schrodinger.trajectory.trajectory_gui_dir.traj_plot_gui module¶

Plot panel for the Trajectory Player.

class schrodinger.trajectory.trajectory_gui_dir.traj_plot_gui.TrajPlotModel(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.models.parameters.CompoundParam

Main model for the trajectory plot GUI

plot_widgets: list¶

A Param to represent lists. Values of this param will have a mutated signal that will be emitted whenever any mutation method is called.

The constructor optionally takes a item_class keyword argument to specify what type of class the items in the list will be. This information will be used for jsonifying the list if specified.

plot_managers: list¶

A Param to represent lists. Values of this param will have a mutated signal that will be emitted whenever any mutation method is called.

The constructor optionally takes a item_class keyword argument to specify what type of class the items in the list will be. This information will be used for jsonifying the list if specified.

DataClass¶

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

__init__(default_value=<object object>, _param_type=<object object>, **kwargs)¶

classmethod addSubParam(name, param, update_owner=True)¶

blockSignals(self, b: bool) → bool¶

block_signal_propagation()¶

childEvent(self, a0: QChildEvent)¶

children(self) → List[QObject]¶

classmethod configureParam()¶: Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, signal: QMetaMethod)¶

customEvent(self, a0: QEvent)¶

classmethod defaultValue()¶

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0

deleteLater(self)¶

destroyed¶: destroyed(self, object: typing.Optional[QObject] = None) [signal]

disconnect(a0: QMetaObject.Connection) → bool¶
disconnect(self) → None

disconnectNotify(self, signal: QMetaMethod)¶

dumpObjectInfo(self)¶

dumpObjectTree(self)¶

dynamicPropertyNames(self) → List[QByteArray]¶

event(self, a0: QEvent) → bool¶

eventFilter(self, a0: QObject, a1: QEvent) → bool¶

findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject¶
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]¶
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

classmethod fromJson(json_obj)¶

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters: json_obj (dict) – A json-loaded dictionary to create an object from.
Returns: An instance of this class.
Return type: cls

classmethod fromJsonImplementation(json_dict)¶: Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam()¶: Return the corresponding abstract param for this instance.

classmethod getJsonBlacklist()¶

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE: Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(obj, signal_type='Changed')¶

classmethod getParamValue(obj)¶

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3

Parameters: param (CompoundParam) – The owner param to get a param value from

classmethod getSubParam(name)¶

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters: name (str) – The name of the subparam to get the value for.

classmethod getSubParams()¶: Return a dictionary mapping subparam names to their values.

getTypeHint()¶

get_version()¶: Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, classname: str) → bool¶

initAbstract()¶

initConcrete()¶: Override to customize initialization of concrete params.

initializeValue()¶: Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, a0: QObject)¶

classmethod isAbstract()¶: Whether the param is an “abstract” param.

isDefault()¶: Whether the current value of this instance matches the default value.

isSignalConnected(self, signal: QMetaMethod) → bool¶

isWidgetType(self) → bool¶

isWindowType(self) → bool¶

killTimer(self, id: int)¶

metaObject(self) → QMetaObject¶

moveToThread(self, thread: QThread)¶

objectName(self) → str¶

objectNameChanged¶: objectNameChanged(self, objectName: str) [signal]

classmethod owner()¶

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a

classmethod ownerChain()¶

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()¶

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'

parent(self) → QObject¶

plot_managersChanged¶

plot_managersReplaced¶

plot_widgetsChanged¶

plot_widgetsReplaced¶

property(self, name: str) → Any¶

pyqtConfigure(...)¶: Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, signal: PYQT_SIGNAL) → int¶

removeEventFilter(self, a0: QObject)¶

reset(*abstract_params)¶

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setObjectName(self, name: str)¶

classmethod setParamValue(obj, value)¶

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10

Parameters

param – The owner param to set a subparam value of.
value – The value to set the subparam value to.

setParent(self, a0: QObject)¶

setProperty(self, name: str, value: Any) → bool¶

classmethod setReference(param1, param2)¶

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6

Parameters

param1 – The first abstract param to keep synced
param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(value=None, **kwargs)¶

Set the value of this CompoundParam to match value.

Parameters

value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.
kwargs – For internal use only.

signalsBlocked(self) → bool¶

skip_eq_check()¶

startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶

staticMetaObject = <PyQt6.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, a0: QTimerEvent)¶

toDict()¶

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}

toJson(_mark_version=True)¶

Create and returns a data structure made up of jsonable items.

Return type: An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()¶: Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str¶

valueChanged¶

class schrodinger.trajectory.trajectory_gui_dir.traj_plot_gui.TrajAnalysisPlotPanel(dockarea=None, **kwargs)¶

Bases: schrodinger.ui.qt.basewidgets.MaestroDockPanel

Overarching panel class for displaying trajectory graphs. This class is typically launched via the Player Toolbar.

