schrodinger.application.bioluminate.protein_structure_quality module

View the Ramachandran plot and Protein Report in a way that is interactive with the workspace. Operates on the workspace structure.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.bioluminate.protein_structure_quality.FakeMaestro

Bases: object

do_nothing(*args, **keyw)
command(astring)
workspace_get()
schrodinger.application.bioluminate.protein_structure_quality.maestro
schrodinger.application.bioluminate.protein_structure_quality.maestro_command(cmd)

Executes cmd as a maestro command and silenty ignores errors. Particularly useful when an ASL may not specify any atoms, which causes Maestro to throw an error even if we don’t care about it.

Parameters

cmd (str) – The maestro command to execute

class schrodinger.application.bioluminate.protein_structure_quality.DataModelWithChart(master)

Bases: schrodinger.application.bioluminate.protein_report_widget.DataModel

A subclass of DataModel that calls a sort callback when sorting

__init__(master)

Create a DataModel instance

data_column

The column that the data to plot is in

restrictByChains(chains)

Restricts the data in the model to the specified chains

Parameters

chains (list of str) – list of chain names (or ‘all’) to display

setData(*args)

Sets the internal data list to the specified list. NOTE: Will use the actual list passed to it (without making a copy)

Overrides the parent class method to store the a copy of the data in self.all_data, since the _data property can be mutated by the restrictByChains method.

Parameters

  • data_list (list) – the list of data for the model. Uses the actual list, not a copy

  • headers (list of str) – The column headers

headerData(section, orientation, role)

Returns the string that should be displayed in the specified header cell. Used by the View.

Parameters

  • section (int) – the row or column index requested

  • orientation (Qt.Orientation (Qt.Horizontal or Qt.Vertical)) – Whether this is for the horizontal or vertical header

  • role (Qt.ItemDataRole) – The data role to return - Qt.DisplayRole to return the text of the header.

Return type

str

Returns

the str representation for the requested header item

sort(*args)

Sort the table (see parent class for argument definition). In addition to sorting, the attribute self.sortCallback() will be called if it exists (with no arguments). This attribute must be set manually by the user.

class CheckIndexOption(value)

Bases: enum.Flag

An enumeration.

NoOption = 0
IndexIsValid = 1
DoNotUseParent = 2
ParentIsInvalid = 4
HorizontalSortHint = 2
class LayoutChangeHint(value)

Bases: enum.Enum

An enumeration.

NoLayoutChangeHint = 0
VerticalSortHint = 1
HorizontalSortHint = 2
NoLayoutChangeHint = 0
VerticalSortHint = 1
beginInsertColumns(self, parent: QModelIndex, first: int, last: int)
beginInsertRows(self, parent: QModelIndex, first: int, last: int)
beginMoveColumns(self, sourceParent: QModelIndex, sourceFirst: int, sourceLast: int, destinationParent: QModelIndex, destinationColumn: int) → bool
beginMoveRows(self, sourceParent: QModelIndex, sourceFirst: int, sourceLast: int, destinationParent: QModelIndex, destinationRow: int) → bool
beginRemoveColumns(self, parent: QModelIndex, first: int, last: int)
beginRemoveRows(self, parent: QModelIndex, first: int, last: int)
beginResetModel(self)
blockSignals(self, b: bool) → bool
buddy(self, index: QModelIndex) → QModelIndex
canDropMimeData(self, data: QMimeData, action: Qt.DropAction, row: int, column: int, parent: QModelIndex) → bool
canFetchMore(self, parent: QModelIndex) → bool
changePersistentIndex(self, from_: QModelIndex, to: QModelIndex)
changePersistentIndexList(self, from_: Iterable[QModelIndex], to: Iterable[QModelIndex])
checkIndex(self, index: QModelIndex, options: QAbstractItemModel.CheckIndexOption = QAbstractItemModel.CheckIndexOption.NoOption) → bool
childEvent(self, a0: QChildEvent)
children(self) → List[QObject]
clearItemData(self, index: QModelIndex) → bool
columnCount(parent=<PyQt6.QtCore.QModelIndex object>)

Returns number of columns

Parameters

parent (QtCore.QModelIndex) – unused

Return type

int

Returns

Number of rows

columnsAboutToBeInserted

columnsAboutToBeInserted(self, parent: QModelIndex, first: int, last: int) [signal]

columnsAboutToBeMoved

columnsAboutToBeMoved(self, sourceParent: QModelIndex, sourceStart: int, sourceEnd: int, destinationParent: QModelIndex, destinationColumn: int) [signal]

columnsAboutToBeRemoved

columnsAboutToBeRemoved(self, parent: QModelIndex, first: int, last: int) [signal]

columnsInserted

columnsInserted(self, parent: QModelIndex, first: int, last: int) [signal]

columnsMoved

columnsMoved(self, parent: QModelIndex, start: int, end: int, destination: QModelIndex, column: int) [signal]

columnsRemoved

columnsRemoved(self, parent: QModelIndex, first: int, last: int) [signal]

connectNotify(self, signal: QMetaMethod)
createIndex(self, row: int, column: int, object: object = 0) → QModelIndex
customEvent(self, a0: QEvent)
data(index, role=ItemDataRole.DisplayRole)

Given a cell index, returns the data that should be displayed in that cell. Used by the view.

