc_sterimol_button)
self.calc_sterimol_button = calc_sterimol_button
remove_sterimol_button = QPushButton("remove Sterimol visualizations")
remove_sterimol_button.clicked.connect(self.del_sterimol)
layout.addRow(remove_sterimol_button)
self.remove_sterimol_button = remove_sterimol_button
self.table = QTableWidget()
self.table.setColumnCount(8)
self.table.setHorizontalHeaderLabels([
'model',
'coord. atoms',
'B\u2081',
'B\u2082',
'B\u2083',
'B\u2084',
'B\u2085',
'L',
])
self.table.setSelectionBehavior(QTableWidget.SelectRows)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.table.resizeColumnToContents(0)
self.table.resizeColumnToContents(1)
self.table.resizeColumnToContents(2)
self.table.resizeColumnToContents(3)
self.table.resizeColumnToContents(4)
self.table.resizeColumnToContents(5)
self.table.resizeColumnToContents(6)
self.table.resizeColumnToContents(7)
self.table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
3, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
4, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
5, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
6, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
7, QHeaderView.Stretch)
layout.addRow(self.table)
menu = QMenuBar()
export = menu.addMenu("&Export")
clear = QAction("Clear data table", self.tool_window.ui_area)
clear.triggered.connect(self.clear_table)
export.addAction(clear)
copy = QAction("&Copy CSV to clipboard", self.tool_window.ui_area)
copy.triggered.connect(self.copy_csv)
shortcut = QKeySequence(Qt.CTRL + Qt.Key_C)
copy.setShortcut(shortcut)
export.addAction(copy)
save = QAction("&Save CSV...", self.tool_window.ui_area)
save.triggered.connect(self.save_csv)
#this shortcut interferes with main window's save shortcut
#I've tried different shortcut contexts to no avail
#thanks Qt...
#shortcut = QKeySequence(Qt.CTRL + Qt.Key_S)
#save.setShortcut(shortcut)
#save.setShortcutContext(Qt.WidgetShortcut)
export.addAction(save)
delimiter = export.addMenu("Delimiter")
comma = QAction("comma", self.tool_window.ui_area, checkable=True)
comma.setChecked(self.settings.delimiter == "comma")
comma.triggered.connect(lambda *args, delim="comma": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(comma)
tab = QAction("tab", self.tool_window.ui_area, checkable=True)
tab.setChecked(self.settings.delimiter == "tab")
tab.triggered.connect(lambda *args, delim="tab": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(tab)
space = QAction("space", self.tool_window.ui_area, checkable=True)
space.setChecked(self.settings.delimiter == "space")
space.triggered.connect(lambda *args, delim="space": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(space)
semicolon = QAction("semicolon",
self.tool_window.ui_area,
checkable=True)
semicolon.setChecked(self.settings.delimiter == "semicolon")
semicolon.triggered.connect(lambda *args, delim="semicolon": self.
settings.__setattr__("delimiter", delim))
delimiter.addAction(semicolon)
add_header = QAction("&Include CSV header",
self.tool_window.ui_area,
checkable=True)
add_header.setChecked(self.settings.include_header)
add_header.triggered.connect(self.header_check)
export.addAction(add_header)
comma.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
comma.triggered.connect(
lambda *args, action=space: action.setChecked(False))
comma.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=space: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
space.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
space.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
space.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=space: action.setChecked(False))
menu.setNativeMenuBar(False)
self._menu = menu
layout.setMenuBar(menu)
menu.setVisible(True)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def __init__(self, parent=None, **kwds):
super(BoolInputWidget, self).__init__(parent=parent, **kwds)
self.cb = QCheckBox(self)
self.setWidget(self.cb)
self.cb.stateChanged.connect(
lambda val: self.dataSetCallback(bool(val)))
class TestRunner(ToolInstance):
def __init__(self, session, name):
super().__init__(session, name)
self.tool_window = MainToolWindow(self)
self._build_ui()
def _build_ui(self):
"""
ui should have:
* table with a list of available tests and show results after they are done
* way to filter tests
* button to run tests
"""
layout = QFormLayout()
# table to list test classes and the results
self.table = QTableWidget()
self.table.setColumnCount(2)
self.table.setHorizontalHeaderLabels(["test", "result"])
self.table.horizontalHeader().setSectionResizeMode(
0,
self.table.horizontalHeader().Interactive)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.table.horizontalHeader().setSectionResizeMode(
1,
self.table.horizontalHeader().Stretch)
self.table.setSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.MinimumExpanding)
self.table.setSelectionBehavior(self.table.SelectRows)
layout.addRow(self.table)
self.filter = QLineEdit()
self.filter.setPlaceholderText("filter test names")
self.filter.setClearButtonEnabled(True)
self.filter.textChanged.connect(self.apply_filter)
layout.addRow(self.filter)
self.profile = QCheckBox()
self.profile.setToolTip("profile functions called during testing "
"using cProfile")
layout.addRow("profile calls:", self.profile)
self.run_button = QPushButton("run tests")
self.run_button.clicked.connect(self.run_tests)
self.run_button.setToolTip(
"if no tests are selected on the table, run all tests\n" +
"otherwise, run selected tests")
layout.addRow(self.run_button)
self.fill_table()
self.table.resizeColumnToContents(0)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def apply_filter(self, text=None):
"""filter table to only show tests matching text"""
if text is None:
text = self.filter.text()
if text:
text = text.replace("(", "\(")
text = text.replace(")", "\)")
m = QRegularExpression(text)
m.setPatternOptions(QRegularExpression.CaseInsensitiveOption)
if m.isValid():
m.optimize()
filter = lambda row_num: m.match(
self.table.item(row_num, 0).text()).hasMatch()
else:
return
else:
filter = lambda row: True
for i in range(0, self.table.rowCount()):
self.table.setRowHidden(i, not filter(i))
def fill_table(self):
"""adds test names to the table"""
mgr = self.session.test_manager
for name in mgr.tests.keys():
row = self.table.rowCount()
self.table.insertRow(row)
test_name = QTableWidgetItem()
test_name.setData(Qt.DisplayRole, name)
self.table.setItem(row, 0, test_name)
def run_tests(self):
"""run the tests selected on the table and show the results"""
from TestManager.commands.test import test
test_list = []
use_selected = True
for row in self.table.selectionModel().selectedRows():
if self.table.isRowHidden(row.row()):
continue
test_name = self.table.item(row.row(), 0).text()
test_list.append(test_name)
if not test_list:
use_selected = False
for i in range(0, self.table.rowCount()):
if self.table.isRowHidden(i):
continue
test_name = self.table.item(i, 0).text()
test_list.append(test_name)
if not test_list:
test_list = ["all"]
results, stats = test(self.session,
test_list,
profile=self.profile.checkState() == Qt.Checked)
cell_widgets = []
for name in results:
widget = QWidget()
widget_layout = QHBoxLayout(widget)
widget_layout.setContentsMargins(0, 0, 0, 0)
success_button = get_button("success")
fail_button = get_button("fail")
skip_button = get_button("skip")
error_button = get_button("error")
expected_fail_button = get_button("expected fail")
unexpected_success_button = get_button("unexpected success")
success_count = 0
fail_count = 0
error_count = 0
unexpected_success_count = 0
expected_fail_count = 0
skip_count = 0
success_tooltip = "Successes:\n"
fail_tooltip = "Failed tests:\n"
error_tooltip = "Errors during test:\n"
unexpected_success_tooltip = "Unexpected successes:\n"
expected_fail_tooltip = "Expected fails:\n"
skip_tooltip = "Skipped tests:\n"
for case in results[name]:
result, msg = results[name][case]
if result == "success":
success_count += 1
success_tooltip += "%s.%s: %s\n" % (
case.__class__.__qualname__, case._testMethodName, msg)
elif result == "fail":
fail_count += 1
fail_tooltip += "%s.%s failed: %s\n" % (
case.__class__.__qualname__, case._testMethodName, msg)
elif result == "error":
error_count += 1
error_tooltip += "error during %s.%s: %s\n" % (
case.__class__.__qualname__, case._testMethodName, msg)
elif result == "expected_failure":
expected_fail_count += 1
expected_fail_tooltip += "intended failure during %s.%s: %s\n" % (
case.__class__.__qualname__, case._testMethodName, msg)
elif result == "skip":
skip_count += 1
skip_tooltip += "%s.%s\n" % (case.__class__.__qualname__,
case._testMethodName)
elif result == "unexpected_success":
unexpected_success_count += 1
unexpected_success_tooltip += "%s.%s should not have worked, but did\n" % (
case.__class__.__qualname__, case._testMethodName)
success_tooltip = success_tooltip.strip()
fail_tooltip = fail_tooltip.strip()
error_tooltip = error_tooltip.strip()
expected_fail_tooltip = expected_fail_tooltip.strip()
skip_tooltip = skip_tooltip.strip()
unexpected_success_tooltip = unexpected_success_tooltip.strip()
icon_count = 0
if success_count:
success_button.setText("%i" % success_count)
success_button.setToolTip(success_tooltip)
success_button.clicked.connect(
lambda *args, t_name=name, res=success_tooltip: self.
tool_window.create_child_window(
"successes for %s" % t_name,
text=res,
window_class=ResultsWindow,
))
widget_layout.insertWidget(icon_count, success_button, 1)
icon_count += 1
if fail_count:
fail_button.setText("%i" % fail_count)
fail_button.setToolTip(fail_tooltip)
fail_button.clicked.connect(
lambda *args, res=fail_tooltip: self.tool_window.
