schrodinger.application.matsci.reordergui module

This module contains classes to enable use of the reorder module in a GUI.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.reordergui.StructureListWidget(master, atomic_constraints=None)

Bases: schrodinger.ui.qt.swidgets.SListWidget

A QListWidget that interacts with a structure picture to select atoms. Clicking on a row will send a signal that an atom has been clicked on. Atoms (rows) can be marked as Mapped or Unmapped, which will result in changing the background color of the row.

There is 1 row in in the ListWidget for each atom in the structure, in the same order as atoms are in the structure. Note that row indexes start at 0 but atom indexes start at 1, so we often have to add/subtract 1 to translate between the two.

atom_clicked

__init__(master, atomic_constraints=None)

Create a StructureListWidget instance

Parameters

• master (ReorderAtomFrame) – The mapping property of the master is used by some subclasses

• atomic_constraints (list or None) – list of atomic constraints for each atom or None

setStructure(struct)

Set the structure object for this widget and fill the widget

Parameters

struct (schrodinger.structure.Structure) – The structure object containing the data for this ListWidget

fill()

Fill the items in the ListWidget using the current structure

selectAtom(index)

Select the item that corresponds to the atom index

Parameters

index (int) – The index of atom whose item should be selected

itemSelected(row)

React to the user selecting an item in the ListWidget

Parameters

row (int) – The row of the item selected

parseAtomText(text)

Parse the given text into an element and atom index

Parameters

text (str) – String describing the atom such as C 13, H 1, etc. Also accepts strings for mapped atoms such as “C 13 - C 12”

Return type

(str, int)

Returns

The element and atom index specified by text

markAtomMapped(index, guess=False)

Mark the row for the given atom index as mapped

Parameters

• index (int) – Atom to mark

• guess (bool) – True if this mark results from a guess, False if not. The background color used depends on this parameter.

Return type

QListWidgetItem

Returns

The list widget item for the affected atom

markAtomUnmapped(index)

Mark the row for the given atom index as unmapped

Parameters

index (int) – Atom to mark

Return type

QListWidgetItem

Returns

The list widget item for the affected atom

getMarkedAtoms(guess=False)

Get atom indexes of marked atoms.

Parameters

guess (bool) – True if this mark results from a guess, False if not. The background color used depends on this parameter.

Return type

list(int)

Returns

Indexes of marked atoms

AboveItem = 1

Adjust = 1

AdjustIgnored = 0

AdjustToContents = 2

AdjustToContentsOnFirstShow = 1

AllEditTriggers = 31

AnimatingState = 6

AnyKeyPressed = 16

Batched = 1

BelowItem = 2

Box = 1

CollapsingState = 5

ContiguousSelection = 4

CurrentChanged = 1

class CursorAction(value)

Bases: enum.Enum

An enumeration.

MoveUp = 0

MoveDown = 1

MoveLeft = 2

MoveRight = 3

MoveHome = 4

MoveEnd = 5

MovePageUp = 6

MovePageDown = 7

MoveNext = 8

MovePrevious = 9

DoubleClicked = 2

DragDrop = 3

class DragDropMode(value)

Bases: enum.Enum

An enumeration.

NoDragDrop = 0

DragOnly = 1

DropOnly = 2

DragDrop = 3

InternalMove = 4

DragOnly = 1

DragSelectingState = 2

DraggingState = 1

DrawChildren = 2

DrawWindowBackground = 1

class DropIndicatorPosition(value)

Bases: enum.Enum

An enumeration.

OnItem = 0

AboveItem = 1

BelowItem = 2

OnViewport = 3

DropOnly = 2

EditKeyPressed = 8

class EditTrigger(value)

Bases: enum.Flag

An enumeration.

NoEditTriggers = 0

CurrentChanged = 1

DoubleClicked = 2

SelectedClicked = 4

EditKeyPressed = 8

AnyKeyPressed = 16

AllEditTriggers = 31

EditingState = 3

EnsureVisible = 0

ExpandingState = 4

ExtendedSelection = 3

Fixed = 0

class Flow(value)

Bases: enum.Enum

An enumeration.

LeftToRight = 0

TopToBottom = 1

Free = 1

HLine = 4

IconMode = 1

IgnoreMask = 4

InternalMove = 4

class LayoutMode(value)

Bases: enum.Enum

An enumeration.

SinglePass = 0

Batched = 1

LeftToRight = 0

ListMode = 0

MoveDown = 1

MoveEnd = 5

MoveHome = 4

MoveLeft = 2

MoveNext = 8

MovePageDown = 7

MovePageUp = 6

MovePrevious = 9

MoveRight = 3

MoveUp = 0

class Movement(value)

Bases: enum.Enum

An enumeration.

Static = 0

Free = 1

Snap = 2

MultiSelection = 2

NoDragDrop = 0

NoEditTriggers = 0

NoFrame = 0

NoSelection = 0

NoState = 0

OnItem = 0

OnViewport = 3

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

PositionAtBottom = 2

PositionAtCenter = 3

PositionAtTop = 1

Raised = 32

class RenderFlag(value)

Bases: enum.Flag

An enumeration.

DrawWindowBackground = 1

DrawChildren = 2

IgnoreMask = 4

class ResizeMode(value)

Bases: enum.Enum

An enumeration.

Fixed = 0

Adjust = 1

class ScrollHint(value)

Bases: enum.Enum

An enumeration.

EnsureVisible = 0

PositionAtTop = 1

PositionAtBottom = 2

PositionAtCenter = 3

class ScrollMode(value)

Bases: enum.Enum

An enumeration.

ScrollPerItem = 0

ScrollPerPixel = 1

ScrollPerItem = 0

ScrollPerPixel = 1

SelectColumns = 2

SelectItems = 0

SelectRows = 1

SelectedClicked = 4

class SelectionBehavior(value)

Bases: enum.Enum

An enumeration.

SelectItems = 0

SelectRows = 1

SelectColumns = 2

class SelectionMode(value)

Bases: enum.Enum

An enumeration.

NoSelection = 0

SingleSelection = 1

MultiSelection = 2

ExtendedSelection = 3

ContiguousSelection = 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

SinglePass = 0

SingleSelection = 1

class SizeAdjustPolicy(value)

Bases: enum.Enum

An enumeration.

AdjustIgnored = 0

AdjustToContentsOnFirstShow = 1

AdjustToContents = 2

Snap = 2

class State(value)

Bases: enum.Enum

An enumeration.

NoState = 0

DraggingState = 1

DragSelectingState = 2

EditingState = 3

ExpandingState = 4

CollapsingState = 5

AnimatingState = 6

Static = 0

class StyleMask(value)

Bases: enum.Enum

An enumeration.

Shadow_Mask = 240

Shape_Mask = 15

StyledPanel = 6

Sunken = 48

TopToBottom = 1

VLine = 5

class ViewMode(value)

Bases: enum.Enum

An enumeration.

ListMode = 0

IconMode = 1

WinPanel = 3

__len__()

Return len(self).

acceptDrops(self) → bool

accessibleDescription(self) → str

accessibleName(self) → str

actionEvent(self, a0: QActionEvent)

actions(self) → List[QAction]

activateWindow(self)

activated

activated(self, index: QModelIndex) [signal]

addAction(self, action: QAction)

addActions(self, actions: Iterable[QAction])

addItem(self, aitem: QListWidgetItem)

addItem(self, label: str) → None

addItems(self, labels: Iterable[str])

addScrollBarWidget(self, widget: QWidget, alignment: Qt.AlignmentFlag)

adjustSize(self)

allItems()

Return all the items in the list widget in order, including hidden ones

Return type

list

Returns

list of all QListWidgetItems in the list widget in order

allItemsIter(role=ItemDataRole.UserRole)

Return a generator over text and data of the list widget, inspired by .items() method of dict.