Graphs are either:

Indexed by frame number (ex. Polar Surface Area for each frame). These are displayed in the main panel view.
Indexed by atom/residue (ex. Residue RMSF over all residues selected) These can be viewed in the advanced graphs section at the bottom.

Variables

displayAsl – Display the asl for the corresponding entry id Signal. args are (asl, entry_id)
displayFrameAndAsl – Change frame and show ASL for given entry id Signal args are (asl, entry_id, frame_number)

model_class¶: alias of schrodinger.trajectory.trajectory_gui_dir.traj_plot_gui.TrajPlotModel

ui_module = <module 'schrodinger.trajectory.trajectory_gui_dir.traj_plot_ui' from '/scr/buildbot/savedbuilds/2023-4/NB/build-133/internal/lib/python3.8/site-packages/schrodinger/trajectory/trajectory_gui_dir/traj_plot_ui.py'>¶

createPlot¶

trajectoryChanged¶

displayFrameAndAsl¶

displayAsl¶

RESIZE_WAIT = 300¶

__init__(dockarea=None, **kwargs)¶

initSetOptions()¶: Suggested subclass use: set instance variables, excluding layouts and subwidgets. Also use here to (optionally) apply the legacy stylesheet spacing settings (PANEL-19101).

initSetUp()¶

Creates widget from ui and stores it ui_widget.

Suggested subclass use: create and initialize subwidgets, and connect signals.

initLayout()¶

defineMappings()¶

Override this in the subclass to define mappings. Should return a list of tuples [(<target>, <param>)]. Targets can be:

a basic widget, like QLineEdit or QComboBox

a custom object that inherits MapperMixin or TargetMixin

a TargetSpec instance

a slot

For common widgets, standard signals and getter/setter methods will be used, as defined in mappers._get_default_access_names().

For more fine-grained custom control, instantiate a TargetSpec object, which allows custom setters, getters, and signals to be specified.

Supplying a slot as the first element of the tuple is equivalent to providing TargetSpec(slot=my_slot).

Note that all target slots are triggered on setModel() as well as in response to the specified signal.

The param is an abstract param reference, e.g. MyModel.my_param.

Example:

def defineMappings(self):
    combo = self.style_combo
    return [(self.name_le, MyModel.name),
            (TargetSpec(combo,
                    getter=combo.currentText,
                    setter=combo.setCurrentText), MyModel.style),
            (self.coord_widget, MyModel.coord),
            (self._onASLTextChanged, MyModel.asl_text)]

getSignalsAndSlots(model)¶

Override this method to specify signal and slot pairs that need to be connected/disconnected whenever the model instance is switched using setModel. The model instance is provided as an argument so that instance-specific signals can be used, but any pairs of signals and slots may be returned from this method.

Returns: a list of 2-tuples where each tuple is a signal, slot pair

event(event)¶

Make sure that scrolling doesn’t cause Workspace zoom.

See Qt documentation for argument documentation.

setPlotVisibleInteractionsAction(action)¶: Set the visible interactions action from the player toolbar

setIncludeEmptyDatasetsAction(action)¶: Set the include empty datasets action from the player toolbar

plotAlreadyExists(settings_hash)¶

Check if a plot already exists.

Parameters: settings_hash (str) – Settings string uniquely identifying a plot.
Returns: True if the specified plot already exists, False otherwise.
Return type: bool

validateTrajectory()¶: Return True if there is a trajectory loaded and it is included in the Workspace; False otherwise.

createTrajectoryPlot(plot_type)¶

Starts the creation of a plot to be displayed in the panel. Shows the panel.

Parameters: plot_type – Type of plot for the panel to create and display
Type: PlotType

getAslIdentifier(asl) → str¶: Get the identifier string for the asl used in the interactions plot :param asl: the asl to get a unique shorthand number for :return: a numbered string associated with the plot’s ASL, to use in plot titles

createPlotManager(plot_cls, *args, show_warning=True, **kwargs)¶

Create a plot manager of given class, with specified options, and start the plot generation. Shows a warning and does nothing if a plot with same settings already exists. Warning is also shown if plot fails to be created or started.

Parameters

plot_cls (AbstractTrajectoryPlotManager) – Class of the plot to create
show_warning (bool) – Whether to show warning if plot with same parameters already exists.

Returns

Plot Manager if valid, None if not

Return type

AbstractTrajectoryPlotManager or None

setupPlotSignals(plot_manager)¶: Hook up plot manager’s signals to panel’s slots.

getNextAvailablePlotNumber(pmanager)¶

Return the plot number that should be used for next plot of given type. For “All Interactions” plots, the plot number is currently not used.