create_child_window(
"failures for %s" % name,
text=res,
window_class=ResultsWindow,
))
widget_layout.insertWidget(icon_count, fail_button, 1)
icon_count += 1
if error_count:
error_button.setText("%i" % error_count)
error_button.setToolTip(error_tooltip)
error_button.clicked.connect(
lambda *args, res=error_tooltip: self.tool_window.
create_child_window(
"errors for %s" % name,
text=res,
window_class=ResultsWindow,
))
widget_layout.insertWidget(icon_count, error_button, 1)
icon_count += 1
if unexpected_success_count:
unexpected_success_button.setText("%i" %
unexpected_success_count)
unexpected_success_button.setToolTip(
unexpected_success_tooltip)
unexpected_success_button.clicked.connect(
lambda *args, res=unexpected_success_tooltip: self.
tool_window.create_child_window(
"unexpected successes for %s" % name,
text=res,
window_class=ResultsWindow,
))
widget_layout.insertWidget(icon_count,
unexpected_success_button, 1)
icon_count += 1
if expected_fail_count:
expected_fail_button.setText("%i" % expected_fail_count)
expected_fail_button.setToolTip(expected_fail_tooltip)
expected_fail_button.clicked.connect(
lambda *args, res=expected_fail_tooltip: self.tool_window.
create_child_window(
"expected failures for %s" % name,
text=res,
window_class=ResultsWindow,
))
widget_layout.insertWidget(icon_count, expected_fail_button, 1)
icon_count += 1
if skip_count:
skip_button.setText("%i" % skip_count)
skip_button.setToolTip(skip_tooltip)
skip_button.clicked.connect(
lambda *args, res=skip_tooltip: self.tool_window.
create_child_window(
"skipped tests for %s" % name,
text=res,
window_class=ResultsWindow,
))
widget_layout.insertWidget(icon_count, skip_button, 1)
cell_widgets.append(widget)
widget_count = 0
if use_selected:
for row in self.table.selectionModel().selectedRows():
if self.table.isRowHidden(row.row()):
continue
self.table.setCellWidget(row.row(), 1,
cell_widgets[widget_count])
self.table.resizeRowToContents(row.row())
widget_count += 1
else:
for i in range(0, self.table.rowCount()):
if self.table.isRowHidden(i):
continue
self.table.setCellWidget(i, 1, cell_widgets[widget_count])
# self.table.resizeRowToContents(i)
widget_count += 1
if self.profile.checkState() == Qt.Checked:
self.tool_window.create_child_window("stats",
text=stats,
window_class=ResultsWindow)
def _build_ui(self):
layout = QGridLayout()
tab_widget = QTabWidget()
layout.addWidget(tab_widget)
structure_widget = QWidget()
structure_layout = QGridLayout(structure_widget)
tab_widget.addTab(structure_widget, "structure")
self.structure_source = QComboBox()
self.structure_source.addItems(
["AARON template", "file", "coordination complexes", "SMILES"])
structure_layout.addWidget(QLabel("structure source:"), 0, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
structure_layout.addWidget(
self.structure_source,
0,
1,
1,
1,
)
open_button = QPushButton("open")
open_button.clicked.connect(self.open_template)
structure_layout.addWidget(
open_button,
0,
2,
1,
1,
)
# SMILES options
self.smiles_options = QGroupBox("SMILES options")
smiles_layout = QFormLayout(self.smiles_options)
structure_layout.addWidget(self.smiles_options, 1, 0, 1, 3,
Qt.AlignTop | Qt.AlignHCenter)
self.smiles_line = QLineEdit()
smiles_layout.addRow("SMILES string:", self.smiles_line)
self.smiles_options.setVisible(
self.structure_source.currentText() == "SMILES")
self.structure_source.currentTextChanged.connect(
lambda text: self.smiles_options.setVisible(text == "SMILES"))
# coordination complexes options
self.coord_comp_options = QGroupBox("Coordination Complex Options")
coord_layout = QFormLayout(self.coord_comp_options)
structure_layout.addWidget(self.coord_comp_options, 1, 0, 1, 3,
Qt.AlignTop | Qt.AlignHCenter)
create_coord_items(self,
coord_layout,
allow_minimization=False,
default_ele="Pd")
self.coord_comp_options.setVisible(
self.structure_source.currentText() == "coordination complexes")
self.structure_source.currentTextChanged.connect(
lambda text: self.coord_comp_options.setVisible(
text == "coordination complexes"))
# aaron template options
self.aaron_options = QGroupBox("AARON template structures")
aaron_layout = QFormLayout(self.aaron_options)
structure_layout.addWidget(self.aaron_options, 1, 0, 1, 3,
Qt.AlignTop | Qt.AlignHCenter)
self.aaron_options.setVisible(
self.structure_source.currentText() == "AARON template")
self.structure_source.currentTextChanged.connect(
lambda text: self.aaron_options.setVisible(text == "AARON template"
))
# file options
self.file_options = QGroupBox("single file options")
file_layout = QFormLayout(self.file_options)
structure_layout.addWidget(self.file_options, 1, 0, 1, 3,
Qt.AlignTop | Qt.AlignHCenter)
file_widget = QWidget()
file_browse_layout = QGridLayout(file_widget)
self.template_file = QLineEdit()
file_browse_layout.addWidget(self.template_file, 0, 0, 1, 1,
Qt.AlignCenter)
browse_button = QPushButton("browse...")
# browse_button.clicked.connect(self.browse_file_template)
file_browse_layout.addWidget(browse_button, 0, 1, 1, 1, Qt.AlignCenter)
file_browse_layout.setColumnStretch(0, 1)
file_browse_layout.setColumnStretch(1, 0)
margins = file_browse_layout.contentsMargins()
file_browse_layout.setContentsMargins(margins.left(), 0,
margins.right(), 0)
file_layout.addRow("file:", file_widget)
self.file_options.setVisible(
self.structure_source.currentText() == "file")
self.structure_source.currentTextChanged.connect(
lambda text: self.file_options.setVisible(text == "file"))
self.optimize_template = QCheckBox()
self.optimize_template.setCheckState(Qt.Checked)
structure_layout.addWidget(
QLabel("optimize template:"),
2,
0,
1,
1,
Qt.AlignLeft | Qt.AlignVCenter,
)
structure_layout.addWidget(
self.optimize_template,
2,
1,
1,
2,
Qt.AlignLeft | Qt.AlignVCenter,
)
structure_layout.setColumnStretch(0, 0)
structure_layout.setColumnStretch(1, 1)
structure_layout.setColumnStretch(2, 0)
# structure changes
changes_widget = QWidget()
changes_layout = QGridLayout(changes_widget)
tab_widget.addTab(changes_widget, "changes")
# HPC settings
hpc_widget = QWidget()
hpc_layout = QGridLayout(hpc_widget)
tab_widget.addTab(hpc_widget, "HPC")
# theory settings
theory_widget = QWidget()
theory_layout = QGridLayout(theory_widget)
tab_widget.addTab(theory_widget, "theory")
# results
results_widget = QWidget()
results_layout = QGridLayout(results_widget)
tab_widget.addTab(results_widget, "results")
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def _build_ui(self):
layout = QGridLayout()
layout.addWidget(QLabel("center of rotation:"), 0, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
self.cor_button = QComboBox()
self.cor_button.addItems(
["automatic", "select atoms", "view's center of rotation"])
layout.addWidget(self.cor_button, 0, 1, 1, 1, Qt.AlignTop)
self.set_cor_selection = QPushButton("set selection")
self.cor_button.currentTextChanged.connect(
lambda t, widget=self.set_cor_selection: widget.setEnabled(
t == "select atoms"))
self.set_cor_selection.clicked.connect(self.manual_cor)
layout.addWidget(self.set_cor_selection, 0, 2, 1, 1, Qt.AlignTop)
self.set_cor_selection.setEnabled(False)
layout.addWidget(QLabel("rotation vector:"), 1, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
self.vector_option = QComboBox()
self.vector_option.addItems([
"axis", "view axis", "bond", "perpendicular to plane",
"centroid of atoms", "custom"
])
layout.addWidget(self.vector_option, 1, 1, 1, 1, Qt.AlignVCenter)
vector = QWidget()
vector.setToolTip("vector will be normalized before rotating")
vector_layout = QHBoxLayout(vector)
vector_layout.setContentsMargins(0, 0, 0, 0)
self.vector_x = QDoubleSpinBox()
self.vector_y = QDoubleSpinBox()
self.vector_z = QDoubleSpinBox()
self.vector_z.setValue(1.0)
for c, t in zip([self.vector_x, self.vector_y, self.vector_z],
[" x", " y", " z"]):
c.setSingleStep(0.01)
c.setRange(-100, 100)
# c.setSuffix(t)
c.valueChanged.connect(self.show_rot_vec)
vector_layout.addWidget(c)
layout.addWidget(vector, 1, 2, 1, 1, Qt.AlignTop)
vector.setVisible(self.vector_option.currentText() == "custom")
self.vector_option.currentTextChanged.connect(
lambda text, widget=vector: widget.setVisible(text == "custom"))
self.view_axis = QComboBox()
self.view_axis.addItems(["z", "y", "x"])
layout.addWidget(self.view_axis, 1, 2, 1, 1, Qt.AlignTop)
self.view_axis.setVisible(
self.vector_option.currentText() == "view axis")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.view_axis: widget.setVisible(text ==
"view axis"))
self.axis = QComboBox()
self.axis.addItems(["z", "y", "x"])
layout.addWidget(self.axis, 1, 2, 1, 1, Qt.AlignTop)
self.axis.setVisible(self.vector_option.currentText() == "axis")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.axis: widget.setVisible(text == "axis"))
self.bond_button = QPushButton("set selected bond")
self.bond_button.clicked.connect(self.set_bonds)
layout.addWidget(self.bond_button, 1, 2, 1, 1, Qt.AlignTop)
self.bond_button.setVisible(self.vector_option.currentText() == "bond")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.bond_button: widget.setVisible(text ==
"bond"))
self.perp_button = QPushButton("set selected atoms")
self.perp_button.clicked.connect(self.set_perpendicular)