Parameters

role (int) – User role to pass do .data function

Return type

generator(tuple(str, type))

Returns

Generator over tupple of text and data of the list widget

allText()

Return the list of all text values, including hidden items

Return type

list

Returns

List of strings

alternatingRowColors(self) → bool

autoFillBackground(self) → bool

autoScrollMargin(self) → int

backgroundRole(self) → QPalette.ColorRole

baseSize(self) → QSize

batchSize(self) → int

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(self)

clearFocus(self)

clearMask(self)

clearPropertyFlags(self)

clearSelection(self)

clicked

clicked(self, index: QModelIndex) [signal]

close(self) → bool

closeEditor(self, editor: QWidget, hint: QAbstractItemDelegate.EndEditHint)

closeEvent(self, a0: QCloseEvent)

closePersistentEditor(self, item: QListWidgetItem)

colorCount(self) → int

commitData(self, editor: QWidget)

connectNotify(self, signal: QMetaMethod)

contentsMargins(self) → QMargins

contentsRect(self) → QRect

contextMenuEvent(self, a0: QContextMenuEvent)

contextMenuPolicy(self) → Qt.ContextMenuPolicy

cornerWidget(self) → QWidget

count(self) → int

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

currentChanged(self, current: QModelIndex, previous: QModelIndex)

currentIndex(self) → QModelIndex

currentItem(self) → QListWidgetItem

currentItemChanged

currentItemChanged(self, current: QListWidgetItem, previous: QListWidgetItem) [signal]

currentRow(self) → int

currentRowChanged

currentRowChanged(self, currentRow: int) [signal]

currentTextChanged

currentTextChanged(self, currentText: str) [signal]

cursor(self) → QCursor

customContextMenuRequested

customContextMenuRequested(self, pos: QPoint) [signal]

customEvent(self, a0: QEvent)

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

defaultDropAction(self) → Qt.DropAction

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

dirtyRegionOffset(self) → QPoint

disconnect(a0: QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, signal: QMetaMethod)

doubleClicked

doubleClicked(self, index: QModelIndex) [signal]

dragDropMode(self) → QAbstractItemView.DragDropMode

dragDropOverwriteMode(self) → bool

dragEnabled(self) → bool

dragEnterEvent(self, e: QDragEnterEvent)

dragLeaveEvent(self, e: QDragLeaveEvent)

dragMoveEvent(self, e: QDragMoveEvent)

drawFrame(self, a0: QPainter)

dropEvent(self, event: QDropEvent)

dropIndicatorPosition(self) → QAbstractItemView.DropIndicatorPosition

dropMimeData(self, index: int, data: QMimeData, action: Qt.DropAction) → bool

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

edit(self, index: QModelIndex)

edit(self, index: QModelIndex, trigger: QAbstractItemView.EditTrigger, event: QEvent) → bool

editItem(self, item: QListWidgetItem)

editTriggers(self) → QAbstractItemView.EditTrigger

editorDestroyed(self, editor: QObject)

effectiveWinId(self) → PyQt6.sip.voidptr

ensurePolished(self)

enterEvent(self, event: QEnterEvent)

entered

entered(self, index: QModelIndex) [signal]

event(self, e: QEvent) → bool

eventFilter(self, object: QObject, event: QEvent) → bool

executeDelayedItemsLayout(self)

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]

findItems(self, text: str, flags: Qt.MatchFlag) → List[QListWidgetItem]

flow(self) → QListView.Flow

focusInEvent(self, e: QFocusEvent)

focusNextChild(self) → bool

focusNextPrevChild(self, next: bool) → bool

focusOutEvent(self, e: 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

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

gridSize(self) → QSize

hasAutoScroll(self) → bool

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)

horizontalOffset(self) → int

horizontalScrollBar(self) → QScrollBar

horizontalScrollBarPolicy(self) → Qt.ScrollBarPolicy

horizontalScrollMode(self) → QAbstractItemView.ScrollMode

horizontalScrollbarAction(self, action: int)

horizontalScrollbarValueChanged(self, value: int)

iconSize(self) → QSize

iconSizeChanged

iconSizeChanged(self, size: QSize) [signal]

indexAt(self, p: QPoint) → QModelIndex

indexFromItem(self, item: QListWidgetItem) → QModelIndex

indexWidget(self, index: QModelIndex) → QWidget

indexesMoved

indexesMoved(self, indexes: Iterable[QModelIndex]) [signal]

inherits(self, classname: str) → bool

initPainter(self, painter: QPainter)

initStyleOption(self, option: QStyleOptionFrame)

initViewItemOption(self, option: QStyleOptionViewItem)

inputMethodEvent(self, event: QInputMethodEvent)

inputMethodHints(self) → Qt.InputMethodHint

inputMethodQuery(self, query: Qt.InputMethodQuery) → Any

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

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

insertItem(self, row: int, item: QListWidgetItem)

insertItem(self, row: int, label: str) → None

insertItems(self, row: int, labels: Iterable[str])

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

isIndexHidden(self, index: QModelIndex) → bool

isLeftToRight(self) → bool

isMaximized(self) → bool

isMinimized(self) → bool

isModal(self) → bool

isPersistentEditorOpen(self, item: QListWidgetItem) → bool

isRightToLeft(self) → bool

isRowHidden(self, row: int) → bool

isSelectionRectVisible(self) → bool

isSignalConnected(self, signal: QMetaMethod) → bool

isSortingEnabled(self) → bool

isVisible(self) → bool

isVisibleTo(self, a0: QWidget) → bool

isWidgetType(self) → bool

isWindow(self) → bool

isWindowModified(self) → bool

isWindowType(self) → bool

isWrapping(self) → bool

item(self, row: int) → QListWidgetItem

itemActivated

itemActivated(self, item: QListWidgetItem) [signal]

itemAlignment(self) → Qt.AlignmentFlag

itemAt(self, p: QPoint) → QListWidgetItem

itemAt(self, ax: int, ay: int) → QListWidgetItem

itemChanged

itemChanged(self, item: QListWidgetItem) [signal]

itemClicked

itemClicked(self, item: QListWidgetItem) [signal]

itemDelegate(self) → QAbstractItemDelegate

itemDelegateForColumn(self, column: int) → QAbstractItemDelegate

itemDelegateForIndex(self, index: QModelIndex) → QAbstractItemDelegate

itemDelegateForRow(self, row: int) → QAbstractItemDelegate

itemDoubleClicked

itemDoubleClicked(self, item: QListWidgetItem) [signal]

itemEntered

itemEntered(self, item: QListWidgetItem) [signal]

itemFromIndex(self, index: QModelIndex) → QListWidgetItem

itemPressed

itemPressed(self, item: QListWidgetItem) [signal]

itemSelectionChanged

itemSelectionChanged(self) [signal]

itemWidget(self, item: QListWidgetItem) → QWidget

items(self, data: QMimeData) → List[QListWidgetItem]

keyPressEvent(self, e: QKeyEvent)

keyReleaseEvent(self, a0: QKeyEvent)

keyboardGrabber() → QWidget

keyboardSearch(self, search: str)