Parameters: pmanager (AbstractTrajectoryPlotManager) – Plot manager instance

updateFsysCt(frame_number)¶

Updates the entry trajectory’s fsys_ct structure coordinates at the frame provided

Parameters: frame_number (int) – frame number of trajectory
Returns: A copy of the frame CT
Return type: cms.Cms

getRmsdReferenceCt()¶

Return fsys_ct structure at the frame that user selected to use for RMSD reference.

Returns: A copy of the frame CT
Return type: cms.Cms

createEnergyPlotForSets(sets)¶

Submit a TrajectoryEnergyJobTask for given sets. A plot window will be created when the job completes.

Parameters: sets (dict) – Dict where keys are set names and values are ASLs.

showRmsdSettingsDialog()¶: Shows the RMSD Settings Dialog

showEnergySettingsDialog()¶: Shows energy job settings dialog in modal mode. Called from “Job Settings…” menu item.

onNewPlotDataAvailable(plot_manager)¶: Called when the given plot manager has finished creating the plot. For multi-series plots, it gets called for every series that is done.

createPlotWidget(plot_manager)¶

Create a new plot widget for displaying the given plot. For simple plots, a CollapsiblePlot is created. For advanced plots, a plot panel with AdvancedPlotShortcut is created.

Parameters: plot (AbstractTrajectoryPlotManager) – Plot object containing the chart.
Returns: Plot widget.
Return type: tplots.CollapsiblePlot or tplots.AdvancedPlotShortcut

countPlotsOfType(mode)¶: Count the number of plots with the given type that are present.

removePlot(plot_manager)¶

Remove the given plot manager from the panel. If it has a plot widget associated with it, it will also be removed.

Parameters: plot_manager (AbstractTrajectoryPlotManager) – Reference to the plot manager.

addWorkspaceMeasurements()¶: Opens the workspace measurement banner, allowing the user to add measurements

getPlotCount()¶

Returns: The current plots count. Used by playertoolbar.py.
Return type: int

exportToExcelFile(sheets, fname)¶

Creates an excel file for the given sheets.

Parameters

sheets (list((str, list(list))) – Data for all tables to be exported from _generateExportData.
fname (str) – Filename

exportToCsvArchive(sheets, fname)¶

Creates a zip archive of CSV files. Each sheet is given a separate CSV file.

Parameters

sheets (list((str, list(list))) – Data for all tables to be exported from _generateExportData.
fname (str) – Filename

deletePlotsForEntry(eid)¶

Remove plots associated with the specified entry id.

Parameters: eid (int) – Entry ID to remove the plots of.

onCurrentFrameChanged(frame)¶

showPlotWarning(msg)¶: Show the given text in a warning dialog, with dialog title set to “Cannot Display Plot” instead of the standard “Warning” title.

resizeShortcuts()¶

resizeEvent(self, a0: QResizeEvent)¶

APPLY_LEGACY_STYLESHEET = True¶

APPLY_PANELX_STYLESHEET = False¶

class BtnPos(value)¶

Bases: enum.IntEnum

An enumeration.

Left = 0¶

Middle = 1¶

Right = 2¶

DockWidgetClosable = 1¶

class DockWidgetFeature(value)¶

Bases: enum.Flag

An enumeration.

DockWidgetClosable = 1¶

DockWidgetMovable = 2¶

DockWidgetFloatable = 4¶

DockWidgetVerticalTitleBar = 8¶

NoDockWidgetFeatures = 0¶

DockWidgetFloatable = 4¶

DockWidgetMovable = 2¶

DockWidgetVerticalTitleBar = 8¶

DrawChildren = 2¶

DrawWindowBackground = 1¶

IgnoreMask = 4¶

NoDockWidgetFeatures = 0¶

PRESETS_FEATURE_FLAG = False¶

class PaintDeviceMetric(value)¶

Bases: enum.Enum

An enumeration.

PdmWidth = 1¶

PdmHeight = 2¶

PdmWidthMM = 3¶

PdmHeightMM = 4¶

PdmNumColors = 5¶

PdmDepth = 6¶

PdmDpiX = 7¶

PdmDpiY = 8¶

PdmPhysicalDpiX = 9¶

PdmPhysicalDpiY = 10¶

PdmDevicePixelRatio = 11¶

PdmDevicePixelRatioScaled = 12¶

PdmDepth = 6¶

PdmDevicePixelRatio = 11¶

PdmDevicePixelRatioScaled = 12¶

PdmDpiX = 7¶

PdmDpiY = 8¶

PdmHeight = 2¶

PdmHeightMM = 4¶

PdmNumColors = 5¶

PdmPhysicalDpiX = 9¶

PdmPhysicalDpiY = 10¶

PdmWidth = 1¶

PdmWidthMM = 3¶

class RenderFlag(value)¶

Bases: enum.Flag

An enumeration.