Parameters

  • index (QtCore.QModelIndex) – index of the cell to return data for

  • role (Qt.ItemDataRole) – The data role to return

Returns

the requested data for the requested index

dataChanged

dataChanged(self, topLeft: QModelIndex, bottomRight: QModelIndex, roles: Iterable[int] = []) [signal]

decodeData(self, row: int, column: int, parent: QModelIndex, stream: QDataStream) → bool
deleteLater(self)
destroyed

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

disconnect(a0: QMetaObject.Connection) → bool
disconnect(self) → None
disconnectNotify(self, signal: QMetaMethod)
dropMimeData(self, data: QMimeData, action: Qt.DropAction, row: int, column: int, parent: QModelIndex) → bool
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
encodeData(self, indexes: Iterable[QModelIndex], stream: QDataStream)
endInsertColumns(self)
endInsertRows(self)
endMoveColumns(self)
endMoveRows(self)
endRemoveColumns(self)
endRemoveRows(self)
endResetModel(self)
event(self, a0: QEvent) → bool
eventFilter(self, a0: QObject, a1: QEvent) → bool
fetchMore(self, parent: QModelIndex)
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]
flags(self, index: QModelIndex) → Qt.ItemFlag
hasChildren(self, parent: QModelIndex = QModelIndex()) → bool
hasIndex(self, row: int, column: int, parent: QModelIndex = QModelIndex()) → bool
headerDataChanged

headerDataChanged(self, orientation: Qt.Orientation, first: int, last: int) [signal]

index(self, row: int, column: int, parent: QModelIndex = QModelIndex()) → QModelIndex
inherits(self, classname: str) → bool
insertColumn(self, column: int, parent: QModelIndex = QModelIndex()) → bool
insertColumns(self, column: int, count: int, parent: QModelIndex = QModelIndex()) → bool
insertRow(self, row: int, parent: QModelIndex = QModelIndex()) → bool
insertRows(self, row: int, count: int, parent: QModelIndex = QModelIndex()) → bool
installEventFilter(self, a0: QObject)
isSignalConnected(self, signal: QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
itemData(self, index: QModelIndex) → Dict[int, Any]
killTimer(self, id: int)
layoutAboutToBeChanged

layoutAboutToBeChanged(self, parents: Iterable[QPersistentModelIndex] = [], hint: QAbstractItemModel.LayoutChangeHint = QAbstractItemModel.NoLayoutChangeHint) [signal]

layoutChanged

layoutChanged(self, parents: Iterable[QPersistentModelIndex] = [], hint: QAbstractItemModel.LayoutChangeHint = QAbstractItemModel.NoLayoutChangeHint) [signal]

match(self, start: QModelIndex, role: int, value: Any, hits: int = 1, flags: Qt.MatchFlag = Qt.MatchFlags(Qt.MatchStartsWith | Qt.MatchWrap)) → List[QModelIndex]
metaObject(self) → QMetaObject
mimeData(self, indexes: Iterable[QModelIndex]) → QMimeData
mimeTypes(self) → List[str]
modelAboutToBeReset

modelAboutToBeReset(self) [signal]

modelReset

modelReset(self) [signal]

moveColumn(self, sourceParent: QModelIndex, sourceColumn: int, destinationParent: QModelIndex, destinationChild: int) → bool
moveColumns(self, sourceParent: QModelIndex, sourceColumn: int, count: int, destinationParent: QModelIndex, destinationChild: int) → bool
moveRow(self, sourceParent: QModelIndex, sourceRow: int, destinationParent: QModelIndex, destinationChild: int) → bool
moveRows(self, sourceParent: QModelIndex, sourceRow: int, count: int, destinationParent: QModelIndex, destinationChild: int) → bool
moveToThread(self, thread: QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

parent(self) → QObject
persistentIndexList(self) → List[QModelIndex]
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
removeColumn(self, column: int, parent: QModelIndex = QModelIndex()) → bool
removeColumns(self, column: int, count: int, parent: QModelIndex = QModelIndex()) → bool
removeEventFilter(self, a0: QObject)
removeRow(self, row: int, parent: QModelIndex = QModelIndex()) → bool
removeRows(self, row: int, count: int, parent: QModelIndex = QModelIndex()) → bool
resetInternalData(self)
revert(self)
roleNames(self) → Dict[int, QByteArray]
rowCount(parent=<PyQt6.QtCore.QModelIndex object>)

Returns number of rows

Parameters

parent (QtCore.QModelIndex) – unused

Return type

int

Returns

Number of rows

rowsAboutToBeInserted

rowsAboutToBeInserted(self, parent: QModelIndex, first: int, last: int) [signal]

rowsAboutToBeMoved

rowsAboutToBeMoved(self, sourceParent: QModelIndex, sourceStart: int, sourceEnd: int, destinationParent: QModelIndex, destinationRow: int) [signal]

rowsAboutToBeRemoved

rowsAboutToBeRemoved(self, parent: QModelIndex, first: int, last: int) [signal]

rowsInserted

rowsInserted(self, parent: QModelIndex, first: int, last: int) [signal]

rowsMoved

rowsMoved(self, parent: QModelIndex, start: int, end: int, destination: QModelIndex, row: int) [signal]

rowsRemoved

rowsRemoved(self, parent: QModelIndex, first: int, last: int) [signal]

sender(self) → QObject
senderSignalIndex(self) → int
setHeaderData(self, section: int, orientation: Qt.Orientation, value: Any, role: int = Qt.EditRole) → bool
setItemData(self, index: QModelIndex, roles: Dict[int, Any]) → bool
setObjectName(self, name: str)
setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) → bool
sibling(self, row: int, column: int, idx: QModelIndex) → QModelIndex
signalsBlocked(self) → bool
span(self, index: QModelIndex) → QSize
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
submit(self) → bool
supportedDragActions(self) → Qt.DropAction
supportedDropActions(self) → Qt.DropAction
thread(self) → QThread
timerEvent(self, a0: QTimerEvent)
tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str
class schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart(*args, **kwargs)

Bases: schrodinger.application.bioluminate.protein_report_widget.ReportFrame

A Protein Report widget that can deal with multiple protein structures and also has a slider chart that can be used to select residues.