killTimer(self, id: int)

layout(self) → QLayout

layoutDirection(self) → Qt.LayoutDirection

layoutMode(self) → QListView.LayoutMode

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

maximumViewportSize(self) → QSize

maximumWidth(self) → int

metaObject(self) → QMetaObject

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

midLineWidth(self) → int

mimeData(self, items: Iterable[QListWidgetItem]) → QMimeData

mimeTypes(self) → List[str]

minimumHeight(self) → int

minimumSize(self) → QSize

minimumSizeHint(self) → QSize

minimumWidth(self) → int

model(self) → QAbstractItemModel

modelColumn(self) → int

mouseDoubleClickEvent(self, e: QMouseEvent)

mouseGrabber() → QWidget

mouseMoveEvent(self, e: QMouseEvent)

mousePressEvent(self, e: QMouseEvent)

mouseReleaseEvent(self, e: QMouseEvent)

move(self, a0: QPoint)

move(self, ax: int, ay: int) → None

moveCursor(self, cursorAction: QAbstractItemView.CursorAction, modifiers: Qt.KeyboardModifier) → QModelIndex

moveEvent(self, a0: QMoveEvent)

moveToThread(self, thread: QThread)

movement(self) → QListView.Movement

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]

openPersistentEditor(self, item: QListWidgetItem)

overrideWindowFlags(self, type: Qt.WindowType)

overrideWindowState(self, state: Qt.WindowState)

paintEngine(self) → QPaintEngine

paintEvent(self, e: QPaintEvent)

paintingActive(self) → bool

palette(self) → QPalette

parent(self) → QObject

parentWidget(self) → QWidget

physicalDpiX(self) → int

physicalDpiY(self) → int

pos(self) → QPoint

pressed

pressed(self, index: QModelIndex) [signal]

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

rectForIndex(self, index: QModelIndex) → QRect

releaseKeyboard(self)

releaseMouse(self)

releaseShortcut(self, id: int)

removeAction(self, action: QAction)

removeEventFilter(self, a0: QObject)

removeItem(item)

Removes and returns the given item

Parameters

item (QListWidgetItem or 0) – The item to be removed from the list widget or 0 if it is not found in the list widget

removeItemByText(text)

Removes and returns the item with the given text

Parameters

text (str) – the text of the item to be removed

Return type

QListWidgetItem or None

Returns

The removed item, or None if an item with the given text is not found.

removeItemWidget(self, aItem: QListWidgetItem)

removeSelectedItems()

Removes selected items.

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

reset(self)

resetHorizontalScrollMode(self)

resetVerticalScrollMode(self)

resize(self, a0: QSize)

resize(self, w: int, h: int) → None

resizeEvent(self, e: QResizeEvent)

resizeMode(self) → QListView.ResizeMode

restoreGeometry(self, geometry: QByteArray) → bool

rootIndex(self) → QModelIndex

row(self, item: QListWidgetItem) → int

rowByText(text, match=MatchFlag.MatchExactly)

Returns the row that a given text is in. Also accounts for hidden items.

Parameters

• text (str) – The text to find

• match (Qt.MatchFlag) – Type of match to search for - default is exact

Return type

int or False

Returns

Row that holds matched text (can be 0), if text is not matched, returns False

rowsAboutToBeRemoved(self, parent: QModelIndex, start: int, end: int)

rowsInserted(self, parent: QModelIndex, start: int, end: int)

saveGeometry(self) → QByteArray

scheduleDelayedItemsLayout(self)

screen(self) → QScreen

scroll(self, dx: int, dy: int)

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

scrollBarWidgets(self, alignment: Qt.AlignmentFlag) → List[QWidget]

scrollContentsBy(self, dx: int, dy: int)

scrollDirtyRegion(self, dx: int, dy: int)

scrollTo(self, index: QModelIndex, hint: QAbstractItemView.ScrollHint = QAbstractItemView.EnsureVisible)

scrollToBottom(self)

scrollToItem(self, item: QListWidgetItem, hint: QAbstractItemView.ScrollHint = QAbstractItemView.EnsureVisible)

scrollToTop(self)

selectAll(self)

selectedIndexes(self) → List[QModelIndex]

selectedItems(self) → List[QListWidgetItem]

selectedText()

Return the list of selected text values, including those of hidden items

Return type

list

Returns

List of strings, each member is the text of a selected item

selectionBehavior(self) → QAbstractItemView.SelectionBehavior

selectionChanged(self, selected: QItemSelection, deselected: QItemSelection)

selectionCommand(self, index: QModelIndex, event: typing.Optional[QEvent] = None) → QItemSelectionModel.SelectionFlag

selectionMode(self) → QAbstractItemView.SelectionMode

selectionModel(self) → QItemSelectionModel

sender(self) → QObject

senderSignalIndex(self) → int

setAcceptDrops(self, on: bool)

setAccessibleDescription(self, description: str)

setAccessibleName(self, name: str)

setAlternatingRowColors(self, enable: bool)

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

setAutoFillBackground(self, enabled: bool)

setAutoScroll(self, enable: bool)

setAutoScrollMargin(self, margin: int)

setBackgroundRole(self, a0: QPalette.ColorRole)

setBaseSize(self, basew: int, baseh: int)

setBaseSize(self, s: QSize) → None

setBatchSize(self, batchSize: int)

setContentsMargins(self, left: int, top: int, right: int, bottom: int)

setContentsMargins(self, margins: QMargins) → None

setContextMenuPolicy(self, policy: Qt.ContextMenuPolicy)

setCornerWidget(self, widget: QWidget)

setCurrentIndex(self, index: QModelIndex)

setCurrentItem(self, item: QListWidgetItem)

setCurrentItem(self, item: QListWidgetItem, command: QItemSelectionModel.SelectionFlag) → None

setCurrentRow(self, row: int)

setCurrentRow(self, row: int, command: QItemSelectionModel.SelectionFlag) → None

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

setDefaultDropAction(self, dropAction: Qt.DropAction)

setDirtyRegion(self, region: QRegion)

setDisabled(self, a0: bool)

setDragDropMode(self, behavior: QAbstractItemView.DragDropMode)

setDragDropOverwriteMode(self, overwrite: bool)

setDragEnabled(self, enable: bool)

setDropIndicatorShown(self, enable: bool)

setEditTriggers(self, triggers: QAbstractItemView.EditTrigger)

setEnabled(self, a0: bool)

setFixedHeight(self, h: int)

setFixedSize(self, a0: QSize)

setFixedSize(self, w: int, h: int) → None

setFixedWidth(self, w: int)

setFlow(self, flow: QListView.Flow)

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)

setGridSize(self, size: QSize)

setHidden(self, hidden: bool)

setHorizontalScrollBar(self, scrollbar: QScrollBar)

setHorizontalScrollBarPolicy(self, a0: Qt.ScrollBarPolicy)

setHorizontalScrollMode(self, mode: QAbstractItemView.ScrollMode)

setIconSize(self, size: QSize)

setIndexWidget(self, index: QModelIndex, widget: QWidget)

setInputMethodHints(self, hints: Qt.InputMethodHint)

setItemAlignment(self, alignment: Qt.AlignmentFlag)

setItemDelegate(self, delegate: QAbstractItemDelegate)

setItemDelegateForColumn(self, column: int, delegate: QAbstractItemDelegate)

setItemDelegateForRow(self, row: int, delegate: QAbstractItemDelegate)

setItemWidget(self, item: QListWidgetItem, widget: QWidget)

setLayout(self, a0: QLayout)

setLayoutDirection(self, direction: Qt.LayoutDirection)

setLayoutMode(self, mode: QListView.LayoutMode)