DrawWindowBackground = 1¶

DrawChildren = 2¶

IgnoreMask = 4¶

SHOW_AS_WINDOW = True¶

class StdBtn(value)¶

Bases: enum.IntEnum

An enumeration.

Ok = 0¶

Cancel = 1¶

Reset = 2¶

Help = 3¶

acceptDrops(self) → bool¶

property accepted¶

accessibleDescription(self) → str¶

accessibleName(self) → str¶

actionEvent(self, a0: QActionEvent)¶

actions(self) → List[QAction]¶

activateWindow(self)¶

addAction(self, action: QAction)¶

addActions(self, actions: Iterable[QAction])¶

adjustSize(self)¶

allowedAreas(self) → Qt.DockWidgetArea¶

allowedAreasChanged¶: allowedAreasChanged(self, allowedAreas: Qt.DockWidgetArea) [signal]

autoFillBackground(self) → bool¶

backgroundRole(self) → QPalette.ColorRole¶

baseSize(self) → QSize¶

blockSignals(self, b: bool) → bool¶

changeEvent(self, event: QEvent)¶

childAt(self, p: QPoint) → QWidget¶
childAt(self, ax: int, ay: int) → QWidget

childEvent(self, a0: QChildEvent)¶

children(self) → List[QObject]¶

childrenRect(self) → QRect¶

childrenRegion(self) → QRegion¶

clearFocus(self)¶

clearMask(self)¶

close(self) → bool¶

closeEvent(event)¶: Do not close the floating python panel and instead emit a SIGNAL to Maestro which redocks the panel back into main window. This is a temporary workaround for Qt5 redock issues

colorCount(self) → int¶

connectNotify(self, signal: QMetaMethod)¶

contentsMargins(self) → QMargins¶

contentsRect(self) → QRect¶

contextMenuEvent(self, a0: QContextMenuEvent)¶

contextMenuPolicy(self) → Qt.ContextMenuPolicy¶

create(self, window: PyQt6.sip.voidptr = 0, initializeWindow: bool = True, destroyOldWindow: bool = True)¶

createWindowContainer(window: QWindow, parent: typing.Optional[QWidget] = None, flags: Qt.WindowType = Qt.WindowFlags()) → QWidget¶

cursor(self) → QCursor¶

customContextMenuRequested¶: customContextMenuRequested(self, pos: QPoint) [signal]

customEvent(self, a0: QEvent)¶

debug()¶

deleteLater(self)¶

depth(self) → int¶

destroy(self, destroyWindow: bool = True, destroySubWindows: bool = True)¶

destroyed¶: destroyed(self, object: typing.Optional[QObject] = None) [signal]

devType(self) → int¶

devicePixelRatio(self) → float¶

devicePixelRatioF(self) → float¶

devicePixelRatioFScale() → float¶

disconnect(a0: QMetaObject.Connection) → bool¶
disconnect(self) → None

disconnectNotify(self, signal: QMetaMethod)¶

dockLocationChanged¶: dockLocationChanged(self, area: Qt.DockWidgetArea) [signal]

dragEnterEvent(self, a0: QDragEnterEvent)¶

dragLeaveEvent(self, a0: QDragLeaveEvent)¶

dragMoveEvent(self, a0: QDragMoveEvent)¶

dropEvent(self, a0: QDropEvent)¶

dumpObjectInfo(self)¶

dumpObjectTree(self)¶

dynamicPropertyNames(self) → List[QByteArray]¶

effectiveWinId(self) → PyQt6.sip.voidptr¶

ensurePolished(self)¶

enterEvent(self, event: QEnterEvent)¶

error(*args, **kwargs)¶: Shows a popup error message box. For parameter documentation see messagebox.MessageBox.

eventFilter(self, a0: QObject, a1: QEvent) → bool¶

features(self) → QDockWidget.DockWidgetFeature¶

featuresChanged¶: featuresChanged(self, features: QDockWidget.DockWidgetFeature) [signal]

find(a0: PyQt6.sip.voidptr) → QWidget¶

findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject¶
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]¶
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

focusInEvent(self, a0: QFocusEvent)¶

focusNextChild(self) → bool¶

focusNextPrevChild(self, next: bool) → bool¶

focusOutEvent(self, a0: QFocusEvent)¶

focusPolicy(self) → Qt.FocusPolicy¶

focusPreviousChild(self) → bool¶

focusProxy(self) → QWidget¶

focusWidget(self) → QWidget¶

font(self) → QFont¶

fontInfo(self) → QFontInfo¶

fontMetrics(self) → QFontMetrics¶

foregroundRole(self) → QPalette.ColorRole¶

forgetMessageBoxResponse(key)¶

Forgets any previously saved response that was stored via a save_response_key.