__init__(*args, **kwargs)

Create the MultiReportWithChart object. See parent class for argument definition.

changeBFactorPlot()
toolbar_feedback_override(message)

Overrides the matplotlib toolbar set_message method to display the information in the first column of the row of the table that corresponds to the current X coordinate of the plot. This will usually be something like a residue name or atom name.

Parameters

message (str) – The string to be displayed in the toolbar. Will usually have x and y coordinates in the form of x=…. y=….

selectRows(rows)

Select the set of rows in the table given by the list rows

Parameters

rows (list) – list (or other iterable) of row numbers to select. Selection will be ONLY these rows - any previous selection is removed.

sliderMoved(slider)

Callback for when the user moves a slider on the sliderchart. Selects those rows of the table that are contained within the sliderchart box.

Parameters

slider (sliderchart.SlidableLine) – The line that was moved

setChanged(selected_title)

In addition to calling the parent class method, this also replots the sliderchart when the user selects a different set of data.

Parameters

selected_title (str) – The title of the new set of data

changeProtein(entry_id, chains='all')

Change the Protein whose data is displayed in the report widget & chart. If the protein has already been calculated, we just replace the Report Widget’s models with the models that contain the data for this protein. If this is a new protein, we run the report and store the data in the models.

Parameters

entry_id (str) – The entry ID of the new protein to display. Use None to clear the table and plot

getDataModelClass()

Returns the proper data model to use, allows easy subclassing of the Model in subclasses

Return type

QtCore.QAbstractTableModel class

Returns

The data model CLASS (not object) to use with this chart

updateTables(*args, **kwargs)

Calculate the data for the current protein and display it in the report widget & chart.

Parameters

entry_id (str) – The entry_id of the protein to calculate. None if the workspace structure should be used.

getSummaryData(chains='all')

Returns a dictionary with the summary data in it

Return type

dict

Returns

Dictionary with summary data

replotChart()

Replot the sliderchart with the current data

workspaceChanged(changed)

Override the parent routine to not change the syncd Value when Everything changes in the workspace, since that’s the signal that we’ve switched proteins, which we do on purpose.

Box = 1
DrawChildren = 2
DrawWindowBackground = 1
HLine = 4
IgnoreMask = 4
NoFrame = 0
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
Panel = 2
PdmDepth = 6
PdmDevicePixelRatio = 11
PdmDevicePixelRatioScaled = 12
PdmDpiX = 7
PdmDpiY = 8
PdmHeight = 2
PdmHeightMM = 4
PdmNumColors = 5
PdmPhysicalDpiX = 9
PdmPhysicalDpiY = 10
PdmWidth = 1
PdmWidthMM = 3
Plain = 16
Raised = 32
class RenderFlag(value)

Bases: enum.Flag

An enumeration.

DrawWindowBackground = 1
DrawChildren = 2
IgnoreMask = 4
class Shadow(value)

Bases: enum.IntEnum

An enumeration.

Plain = 16
Raised = 32
Sunken = 48
Shadow_Mask = 240
class Shape(value)

Bases: enum.IntEnum

An enumeration.

NoFrame = 0
Box = 1
Panel = 2
WinPanel = 3
HLine = 4
VLine = 5
StyledPanel = 6
Shape_Mask = 15
class StyleMask(value)

Bases: enum.Enum

An enumeration.

Shadow_Mask = 240
Shape_Mask = 15
StyledPanel = 6
Sunken = 48
VLine = 5
WinPanel = 3
acceptDrops(self) → bool
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
clear()

Clear the widget. Used by PrepWizard.

clearFocus(self)
clearMask(self)
close()

Close the frame, and clean up anything that needs to happen upon closing

closeEvent(self, a0: QCloseEvent)
closePanel()

Hide the panel

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)
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)
drawFrame(self, a0: QPainter)
dropEvent(self, a0: QDropEvent)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
effectiveWinId(self) → PyQt6.sip.voidptr
ensurePolished(self)
enterEvent(self, event: QEnterEvent)
event(self, e: QEvent) → bool
eventFilter(self, a0: QObject, a1: QEvent) → bool
exportAllTables()

Export all tables.

exportCurrentTable()

Export only the current table.

exportTables(filename, tables_to_write)

Export the specified tables to the <filename> file.

Parameters

  • filename (str) – the path to the output file

  • tables_to_write (str) – the name of the set of data to write out

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
frameGeometry(self) → QRect
frameRect(self) → QRect
frameShadow(self) → QFrame.Shadow
frameShape(self) → QFrame.Shape
frameSize(self) → QSize
frameStyle(self) → int
frameWidth(self) → int
geometry(self) → QRect
getSelectedDataTitles(model)

Returns a list of selected data titles (the value in the first column)

Parameters

model (DataModel) – The model the data comes from

Return type

list

Returns

list of data titles (the value in the first column) for each selected row

getStructure(entry_id=None)

Return the structure to report on.