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)

setModel(self, model: QAbstractItemModel)

setModelColumn(self, column: int)

setMouseTracking(self, enable: bool)

setMovement(self, movement: QListView.Movement)

setObjectName(self, name: str)

setPalette(self, a0: QPalette)

setParent(self, parent: QWidget)

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

setPositionForIndex(self, position: QPoint, index: QModelIndex)

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

setResizeMode(self, mode: QListView.ResizeMode)

setRootIndex(self, index: QModelIndex)

setRowHidden(self, row: int, hide: bool)

setScreen(self, a0: QScreen)

setSelection(self, rect: QRect, command: QItemSelectionModel.SelectionFlag)

setSelectionBehavior(self, behavior: QAbstractItemView.SelectionBehavior)

setSelectionMode(self, mode: QAbstractItemView.SelectionMode)

setSelectionModel(self, selectionModel: QItemSelectionModel)

setSelectionRectVisible(self, show: bool)

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

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

setSizeAdjustPolicy(self, policy: QAbstractScrollArea.SizeAdjustPolicy)

setSizeIncrement(self, w: int, h: int)

setSizeIncrement(self, s: QSize) → None

setSizePolicy(self, a0: QSizePolicy)

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

setSortingEnabled(self, enable: bool)

setSpacing(self, space: int)

setState(self, state: QAbstractItemView.State)

setStatusTip(self, a0: str)

setStyle(self, a0: QStyle)

setStyleSheet(self, styleSheet: str)

setTabKeyNavigation(self, enable: bool)

setTabOrder(a0: QWidget, a1: QWidget)

setTabletTracking(self, enable: bool)

setTextElideMode(self, mode: Qt.TextElideMode)

setTextSelected(text, selected=True)

Selects the item with the given text. Will select hidden items too.

Parameters

• text (str) – the text of the item to be selected

• selected (bool) – True if the item should be selected, False if it should be deselected.

Return type

bool

Returns

True if an item with the given text is found, False if not

setToolTip(self, a0: str)

setToolTipDuration(self, msec: int)

setUniformItemSizes(self, enable: bool)

setUpdatesEnabled(self, enable: bool)

setVerticalScrollBar(self, scrollbar: QScrollBar)

setVerticalScrollBarPolicy(self, a0: Qt.ScrollBarPolicy)

setVerticalScrollMode(self, mode: QAbstractItemView.ScrollMode)

setViewMode(self, mode: QListView.ViewMode)

setViewport(self, widget: QWidget)

setViewportMargins(self, left: int, top: int, right: int, bottom: int)

setViewportMargins(self, margins: QMargins) → None

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)

setWordWrap(self, on: bool)

setWrapping(self, enable: bool)

setupViewport(self, viewport: QWidget)

sharedPainter(self) → QPainter

show(self)

showDropIndicator(self) → bool

showEvent(self, a0: QShowEvent)

showFullScreen(self)

showMaximized(self)

showMinimized(self)

showNormal(self)

signalsBlocked(self) → bool

size(self) → QSize

sizeAdjustPolicy(self) → QAbstractScrollArea.SizeAdjustPolicy

sizeHint(self) → QSize

sizeHintForColumn(self, column: int) → int

sizeHintForIndex(self, index: QModelIndex) → QSize

sizeHintForRow(self, row: int) → int

sizeIncrement(self) → QSize

sizePolicy(self) → QSizePolicy

sortItems(self, order: Qt.SortOrder = Qt.AscendingOrder)

spacing(self) → int

stackUnder(self, a0: QWidget)

startDrag(self, supportedActions: Qt.DropAction)

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

state(self) → QAbstractItemView.State

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

statusTip(self) → str

style(self) → QStyle

styleSheet(self) → str

supportedDropActions(self) → Qt.DropAction

tabKeyNavigation(self) → bool

tabletEvent(self, a0: QTabletEvent)

takeItem(self, row: int) → QListWidgetItem

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

textElideMode(self) → Qt.TextElideMode

thread(self) → QThread

timerEvent(self, e: 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)

uniformItemSizes(self) → bool

unsetCursor(self)

unsetLayoutDirection(self)

unsetLocale(self)

update(self)

update(self, index: QModelIndex) → None

updateEditorData(self)

updateEditorGeometries(self)

updateGeometries(self)

updateGeometry(self)

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

updatesEnabled(self) → bool

verticalOffset(self) → int

verticalScrollBar(self) → QScrollBar

verticalScrollBarPolicy(self) → Qt.ScrollBarPolicy

verticalScrollMode(self) → QAbstractItemView.ScrollMode

verticalScrollbarAction(self, action: int)

verticalScrollbarValueChanged(self, value: int)

viewMode(self) → QListView.ViewMode

viewport(self) → QWidget

viewportEntered

viewportEntered(self) [signal]

viewportEvent(self, e: QEvent) → bool

viewportMargins(self) → QMargins

viewportSizeHint(self) → QSize

visibleRegion(self) → QRegion

visualItemRect(self, item: QListWidgetItem) → QRect

visualRect(self, index: QModelIndex) → QRect

visualRegionForSelection(self, selection: QItemSelection) → QRegion

whatsThis(self) → str

wheelEvent(self, e: 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

wordWrap(self) → bool

x(self) → int

y(self) → int

class schrodinger.application.matsci.reordergui.ComparisonListWidget(*args, **kwargs)

Bases: schrodinger.application.matsci.reordergui.StructureListWidget

The list widget for the Comparison structure.

__init__(*args, **kwargs)

See parent method for the documentation. Here defaults are set.

getAtomText(atom)

Get the text to display in a row of the ListWidget

The atom text for an item is just the atom element plus index

Parameters

atom (int or _StructureAtom) – A reference to the atom to create text for

Return type

str

Returns

The text to display for this atom

markAtomMapped(index, guess=False)

Mark the row for the given atom index as mapped

Adds to the parent method by deselecting the row

Parameters

• index (int) – Atom to mark

• guess (bool) – True if this mark results from a guess, False if not. The background color used depends on this parameter.

Return type

QListWidgetItem

Returns

The list widget item for the affected atom

markSuggestedAtom(index)

Mark foreground of the suggested atom item with SUGGEST_COLOR, previously suggested atom with BLACK.

Parameters

index (int) – Atom to mark

AboveItem = 1

Adjust = 1

AdjustIgnored = 0

AdjustToContents = 2

AdjustToContentsOnFirstShow = 1

AllEditTriggers = 31

AnimatingState = 6

AnyKeyPressed = 16

Batched = 1

BelowItem = 2

Box = 1

CollapsingState = 5

ContiguousSelection = 4

CurrentChanged = 1

class CursorAction(value)

Bases: enum.Enum

An enumeration.

MoveUp = 0

MoveDown = 1

MoveLeft = 2

MoveRight = 3

MoveHome = 4

MoveEnd = 5

MovePageUp = 6

MovePageDown = 7

MoveNext = 8

MovePrevious = 9

DoubleClicked = 2

DragDrop = 3

class DragDropMode(value)

Bases: enum.Enum

An enumeration.