layout.addWidget(self.perp_button, 1, 2, 1, 1, Qt.AlignTop)
self.perp_button.setVisible(
self.vector_option.currentText() == "perpendicular to plane")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.perp_button: widget.setVisible(
text == "perpendicular to plane"))
self.group_button = QPushButton("set selected atoms")
self.group_button.clicked.connect(self.set_group)
layout.addWidget(self.group_button, 1, 2, 1, 1, Qt.AlignTop)
self.group_button.setVisible(
self.vector_option.currentText() == "centroid of atoms")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.group_button: widget.setVisible(
text == "centroid of atoms"))
layout.addWidget(QLabel("angle:"), 2, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
self.angle = QDoubleSpinBox()
self.angle.setRange(-360, 360)
self.angle.setSingleStep(5)
self.angle.setSuffix("°")
layout.addWidget(self.angle, 2, 1, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
layout.addWidget(QLabel("preview rotation axis:"), 3, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
self.display_rot_vec = QCheckBox()
self.display_rot_vec.setCheckState(Qt.Checked)
self.display_rot_vec.stateChanged.connect(self.show_rot_vec)
layout.addWidget(self.display_rot_vec, 3, 1, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
rotate_button = QPushButton("rotate selected atoms")
rotate_button.clicked.connect(self.do_rotate)
layout.addWidget(rotate_button, 4, 0, 1, 3, Qt.AlignTop)
self.rotate_button = rotate_button
self.status_bar = QStatusBar()
self.status_bar.setSizeGripEnabled(False)
layout.addWidget(self.status_bar, 5, 0, 1, 3, Qt.AlignTop)
self.vector_option.currentTextChanged.connect(self.show_auto_status)
self.cor_button.currentIndexChanged.connect(
lambda *args: self.show_auto_status("select atoms"))
self.cor_button.currentIndexChanged.connect(self.show_rot_vec)
self.set_cor_selection.clicked.connect(self.show_rot_vec)
self.vector_option.currentIndexChanged.connect(self.show_rot_vec)
self.axis.currentIndexChanged.connect(self.show_rot_vec)
self.view_axis.currentIndexChanged.connect(self.show_rot_vec)
self.bond_button.clicked.connect(self.show_rot_vec)
self.perp_button.clicked.connect(self.show_rot_vec)
self.group_button.clicked.connect(self.show_rot_vec)
layout.setRowStretch(0, 0)
layout.setRowStretch(1, 0)
layout.setRowStretch(2, 0)
layout.setRowStretch(3, 0)
layout.setRowStretch(4, 0)
layout.setRowStretch(5, 1)
layout.setColumnStretch(0, 0)
layout.setColumnStretch(1, 1)
layout.setColumnStretch(2, 1)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def addAttributeSlot(self):
""" Adds a new attribute (column) to the table """
dialog = QDialog(self)
dialog.setModal(True)
dialog.setWindowTitle('Add Attribute')
layout = QVBoxLayout()
dialog.setLayout(layout)
form = QFormLayout()
nameBox = QLineEdit()
typeCombo = QComboBox()
for attrType in _attrTypes:
typeName = partio.TypeName(attrType)
typeCombo.addItem(typeName)
typeCombo.setCurrentIndex(partio.FLOAT)
countBox = QLineEdit()
countBox.setValidator(QIntValidator())
countBox.setText('1')
fixedCheckbox = QCheckBox()
valueBox = QLineEdit()
valueBox.setText('0')
form.addRow('Name:', nameBox)
form.addRow('Type:', typeCombo)
form.addRow('Count:', countBox)
form.addRow('Fixed:', fixedCheckbox)
form.addRow('Default Value:', valueBox)
layout.addLayout(form)
buttons = QHBoxLayout()
layout.addLayout(buttons)
add = QPushButton('Add')
add.clicked.connect(dialog.accept)
buttons.addWidget(add)
cancel = QPushButton('Cancel')
cancel.clicked.connect(dialog.reject)
buttons.addWidget(cancel)
if not dialog.exec_():
return
name = str(nameBox.text())
if not name:
print 'Please supply a name for the new attribute' # TODO: prompt
return
attrType = typeCombo.currentIndex()
count = int(countBox.text())
fixed = fixedCheckbox.isChecked()
values = list(str(valueBox.text()).strip().split())
for i in range(count):
if i < len(values):
value = values[i]
else:
value = values[-1]
if attrType == partio.INT or attrType == partio.INDEXEDSTR:
values[i] = int(value)
elif attrType == partio.FLOAT or attrType == partio.VECTOR:
values[i] = float(value) # pylint:disable=R0204
else:
values[i] = 0.0 # pylint:disable=R0204
value = tuple(values)
self.data.addAttribute(name, attrType, count, fixed, value)
class _SubstituentSelector(ToolInstance):
def __init__(self, session, name):
super().__init__(session, name)
self.tool_window = MainToolWindow(self)
self._build_ui()
def _build_ui(self):
layout = QFormLayout()
self.substituent_table = SubstituentTable(singleSelect=True)
layout.addRow(self.substituent_table)
self.new_residue = QCheckBox()
self.new_residue.setCheckState(
Qt.Checked if SubstituteMouseMode.newRes else Qt.Unchecked)
layout.addRow("new residue:", self.new_residue)
self.res_name = QLineEdit()
self.res_name.setPlaceholderText("leave blank to keep current")
layout.addRow("set residue name:", self.res_name)
self.distance_names = QCheckBox()
self.distance_names.setCheckState(
Qt.Checked if SubstituteMouseMode.useRemoteness else Qt.Unchecked)
layout.addRow("distance atom names:", self.distance_names)
self.keep_open = QCheckBox()
layout.addRow("keep list open:", self.keep_open)
do_it = QPushButton("set substituent")
do_it.clicked.connect(self.set_sub)
layout.addRow(do_it)
self.keep_open.stateChanged.connect(
lambda state: do_it.setVisible(state != Qt.Checked))
self.keep_open.stateChanged.connect(self.sub_changed)
self.substituent_table.table.itemSelectionChanged.connect(
self.sub_changed)
self.new_residue.stateChanged.connect(self.sub_changed)
self.res_name.textChanged.connect(self.sub_changed)
self.distance_names.stateChanged.connect(self.sub_changed)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def sub_changed(self):
if self.keep_open.checkState() == Qt.Checked:
self.set_sub()
def set_sub(self):
sub_names = []
for row in self.substituent_table.table.selectionModel().selectedRows(
):
if self.substituent_table.table.isRowHidden(row.row()):
continue
sub_names.append(row.data())
if sub_names:
SubstituteMouseMode.substituent = sub_names[0]
SubstituteMouseMode.newRes = self.new_residue.checkState(
) == Qt.Checked
SubstituteMouseMode.useRemoteness = self.distance_names.checkState(
) == Qt.Checked
sub_name = self.res_name.text()
SubstituteMouseMode.resName = sub_name
if self.keep_open.checkState() != Qt.Checked:
self.delete()
def close(self):
sub_names = []
for row in self.substituent_table.table.selectionModel().selectedRows(
):
if self.substituent_table.table.isRowHidden(row.row()):
continue
sub_names.append(row.data())
if sub_names:
SubstituteMouseMode.substituent = sub_names[0]
SubstituteMouseMode.newRes = self.new_residue.checkState(
) == Qt.Checked
SubstituteMouseMode.useRemoteness = self.distance_names.checkState(
) == Qt.Checked
sub_name = self.res_name.text()
SubstituteMouseMode.resName = sub_name
super().close()
def _build_ui(self):
layout = QFormLayout()
initial_elements = []
if ChangeElementMouseMode.element:
initial_elements = [ChangeElementMouseMode.element]
else:
initial_elements = ["C"]
self.periodic_table = PeriodicTable(select_multiple=False,
initial_elements=initial_elements)
self.periodic_table.elementSelectionChanged.connect(
self.element_changed)
layout.addRow(self.periodic_table)
self.vsepr = QComboBox()
self.vsepr.addItems([
"do not change", # 0
"linear (1 bond)", # 1
"linear (2 bonds)", # 2
"trigonal planar (2 bonds)", # 3
"tetrahedral (2 bonds)", # 4
"trigonal planar", # 5
"tetrahedral (3 bonds)", # 6
"T-shaped", # 7
"trigonal pyramidal", # 8
"tetrahedral", # 9
"sawhorse", #10
"seesaw", #11
"square planar", #12
"trigonal bipyramidal", #13
"square pyramidal", #14
"pentagonal", #15
"octahedral", #16
"hexagonal", #17
"trigonal prismatic", #18
"pentagonal pyramidal", #19
"capped octahedral", #20
"capped trigonal prismatic", #21
"heptagonal", #22
"hexagonal pyramidal", #23
"pentagonal bipyramidal", #24
"biaugmented trigonal prismatic", #25
"cubic", #26
"elongated trigonal bipyramidal", #27
"hexagonal bipyramidal", #28
"heptagonal pyramidal", #29
"octagonal", #30
"square antiprismatic", #31
"trigonal dodecahedral", #32
"capped cube", #33
"capped square antiprismatic", #34
"enneagonal", #35
"heptagonal bipyramidal", #36
"hula-hoop", #37
"triangular cupola", #38
"tridiminished icosahedral", #39
"muffin", #40
"octagonal pyramidal", #41
"tricapped trigonal prismatic", #42
])
self.vsepr.setCurrentIndex(9)
self.vsepr.insertSeparator(33)
self.vsepr.insertSeparator(25)
self.vsepr.insertSeparator(20)
self.vsepr.insertSeparator(16)
self.vsepr.insertSeparator(13)
self.vsepr.insertSeparator(8)
self.vsepr.insertSeparator(5)
self.vsepr.insertSeparator(2)
self.vsepr.insertSeparator(1)
self.vsepr.insertSeparator(0)
self.vsepr.currentTextChanged.connect(self.element_changed)
layout.addRow("shape:", self.vsepr)
self.keep_open = QCheckBox()
layout.addRow("keep table open:", self.keep_open)
if ChangeElementMouseMode.vsepr:
ndx = self.vsepr.findText(ChangeElementMouseMode.vsepr,
Qt.MatchExactly)
if ndx != -1:
self.vsepr.setCurrentIndex(ndx)
do_it = QPushButton("set element and shape")
do_it.clicked.connect(self.set_selected)
layout.addRow(do_it)
self.keep_open.stateChanged.connect(
lambda state: do_it.setVisible(state != Qt.Checked))