Parameters: key – the key for the response to forget

frameGeometry(self) → QRect¶

frameSize(self) → QSize¶

geometry(self) → QRect¶

getModel()¶

classmethod getPanelInstance(create=True)¶

Return the singleton instance of this panel, creating one if necessary.

Parameters: create (bool) – Whether to create an instance of the panel if none exists
Returns: instance of this panel.
Return type: PanelMixin

grab(self, rectangle: QRect = QRect(QPoint(0, 0), QSize(- 1, - 1))) → QPixmap¶

grabGesture(self, type: Qt.GestureType, flags: Qt.GestureFlag = Qt.GestureFlags())¶

grabKeyboard(self)¶

grabMouse(self)¶
grabMouse(self, a0: Union[QCursor, Qt.CursorShape]) → None

grabShortcut(self, key: Union[QKeySequence, QKeySequence.StandardKey, str, int], context: Qt.ShortcutContext = Qt.WindowShortcut) → int¶

graphicsEffect(self) → QGraphicsEffect¶

graphicsProxyWidget(self) → QGraphicsProxyWidget¶

hasFocus(self) → bool¶

hasHeightForWidth(self) → bool¶

hasMouseTracking(self) → bool¶

hasTabletTracking(self) → bool¶

height(self) → int¶

heightForWidth(self, a0: int) → int¶

heightMM(self) → int¶

hide(self)¶

hideEvent(self, a0: QHideEvent)¶

info(*args, **kwargs)¶: Shows a popup information message box. For parameter documentation see messagebox.MessageBox.

inherits(self, classname: str) → bool¶

initFinalize()¶: Suggested subclass use: perform any remaining initialization.

initLayOut()¶: @overrides: widgetmixins.InitMixin

initPainter(self, painter: QPainter)¶

initSetDefaults()¶: @overrides: widgetmixins.InitMixin

initStyleOption(self, option: QStyleOptionDockWidget)¶

inputMethodEvent(self, a0: QInputMethodEvent)¶

inputMethodHints(self) → Qt.InputMethodHint¶

inputMethodQuery(self, a0: Qt.InputMethodQuery) → Any¶

insertAction(self, before: QAction, action: QAction)¶

insertActions(self, before: QAction, actions: Iterable[QAction])¶

installEventFilter(self, a0: QObject)¶

isActiveWindow(self) → bool¶

isAncestorOf(self, child: QWidget) → bool¶

isAreaAllowed(self, area: Qt.DockWidgetArea) → bool¶

isEnabled(self) → bool¶

isEnabledTo(self, a0: QWidget) → bool¶

isFloating(self) → bool¶

isFullScreen(self) → bool¶

isHidden(self) → bool¶

isLeftToRight(self) → bool¶

isMaximized(self) → bool¶

isMinimized(self) → bool¶

isModal(self) → bool¶

isRightToLeft(self) → bool¶

isSignalConnected(self, signal: QMetaMethod) → bool¶

isVisible(self) → bool¶

isVisibleTo(self, a0: QWidget) → bool¶

isWidgetType(self) → bool¶

isWindow(self) → bool¶

isWindowModified(self) → bool¶

isWindowType(self) → bool¶

keyPressEvent(self, a0: QKeyEvent)¶

keyReleaseEvent(self, a0: QKeyEvent)¶

keyboardGrabber() → QWidget¶

killTimer(self, id: int)¶

layout(self) → QLayout¶

layoutDirection(self) → Qt.LayoutDirection¶

leaveEvent(self, a0: QEvent)¶

locale(self) → QLocale¶

logicalDpiX(self) → int¶

logicalDpiY(self) → int¶

lower(self)¶

makeInitialModel()¶

mapFrom(self, a0: QWidget, a1: QPoint) → QPoint¶
mapFrom(self, a0: QWidget, a1: QPointF) → QPointF

mapFromGlobal(self, a0: QPoint) → QPoint¶
mapFromGlobal(self, a0: QPointF) → QPointF

mapFromParent(self, a0: QPoint) → QPoint¶
mapFromParent(self, a0: QPointF) → QPointF

mapTo(self, a0: QWidget, a1: QPoint) → QPoint¶
mapTo(self, a0: QWidget, a1: QPointF) → QPointF

mapToGlobal(self, a0: QPoint) → QPoint¶
mapToGlobal(self, a0: QPointF) → QPointF

mapToParent(self, a0: QPoint) → QPoint¶
mapToParent(self, a0: QPointF) → QPointF

mappedParams()¶: Return a list of the abstract params that are mapped to.