NoDragDrop = 0

DragOnly = 1

DropOnly = 2

DragDrop = 3

InternalMove = 4

DragOnly = 1

DragSelectingState = 2

DraggingState = 1

DrawChildren = 2

DrawWindowBackground = 1

class DropIndicatorPosition(value)

Bases: enum.Enum

An enumeration.

OnItem = 0

AboveItem = 1

BelowItem = 2

OnViewport = 3

DropOnly = 2

EditKeyPressed = 8

class EditTrigger(value)

Bases: enum.Flag

An enumeration.

NoEditTriggers = 0

CurrentChanged = 1

DoubleClicked = 2

SelectedClicked = 4

EditKeyPressed = 8

AnyKeyPressed = 16

AllEditTriggers = 31

EditingState = 3

EnsureVisible = 0

ExpandingState = 4

ExtendedSelection = 3

Fixed = 0

class Flow(value)

Bases: enum.Enum

An enumeration.

LeftToRight = 0

TopToBottom = 1

Free = 1

HLine = 4

IconMode = 1

IgnoreMask = 4

InternalMove = 4

class LayoutMode(value)

Bases: enum.Enum

An enumeration.

SinglePass = 0

Batched = 1

LeftToRight = 0

ListMode = 0

MoveDown = 1

MoveEnd = 5

MoveHome = 4

MoveLeft = 2

MoveNext = 8

MovePageDown = 7

MovePageUp = 6

MovePrevious = 9

MoveRight = 3

MoveUp = 0

class Movement(value)

Bases: enum.Enum

An enumeration.

Static = 0

Free = 1

Snap = 2

MultiSelection = 2

NoDragDrop = 0

NoEditTriggers = 0

NoFrame = 0

NoSelection = 0

NoState = 0

OnItem = 0

OnViewport = 3

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

PositionAtBottom = 2

PositionAtCenter = 3

PositionAtTop = 1

Raised = 32

class RenderFlag(value)

Bases: enum.Flag

An enumeration.

DrawWindowBackground = 1

DrawChildren = 2

IgnoreMask = 4

class ResizeMode(value)

Bases: enum.Enum

An enumeration.

Fixed = 0

Adjust = 1

class ScrollHint(value)

Bases: enum.Enum

An enumeration.

EnsureVisible = 0

PositionAtTop = 1

PositionAtBottom = 2

PositionAtCenter = 3

class ScrollMode(value)

Bases: enum.Enum

An enumeration.

ScrollPerItem = 0

ScrollPerPixel = 1

ScrollPerItem = 0

ScrollPerPixel = 1

SelectColumns = 2

SelectItems = 0

SelectRows = 1

SelectedClicked = 4

class SelectionBehavior(value)

Bases: enum.Enum

An enumeration.

SelectItems = 0

SelectRows = 1

SelectColumns = 2

class SelectionMode(value)

Bases: enum.Enum

An enumeration.

NoSelection = 0

SingleSelection = 1

MultiSelection = 2

ExtendedSelection = 3

ContiguousSelection = 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

SinglePass = 0

SingleSelection = 1

class SizeAdjustPolicy(value)

Bases: enum.Enum

An enumeration.

AdjustIgnored = 0

AdjustToContentsOnFirstShow = 1

AdjustToContents = 2

Snap = 2

class State(value)

Bases: enum.Enum

An enumeration.

NoState = 0

DraggingState = 1

DragSelectingState = 2

EditingState = 3

ExpandingState = 4

CollapsingState = 5

AnimatingState = 6

Static = 0

class StyleMask(value)

Bases: enum.Enum

An enumeration.

Shadow_Mask = 240

Shape_Mask = 15

StyledPanel = 6

Sunken = 48

TopToBottom = 1

VLine = 5

class ViewMode(value)

Bases: enum.Enum

An enumeration.

ListMode = 0

IconMode = 1

WinPanel = 3

__len__()

Return len(self).

acceptDrops(self) → bool

accessibleDescription(self) → str

accessibleName(self) → str

actionEvent(self, a0: QActionEvent)

actions(self) → List[QAction]

activateWindow(self)

activated

activated(self, index: QModelIndex) [signal]

addAction(self, action: QAction)

addActions(self, actions: Iterable[QAction])

addItem(self, aitem: QListWidgetItem)

addItem(self, label: str) → None

addItems(self, labels: Iterable[str])

addScrollBarWidget(self, widget: QWidget, alignment: Qt.AlignmentFlag)

adjustSize(self)

allItems()

Return all the items in the list widget in order, including hidden ones

Return type

list

Returns

list of all QListWidgetItems in the list widget in order

allItemsIter(role=ItemDataRole.UserRole)

Return a generator over text and data of the list widget, inspired by .items() method of dict.

Parameters

role (int) – User role to pass do .data function

Return type

generator(tuple(str, type))

Returns

Generator over tupple of text and data of the list widget

allText()

Return the list of all text values, including hidden items

Return type

list

Returns

List of strings

alternatingRowColors(self) → bool

atom_clicked

autoFillBackground(self) → bool

autoScrollMargin(self) → int

backgroundRole(self) → QPalette.ColorRole

baseSize(self) → QSize

batchSize(self) → int

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(self)

clearFocus(self)

clearMask(self)

clearPropertyFlags(self)

clearSelection(self)

clicked

clicked(self, index: QModelIndex) [signal]

close(self) → bool

closeEditor(self, editor: QWidget, hint: QAbstractItemDelegate.EndEditHint)

closeEvent(self, a0: QCloseEvent)

closePersistentEditor(self, item: QListWidgetItem)

colorCount(self) → int

commitData(self, editor: QWidget)

connectNotify(self, signal: QMetaMethod)

contentsMargins(self) → QMargins

contentsRect(self) → QRect

contextMenuEvent(self, a0: QContextMenuEvent)

contextMenuPolicy(self) → Qt.ContextMenuPolicy

cornerWidget(self) → QWidget

count(self) → int

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

currentChanged(self, current: QModelIndex, previous: QModelIndex)

currentIndex(self) → QModelIndex

currentItem(self) → QListWidgetItem

currentItemChanged

currentItemChanged(self, current: QListWidgetItem, previous: QListWidgetItem) [signal]

currentRow(self) → int

currentRowChanged

currentRowChanged(self, currentRow: int) [signal]

currentTextChanged

currentTextChanged(self, currentText: str) [signal]

cursor(self) → QCursor

customContextMenuRequested

customContextMenuRequested(self, pos: QPoint) [signal]

customEvent(self, a0: QEvent)

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

defaultDropAction(self) → Qt.DropAction

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

dirtyRegionOffset(self) → QPoint

disconnect(a0: QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, signal: QMetaMethod)

doubleClicked

doubleClicked(self, index: QModelIndex) [signal]

dragDropMode(self) → QAbstractItemView.DragDropMode

dragDropOverwriteMode(self) → bool

dragEnabled(self) → bool

dragEnterEvent(self, e: QDragEnterEvent)

dragLeaveEvent(self, e: QDragLeaveEvent)

dragMoveEvent(self, e: QDragMoveEvent)

drawFrame(self, a0: QPainter)

dropEvent(self, event: QDropEvent)

dropIndicatorPosition(self) → QAbstractItemView.DropIndicatorPosition

dropMimeData(self, index: int, data: QMimeData, action: Qt.DropAction) → bool

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

edit(self, index: QModelIndex)

edit(self, index: QModelIndex, trigger: QAbstractItemView.EditTrigger, event: QEvent) → bool

editItem(self, item: QListWidgetItem)

editTriggers(self) → QAbstractItemView.EditTrigger

editorDestroyed(self, editor: QObject)

effectiveWinId(self) → PyQt6.sip.voidptr

ensurePolished(self)

enterEvent(self, event: QEnterEvent)

entered

entered(self, index: QModelIndex) [signal]

event(self, e: QEvent) → bool

eventFilter(self, object: QObject, event: QEvent) → bool

executeDelayedItemsLayout(self)

fill()

Fill the items in the ListWidget using the current structure

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]

findItems(self, text: str, flags: Qt.MatchFlag) → List[QListWidgetItem]

flow(self) → QListView.Flow

focusInEvent(self, e: QFocusEvent)

focusNextChild(self) → bool

focusNextPrevChild(self, next: bool) → bool

focusOutEvent(self, e: 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

getMarkedAtoms(guess=False)

Get atom indexes of marked atoms.