self.keep_open.stateChanged.connect(self.element_changed)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
class ConeAngle(ToolInstance):
help = "https://github.com/QChASM/SEQCROW/wiki/Cone-Angle-Tool"
def __init__(self, session, name):
super().__init__(session, name)
from chimerax.ui import MainToolWindow
self.tool_window = MainToolWindow(self)
self.settings = _ConeAngleSettings(self.session, name)
self.ligands = dict()
self._build_ui()
def _build_ui(self):
layout = QFormLayout()
self.cone_option = QComboBox()
self.cone_option.addItems(["Tolman (Unsymmetrical)", "Exact"])
ndx = self.cone_option.findText(self.settings.cone_option,
Qt.MatchExactly)
self.cone_option.setCurrentIndex(ndx)
layout.addRow("method:", self.cone_option)
self.radii_option = QComboBox()
self.radii_option.addItems(["Bondi", "UMN"])
ndx = self.radii_option.findText(self.settings.radii, Qt.MatchExactly)
self.radii_option.setCurrentIndex(ndx)
layout.addRow("radii:", self.radii_option)
self.display_cone = QCheckBox()
self.display_cone.setChecked(self.settings.display_cone)
layout.addRow("show cone:", self.display_cone)
self.display_radii = QCheckBox()
self.display_radii.setChecked(self.settings.display_radii)
layout.addRow("show radii:", self.display_radii)
set_ligand_button = QPushButton("set ligand to current selection")
set_ligand_button.clicked.connect(self.set_ligand)
layout.addRow(set_ligand_button)
self.set_ligand_button = set_ligand_button
calc_cone_button = QPushButton(
"calculate cone angle for ligand on selected center")
calc_cone_button.clicked.connect(self.calc_cone)
layout.addRow(calc_cone_button)
self.calc_cone_button = calc_cone_button
remove_cone_button = QPushButton("remove cone visualizations")
remove_cone_button.clicked.connect(self.del_cone)
layout.addRow(remove_cone_button)
self.remove_cone_button = remove_cone_button
self.table = QTableWidget()
self.table.setColumnCount(3)
self.table.setHorizontalHeaderLabels([
'model',
'center',
'cone angle (°)',
])
self.table.setSelectionBehavior(QTableWidget.SelectRows)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.table.resizeColumnToContents(0)
self.table.resizeColumnToContents(1)
self.table.resizeColumnToContents(2)
self.table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.Stretch)
layout.addRow(self.table)
menu = QMenuBar()
export = menu.addMenu("&Export")
clear = QAction("Clear data table", self.tool_window.ui_area)
clear.triggered.connect(self.clear_table)
export.addAction(clear)
copy = QAction("&Copy CSV to clipboard", self.tool_window.ui_area)
copy.triggered.connect(self.copy_csv)
shortcut = QKeySequence(Qt.CTRL + Qt.Key_C)
copy.setShortcut(shortcut)
export.addAction(copy)
save = QAction("&Save CSV...", self.tool_window.ui_area)
save.triggered.connect(self.save_csv)
#this shortcut interferes with main window's save shortcut
#I've tried different shortcut contexts to no avail
#thanks Qt...
#shortcut = QKeySequence(Qt.CTRL + Qt.Key_S)
#save.setShortcut(shortcut)
#save.setShortcutContext(Qt.WidgetShortcut)
export.addAction(save)
delimiter = export.addMenu("Delimiter")
comma = QAction("comma", self.tool_window.ui_area, checkable=True)
comma.setChecked(self.settings.delimiter == "comma")
comma.triggered.connect(lambda *args, delim="comma": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(comma)
tab = QAction("tab", self.tool_window.ui_area, checkable=True)
tab.setChecked(self.settings.delimiter == "tab")
tab.triggered.connect(lambda *args, delim="tab": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(tab)
space = QAction("space", self.tool_window.ui_area, checkable=True)
space.setChecked(self.settings.delimiter == "space")
space.triggered.connect(lambda *args, delim="space": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(space)
semicolon = QAction("semicolon",
self.tool_window.ui_area,
checkable=True)
semicolon.setChecked(self.settings.delimiter == "semicolon")
semicolon.triggered.connect(lambda *args, delim="semicolon": self.
settings.__setattr__("delimiter", delim))
delimiter.addAction(semicolon)
add_header = QAction("&Include CSV header",
self.tool_window.ui_area,
checkable=True)
add_header.setChecked(self.settings.include_header)
add_header.triggered.connect(self.header_check)
export.addAction(add_header)
comma.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
comma.triggered.connect(
lambda *args, action=space: action.setChecked(False))
comma.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=space: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
space.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
space.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
space.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=space: action.setChecked(False))
menu.setNativeMenuBar(False)
self._menu = menu
layout.setMenuBar(menu)
menu.setVisible(True)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def clear_table(self):
are_you_sure = QMessageBox.question(
None,
"Clear table?",
"Are you sure you want to clear the data table?",
)
if are_you_sure != QMessageBox.Yes:
return
self.table.setRowCount(0)
def header_check(self, state):
"""user has [un]checked the 'include header' option on the menu"""
if state:
self.settings.include_header = True
else:
self.settings.include_header = False
def get_csv(self):
if self.settings.delimiter == "comma":
delim = ","
elif self.settings.delimiter == "space":
delim = " "
elif self.settings.delimiter == "tab":
delim = "\t"
elif self.settings.delimiter == "semicolon":
delim = ";"
if self.settings.include_header:
s = delim.join(["model", "center_atom", "cone_angle"])
s += "\n"
else:
s = ""
for i in range(0, self.table.rowCount()):
s += delim.join([
item.data(Qt.DisplayRole)
for item in [self.table.item(i, j) for j in range(0, 3)]
])
s += "\n"
return s
def copy_csv(self):
app = QApplication.instance()
clipboard = app.clipboard()
csv = self.get_csv()
clipboard.setText(csv)
self.session.logger.status("copied to clipboard")
def save_csv(self):
"""save data on current tab to CSV file"""
filename, _ = QFileDialog.getSaveFileName(filter="CSV Files (*.csv)")
if filename:
s = self.get_csv()
with open(filename, 'w') as f:
f.write(s.strip())
self.session.logger.status("saved to %s" % filename)
def del_cone(self):
for model in self.session.models.list(type=Generic3DModel):
if model.name.startswith("Cone angle"):
model.delete()
def set_ligand(self, *args):
self.ligands = {}
for atom in selected_atoms(self.session):
if atom.structure not in self.ligands:
self.ligands[atom.structure] = []
self.ligands[atom.structure].append(atom)
self.session.logger.status("set ligand to current selection")
def calc_cone(self, *args):
self.settings.cone_option = self.cone_option.currentText()
self.settings.radii = self.radii_option.currentText()
self.settings.display_radii = self.display_radii.checkState(
) == Qt.Checked
self.settings.display_cone = self.display_cone.checkState(
) == Qt.Checked
if self.cone_option.currentText() == "Tolman (Unsymmetrical)":
method = "tolman"
else:
method = self.cone_option.currentText()
radii = self.radii_option.currentText()
return_cones = self.display_cone.checkState() == Qt.Checked
display_radii = self.display_radii.checkState() == Qt.Checked
# self.table.setRowCount(0)
for center_atom in selected_atoms(self.session):
rescol = ResidueCollection(center_atom.structure)
at_center = rescol.find_exact(AtomSpec(center_atom.atomspec))[0]
if center_atom.structure in self.ligands:
comp = Component(
rescol.find([
AtomSpec(atom.atomspec)
for atom in self.ligands[center_atom.structure]
]),
to_center=rescol.find_exact(AtomSpec(
center_atom.atomspec)),
key_atoms=rescol.find(BondedTo(at_center)),
)
else:
comp = Component(
rescol.find(NotAny(at_center)),
to_center=rescol.find_exact(AtomSpec(
center_atom.atomspec)),
key_atoms=rescol.find(BondedTo(at_center)),
)
cone_angle = comp.cone_angle(
center=rescol.find(AtomSpec(center_atom.atomspec)),
method=method,
radii=radii,
return_cones=return_cones,
)
if return_cones:
cone_angle, cones = cone_angle
s = ".transparency 0.5\n"
for cone in cones:
apex, base, radius = cone
s += ".cone %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f %.3f open\n" % (
*apex, *base, radius)
stream = BytesIO(bytes(s, "utf-8"))
bild_obj, status = read_bild(self.session, stream,
"Cone angle %s" % center_atom)
self.session.models.add(bild_obj, parent=center_atom.structure)
if display_radii:
s = ".note radii\n"
s += ".transparency 75\n"
color = None
for atom in comp.atoms:
chix_atom = atom.chix_atom
if radii.lower() == "umn":
r = VDW_RADII[chix_atom.element.name]
elif radii.lower() == "bondi":
r = BONDI_RADII[chix_atom.element.name]
if color is None or chix_atom.color != color:
color = chix_atom.color
rgb = [x / 255. for x in chix_atom.color]
rgb.pop(-1)
s += ".color %f %f %f\n" % tuple(rgb)
s += ".sphere %f %f %f %f\n" % (*chix_atom.coord, r)
stream = BytesIO(bytes(s, "utf-8"))
bild_obj, status = read_bild(self.session, stream,
"Cone angle radii")
self.session.models.add(bild_obj, parent=center_atom.structure)
row = self.table.rowCount()
self.table.insertRow(row)
name = QTableWidgetItem()
name.setData(Qt.DisplayRole, center_atom.structure.name)
self.table.setItem(row, 0, name)
center = QTableWidgetItem()