Parameters

entry_id (str or None) – Entry ID of the structure to use, or None (default) if the workspace structure is to be used. If entry_id is given, the structure is taken from the project table row for that entry_id (which may be different from the current workspace structure). If entry_id is None, the workspace structure is used, but crystal structure properties are taken from the included project table row

Return type

schrodinger.structure.Structure

Returns

The structure requested

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)
inherits(self, classname: str) → bool
initPainter(self, painter: QPainter)
initStyleOption(self, option: QStyleOptionFrame)
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)
lineWidth(self) → int
locale(self) → QLocale
logicalDpiX(self) → int
logicalDpiY(self) → int
lower(self)
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
mask(self) → QRegion
maximumHeight(self) → int
maximumSize(self) → QSize
maximumWidth(self) → int
metaObject(self) → QMetaObject
metric(self, a0: QPaintDevice.PaintDeviceMetric) → int
midLineWidth(self) → int
minimumHeight(self) → int
minimumSize(self) → QSize
minimumSizeHint(self) → QSize
minimumWidth(self) → int
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]

openHelp()

Display the help topic

overrideWindowFlags(self, type: Qt.WindowType)
overrideWindowState(self, state: Qt.WindowState)
paintEngine(self) → QPaintEngine
paintEvent(self, a0: QPaintEvent)
paintingActive(self) → bool
palette(self) → QPalette
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.

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
resize(self, a0: QSize)
resize(self, w: int, h: int) → None
resizeEvent(self, a0: QResizeEvent)
restoreGeometry(self, geometry: QByteArray) → bool
saveGeometry(self) → QByteArray
screen(self) → QScreen
scroll(self, dx: int, dy: int)
scroll(self, dx: int, dy: int, a2: QRect) → None
selectionChangedCallback(selected=None, deselected=None)

Called when table selection is changed

Parameters

  • selected (QItemSelection) – Unused callback-required parameters

  • deselected (QItemSelection) – Unused callback-required parameters

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])
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)
setFrameRect(self, a0: QRect)
setFrameShadow(self, a0: QFrame.Shadow)
setFrameShape(self, a0: QFrame.Shape)
setFrameStyle(self, a0: int)
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)
setLineWidth(self, a0: int)
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)
setMidLineWidth(self, a0: int)
setMinimumHeight(self, minh: int)
setMinimumSize(self, minw: int, minh: int)
setMinimumSize(self, s: QSize) → None
setMinimumWidth(self, minw: int)
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)
setSets(all_titles, all_tooltips)

Populate the sets menu with the given items. Also takes in a list of tooltips, for each item.

Parameters

  • all_titles (list(str)) – List of item texts to add.

  • all_tooltips – List of tool tips for each item.

Type

all_tooltips: list(str)

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)
setWindowFilePath(self, filePath: str)
setWindowFlag(self, a0: Qt.WindowType, on: bool = True)
setWindowFlags(self, type: Qt.WindowType)
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)
sharedPainter(self) → QPainter
show(self)
showEvent(self, a0: QShowEvent)
showFullScreen(self)
showMaximized(self)
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
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.application.bioluminate.protein_structure_quality.HomologyRama(*args, **kwargs)

Bases: schrodinger.ui.qt.rama.Rama

A Ramachandran plot customized for the Protein Structure Quality Viewer

DEFAULT_MARKER_SIZE = 2.0
MARKER_SCALING_FACTOR = 1.0
PICK_RADIUS = 1.5
__init__(*args, **kwargs)

Create a HomologyRama object.

See parent class for argument documentation

change_current_pick(new_pick, multi=False)

React to picking a new point in the plot by changing the phi/psi counters if used and highlighting the selection in the workspace.

Parameters

new_pick (int) – the index of the picked point in self.dihedral_list

getCategory(xval, yval)

Get the favorable, allowed or disallowed status of a point

Parameters

  • xval (float) – the x value of the point

  • yval (float) – the y value of the point

Return type

str

Returns

one of HomologyRama.FAVORABLE, HomologyRama.ALLOWED, HomologyRama.DISALLOWED

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

Draw the various regions on the Ramachandran plot, and define the favorable, allowed and disallowed bins

recolorPlot(favorable, allowed, disallowed)

Change the color of the regions on the plot

Parameters

  • favorable (str) – matplotlib-recognized color string for the favorable regions

  • allowed (str) – matplotlib-recognized color string for the allowed regions

  • disallowed (str) – matplotlib-recognized color string for the disallowed regions

makeBinPoint(xval, yval)

Return the bottom left corner of a 10x10 degree patch of the plot that contains xval, yval

Parameters

  • xval (float) – the x value of the point

  • yval (float) – the y value of the point

Return type

tuple

Returns

(X, Y) of the bottom left corner of the patch that contains (xval, yval). Will be integer multiples of 10.

defineBins(allowed, favorable)

Define the 10x10 degree bins for what is allowed and what is favorable

Parameters

  • allowed (list) – matplotlib Polygon object defining an allowed region

  • favorable (list) – matplotlib Polygon object defining a favorable region

display_structure(ct, ca_list=None, chains='all')

Plot the dihedrals for a new structure

Parameters

  • ct (schrodinger.structure.Structure) – structure with dihedrals to plot

  • ca_list (list) – list of Calpha carbons to plot (default is all)

  • chains ('all' or list of str) – What chains to display, default is ‘all’, otherwise should be a list of chain names

updateScatterPlot()

Updates the plot to show the displayed structure. Overrides the parent class method in order to only show dihedrals from the specified chains.

find_closest_point(event)

Find the dihedral closes to the point (x, y). Overrides the parent class method in order to only choose points from the displayed chain.