Parameters

guess (bool) – True if this mark results from a guess, False if not. The background color used depends on this parameter.

Return type

list(int)

Returns

Indexes of marked atoms

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

gridSize(self) → QSize

hasAutoScroll(self) → bool

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)

horizontalOffset(self) → int

horizontalScrollBar(self) → QScrollBar

horizontalScrollBarPolicy(self) → Qt.ScrollBarPolicy

horizontalScrollMode(self) → QAbstractItemView.ScrollMode

horizontalScrollbarAction(self, action: int)

horizontalScrollbarValueChanged(self, value: int)

iconSize(self) → QSize

iconSizeChanged

iconSizeChanged(self, size: QSize) [signal]

indexAt(self, p: QPoint) → QModelIndex

indexFromItem(self, item: QListWidgetItem) → QModelIndex

indexWidget(self, index: QModelIndex) → QWidget

indexesMoved

indexesMoved(self, indexes: Iterable[QModelIndex]) [signal]

inherits(self, classname: str) → bool

initPainter(self, painter: QPainter)

initStyleOption(self, option: QStyleOptionFrame)

initViewItemOption(self, option: QStyleOptionViewItem)

inputMethodEvent(self, event: QInputMethodEvent)

inputMethodHints(self) → Qt.InputMethodHint

inputMethodQuery(self, query: Qt.InputMethodQuery) → Any

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

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

insertItem(self, row: int, item: QListWidgetItem)

insertItem(self, row: int, label: str) → None

insertItems(self, row: int, labels: Iterable[str])

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

isIndexHidden(self, index: QModelIndex) → bool

isLeftToRight(self) → bool

isMaximized(self) → bool

isMinimized(self) → bool

isModal(self) → bool

isPersistentEditorOpen(self, item: QListWidgetItem) → bool

isRightToLeft(self) → bool

isRowHidden(self, row: int) → bool

isSelectionRectVisible(self) → bool

isSignalConnected(self, signal: QMetaMethod) → bool

isSortingEnabled(self) → bool

isVisible(self) → bool

isVisibleTo(self, a0: QWidget) → bool

isWidgetType(self) → bool

isWindow(self) → bool

isWindowModified(self) → bool

isWindowType(self) → bool

isWrapping(self) → bool

item(self, row: int) → QListWidgetItem

itemActivated

itemActivated(self, item: QListWidgetItem) [signal]

itemAlignment(self) → Qt.AlignmentFlag

itemAt(self, p: QPoint) → QListWidgetItem

itemAt(self, ax: int, ay: int) → QListWidgetItem

itemChanged

itemChanged(self, item: QListWidgetItem) [signal]

itemClicked

itemClicked(self, item: QListWidgetItem) [signal]

itemDelegate(self) → QAbstractItemDelegate

itemDelegateForColumn(self, column: int) → QAbstractItemDelegate

itemDelegateForIndex(self, index: QModelIndex) → QAbstractItemDelegate

itemDelegateForRow(self, row: int) → QAbstractItemDelegate

itemDoubleClicked

itemDoubleClicked(self, item: QListWidgetItem) [signal]

itemEntered

itemEntered(self, item: QListWidgetItem) [signal]

itemFromIndex(self, index: QModelIndex) → QListWidgetItem

itemPressed

itemPressed(self, item: QListWidgetItem) [signal]

itemSelected(row)

React to the user selecting an item in the ListWidget

Parameters

row (int) – The row of the item selected

itemSelectionChanged

itemSelectionChanged(self) [signal]

itemWidget(self, item: QListWidgetItem) → QWidget

items(self, data: QMimeData) → List[QListWidgetItem]

keyPressEvent(self, e: QKeyEvent)

keyReleaseEvent(self, a0: QKeyEvent)

keyboardGrabber() → QWidget

keyboardSearch(self, search: str)

killTimer(self, id: int)

layout(self) → QLayout

layoutDirection(self) → Qt.LayoutDirection

layoutMode(self) → QListView.LayoutMode

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

markAtomUnmapped(index)

Mark the row for the given atom index as unmapped

Parameters

index (int) – Atom to mark

Return type

QListWidgetItem

Returns

The list widget item for the affected atom

mask(self) → QRegion

maximumHeight(self) → int

maximumSize(self) → QSize

maximumViewportSize(self) → QSize

maximumWidth(self) → int

metaObject(self) → QMetaObject

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

midLineWidth(self) → int

mimeData(self, items: Iterable[QListWidgetItem]) → QMimeData

mimeTypes(self) → List[str]

minimumHeight(self) → int

minimumSize(self) → QSize

minimumSizeHint(self) → QSize

minimumWidth(self) → int

model(self) → QAbstractItemModel

modelColumn(self) → int

mouseDoubleClickEvent(self, e: QMouseEvent)

mouseGrabber() → QWidget

mouseMoveEvent(self, e: QMouseEvent)

mousePressEvent(self, e: QMouseEvent)

mouseReleaseEvent(self, e: QMouseEvent)

move(self, a0: QPoint)

move(self, ax: int, ay: int) → None

moveCursor(self, cursorAction: QAbstractItemView.CursorAction, modifiers: Qt.KeyboardModifier) → QModelIndex

moveEvent(self, a0: QMoveEvent)

moveToThread(self, thread: QThread)

movement(self) → QListView.Movement

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]

openPersistentEditor(self, item: QListWidgetItem)

overrideWindowFlags(self, type: Qt.WindowType)

overrideWindowState(self, state: Qt.WindowState)

paintEngine(self) → QPaintEngine

paintEvent(self, e: QPaintEvent)

paintingActive(self) → bool

palette(self) → QPalette

parent(self) → QObject

parentWidget(self) → QWidget

parseAtomText(text)

Parse the given text into an element and atom index

Parameters

text (str) – String describing the atom such as C 13, H 1, etc. Also accepts strings for mapped atoms such as “C 13 - C 12”

Return type

(str, int)

Returns

The element and atom index specified by text

physicalDpiX(self) → int

physicalDpiY(self) → int

pos(self) → QPoint

pressed

pressed(self, index: QModelIndex) [signal]

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

rectForIndex(self, index: QModelIndex) → QRect

releaseKeyboard(self)

releaseMouse(self)

releaseShortcut(self, id: int)

removeAction(self, action: QAction)

removeEventFilter(self, a0: QObject)

removeItem(item)

Removes and returns the given item

Parameters

item (QListWidgetItem or 0) – The item to be removed from the list widget or 0 if it is not found in the list widget

removeItemByText(text)

Removes and returns the item with the given text

Parameters

text (str) – the text of the item to be removed

Return type

QListWidgetItem or None

Returns

The removed item, or None if an item with the given text is not found.

removeItemWidget(self, aItem: QListWidgetItem)

removeSelectedItems()

Removes selected items.