center.setData(Qt.DisplayRole, center_atom.atomspec)
self.table.setItem(row, 1, center)
ca = QTableWidgetItem()
ca.setData(Qt.DisplayRole, "%.2f" % cone_angle)
self.table.setItem(row, 2, ca)
self.table.resizeColumnToContents(0)
self.table.resizeColumnToContents(1)
self.table.resizeColumnToContents(2)
class PrecisionRotate(ToolInstance):
help = "https://github.com/QChASM/SEQCROW/wiki/Rotate-Tool"
SESSION_ENDURING = False
SESSION_SAVE = False
def __init__(self, session, name):
super().__init__(session, name)
self.tool_window = MainToolWindow(self)
self.settings = _PrecisionRotateSettings(session, name)
self.bonds = {}
self.bond_centers = {}
self.groups = {}
self.perpendiculars = {}
self.perp_centers = {}
self.manual_center = {}
self._build_ui()
self._show_rot_vec = self.session.triggers.add_handler(
SELECTION_CHANGED, self.show_rot_vec)
global_triggers = get_triggers()
self._changes = global_triggers.add_handler("changes done",
self.show_rot_vec)
self.show_rot_vec()
def _build_ui(self):
layout = QGridLayout()
layout.addWidget(QLabel("center of rotation:"), 0, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
self.cor_button = QComboBox()
self.cor_button.addItems(
["automatic", "select atoms", "view's center of rotation"])
layout.addWidget(self.cor_button, 0, 1, 1, 1, Qt.AlignTop)
self.set_cor_selection = QPushButton("set selection")
self.cor_button.currentTextChanged.connect(
lambda t, widget=self.set_cor_selection: widget.setEnabled(
t == "select atoms"))
self.set_cor_selection.clicked.connect(self.manual_cor)
layout.addWidget(self.set_cor_selection, 0, 2, 1, 1, Qt.AlignTop)
self.set_cor_selection.setEnabled(False)
layout.addWidget(QLabel("rotation vector:"), 1, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
self.vector_option = QComboBox()
self.vector_option.addItems([
"axis", "view axis", "bond", "perpendicular to plane",
"centroid of atoms", "custom"
])
layout.addWidget(self.vector_option, 1, 1, 1, 1, Qt.AlignVCenter)
vector = QWidget()
vector.setToolTip("vector will be normalized before rotating")
vector_layout = QHBoxLayout(vector)
vector_layout.setContentsMargins(0, 0, 0, 0)
self.vector_x = QDoubleSpinBox()
self.vector_y = QDoubleSpinBox()
self.vector_z = QDoubleSpinBox()
self.vector_z.setValue(1.0)
for c, t in zip([self.vector_x, self.vector_y, self.vector_z],
[" x", " y", " z"]):
c.setSingleStep(0.01)
c.setRange(-100, 100)
# c.setSuffix(t)
c.valueChanged.connect(self.show_rot_vec)
vector_layout.addWidget(c)
layout.addWidget(vector, 1, 2, 1, 1, Qt.AlignTop)
vector.setVisible(self.vector_option.currentText() == "custom")
self.vector_option.currentTextChanged.connect(
lambda text, widget=vector: widget.setVisible(text == "custom"))
self.view_axis = QComboBox()
self.view_axis.addItems(["z", "y", "x"])
layout.addWidget(self.view_axis, 1, 2, 1, 1, Qt.AlignTop)
self.view_axis.setVisible(
self.vector_option.currentText() == "view axis")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.view_axis: widget.setVisible(text ==
"view axis"))
self.axis = QComboBox()
self.axis.addItems(["z", "y", "x"])
layout.addWidget(self.axis, 1, 2, 1, 1, Qt.AlignTop)
self.axis.setVisible(self.vector_option.currentText() == "axis")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.axis: widget.setVisible(text == "axis"))
self.bond_button = QPushButton("set selected bond")
self.bond_button.clicked.connect(self.set_bonds)
layout.addWidget(self.bond_button, 1, 2, 1, 1, Qt.AlignTop)
self.bond_button.setVisible(self.vector_option.currentText() == "bond")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.bond_button: widget.setVisible(text ==
"bond"))
self.perp_button = QPushButton("set selected atoms")
self.perp_button.clicked.connect(self.set_perpendicular)
layout.addWidget(self.perp_button, 1, 2, 1, 1, Qt.AlignTop)
self.perp_button.setVisible(
self.vector_option.currentText() == "perpendicular to plane")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.perp_button: widget.setVisible(
text == "perpendicular to plane"))
self.group_button = QPushButton("set selected atoms")
self.group_button.clicked.connect(self.set_group)
layout.addWidget(self.group_button, 1, 2, 1, 1, Qt.AlignTop)
self.group_button.setVisible(
self.vector_option.currentText() == "centroid of atoms")
self.vector_option.currentTextChanged.connect(
lambda text, widget=self.group_button: widget.setVisible(
text == "centroid of atoms"))
layout.addWidget(QLabel("angle:"), 2, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
self.angle = QDoubleSpinBox()
self.angle.setRange(-360, 360)
self.angle.setSingleStep(5)
self.angle.setSuffix("°")
layout.addWidget(self.angle, 2, 1, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
layout.addWidget(QLabel("preview rotation axis:"), 3, 0, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
self.display_rot_vec = QCheckBox()
self.display_rot_vec.setCheckState(Qt.Checked)
self.display_rot_vec.stateChanged.connect(self.show_rot_vec)
layout.addWidget(self.display_rot_vec, 3, 1, 1, 1,
Qt.AlignLeft | Qt.AlignVCenter)
rotate_button = QPushButton("rotate selected atoms")
rotate_button.clicked.connect(self.do_rotate)
layout.addWidget(rotate_button, 4, 0, 1, 3, Qt.AlignTop)
self.rotate_button = rotate_button
self.status_bar = QStatusBar()
self.status_bar.setSizeGripEnabled(False)
layout.addWidget(self.status_bar, 5, 0, 1, 3, Qt.AlignTop)
self.vector_option.currentTextChanged.connect(self.show_auto_status)
self.cor_button.currentIndexChanged.connect(
lambda *args: self.show_auto_status("select atoms"))
self.cor_button.currentIndexChanged.connect(self.show_rot_vec)
self.set_cor_selection.clicked.connect(self.show_rot_vec)
self.vector_option.currentIndexChanged.connect(self.show_rot_vec)
self.axis.currentIndexChanged.connect(self.show_rot_vec)
self.view_axis.currentIndexChanged.connect(self.show_rot_vec)
self.bond_button.clicked.connect(self.show_rot_vec)
self.perp_button.clicked.connect(self.show_rot_vec)
self.group_button.clicked.connect(self.show_rot_vec)
layout.setRowStretch(0, 0)
layout.setRowStretch(1, 0)
layout.setRowStretch(2, 0)
layout.setRowStretch(3, 0)
layout.setRowStretch(4, 0)
layout.setRowStretch(5, 1)
layout.setColumnStretch(0, 0)
layout.setColumnStretch(1, 1)
layout.setColumnStretch(2, 1)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def manual_cor(self, *args):
selection = selected_atoms(self.session)
models = {}
for atom in selection:
if atom.structure not in models:
models[atom.structure] = [atom]
else:
models[atom.structure].append(atom)
self.manual_center = {}
for model in models:
atoms = models[model]
coords = np.array([atom.coord for atom in atoms])
self.manual_center[model] = np.mean(coords, axis=0)
def show_auto_status(self, text):
if self.cor_button.currentText() == "automatic":
if text == "bond":
self.status_bar.showMessage(
"center set to one of the bonded atoms")
elif text == "perpendicular to plane":
self.status_bar.showMessage("center set to centroid of atoms")
else:
self.status_bar.showMessage(
"center set to centroid of rotating atoms")
elif self.cor_button.currentText() == "select atoms":
self.status_bar.showMessage(
"center set to centroid of specified atoms")
else:
self.status_bar.showMessage(
"center set to view's center of rotation")
def set_bonds(self, *args):
bonds = selected_bonds(self.session)
if len(bonds) == 0:
self.session.logger.error("no bonds selected")
return
models = [bond.structure for bond in bonds]
if any(models.count(m) > 1 for m in models):
self.session.logger.error(
"multiple bonds selected on the same structure")
return
self.bonds = {
model: (bond.atoms[0].coord - bond.atoms[1].coord)
for model, bond in zip(models, bonds)
}
self.bond_centers = {
model: bond.atoms[1].coord
for model, bond in zip(models, bonds)
}
def set_perpendicular(self, *args):
atoms = selected_atoms(self.session)
if len(atoms) == 0:
self.session.logger.error("no atoms selected")
return
self.perpendiculars = {}
self.perp_centers = {}
models = set(atom.structure for atom in atoms)
for model in models:
atom_coords = []
for atom in atoms:
if atom.structure is model:
atom_coords.append(atom.coord)
if len(atom_coords) < 3:
self.session.logger.error("fewer than 3 atoms selected on %s" %
model.atomspec)
continue
xyz = np.array(atom_coords)
xyz -= np.mean(atom_coords, axis=0)
R = np.dot(xyz.T, xyz)
u, s, vh = np.linalg.svd(R, compute_uv=True)
vector = u[:, -1]
self.perpendiculars[model] = vector
self.perp_centers[model] = np.mean(atom_coords, axis=0)
def set_group(self, *args):
atoms = selected_atoms(self.session)
if len(atoms) == 0:
self.session.logger.error("no atoms selected")
return
self.groups = {}
models = set(atom.structure for atom in atoms)
for model in models:
atom_coords = []
for atom in atoms:
if atom.structure is model:
atom_coords.append(atom.coord)
self.groups[model] = np.mean(atom_coords, axis=0)
def do_rotate(self, *args):
selection = selected_atoms(self.session)
models = {}
for atom in selection:
if atom.structure not in models:
models[atom.structure] = [atom]
else:
models[atom.structure].append(atom)
if len(models.keys()) == 0:
return
if self.vector_option.currentText() == "axis":
if self.axis.currentText() == "z":
vector = np.array([0., 0., 1.])