Parameters

event (MouseEvent) – The matplotlib mouse event that generates this call

isInDisplayedChain(dihedral)

Returns True if the dihedral is from one of the displayed chains, False if not

Parameters

dihedral (rama.Rama.backbone_dihedral) – The object to test to see if it belongs to one of the displayed chains

Return type

bool

Returns

True if the dihedral is from one of the displayed chains, False if not

ALLOWED_COLOR = '#ffffe0'
CROSSHAIR_COLOR = '#cccccc'
CROSSHAIR_LINEWIDTH = 0.5
DATA_MAX = 180.0
DATA_MIN = -180.0
FAVORABLE_COLOR = '#ffa07a'
SPINBOX_ADJUST_THRESH = 0.049
TEXT_SIZE = 'small'
TICK_LABEL_SIZE = 'x-small'
TICK_SPACING = 30
adjust_phi(value)

React to changed value of the Phi spinbox

The method only makes sense with multiselect == False

Parameters

value (float) – new value of the spinbox

adjust_psi(value)

React to changed value of the Psi spinbox

The method only makes sense with multiselect == False

Parameters

value (float) – new value of the spinbox

adjust_symbol_size(value)
apply_dihedral(idihedral)

Change the value of a dihedral

Parameters

idihedral (int) – The index of the dihedral to change

clearGraph()

Gets called when project is closed

clear_selection(event)

Clear the selected points

Parameters

event (event or None) – The event that generated this call, or None if not being called as a response to an event. This parameter is unused.

display_residue(which='all')

Select residues in the workspace corresponding to the given points

Parameters

which (int, None or 'all') – If None, all residues are deselected. If an integer, that integer is taken as the index in the dihedral list to select. If ‘all’, residues for all selected points are selected.

drag(event)

As the user moves the mouse over a point, display information for that point in the toolbar and select the corresponding residue in the workspace.

Parameters

event (matplotlib MouseEvent) – The event that generated the call to this method.

draw_axes()
get_marker_color(idx: int) → str

Get the color to use for the scatterplot marker corresponding to dihedral idx.

get_picked()

Get the BackboneDihedral object for the selected dihedral that was most recently selected.

Return type

Optional[BackboneDihedral]

Returns

The BackboneDihedral object for the selected dihedral that was most recently selected, or None if there are no selected dihedrals.

get_residue_label(residue)

Format the label displayed in the toolbar for the currently moused-over residue.

Parameters

residue (Residue) – The residue to label

Return type

str

Returns

The label for the residue

options_quit()
pick_by_atom(iatom)
pick_by_point(event)
revert_to_original()

Set the current point to its original phi & psi values

This method only makes sense with multiselect == False

revert_to_saved()

Set the current point to its previously saved phi & psi values

This method only makes sense with multiselect == False

save()

Store the current phi & psi values of the current point.

This method only makes sense with multiselect == False

set_symbol_size(value=None)
setup_counters(layout)

Add additional widgets for angle manipulation to the layout

update_display()
update_point_faces(indexes)

Update the face colors for points on the plot - faster than doing a complete replot.

Parameters

indexes (list) – List of indexes to recolor. Should be the index of the point in the self.dihedral_list list

update_point_xval(index, xval)

Update the x-value of a point on the plot

Parameters

index (int) – The index of the point in the self.dihedral_list list

update_point_yval(index, yval)

Update the y-value of a point

Parameters

index (int) – The index of the point in the self.dihedral_list list

write_file(filename)
class schrodinger.application.bioluminate.protein_structure_quality.ProteinStructureQualityViewer(models=None)

Bases: schrodinger.ui.qt.appframework.AppFramework

The Main Panel Class

__init__(models=None)

Create a ProteinStructureQualityViewer instance

Parameters

models (list) – list of Homology models to view in the panel

toggleFavorable()

Refresh the workspace view when the user changes what regions to color

toggleAllowed()

Refresh the workspace view when the user changes what regions to color

toggleDisallowed()

Refresh the workspace view when the user changes what regions to color

loadModels(models=None)

Load the models into the viewer

Parameters

models (list or None) – list of Homology models to view in the panel, or None if the selected rows of the project table should be used.

changeModel()

Switch which model the panel is displaying data for

tabSelected(index)

When the user switches to the report tab, show everything as wire

Parameters

index (int) – The index of the current tab

showNewStructure(struct, chains='all')

Show data for a new structure in the Ramachandran plot

Parameters

  • struct (schrodinger.structure.Structure object) – The structure to display in the plot

  • chains (list or 'all') – list of chain names (or ‘all’) to display

changePreset(choice)

Change which preset set of appearances to use when modifying the workspace structure appearances based on the Ramachandran plot regions.

Parameters

choice (str) – Which preset set of appearances to use

updateWorkspaceView(all=False, favorable=False, allowed=False, disallowed=False)

Change the workspace appearance based on the Ramachandran plot regions

Parameters

  • all (bool) – If True, all residue appearances will be updated. False is default

  • favorable (bool) – If True, modify the appearance of residues in the favorable regions. If False, do not.

  • allowed (bool) – If True, modify the appearance of residues in the allowed regions. If False, do not.

