schrodinger.trajectory.trajectory_gui_dir.ramachandran_plots module¶

class schrodinger.trajectory.trajectory_gui_dir.ramachandran_plots.RamaPlot(*args, **kwargs)¶

Bases: schrodinger.ui.qt.rama.RamaContourMixin, PyQt6.QtCore.QObject

Ramachandran Plot. Has functionality for creating regions and plotting points.

Variables

pointClicked – Emitted with a clicked point’s frame number
mouseRightButtonClicked – Emitted when mouse right click button pressed on plot

pointClicked¶

mouseRightButtonClicked¶

DEFAULT_POINT_HEX = '#000000'¶

START_TIME_RGB = (221, 221, 221)¶

END_TIME_RGB = (0, 0, 0)¶

TICK_SPACING = 45¶

TEXT_SIZING = 'medium'¶

__init__(*args, **kwargs)¶

loadResults(labels=None, results=None, trajectories=None, residue_type=None)¶

Loads results from task and populate graph

Parameters

labels – List of residue labels
results (list(tuple(float, float))) – List of (phi, psi) angles
trajectories – list(Frame)
residue_type – rama.RamaResidueType

findClosestFrame(x: float, y: float)¶: Finds closest frame to the x and y coordinates given

setColorByTimeMode(color_by_time)¶

calculateColor(frame: int)¶: Calculates the color needed for a point on the plot for the given frame

ALLOWED_COLOR = '#ffffe0'¶

CROSSHAIR_COLOR = '#cccccc'¶

CROSSHAIR_LINEWIDTH = 0.5¶

DATA_MAX = 180.0¶

DATA_MIN = -180.0¶

FAVORABLE_COLOR = '#ffa07a'¶

TEXT_SIZE = 'small'¶

TICK_LABEL_SIZE = 'x-small'¶

blockSignals(self, b: bool) → bool¶

childEvent(self, a0: QChildEvent)¶

children(self) → List[QObject]¶

connectNotify(self, signal: QMetaMethod)¶

customEvent(self, a0: QEvent)¶

deleteLater(self)¶

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

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

disconnectNotify(self, signal: QMetaMethod)¶

draw_axes()¶

draw_regions(residue_type: schrodinger.ui.qt.rama.RamaResidueType = RamaResidueType.GENERAL)¶

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]

inherits(self, classname: str) → bool¶

installEventFilter(self, a0: QObject)¶

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]

parent(self) → QObject¶

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)¶

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setObjectName(self, name: str)¶

setParent(self, a0: QObject)¶

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

signalsBlocked(self) → bool¶

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

staticMetaObject = <PyQt6.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, a0: QTimerEvent)¶

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

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

Bases: schrodinger.models.parameters.CompoundParam

color_by_time: bool¶

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

end_time: str¶

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

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]¶

color_by_timeChanged¶

color_by_timeReplaced¶

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]¶

end_timeChanged¶

end_timeReplaced¶

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¶

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.ramachandran_plots.RamachandranPlotPanel(plot_manager, parent=None)¶

Bases: schrodinger.trajectory.trajectory_gui_dir.plots.BaseAdvancedPlotPanel

Panel containing clickable Ramachandran Plot

model_class¶: alias of schrodinger.trajectory.trajectory_gui_dir.ramachandran_plots.RamachandranPlotModel

ui_module = <module 'schrodinger.trajectory.trajectory_gui_dir.rama_plot_panel_ui' from '/scr/buildbot/savedbuilds/2024-1/NB/build-133/internal/lib/python3.8/site-packages/schrodinger/trajectory/trajectory_gui_dir/rama_plot_panel_ui.py'>¶

SHORTCUT_PREFIX = 'Phi-Psi'¶

__init__(plot_manager, parent=None)¶

initSetUp()¶

Creates widget from ui and stores it ui_widget.

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

initLayOut()¶: @overrides: widgetmixins.InitMixin

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)]

updateSimulationTime(sim_time)¶

setResTypeLabel(res_type: schrodinger.ui.qt.rama.RamaResidueType)¶

mousePressEvent(self, a0: QMouseEvent)¶

APPLY_LEGACY_STYLESHEET = True¶

APPLY_PANELX_STYLESHEET = False¶

class BtnPos(value)¶

Bases: enum.IntEnum

An enumeration.

Left = 0¶

Middle = 1¶

Right = 2¶

DrawChildren = 2¶

DrawWindowBackground = 1¶

IgnoreMask = 4¶

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)¶

autoFillBackground(self) → bool¶

backgroundRole(self) → QPalette.ColorRole¶

baseSize(self) → QSize¶

blockSignals(self, b: bool) → bool¶

changeEvent(self, a0: 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)¶: Ensures proper handling of OK, Cancel, and [X] button clicks

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)¶

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.

event(self, a0: QEvent) → bool¶

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

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

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

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.

initPainter(self, painter: QPainter)¶

initSetDefaults()¶: @overrides: widgetmixins.InitMixin

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

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¶

isEnabled(self) → bool¶

isEnabledTo(self, a0: QWidget) → 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)¶

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, a0: 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.