elif self.axis.currentText() == "y":
vector = np.array([0., 1., 0.])
elif self.axis.currentText() == "x":
vector = np.array([1., 0., 0.])
elif self.vector_option.currentText() == "view axis":
if self.view_axis.currentText() == "z":
vector = self.session.view.camera.get_position().axes()[2]
elif self.view_axis.currentText() == "y":
vector = self.session.view.camera.get_position().axes()[1]
elif self.view_axis.currentText() == "x":
vector = self.session.view.camera.get_position().axes()[0]
elif self.vector_option.currentText() == "bond":
vector = self.bonds
elif self.vector_option.currentText() == "perpendicular to plane":
vector = self.perpendiculars
elif self.vector_option.currentText() == "centroid of atoms":
vector = self.groups
elif self.vector_option.currentText() == "custom":
x = self.vector_x.value()
y = self.vector_y.value()
z = self.vector_z.value()
vector = np.array([x, y, z])
angle = np.deg2rad(self.angle.value())
center = {}
for model in models:
atoms = models[model]
coords = np.array([atom.coord for atom in atoms])
center[model] = np.mean(coords, axis=0)
if self.cor_button.currentText() == "automatic":
if self.vector_option.currentText() == "perpendicular to plane":
center = self.perp_centers
elif self.vector_option.currentText() == "bond":
center = self.bond_centers
elif self.cor_button.currentText() == "select atoms":
center = self.manual_center
else:
center = self.session.main_view.center_of_rotation
for model in models:
if isinstance(vector, dict):
if model not in vector.keys():
continue
else:
v = vector[model]
else:
v = vector
if isinstance(center, dict):
if model not in center.keys():
continue
else:
c = center[model]
else:
c = center
if self.vector_option.currentText(
) == "centroid of atoms" and self.cor_button.currentText(
) != "automatic":
v = v - c
v = v / np.linalg.norm(v)
q = np.hstack(([np.cos(angle / 2)], v * np.sin(angle / 2)))
q /= np.linalg.norm(q)
qs = q[0]
qv = q[1:]
xyz = np.array([a.coord for a in models[model]])
xyz -= c
xprod = np.cross(qv, xyz)
qs_xprod = 2 * qs * xprod
qv_xprod = 2 * np.cross(qv, xprod)
xyz += qs_xprod + qv_xprod + c
for t, coord in zip(models[model], xyz):
t.coord = coord
def show_rot_vec(self, *args):
for model in self.session.models.list(type=Generic3DModel):
if model.name == "rotation vector":
model.delete()
if self.display_rot_vec.checkState() == Qt.Unchecked:
return
selection = selected_atoms(self.session)
if len(selection) == 0:
return
models = {}
for atom in selection:
if atom.structure not in models:
models[atom.structure] = [atom]
else:
models[atom.structure].append(atom)
if len(models.keys()) == 0:
return
if self.vector_option.currentText() == "axis":
if self.axis.currentText() == "z":
vector = np.array([0., 0., 1.])
elif self.axis.currentText() == "y":
vector = np.array([0., 1., 0.])
elif self.axis.currentText() == "x":
vector = np.array([1., 0., 0.])
elif self.vector_option.currentText() == "view axis":
if self.view_axis.currentText() == "z":
vector = self.session.view.camera.get_position().axes()[2]
elif self.view_axis.currentText() == "y":
vector = self.session.view.camera.get_position().axes()[1]
elif self.view_axis.currentText() == "x":
vector = self.session.view.camera.get_position().axes()[0]
elif self.vector_option.currentText() == "bond":
vector = self.bonds
elif self.vector_option.currentText() == "perpendicular to plane":
vector = self.perpendiculars
elif self.vector_option.currentText() == "centroid of atoms":
vector = self.groups
elif self.vector_option.currentText() == "custom":
x = self.vector_x.value()
y = self.vector_y.value()
z = self.vector_z.value()
vector = np.array([x, y, z])
center = {}
for model in models:
atoms = models[model]
coords = np.array([atom.coord for atom in atoms])
center[model] = np.mean(coords, axis=0)
if self.cor_button.currentText() == "automatic":
if self.vector_option.currentText() == "perpendicular to plane":
center = self.perp_centers
elif self.vector_option.currentText() == "bond":
center = self.bond_centers
elif self.cor_button.currentText() == "select atoms":
center = self.manual_center
else:
center = self.session.main_view.center_of_rotation
for model in models:
if isinstance(vector, dict):
if model not in vector.keys():
continue
else:
v = vector[model]
else:
v = vector
if isinstance(center, dict):
if model not in center.keys():
continue
else:
c = center[model]
else:
c = center
if self.vector_option.currentText(
) == "centroid of atoms" and self.cor_button.currentText(
) != "automatic":
v = v - c
if np.linalg.norm(v) == 0:
continue
residues = []
for atom in models[model]:
if atom.residue not in residues:
residues.append(atom.residue)
v_c = c + v
s = ".color red\n"
s += ".arrow %10.6f %10.6f %10.6f %10.6f %10.6f %10.6f 0.2 0.4 0.7\n" % (
*c, *v_c)
stream = BytesIO(bytes(s, 'utf-8'))
bild_obj, status = read_bild(self.session, stream,
"rotation vector")
self.session.models.add(bild_obj, parent=model)
def delete(self):
self.session.triggers.remove_handler(self._show_rot_vec)
global_triggers = get_triggers()
global_triggers.remove_handler(self._changes)
for model in self.session.models.list(type=Generic3DModel):
if model.name == "rotation vector":
model.delete()
return super().delete()
def close(self):
self.session.triggers.remove_handler(self._show_rot_vec)
global_triggers = get_triggers()
global_triggers.remove_handler(self._changes)
for model in self.session.models.list(type=Generic3DModel):
if model.name == "rotation vector":
model.delete()
return super().close()
def _build_ui(self):
layout = QFormLayout()
self.cone_option = QComboBox()
self.cone_option.addItems(["Tolman (Unsymmetrical)", "Exact"])
ndx = self.cone_option.findText(self.settings.cone_option,
Qt.MatchExactly)
self.cone_option.setCurrentIndex(ndx)
layout.addRow("method:", self.cone_option)
self.radii_option = QComboBox()
self.radii_option.addItems(["Bondi", "UMN"])
ndx = self.radii_option.findText(self.settings.radii, Qt.MatchExactly)
self.radii_option.setCurrentIndex(ndx)
layout.addRow("radii:", self.radii_option)
self.display_cone = QCheckBox()
self.display_cone.setChecked(self.settings.display_cone)
layout.addRow("show cone:", self.display_cone)
self.display_radii = QCheckBox()
self.display_radii.setChecked(self.settings.display_radii)
layout.addRow("show radii:", self.display_radii)
set_ligand_button = QPushButton("set ligand to current selection")
set_ligand_button.clicked.connect(self.set_ligand)
layout.addRow(set_ligand_button)
self.set_ligand_button = set_ligand_button
calc_cone_button = QPushButton(
"calculate cone angle for ligand on selected center")
calc_cone_button.clicked.connect(self.calc_cone)
layout.addRow(calc_cone_button)
self.calc_cone_button = calc_cone_button
remove_cone_button = QPushButton("remove cone visualizations")
remove_cone_button.clicked.connect(self.del_cone)
layout.addRow(remove_cone_button)
self.remove_cone_button = remove_cone_button
self.table = QTableWidget()
self.table.setColumnCount(3)
self.table.setHorizontalHeaderLabels([
'model',
'center',
'cone angle (°)',
])
self.table.setSelectionBehavior(QTableWidget.SelectRows)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.table.resizeColumnToContents(0)
self.table.resizeColumnToContents(1)
self.table.resizeColumnToContents(2)
self.table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.Stretch)
layout.addRow(self.table)
menu = QMenuBar()
export = menu.addMenu("&Export")
clear = QAction("Clear data table", self.tool_window.ui_area)
clear.triggered.connect(self.clear_table)
export.addAction(clear)
copy = QAction("&Copy CSV to clipboard", self.tool_window.ui_area)
copy.triggered.connect(self.copy_csv)
shortcut = QKeySequence(Qt.CTRL + Qt.Key_C)
copy.setShortcut(shortcut)
export.addAction(copy)
save = QAction("&Save CSV...", self.tool_window.ui_area)
save.triggered.connect(self.save_csv)
#this shortcut interferes with main window's save shortcut
#I've tried different shortcut contexts to no avail
#thanks Qt...