  • disallowed (bool) – If True, modify the appearance of residues in the disallowed regions. If False, do not.

AllowNestedDocks = 2
AllowTabbedDocks = 4
AnimatedDocks = 1
class DockOption(value)

Bases: enum.Flag

An enumeration.

AnimatedDocks = 1
AllowNestedDocks = 2
AllowTabbedDocks = 4
ForceTabbedDocks = 8
VerticalTabs = 16
GroupedDragging = 32
DrawChildren = 2
DrawWindowBackground = 1
ForceTabbedDocks = 8
GroupedDragging = 32
IgnoreMask = 4
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
VerticalTabs = 16
acceptDrops(self) → bool
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])
addButtonToBottomLayout(text, command)

Adds a button to the bottom bar, to go to the right of Job Start buttons. Useful when you need a button on the bottom which is not standard job launching.

Buttons are added from left to right in the order that this function is called..

:param text text that goes on the button :type text str

:param command the slot that the button will run :param callable

Return type

str

Returns

name of button, to be used in setButtonEnabled

addCentralWidget(w)

Add a widget to the central area of the AppFramework dialog

addDockWidget(self, area: Qt.DockWidgetArea, dockwidget: QDockWidget)
addDockWidget(self, area: Qt.DockWidgetArea, dockwidget: QDockWidget, orientation: Qt.Orientation) → None
addToolBar(self, area: Qt.ToolBarArea, toolbar: QToolBar)
addToolBar(self, toolbar: QToolBar) → None
addToolBar(self, title: str) → QToolBar
addToolBarBreak(self, area: Qt.ToolBarArea = Qt.TopToolBarArea)
adjustSize(self)
askOverwrite(files=None, parent=None)

Display a dialog asking the user whether to overwrite existing files. Returns True if user chose to overwrite, False otherwise.

Optionally specify a list of files that will be overwritten if the user presses the Overwrite button.

askOverwriteIfNecessary(files)

If any of the files in the <files> list exists, will bring up a dialog box asking the user whether they want to overwrite them. Returns True if the user chose to overwrite or if specified files do not exist. Returns False if the user cancelled.

autoFillBackground(self) → bool
backgroundRole(self) → QPalette.ColorRole
baseSize(self) → QSize
blockSignals(self, b: bool) → bool
centralWidget(self) → QWidget
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)

Called by QApplication when the user clicked on the “x” button to close the window. Will call the user-specified close command (if specified).

closePanel()

Hide panel, if in Maestro. Otherwise close it.

colorCount(self) → int
connectNotify(self, signal: QMetaMethod)
contentsMargins(self) → QMargins
contentsRect(self) → QRect
contextMenuEvent(self, event: QContextMenuEvent)
contextMenuPolicy(self) → Qt.ContextMenuPolicy
corner(self, corner: Qt.Corner) → Qt.DockWidgetArea
create(self, window: PyQt6.sip.voidptr = 0, initializeWindow: bool = True, destroyOldWindow: bool = True)
createMenus(d)

Setup for making individual menus, create MainMenuBar.

createPopupMenu(self) → QMenu
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)
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)
dockOptions(self) → QMainWindow.DockOption
dockWidgetArea(self, dockwidget: QDockWidget) → Qt.DockWidgetArea
documentMode(self) → bool
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(text, preferences=None, key=None)

Display an error dialog with the specified text. If preferences and key are both supplied, then the dialog will contain a “Don’t show this again” checkbox. Future invocations of this dialog with the same preferences and key values will obey the user’s show preference.

Parameters

  • text (str) – The information to display in the dialog

  • preferences – obsolete; ignored.

  • key (str) – The key to store the preference under. If specified, a “Do not show again” checkbox will be rendered in the dialog box.

Return type

None

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

Calls exec() method of the application.

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
frameGeometry(self) → QRect
frameSize(self) → QSize
geometry(self) → QRect
getApp()

Return QApplication instance which this panel is running under. If in Maestro, returns Maestro’s global QApplication instance.

getInputFile()

Return the selected input file path (Python string).

If the panel has no input frame, raises RuntimeError. If FILE source is not allowed, raises RuntimeError.

getInputSource()

Return the selected input source. Available values (module constants):

  • WORKSPACE

  • SELECTED_ENTRIES

  • INCLUDED_ENTRIES

  • INCLUDED_ENTRY

  • FILE

If the panel has no input frame, raises RuntimeError.

getOpenFileName(caption='Select a file', initial_dir=None, support_mae=True, support_sd=True, support_pdb=True)

Brings up an open file dialog box for selecting structure files. By default reads Maestro, SD, and PDB formats. Returns file path that is readable by StructureReader. Is user pressed cancel, empty string is returned.

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
help()

Display the help dialog (or a warning dialog if no help can be found). This function requires help_topic to have been given when the class was initialized.

hide(self)
hideEvent(self, a0: QHideEvent)
iconSize(self) → QSize
iconSizeChanged

iconSizeChanged(self, iconSize: QSize) [signal]

info(text, preferences=None, key=None)

Display an information dialog with the specified text. If preferences and key are both supplied, then the dialog will contain a “Don’t show this again” checkbox. Future invocations of this dialog with the same preferences and key values will obey the user’s show preference.

Parameters

  • text (str) – The information to display in the dialog

  • preferences – obsolete; ignored.

  • key (str) – The key to store the preference under. If specified, a “Do not show again” checkbox will be rendered in the dialog box.