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

raise_(self)¶

receivers(self, signal: PYQT_SIGNAL) → int¶

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

resizeEvent(self, a0: QResizeEvent)¶

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)¶

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)¶

setFixedHeight(self, h: int)¶

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

setFixedWidth(self, w: int)¶

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)¶

setToolTip(self, a0: str)¶

setToolTipDuration(self, msec: int)¶

setUpdatesEnabled(self, enable: bool)¶

setVisible(self, visible: bool)¶

setWhatsThis(self, a0: str)¶

setWidgetLayout()¶: Set the widget layout

setWindowFilePath(self, filePath: str)¶

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

setWindowFlags(self, type: Qt.WindowType)¶

setWindowFlagsForRun()¶

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()¶

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)¶

toolTip(self) → str¶

toolTipDuration(self) → int¶

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¶

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)¶

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¶

class schrodinger.trajectory.trajectory_gui_dir.ramachandran_plots.RamachandranPlotManager(panel, res_asl, residue_type)¶

Bases: schrodinger.trajectory.trajectory_gui_dir.plots.AbstractAdvancedTrajectoryPlotManager

PANEL_CLASS¶: alias of schrodinger.trajectory.trajectory_gui_dir.ramachandran_plots.RamachandranPlotPanel

__init__(panel, res_asl, residue_type)¶

createShortcutWidget(plot_panel)¶

Create and store reference to a shortcut widget for a given Advanced Plot

Parameters: plot_panel (BaseAdvancedPlotPanel) – Plot panel that shortcut will launch
Returns: Shortcut for the Advanced Plot
Return type: AdvancedPlotShortcut

onPlotClicked(frame)¶

getInitialPlotTitleAndTooltip(shortcut_title: str)¶

Return the plot title and tooltip for this plot.

Returns: Plot title, Plot tooltip.
Return type: (str, str or None)

configureTask(task, res_asl, residue_type)¶: Configure the specified task by assigning it the analysis mode, and assigning inputs based on the currently selected trajectory. Task’s taskDone signal is connected to self._onTaskEnded().

getPlotType()¶: Returns what type of plot this class uses; used for grouping export data.

loadFromTask(task)¶

Load in results from the given task.

Parameters: task (tasks.AbstractTask) – Task to get result data from.

getDataForExport()¶

Return a list of row data to export to CSV or Excel.

Returns: Data to be exported
Return type: list(list)

saveImage()¶: Save a .png file of the plot

blockSignals(self, b: bool) → bool¶

childEvent(self, a0: QChildEvent)¶

children(self) → List[QObject]¶

colorEntryByScheme¶

connectNotify(self, signal: QMetaMethod)¶

createAndDisplayMeasurement¶

createPanel()¶: For advanced plots, creates an instance of a plot panel and returns it. For simple (panel-less) plots, returns None.

customEvent(self, a0: QEvent)¶

deleteLater(self)¶

deletePlot¶

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

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

disconnectNotify(self, signal: QMetaMethod)¶

displayAsl¶

displayFrameAndAsl¶

dumpObjectInfo(self)¶

dumpObjectTree(self)¶

dynamicPropertyNames(self) → List[QByteArray]¶

event(self, a0: QEvent) → bool¶

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

exportToCSV(parent=None)¶: Export plot data to a CSV file

exportToExcel(parent=None)¶: Export data to an .xls file

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]

generateASL(aids)¶

Generates an ASL string selecting given atom IDs.

Parameters: aids (Union[int, list(int)]) – Single atom id OR list of atom ids
Returns: ASL which selects given atoms.
Return type: str

generateSettingsHash(settings_list)¶

Return a tuple that uniquely identifies this plot.

Parameters: settings_list (list) – List of settings that can uniquely identify the plot. In addition to these, the plot class name and trajectory path will be added.
Returns: Unique identifier for the plot.
Return type: tuple

getExportData()¶: Most panels export the same data whether export was selected from the plot panel or the main panel. Override this method to export different type of data when exporting from the parent panel, via the “Export Results…” button.

getPlotTitle()¶

getSettingsHash()¶

inherits(self, classname: str) → bool¶

installEventFilter(self, a0: QObject)¶

isRunning()¶: Return True if the plot is still generating data.

isSignalConnected(self, signal: QMetaMethod) → bool¶

isWidgetType(self) → bool¶

isWindowType(self) → bool¶

killTimer(self, id: int)¶

metaObject(self) → QMetaObject¶

moveToThread(self, thread: QThread)¶

newDataAvailable¶

objectName(self) → str¶

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

parent(self) → QObject¶

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)¶

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setObjectName(self, name: str)¶

setParent(self, a0: QObject)¶

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

showContextMenu(parent=None)¶

showWarning¶

signalsBlocked(self) → bool¶

start()¶

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

staticMetaObject = <PyQt6.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, a0: QTimerEvent)¶

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