#shortcut = QKeySequence(Qt.CTRL + Qt.Key_S)
#save.setShortcut(shortcut)
#save.setShortcutContext(Qt.WidgetShortcut)
export.addAction(save)
delimiter = export.addMenu("Delimiter")
comma = QAction("comma", self.tool_window.ui_area, checkable=True)
comma.setChecked(self.settings.delimiter == "comma")
comma.triggered.connect(lambda *args, delim="comma": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(comma)
tab = QAction("tab", self.tool_window.ui_area, checkable=True)
tab.setChecked(self.settings.delimiter == "tab")
tab.triggered.connect(lambda *args, delim="tab": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(tab)
space = QAction("space", self.tool_window.ui_area, checkable=True)
space.setChecked(self.settings.delimiter == "space")
space.triggered.connect(lambda *args, delim="space": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(space)
semicolon = QAction("semicolon",
self.tool_window.ui_area,
checkable=True)
semicolon.setChecked(self.settings.delimiter == "semicolon")
semicolon.triggered.connect(lambda *args, delim="semicolon": self.
settings.__setattr__("delimiter", delim))
delimiter.addAction(semicolon)
add_header = QAction("&Include CSV header",
self.tool_window.ui_area,
checkable=True)
add_header.setChecked(self.settings.include_header)
add_header.triggered.connect(self.header_check)
export.addAction(add_header)
comma.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
comma.triggered.connect(
lambda *args, action=space: action.setChecked(False))
comma.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=space: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
space.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
space.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
space.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=space: action.setChecked(False))
menu.setNativeMenuBar(False)
self._menu = menu
layout.setMenuBar(menu)
menu.setVisible(True)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def addAttributeSlot(self):
""" Adds a new attribute (column) to the table """
dialog = QDialog(self)
dialog.setModal(True)
dialog.setWindowTitle('Add Attribute')
layout = QVBoxLayout()
dialog.setLayout(layout)
form = QFormLayout()
nameBox = QLineEdit()
typeCombo = QComboBox()
for attrType in _attrTypes:
typeName = partio.TypeName(attrType)
typeCombo.addItem(typeName)
typeCombo.setCurrentIndex(partio.FLOAT)
countBox = QLineEdit()
countBox.setValidator(QIntValidator())
countBox.setText('1')
fixedCheckbox = QCheckBox()
valueBox = QLineEdit()
valueBox.setText('0')
form.addRow('Name:', nameBox)
form.addRow('Type:', typeCombo)
form.addRow('Count:', countBox)
form.addRow('Fixed:', fixedCheckbox)
form.addRow('Default Value:', valueBox)
layout.addLayout(form)
buttons = QHBoxLayout()
layout.addLayout(buttons)
add = QPushButton('Add')
add.clicked.connect(dialog.accept)
buttons.addWidget(add)
cancel = QPushButton('Cancel')
cancel.clicked.connect(dialog.reject)
buttons.addWidget(cancel)
if not dialog.exec_():
return
name = str(nameBox.text())
if not name:
print('Please supply a name for the new attribute') # TODO: prompt
return
attrType = typeCombo.currentIndex()
count = int(countBox.text())
fixed = fixedCheckbox.isChecked()
values = list(str(valueBox.text()).strip().split())
for i in range(count):
if i < len(values):
value = values[i]
else:
value = values[-1]
if attrType == partio.INT or attrType == partio.INDEXEDSTR:
values[i] = int(value)
elif attrType == partio.FLOAT or attrType == partio.VECTOR:
values[i] = float(value) # pylint:disable=R0204
else:
values[i] = 0.0 # pylint:disable=R0204
value = tuple(values)
self.data.addAttribute(name, attrType, count, fixed, value)
def __init__(self):
super(Second, self).__init__()
self.setWindowTitle("Add new device")
self.nameLabel = QLabel(self)
self.nameLabel.move(10, 10)
self.nameLabel.setText("Device name")
self.nameEntry = QLineEdit(self)
self.nameEntry.move(10, 40)
self.nameEntry.resize(100, 30)
self.colorLabel = QLabel(self)
self.colorLabel.move(120, 10)
self.colorLabel.setText("Color cameras")
self.colorEntry = QLineEdit(self)
self.colorEntry.move(140, 40)
self.colorEntry.resize(70, 30)
self.colorEntry.setValidator(QtGui.QIntValidator())
self.monoLabel = QLabel(self)
self.monoLabel.move(230, 10)
self.monoLabel.setText("Mono cameras")
self.monoEntry = QLineEdit(self)
self.monoEntry.move(250, 40)
self.monoEntry.resize(70, 30)
self.monoEntry.setValidator(QtGui.QIntValidator())
self.depthPresent = QCheckBox("Include depth", self)
self.depthPresent.move(10, 80)
self.depthPresent.resize(150, 30)
self.depthPresent.stateChanged.connect(self.toggle_depth)
self.leftfovLabel = QLabel(self)
self.leftfovLabel.move(10, 120)
self.leftfovLabel.setText("Left FOV deg.")
self.leftfovEntry = QLineEdit(self)
self.leftfovEntry.move(180, 120)
self.leftfovEntry.resize(140, 30)
self.leftfovEntry.setValidator(QtGui.QDoubleValidator())
self.rightfovLabel = QLabel(self)
self.rightfovLabel.move(10, 160)
self.rightfovLabel.setText("Right FOV deg.")
self.rightfovEntry = QLineEdit(self)
self.rightfovEntry.move(180, 160)
self.rightfovEntry.resize(140, 30)
self.rightfovEntry.setValidator(QtGui.QDoubleValidator())
self.rgbfovLabel = QLabel(self)
self.rgbfovLabel.move(10, 200)
self.rgbfovLabel.setText("RGB FOV deg.")
self.rgbfovEntry = QLineEdit(self)
self.rgbfovEntry.move(180, 200)
self.rgbfovEntry.resize(140, 30)
self.rgbfovEntry.setValidator(QtGui.QDoubleValidator())
self.lrdistanceLabel = QLabel(self)
self.lrdistanceLabel.move(10, 240)
self.lrdistanceLabel.resize(200, 30)
self.lrdistanceLabel.setText("Left - Right distance cm.")
self.lrdistanceEntry = QLineEdit(self)
self.lrdistanceEntry.move(180, 240)
self.lrdistanceEntry.resize(140, 30)
self.lrdistanceEntry.setValidator(QtGui.QDoubleValidator())
self.lrgbdistanceLabel = QLabel(self)
self.lrgbdistanceLabel.move(10, 280)
self.lrgbdistanceLabel.resize(200, 30)
self.lrgbdistanceLabel.setText("Left - RGB distance cm.")