Return type

None

inherits(self, classname: str) → bool
initPainter(self, painter: QPainter)
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])
insertToolBar(self, before: QToolBar, toolbar: QToolBar)
insertToolBarBreak(self, before: QToolBar)
installEventFilter(self, a0: QObject)
interior()

Return the interior frame where client widgets should be parented from

isActiveWindow(self) → bool
isAncestorOf(self, child: QWidget) → bool
isAnimated(self) → bool
isDockNestingEnabled(self) → bool
isDockableInMaestro()

Returns True if the PyQt panel can be docked into Maestro mainwindow. Otherwise returns false. This function should be called only after parsing the ‘dockable’ argument inside the constructor.

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
isSeparator(self, pos: QPoint) → 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
jobCompleted
keyPressEvent(self, a0: QKeyEvent)
keyReleaseEvent(self, a0: QKeyEvent)
keyboardGrabber() → QWidget
killTimer(self, id: int)
launchJobCmd(cmd)

Launches job control command. Automatically tracked by the job status button (no need to call monitorJob method afterwards). NOTE: Unlike similar method in AF2, this method does not add -HOST etc options.

layout(self) → QLayout
layoutDirection(self) → Qt.LayoutDirection
leaveEvent(self, a0: QEvent)
locale(self) → QLocale
logicalDpiX(self) → int
logicalDpiY(self) → int
lower(self)
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
mask(self) → QRegion
maximumHeight(self) → int
maximumSize(self) → QSize
maximumWidth(self) → int
menuBar(self) → QMenuBar
menuWidget(self) → QWidget
metaObject(self) → QMetaObject
metric(self, a0: QPaintDevice.PaintDeviceMetric) → int
minimumHeight(self) → int
minimumSize(self) → QSize
minimumSizeHint(self) → QSize
minimumWidth(self) → int
monitorJob(jobid, showpanel=False)

Monitor the given jobid and show the monitor panel; if in maestro.

Parameters

  • jobid – jobid of the job to monitor

  • showpanel – whether to bring up the Monitor panel. By default, the panel will open if the “Open Monitor panel” preference is set.

Example, after launching the job, use the jobid to issue the command:

<AppFramework_instance>.monitorJob(<jobid>)
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, a0: QPaintEvent)
paintingActive(self) → bool
palette(self) → QPalette
parent(self) → QObject
parentWidget(self) → QWidget
physicalDpiX(self) → int
physicalDpiY(self) → int
pos(self) → QPoint
previousInFocusChain(self) → QWidget
processEvents()

Allow the QApplication’s or Maestro’s main event loop to process pending events.

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(msg, button1='OK', button2='Cancel', title='Question')

Display a prompt dialog window with specified text. Returns True if first button (default OK) is pressed, False otherwise.

quitPanel()

Quit the panel (even if in Maestro)

Note that the calling script needs to unset the variable that holds this panel instance in order to truly delete the panel. For example, this method should be subclassed as follows:

def quitPanel(self):

global mypanel # Where mypanel is the variable holding this object appframework.AppFramework.quitPanel(self) mypanel = None

raise_(self)
receivers(self, signal: PYQT_SIGNAL) → int
rect(self) → QRect
releaseKeyboard(self)
releaseMouse(self)
releaseShortcut(self, id: int)
removeAction(self, action: QAction)
removeDockWidget(self, dockwidget: QDockWidget)
removeEventFilter(self, a0: QObject)
removeToolBar(self, toolbar: QToolBar)
removeToolBarBreak(self, before: QToolBar)
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
resize(self, a0: QSize)
resize(self, w: int, h: int) → None
resizeDocks(self, docks: Iterable[QDockWidget], sizes: Iterable[int], orientation: Qt.Orientation)
resizeEvent(self, a0: QResizeEvent)
restoreCursor(app_wide=True)

Restore the application level cursor to the default. If ‘app_wide’ is True then if will be restored for the entire application, if it’s False, it will be just for this panel.

restoreDockWidget(self, dockwidget: QDockWidget) → bool
restoreGeometry(self, geometry: QByteArray) → bool
restoreState(self, state: QByteArray, version: int = 0) → bool
saveGeometry(self) → QByteArray
saveState(self, version: int = 0) → 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)
setAnimated(self, enabled: bool)
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
setButtonEnabled(button, enabled)

Enable / disable the specified button, e.g.,

self.setButtonEnabled(‘start’, False)

Raises a RuntimeError if the button doesn’t exist.

setButtonState(button, state)

Set the state of the specified button, e.g.,

self.setButtonState(‘start’, ‘disabled’)

The standard state is ‘normal’. Raises a RuntimeError if the button doesn’t exist or if the requested state can’t be set.