mask(self) → QRegion¶

maximumHeight(self) → int¶

maximumSize(self) → QSize¶

maximumWidth(self) → int¶

metaObject(self) → QMetaObject¶

metric(self, a0: QPaintDevice.PaintDeviceMetric) → int¶

minimumHeight(self) → int¶

minimumSize(self) → QSize¶

minimumSizeHint(self) → QSize¶

minimumWidth(self) → int¶

property model¶

mouseDoubleClickEvent(self, a0: QMouseEvent)¶

mouseGrabber() → QWidget¶

mouseMoveEvent(self, a0: QMouseEvent)¶

mousePressEvent(self, a0: QMouseEvent)¶

mouseReleaseEvent(self, a0: QMouseEvent)¶

move(self, a0: QPoint)¶
move(self, ax: int, ay: int) → None

moveEvent(self, a0: QMoveEvent)¶

moveToThread(self, thread: QThread)¶

nativeEvent(self, eventType: QByteArray, message: PyQt6.sip.voidptr) → Tuple[bool, PyQt6.sip.voidptr]¶

nativeParentWidget(self) → QWidget¶

nextInFocusChain(self) → QWidget¶

normalGeometry(self) → QRect¶

objectName(self) → str¶

objectNameChanged¶: objectNameChanged(self, objectName: str) [signal]

overrideWindowFlags(self, type: Qt.WindowType)¶

overrideWindowState(self, state: Qt.WindowState)¶

paintEngine(self) → QPaintEngine¶

paintEvent(self, event: QPaintEvent)¶

paintingActive(self) → bool¶

palette(self) → QPalette¶

classmethod panel(blocking=False, modal=False, finished_callback=None)¶

Open an instance of this class.

For full argument documentation, see ExecutionMixin.run.

parent(self) → QObject¶

parentWidget(self) → QWidget¶

physicalDpiX(self) → int¶

physicalDpiY(self) → int¶

pos(self) → QPoint¶

previousInFocusChain(self) → QWidget¶

property(self, name: str) → Any¶

pyqtConfigure(...)¶: Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

pythonPanelAboutToBeClosed¶: pythonPanelAboutToBeClosed(self, widget: QWidget) [signal]

question(*args, **kwargs)¶: Shows a popup question message box. For parameter documentation see messagebox.QuestionMessageBox.

raise_(self)¶

receivers(self, signal: PYQT_SIGNAL) → int¶

reconfigureDockWidget¶: reconfigureDockWidget(self, widget: QWidget) [signal]

rect(self) → QRect¶

releaseKeyboard(self)¶

releaseMouse(self)¶

releaseShortcut(self, id: int)¶

removeAction(self, action: QAction)¶

removeEventFilter(self, a0: QObject)¶

render(self, target: QPaintDevice, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: QWidget.RenderFlag = QWidget.RenderFlags(QWidget.DrawWindowBackground | QWidget.DrawChildren))¶
render(self, painter: QPainter, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: QWidget.RenderFlag = QWidget.RenderFlags(QWidget.DrawWindowBackground | QWidget.DrawChildren)) → None

repaint(self)¶
repaint(self, x: int, y: int, w: int, h: int) → None
repaint(self, a0: QRect) → None
repaint(self, a0: QRegion) → None

reportValidation(results)¶

Present validation messages to the user. This is an implmentation of the ValidationMixin interface and does not need to be called directly.

This method assumes that error and question methods have been defined in the subclass, as in e.g. widget_mixins.MessageBoxMixin.

Parameters: results (validation.ValidationResults) – Set of validation results generated by validate
Returns: if True, there were no validation errors and the user decided to continue despite any warnings. If False, there was at least one validation error or the user decided to abort when faced with a warning.

resetMappedParams()¶

resize(self, a0: QSize)¶
resize(self, w: int, h: int) → None

restoreGeometry(self, geometry: QByteArray) → bool¶

run(blocking=False, modal=False, finished_callback=None)¶

Show this widget, while optionally blocking, making the widget window modal, and registering a callback for when the widget is closed again.

Parameters

blocking (bool) – if True, block progress in the calling method until the widget is closed again.
modal (bool) – if True, open this widget as window modal. Otherwise, open this widget as nonmodal.
finished_callback (a callable object) – an object that will be called with no arguments when this widget is closed.

runAllSlots()¶

runValidation(silent=False, validate_children=True, stop_on_fail=True)¶

Runs validation and reports the results (unless run silently).