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

reset(self)

resetHorizontalScrollMode(self)

resetVerticalScrollMode(self)

resize(self, a0: QSize)

resize(self, w: int, h: int) → None

resizeEvent(self, e: QResizeEvent)

resizeMode(self) → QListView.ResizeMode

restoreGeometry(self, geometry: QByteArray) → bool

rootIndex(self) → QModelIndex

row(self, item: QListWidgetItem) → int

rowByText(text, match=MatchFlag.MatchExactly)

Returns the row that a given text is in. Also accounts for hidden items.

Parameters

• text (str) – The text to find

• match (Qt.MatchFlag) – Type of match to search for - default is exact

Return type

int or False

Returns

Row that holds matched text (can be 0), if text is not matched, returns False

rowsAboutToBeRemoved(self, parent: QModelIndex, start: int, end: int)

rowsInserted(self, parent: QModelIndex, start: int, end: int)

saveGeometry(self) → QByteArray

scheduleDelayedItemsLayout(self)

screen(self) → QScreen

scroll(self, dx: int, dy: int)

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

scrollBarWidgets(self, alignment: Qt.AlignmentFlag) → List[QWidget]

scrollContentsBy(self, dx: int, dy: int)

scrollDirtyRegion(self, dx: int, dy: int)

scrollTo(self, index: QModelIndex, hint: QAbstractItemView.ScrollHint = QAbstractItemView.EnsureVisible)

scrollToBottom(self)

scrollToItem(self, item: QListWidgetItem, hint: QAbstractItemView.ScrollHint = QAbstractItemView.EnsureVisible)

scrollToTop(self)

selectAll(self)

selectAtom(index)

Select the item that corresponds to the atom index

Parameters

index (int) – The index of atom whose item should be selected

selectedIndexes(self) → List[QModelIndex]

selectedItems(self) → List[QListWidgetItem]

selectedText()

Return the list of selected text values, including those of hidden items

Return type

list

Returns

List of strings, each member is the text of a selected item

selectionBehavior(self) → QAbstractItemView.SelectionBehavior

selectionChanged(self, selected: QItemSelection, deselected: QItemSelection)

selectionCommand(self, index: QModelIndex, event: typing.Optional[QEvent] = None) → QItemSelectionModel.SelectionFlag

selectionMode(self) → QAbstractItemView.SelectionMode

selectionModel(self) → QItemSelectionModel

sender(self) → QObject

senderSignalIndex(self) → int

setAcceptDrops(self, on: bool)

setAccessibleDescription(self, description: str)

setAccessibleName(self, name: str)

setAlternatingRowColors(self, enable: bool)

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

setAutoFillBackground(self, enabled: bool)

setAutoScroll(self, enable: bool)

setAutoScrollMargin(self, margin: int)

setBackgroundRole(self, a0: QPalette.ColorRole)

setBaseSize(self, basew: int, baseh: int)

setBaseSize(self, s: QSize) → None

setBatchSize(self, batchSize: int)

setContentsMargins(self, left: int, top: int, right: int, bottom: int)

setContentsMargins(self, margins: QMargins) → None

setContextMenuPolicy(self, policy: Qt.ContextMenuPolicy)

setCornerWidget(self, widget: QWidget)

setCurrentIndex(self, index: QModelIndex)

setCurrentItem(self, item: QListWidgetItem)

setCurrentItem(self, item: QListWidgetItem, command: QItemSelectionModel.SelectionFlag) → None

setCurrentRow(self, row: int)

setCurrentRow(self, row: int, command: QItemSelectionModel.SelectionFlag) → None

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

setDefaultDropAction(self, dropAction: Qt.DropAction)

setDirtyRegion(self, region: QRegion)

setDisabled(self, a0: bool)

setDragDropMode(self, behavior: QAbstractItemView.DragDropMode)

setDragDropOverwriteMode(self, overwrite: bool)

setDragEnabled(self, enable: bool)

setDropIndicatorShown(self, enable: bool)

setEditTriggers(self, triggers: QAbstractItemView.EditTrigger)

setEnabled(self, a0: bool)

setFixedHeight(self, h: int)

setFixedSize(self, a0: QSize)

setFixedSize(self, w: int, h: int) → None

setFixedWidth(self, w: int)

setFlow(self, flow: QListView.Flow)

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)

setGridSize(self, size: QSize)

setHidden(self, hidden: bool)

setHorizontalScrollBar(self, scrollbar: QScrollBar)

setHorizontalScrollBarPolicy(self, a0: Qt.ScrollBarPolicy)

setHorizontalScrollMode(self, mode: QAbstractItemView.ScrollMode)

setIconSize(self, size: QSize)

setIndexWidget(self, index: QModelIndex, widget: QWidget)

setInputMethodHints(self, hints: Qt.InputMethodHint)

setItemAlignment(self, alignment: Qt.AlignmentFlag)

setItemDelegate(self, delegate: QAbstractItemDelegate)

setItemDelegateForColumn(self, column: int, delegate: QAbstractItemDelegate)

setItemDelegateForRow(self, row: int, delegate: QAbstractItemDelegate)

setItemWidget(self, item: QListWidgetItem, widget: QWidget)

setLayout(self, a0: QLayout)

setLayoutDirection(self, direction: Qt.LayoutDirection)

setLayoutMode(self, mode: QListView.LayoutMode)

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)

setModel(self, model: QAbstractItemModel)

setModelColumn(self, column: int)

setMouseTracking(self, enable: bool)

setMovement(self, movement: QListView.Movement)

setObjectName(self, name: str)

setPalette(self, a0: QPalette)

setParent(self, parent: QWidget)

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

setPositionForIndex(self, position: QPoint, index: QModelIndex)

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

setResizeMode(self, mode: QListView.ResizeMode)

setRootIndex(self, index: QModelIndex)

setRowHidden(self, row: int, hide: bool)

setScreen(self, a0: QScreen)

setSelection(self, rect: QRect, command: QItemSelectionModel.SelectionFlag)

setSelectionBehavior(self, behavior: QAbstractItemView.SelectionBehavior)

setSelectionMode(self, mode: QAbstractItemView.SelectionMode)

setSelectionModel(self, selectionModel: QItemSelectionModel)

setSelectionRectVisible(self, show: bool)

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

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

setSizeAdjustPolicy(self, policy: QAbstractScrollArea.SizeAdjustPolicy)

setSizeIncrement(self, w: int, h: int)

setSizeIncrement(self, s: QSize) → None

setSizePolicy(self, a0: QSizePolicy)

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

setSortingEnabled(self, enable: bool)

setSpacing(self, space: int)

setState(self, state: QAbstractItemView.State)

setStatusTip(self, a0: str)

setStructure(struct)

Set the structure object for this widget and fill the widget

Parameters

struct (schrodinger.structure.Structure) – The structure object containing the data for this ListWidget

setStyle(self, a0: QStyle)

setStyleSheet(self, styleSheet: str)

setTabKeyNavigation(self, enable: bool)

setTabOrder(a0: QWidget, a1: QWidget)

setTabletTracking(self, enable: bool)

setTextElideMode(self, mode: Qt.TextElideMode)

setTextSelected(text, selected=True)

Selects the item with the given text. Will select hidden items too.