Obsolete. Please use setButtonEnabled() method instead.

setCentralWidget(self, widget: QWidget)
setContentsMargins(self, left: int, top: int, right: int, bottom: int)
setContentsMargins(self, margins: QMargins) → None
setContextMenuPolicy(self, policy: Qt.ContextMenuPolicy)
setCorner(self, corner: Qt.Corner, area: Qt.DockWidgetArea)
setCursor(self, a0: Union[QCursor, Qt.CursorShape])
setDisabled(self, a0: bool)
setDockNestingEnabled(self, enabled: bool)
setDockOptions(self, options: QMainWindow.DockOption)
setDocumentMode(self, enabled: 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)
setIconSize(self, iconSize: QSize)
setInputMethodHints(self, hints: Qt.InputMethodHint)
setJobname(jobname)
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)
setMenuBar(self, menubar: QMenuBar)
setMenuWidget(self, menubar: QWidget)
setMinimumHeight(self, minh: int)
setMinimumSize(self, minw: int, minh: int)
setMinimumSize(self, s: QSize) → None
setMinimumWidth(self, minw: int)
setMouseTracking(self, enable: bool)
setObjectName(self, name: str)
setPalette(self, a0: QPalette)
setParent(self, parent: QWidget)
setParent(self, parent: QWidget, f: Qt.WindowType) → None
setProgress(step, total_steps)

Set the progress bar value (bottom of the panel) to <step> out of <total_steps>

Set both to 0 to hide the progress bar.

setProgressError(error)

Set the color of the progress bar to red (error=True) or normal color (error=False).

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
setStatusBar(self, statusbar: QStatusBar)
setStatusTip(self, a0: str)
setStyle(self, a0: QStyle)
setStyleSheet(self, styleSheet: str)
setTabOrder(a0: QWidget, a1: QWidget)
setTabPosition(self, areas: Qt.DockWidgetArea, tabPosition: QTabWidget.TabPosition)
setTabShape(self, tabShape: QTabWidget.TabShape)
setTabletTracking(self, enable: bool)
setToolButtonStyle(self, toolButtonStyle: Qt.ToolButtonStyle)
setToolTip(self, a0: str)
setToolTipDuration(self, msec: int)
setUnifiedTitleAndToolBarOnMac(self, set: bool)
setUpdatesEnabled(self, enable: bool)
setVisible(self, visible: bool)
setWaitCursor(app_wide=True)

Set the cursor to the wait cursor. This will be an hourglass, clock or similar. Call restoreCursor() to return to the default cursor. If ‘app_wide’ is True then it will apply to the entire application (including Maestro if running there). If it’s False then it will apply only to this panel.

setWhatsThis(self, a0: str)
setWindowFilePath(self, filePath: str)
setWindowFlag(self, a0: Qt.WindowType, on: bool = True)
setWindowFlags(self, type: Qt.WindowType)
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)
setupJobParameters()

Setups up the job parameters from the state of the input frame. Do not call directly from your script.

Returns True if success, False on error (after displaying an error message).

sharedPainter(self) → QPainter
show(also_raise=True, also_activate=True)

Redefine the show() method to deiconize if necessary and also raise_() the panel if ‘also_raise’ is specified as True.

Parameters

  • also_raise (bool) – If True (default), the raise_ method will also be called on the window. If False it is not. This is important on some Window managers to ensure the window is placed on top of other windows.

  • also_activate (bool) – If True (default), the activateWindow method will also be called on the window. If False it is not. This is important on some Window managers to ensure the window is placed on top of other windows.

showEvent(show_event)

Override the normal processing when the panel is shown.

showFullScreen(self)
showMaximized(self)
showMinimized(self)
showNormal(self)
signalsBlocked(self) → bool
size(self) → QSize
sizeHint(self) → QSize
sizeIncrement(self) → QSize
sizePolicy(self) → QSizePolicy
splitDockWidget(self, after: QDockWidget, dockwidget: QDockWidget, orientation: Qt.Orientation)
stackUnder(self, a0: QWidget)
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
start_wrapper_timeout = 3000
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
statusBar(self) → QStatusBar
statusTip(self) → str
style(self) → QStyle
styleSheet(self) → str
tabPosition(self, area: Qt.DockWidgetArea) → QTabWidget.TabPosition
tabShape(self) → QTabWidget.TabShape
tabifiedDockWidgetActivated

tabifiedDockWidgetActivated(self, dockWidget: QDockWidget) [signal]

tabifiedDockWidgets(self, dockwidget: QDockWidget) → List[QDockWidget]
tabifyDockWidget(self, first: QDockWidget, second: QDockWidget)
tabletEvent(self, a0: QTabletEvent)
takeCentralWidget(self) → QWidget
testAttribute(self, attribute: Qt.WidgetAttribute) → bool
thread(self) → QThread
timerEvent(self, a0: QTimerEvent)
toolBarArea(self, toolbar: QToolBar) → Qt.ToolBarArea
toolBarBreak(self, toolbar: QToolBar) → bool
toolButtonStyle(self) → Qt.ToolButtonStyle
toolButtonStyleChanged

toolButtonStyleChanged(self, toolButtonStyle: Qt.ToolButtonStyle) [signal]

toolTip(self) → str
toolTipDuration(self) → int
tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str
trackJobProgress(job)

Display a progress dialog showing the progress of this job. (Any previously tracked job will no longer be tracked)

job - a jobcontrol.Job object.

underMouse(self) → bool
ungrabGesture(self, type: Qt.GestureType)
unifiedTitleAndToolBarOnMac(self) → bool
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)
updateJobname()

Update jobname in parameters from main window.

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

Updates the status bar.

updatesEnabled(self) → bool
visibleRegion(self) → QRegion
warning(text, preferences=None, key=None)

Display a warning dialog with the specified text. If preferences and key are both supplied, then the dialog will contain a “Don’t show this again” checkbox. Future invocations of this dialog with the same preferences and key values will obey the user’s show preference.

Parameters

  • text (str) – The information to display in the dialog

  • preferences – obsolete; ignored.

  • key (str) – The key to store the preference under. If specified, a “Do not show again” checkbox will be rendered in the dialog box.

Return type

None

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
null()