self.lrgbdistanceEntry = QLineEdit(self)
self.lrgbdistanceEntry.move(180, 280)
self.lrgbdistanceEntry.resize(140, 30)
self.lrgbdistanceEntry.setValidator(QtGui.QDoubleValidator())
self.saveButton = QPushButton("Save", self)
self.saveButton.resize(100, 30)
self.saveButton.clicked.connect(self.save)
self.cancelButton = QPushButton("Cancel", self)
self.cancelButton.resize(100, 30)
self.cancelButton.clicked.connect(self.cancel)
self.toggle_depth(False)
class LigandSterimol(ToolInstance):
help = "https://github.com/QChASM/SEQCROW/wiki/Ligand-Sterimol-Tool"
SESSION_ENDURING = False
SESSION_SAVE = False
def __init__(self, session, name):
super().__init__(session, name)
from chimerax.ui import MainToolWindow
self.tool_window = MainToolWindow(self)
self.settings = _SterimolSettings(self.session, name)
self._build_ui()
def _build_ui(self):
layout = QFormLayout()
self.radii_option = QComboBox()
self.radii_option.addItems(["Bondi", "UMN"])
ndx = self.radii_option.findText(self.settings.radii, Qt.MatchExactly)
self.radii_option.setCurrentIndex(ndx)
layout.addRow("radii:", self.radii_option)
self.L_option = QComboBox()
self.L_option.addItems([
"to centroid of coordinating atoms",
"bisect angle between coordinating atoms"
])
ndx = self.L_option.findText(self.settings.L_option, Qt.MatchExactly)
self.L_option.setCurrentIndex(ndx)
layout.addRow("L axis:", self.L_option)
self.sterimol2vec = QGroupBox("Sterimol2Vec")
sterimol2vec_layout = QFormLayout(self.sterimol2vec)
self.at_L = QDoubleSpinBox()
self.at_L.setRange(-10, 30)
self.at_L.setDecimals(2)
self.at_L.setSingleStep(0.25)
self.at_L.setValue(self.settings.at_L)
sterimol2vec_layout.addRow("L value:", self.at_L)
layout.addRow(self.sterimol2vec)
self.sterimol2vec.setCheckable(True)
self.sterimol2vec.toggled.connect(lambda x: self.at_L.setEnabled(x))
self.sterimol2vec.setChecked(self.settings.sterimol2vec)
self.display_vectors = QCheckBox()
self.display_vectors.setChecked(self.settings.display_vectors)
layout.addRow("show vectors:", self.display_vectors)
self.display_radii = QCheckBox()
self.display_radii.setChecked(self.settings.display_radii)
layout.addRow("show radii:", self.display_radii)
calc_sterimol_button = QPushButton(
"calculate parameters for selected ligands")
calc_sterimol_button.clicked.connect(self.calc_sterimol)
layout.addRow(calc_sterimol_button)
self.calc_sterimol_button = calc_sterimol_button
remove_sterimol_button = QPushButton("remove Sterimol visualizations")
remove_sterimol_button.clicked.connect(self.del_sterimol)
layout.addRow(remove_sterimol_button)
self.remove_sterimol_button = remove_sterimol_button
self.table = QTableWidget()
self.table.setColumnCount(8)
self.table.setHorizontalHeaderLabels([
'model',
'coord. atoms',
'B\u2081',
'B\u2082',
'B\u2083',
'B\u2084',
'B\u2085',
'L',
])
self.table.setSelectionBehavior(QTableWidget.SelectRows)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.table.resizeColumnToContents(0)
self.table.resizeColumnToContents(1)
self.table.resizeColumnToContents(2)
self.table.resizeColumnToContents(3)
self.table.resizeColumnToContents(4)
self.table.resizeColumnToContents(5)
self.table.resizeColumnToContents(6)
self.table.resizeColumnToContents(7)
self.table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
3, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
4, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
5, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
6, QHeaderView.Stretch)
self.table.horizontalHeader().setSectionResizeMode(
7, QHeaderView.Stretch)
layout.addRow(self.table)
menu = QMenuBar()
export = menu.addMenu("&Export")
clear = QAction("Clear data table", self.tool_window.ui_area)
clear.triggered.connect(self.clear_table)
export.addAction(clear)
copy = QAction("&Copy CSV to clipboard", self.tool_window.ui_area)
copy.triggered.connect(self.copy_csv)
shortcut = QKeySequence(Qt.CTRL + Qt.Key_C)
copy.setShortcut(shortcut)
export.addAction(copy)
save = QAction("&Save CSV...", self.tool_window.ui_area)
save.triggered.connect(self.save_csv)
#this shortcut interferes with main window's save shortcut
#I've tried different shortcut contexts to no avail
#thanks Qt...
#shortcut = QKeySequence(Qt.CTRL + Qt.Key_S)
#save.setShortcut(shortcut)
#save.setShortcutContext(Qt.WidgetShortcut)
export.addAction(save)
delimiter = export.addMenu("Delimiter")
comma = QAction("comma", self.tool_window.ui_area, checkable=True)
comma.setChecked(self.settings.delimiter == "comma")
comma.triggered.connect(lambda *args, delim="comma": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(comma)
tab = QAction("tab", self.tool_window.ui_area, checkable=True)
tab.setChecked(self.settings.delimiter == "tab")
tab.triggered.connect(lambda *args, delim="tab": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(tab)
space = QAction("space", self.tool_window.ui_area, checkable=True)
space.setChecked(self.settings.delimiter == "space")
space.triggered.connect(lambda *args, delim="space": self.settings.
__setattr__("delimiter", delim))
delimiter.addAction(space)
semicolon = QAction("semicolon",
self.tool_window.ui_area,
checkable=True)
semicolon.setChecked(self.settings.delimiter == "semicolon")
semicolon.triggered.connect(lambda *args, delim="semicolon": self.
settings.__setattr__("delimiter", delim))
delimiter.addAction(semicolon)
add_header = QAction("&Include CSV header",
self.tool_window.ui_area,
checkable=True)
add_header.setChecked(self.settings.include_header)
add_header.triggered.connect(self.header_check)
export.addAction(add_header)
comma.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
comma.triggered.connect(
lambda *args, action=space: action.setChecked(False))
comma.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=space: action.setChecked(False))
tab.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
space.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
space.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
space.triggered.connect(
lambda *args, action=semicolon: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=comma: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=tab: action.setChecked(False))
semicolon.triggered.connect(
lambda *args, action=space: action.setChecked(False))
menu.setNativeMenuBar(False)
self._menu = menu
layout.setMenuBar(menu)
menu.setVisible(True)
self.tool_window.ui_area.setLayout(layout)
self.tool_window.manage(None)
def clear_table(self):
are_you_sure = QMessageBox.question(
None,
"Clear table?",
"Are you sure you want to clear the data table?",
)
if are_you_sure != QMessageBox.Yes:
return
self.table.setRowCount(0)
def calc_sterimol(self, *args):
self.settings.radii = self.radii_option.currentText()
self.settings.display_radii = self.display_radii.checkState(
) == Qt.Checked
self.settings.display_vectors = self.display_vectors.checkState(
) == Qt.Checked
self.settings.at_L = self.at_L.value()
self.settings.sterimol2vec = self.sterimol2vec.isChecked()
self.settings.L_option = self.L_option.currentText()
targets, neighbors, datas = sterimol_cmd(
self.session,
selected_atoms(self.session),
radii=self.radii_option.currentText(),
showVectors=self.display_vectors.checkState() == Qt.Checked,
showRadii=self.display_radii.checkState() == Qt.Checked,
return_values=True,
at_L=self.at_L.value() if self.sterimol2vec.isChecked() else None,
bisect_L=self.L_option.currentText() ==
"bisect angle between coordinating atoms",
)
if len(targets) == 0:
return
if self.settings.delimiter == "comma":
delim = ","
elif self.settings.delimiter == "space":
delim = " "
elif self.settings.delimiter == "tab":
delim = "\t"
elif self.settings.delimiter == "semicolon":
delim = ";"
# self.table.setRowCount(0)
for t, b, data in zip(targets, neighbors, datas):
row = self.table.rowCount()
self.table.insertRow(row)
targ = QTableWidgetItem()
targ.setData(Qt.DisplayRole, t)
self.table.setItem(row, 0, targ)
neigh = QTableWidgetItem()
neigh.setData(Qt.DisplayRole, delim.join(b))
self.table.setItem(row, 1, neigh)
l = np.linalg.norm(data["L"][1] - data["L"][0])
b1 = np.linalg.norm(data["B1"][1] - data["B1"][0])
b2 = np.linalg.norm(data["B2"][1] - data["B2"][0])
b3 = np.linalg.norm(data["B3"][1] - data["B3"][0])
b4 = np.linalg.norm(data["B4"][1] - data["B4"][0])
b5 = np.linalg.norm(data["B5"][1] - data["B5"][0])
li = QTableWidgetItem()
li.setData(Qt.DisplayRole, "%.2f" % l)
self.table.setItem(row, 7, li)
b1i = QTableWidgetItem()
b1i.setData(Qt.DisplayRole, "%.2f" % b1)
self.table.setItem(row, 2, b1i)
b2i = QTableWidgetItem()
b2i.setData(Qt.DisplayRole, "%.2f" % b2)
self.table.setItem(row, 3, b2i)
b3i = QTableWidgetItem()
b3i.setData(Qt.DisplayRole, "%.2f" % b3)
self.table.setItem(row, 4, b3i)
b4i = QTableWidgetItem()
b4i.setData(Qt.DisplayRole, "%.2f" % b4)
self.table.setItem(row, 5, b4i)
b5i = QTableWidgetItem()
b5i.setData(Qt.DisplayRole, "%.2f" % b5)
self.table.setItem(row, 6, b5i)
for i in range(0, 7):
if i == 1:
continue
self.table.resizeColumnToContents(i)
def header_check(self, state):
"""user has [un]checked the 'include header' option on the menu"""
if state:
self.settings.include_header = True
else:
self.settings.include_header = False
def get_csv(self):
if self.settings.delimiter == "comma":
delim = ","
elif self.settings.delimiter == "space":
delim = " "
elif self.settings.delimiter == "tab":
delim = "\t"
elif self.settings.delimiter == "semicolon":
delim = ";"
if self.settings.include_header:
s = delim.join([
"substituent_atom", "bonded_atom", "B1", "B2", "B3", "B4",
"B5", "L"
])
s += "\n"
else:
s = ""
for i in range(0, self.table.rowCount()):
s += delim.join([
item.data(Qt.DisplayRole)
for item in [self.table.item(i, j) for j in range(0, 8)]
])
s += "\n"
return s
def copy_csv(self):
app = QApplication.instance()
clipboard = app.clipboard()
csv = self.get_csv()
clipboard.setText(csv)
self.session.logger.status("copied to clipboard")
def save_csv(self):
"""save data on current tab to CSV file"""
filename, _ = QFileDialog.getSaveFileName(filter="CSV Files (*.csv)")
if filename:
s = self.get_csv()
with open(filename, 'w') as f:
f.write(s.strip())
self.session.logger.status("saved to %s" % filename)
def del_sterimol(self):
for model in self.session.models.list(type=Generic3DModel):
if model.name.startswith("Sterimol"):
model.delete()
def display_help(self):
"""Show the help for this tool in the help viewer."""
from chimerax.core.commands import run
run(self.session,
'open %s' % self.help if self.help is not None else "")