Parameters

silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.
validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.
stop_on_fail (bool) – stop validation when first failure is encountered

Returns

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type

ValidationResults or bool

saveGeometry(self) → QByteArray¶

screen(self) → QScreen¶

scroll(self, dx: int, dy: int)¶
scroll(self, dx: int, dy: int, a2: QRect) → None

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setAcceptDrops(self, on: bool)¶

setAccessibleDescription(self, description: str)¶

setAccessibleName(self, name: str)¶

setAllowedAreas(self, areas: Qt.DockWidgetArea)¶

setAttribute(self, attribute: Qt.WidgetAttribute, on: bool = True)¶

setAutoFillBackground(self, enabled: bool)¶

setBackgroundRole(self, a0: QPalette.ColorRole)¶

setBaseSize(self, basew: int, baseh: int)¶
setBaseSize(self, s: QSize) → None

setContentsMargins(self, left: int, top: int, right: int, bottom: int)¶
setContentsMargins(self, margins: QMargins) → None

setContextMenuPolicy(self, policy: Qt.ContextMenuPolicy)¶

setCursor(self, a0: Union[QCursor, Qt.CursorShape])¶

setDefaults()¶: @overrides: af2.App

setDisabled(self, a0: bool)¶

setEnabled(self, a0: bool)¶

setFeatures(self, features: QDockWidget.DockWidgetFeature)¶

setFixedHeight(self, h: int)¶

setFixedSize(self, a0: QSize)¶
setFixedSize(self, w: int, h: int) → None

setFixedWidth(self, w: int)¶

setFloating(self, floating: bool)¶

setFocus(self)¶
setFocus(self, reason: Qt.FocusReason) → None

setFocusPolicy(self, policy: Qt.FocusPolicy)¶

setFocusProxy(self, a0: QWidget)¶

setFont(self, a0: QFont)¶

setForegroundRole(self, a0: QPalette.ColorRole)¶

setGeometry(self, a0: QRect)¶
setGeometry(self, ax: int, ay: int, aw: int, ah: int) → None

setGraphicsEffect(self, effect: QGraphicsEffect)¶

setHidden(self, hidden: bool)¶

setInputMethodHints(self, hints: Qt.InputMethodHint)¶

setLayout(self, a0: QLayout)¶

setLayoutDirection(self, direction: Qt.LayoutDirection)¶

setLocale(self, locale: QLocale)¶

setMask(self, a0: QBitmap)¶
setMask(self, a0: QRegion) → None

setMaximumHeight(self, maxh: int)¶

setMaximumSize(self, maxw: int, maxh: int)¶
setMaximumSize(self, s: QSize) → None

setMaximumWidth(self, maxw: int)¶

setMinimumHeight(self, minh: int)¶

setMinimumSize(self, minw: int, minh: int)¶
setMinimumSize(self, s: QSize) → None

setMinimumWidth(self, minw: int)¶

setModel(model)¶

Sets the model object for the mapper. Disconnects the old model, if one is set, and connects the new model. Pass in None to have no model set.

Parameters: model – the model instance or None

setModelWithoutSlots(model)¶: This is called when this MapperMixin is a sub-widget of a parent MapperMixin. Since the slots will all be called at the end of the parent setModel, they shouldn’t be called during the sub-widget’s setModel.

setMouseTracking(self, enable: bool)¶

setObjectName(self, name: str)¶

setPalette(self, a0: QPalette)¶

setParent(self, parent: QWidget)¶
setParent(self, parent: QWidget, f: Qt.WindowType) → None

setProperty(self, name: str, value: Any) → bool¶

setScreen(self, a0: QScreen)¶

setShortcutAutoRepeat(self, id: int, enabled: bool = True)¶

setShortcutEnabled(self, id: int, enabled: bool = True)¶

setSizeIncrement(self, w: int, h: int)¶
setSizeIncrement(self, s: QSize) → None

setSizePolicy(self, a0: QSizePolicy)¶
setSizePolicy(self, hor: QSizePolicy.Policy, ver: QSizePolicy.Policy) → None

setStatusTip(self, a0: str)¶

setStyle(self, a0: QStyle)¶

setStyleSheet(self, styleSheet: str)¶

setTabOrder(a0: QWidget, a1: QWidget)¶

setTabletTracking(self, enable: bool)¶

setTitleBarWidget(self, widget: QWidget)¶

setToolTip(self, a0: str)¶

setToolTipDuration(self, msec: int)¶

setUpdatesEnabled(self, enable: bool)¶

setVisible(self, visible: bool)¶

setWhatsThis(self, a0: str)¶

setWidget(self, widget: QWidget)¶

setWidgetLayout()¶: Set the widget layout. A QDockWidget’s layout does not allow nested layouts so we create a container widget to hold the widget layout.

setWindowFilePath(self, filePath: str)¶

setWindowFlag(self, a0: Qt.WindowType, on: bool = True)¶

setWindowFlags(self, type: Qt.WindowType)¶

setWindowFlagsForRun()¶: Don’t set any window flags for run

setWindowIcon(self, icon: QIcon)¶

setWindowIconText(self, a0: str)¶

setWindowModality(self, windowModality: Qt.WindowModality)¶

setWindowModified(self, a0: bool)¶

setWindowOpacity(self, level: float)¶

setWindowRole(self, a0: str)¶

setWindowState(self, state: Qt.WindowState)¶

setWindowTitle(self, a0: str)¶

setting_model()¶

setupDockWidget¶: setupDockWidget(self) [signal]

sharedPainter(self) → QPainter¶

show()¶: Override the show method to clear and previous value of self.accepted

showEvent(self, a0: QShowEvent)¶

showFullScreen(self)¶

showMaximized(self)¶

showMessageBox(*args, **kwargs)¶: Shows a popup message box. For parameter documentation see messagebox.MessageBox.

showMinimized(self)¶

showNormal(self)¶

signalsBlocked(self) → bool¶

size(self) → QSize¶

sizeHint(self) → QSize¶

sizeIncrement(self) → QSize¶

sizePolicy(self) → QSizePolicy¶

stackUnder(self, a0: QWidget)¶

startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶

staticMetaObject = <PyQt6.QtCore.QMetaObject object>¶

statusTip(self) → str¶

style(self) → QStyle¶

styleSheet(self) → str¶

tabletEvent(self, a0: QTabletEvent)¶

testAttribute(self, attribute: Qt.WidgetAttribute) → bool¶

thread(self) → QThread¶

timerEvent(self, a0: QTimerEvent)¶

titleBarWidget(self) → QWidget¶

toggleViewAction(self) → QAction¶

toolTip(self) → str¶

toolTipDuration(self) → int¶

topLevelChanged¶: topLevelChanged(self, topLevel: bool) [signal]

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str¶

underMouse(self) → bool¶

ungrabGesture(self, type: Qt.GestureType)¶

unsetCursor(self)¶

unsetLayoutDirection(self)¶

unsetLocale(self)¶

update(self)¶
update(self, a0: QRect) → None
update(self, a0: QRegion) → None
update(self, ax: int, ay: int, aw: int, ah: int) → None

updateGeometry(self)¶

updateMicroFocus(self, query: Qt.InputMethodQuery = Qt.ImQueryAll)¶

updatesEnabled(self) → bool¶

visibilityChanged¶: visibilityChanged(self, visible: bool) [signal]

visibleRegion(self) → QRegion¶

warning(*args, **kwargs)¶: Shows a popup warning message box. For parameter documentation see messagebox.MessageBox.

whatsThis(self) → str¶

wheelEvent(self, a0: QWheelEvent)¶

widget(self) → QWidget¶

width(self) → int¶

widthMM(self) → int¶

winId(self) → PyQt6.sip.voidptr¶

window(self) → QWidget¶

windowFilePath(self) → str¶

windowFlags(self) → Qt.WindowType¶

windowHandle(self) → QWindow¶

windowIcon(self) → QIcon¶

windowIconChanged¶: windowIconChanged(self, icon: QIcon) [signal]

windowIconText(self) → str¶

windowIconTextChanged¶: windowIconTextChanged(self, iconText: str) [signal]

windowModality(self) → Qt.WindowModality¶

windowOpacity(self) → float¶

windowRole(self) → str¶

windowState(self) → Qt.WindowState¶

windowTitle(self) → str¶

windowTitleChanged¶: windowTitleChanged(self, title: str) [signal]

windowType(self) → Qt.WindowType¶

x(self) → int¶

y(self) → int¶

schrodinger.trajectory.trajectory_gui_dir.traj_plot_gui.res_has_backbone_atoms(res: schrodinger.structure._structure._Residue) → bool¶

Checks to see if given residue has backbone atoms needed for Ramachandran analysis

Parameters: res – Residue to check
Returns: Whether residue has requisite backbone atoms

schrodinger.trajectory.trajectory_gui_dir.traj_plot_gui.res_has_nucleotide_atoms(res) → bool¶

Checks to see if given residue has nucleotide PDB names

Parameters: res – Residue to check
Returns: Whether residue has requisite nucleotide backbone atoms

schrodinger.trajectory.trajectory_gui_dir.traj_plot_gui.res_has_rotatable_bonds(res) → bool¶

schrodinger.trajectory.trajectory_gui_dir.traj_plot_gui.res_is_solvent(res) → bool¶