Parameters

• text (str) – the text of the item to be selected

• selected (bool) – True if the item should be selected, False if it should be deselected.

Return type

bool

Returns

True if an item with the given text is found, False if not

setToolTip(self, a0: str)

setToolTipDuration(self, msec: int)

setUniformItemSizes(self, enable: bool)

setUpdatesEnabled(self, enable: bool)

setVerticalScrollBar(self, scrollbar: QScrollBar)

setVerticalScrollBarPolicy(self, a0: Qt.ScrollBarPolicy)

setVerticalScrollMode(self, mode: QAbstractItemView.ScrollMode)

setViewMode(self, mode: QListView.ViewMode)

setViewport(self, widget: QWidget)

setViewportMargins(self, left: int, top: int, right: int, bottom: int)

setViewportMargins(self, margins: QMargins) → None

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)

setWordWrap(self, on: bool)

setWrapping(self, enable: bool)

setupViewport(self, viewport: QWidget)

sharedPainter(self) → QPainter

show(self)

showDropIndicator(self) → bool

showEvent(self, a0: QShowEvent)

showFullScreen(self)

showMaximized(self)

showMinimized(self)

showNormal(self)

signalsBlocked(self) → bool

size(self) → QSize

sizeAdjustPolicy(self) → QAbstractScrollArea.SizeAdjustPolicy

sizeHint(self) → QSize

sizeHintForColumn(self, column: int) → int

sizeHintForIndex(self, index: QModelIndex) → QSize

sizeHintForRow(self, row: int) → int

sizeIncrement(self) → QSize

sizePolicy(self) → QSizePolicy

sortItems(self, order: Qt.SortOrder = Qt.AscendingOrder)

spacing(self) → int

stackUnder(self, a0: QWidget)

startDrag(self, supportedActions: Qt.DropAction)

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

state(self) → QAbstractItemView.State

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

statusTip(self) → str

style(self) → QStyle

styleSheet(self) → str

supportedDropActions(self) → Qt.DropAction

tabKeyNavigation(self) → bool

tabletEvent(self, a0: QTabletEvent)

takeItem(self, row: int) → QListWidgetItem

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

textElideMode(self) → Qt.TextElideMode

thread(self) → QThread

timerEvent(self, e: 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)

uniformItemSizes(self) → bool

unsetCursor(self)

unsetLayoutDirection(self)

unsetLocale(self)

update(self)

update(self, index: QModelIndex) → None

updateEditorData(self)

updateEditorGeometries(self)

updateGeometries(self)

updateGeometry(self)

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

updatesEnabled(self) → bool

verticalOffset(self) → int

verticalScrollBar(self) → QScrollBar

verticalScrollBarPolicy(self) → Qt.ScrollBarPolicy

verticalScrollMode(self) → QAbstractItemView.ScrollMode

verticalScrollbarAction(self, action: int)

verticalScrollbarValueChanged(self, value: int)

viewMode(self) → QListView.ViewMode

viewport(self) → QWidget

viewportEntered

viewportEntered(self) [signal]

viewportEvent(self, e: QEvent) → bool

viewportMargins(self) → QMargins

viewportSizeHint(self) → QSize

visibleRegion(self) → QRegion

visualItemRect(self, item: QListWidgetItem) → QRect

visualRect(self, index: QModelIndex) → QRect

visualRegionForSelection(self, selection: QItemSelection) → QRegion

whatsThis(self) → str

wheelEvent(self, e: 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

wordWrap(self) → bool

x(self) → int

y(self) → int

class schrodinger.application.matsci.reordergui.ReferenceListWidget(master, atomic_constraints=None)

Bases: schrodinger.application.matsci.reordergui.StructureListWidget

The ListWidget for the reference structure.

markAtomMapped(index, guess=False)

Mark the row for the given atom index as mapped and update the text

Adds to the parent method by changing the text of the marked item to reflect the mapping.

Parameters

• index (int) – Atom to mark

• guess (bool) – True if this mark results from a guess, False if not. The background color used depends on this parameter.

Return type

QListWidgetItem

Returns

The list widget item for the affected atom

markAtomUnmapped(index)

Remove the mapping for atom index

Adds to the parent method by changing the text of the marked item to reflect the unmapping.

Parameters

index (int) – The atom index to unmap

Return type

QListWidgetItem

Returns

The list widget item for the affected atom

getAtomText(atom)

Get the text to display in a row of the ListWidget

The atom text for an item is the atom element plus index for the Reference atom, plus the atom index of any Comparison atom mapped to this atom.

Parameters

atom (int or _StructureAtom) – A reference to the atom to create text for

Return type

str

Returns

The text to display for this atom

AboveItem = 1

Adjust = 1

AdjustIgnored = 0

AdjustToContents = 2

AdjustToContentsOnFirstShow = 1

AllEditTriggers = 31

AnimatingState = 6

AnyKeyPressed = 16

Batched = 1

BelowItem = 2

Box = 1

CollapsingState = 5

ContiguousSelection = 4

CurrentChanged = 1

class CursorAction(value)

Bases: enum.Enum

An enumeration.

MoveUp = 0

MoveDown = 1

MoveLeft = 2

MoveRight = 3

MoveHome = 4

MoveEnd = 5

MovePageUp = 6

MovePageDown = 7

MoveNext = 8

MovePrevious = 9

DoubleClicked = 2

DragDrop = 3

class DragDropMode(value)

Bases: enum.Enum

An enumeration.

NoDragDrop = 0

DragOnly = 1

DropOnly = 2

DragDrop = 3

InternalMove = 4

DragOnly = 1

DragSelectingState = 2

DraggingState = 1

DrawChildren = 2

DrawWindowBackground = 1

class DropIndicatorPosition(value)

Bases: enum.Enum

An enumeration.

OnItem = 0

AboveItem = 1

BelowItem = 2

OnViewport = 3

DropOnly = 2

EditKeyPressed = 8

class EditTrigger(value)

Bases: enum.Flag

An enumeration.

NoEditTriggers = 0

CurrentChanged = 1

DoubleClicked = 2

SelectedClicked = 4

EditKeyPressed = 8

AnyKeyPressed = 16

AllEditTriggers = 31

EditingState = 3

EnsureVisible = 0

ExpandingState = 4

ExtendedSelection = 3

Fixed = 0

class Flow(value)

Bases: enum.Enum

An enumeration.

LeftToRight = 0

TopToBottom = 1

Free = 1

HLine = 4

IconMode = 1

IgnoreMask = 4

InternalMove = 4

class LayoutMode(value)

Bases: enum.Enum

An enumeration.

SinglePass = 0

Batched = 1

LeftToRight = 0

ListMode = 0

MoveDown = 1

MoveEnd = 5

MoveHome = 4

MoveLeft = 2

MoveNext = 8

MovePageDown = 7

MovePageUp = 6

MovePrevious = 9

MoveRight = 3

MoveUp = 0

class Movement(value)

Bases: enum.Enum

An enumeration.

Static = 0

Free = 1

Snap = 2

MultiSelection = 2

NoDragDrop = 0

NoEditTriggers = 0

NoFrame = 0

NoSelection = 0

NoState = 0

OnItem = 0

OnViewport = 3

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

PositionAtBottom = 2

PositionAtCenter = 3

PositionAtTop = 1

Raised = 32

class RenderFlag(value)

Bases: enum.Flag

An enumeration.

DrawWindowBackground = 1

DrawChildren = 2

IgnoreMask = 4

class ResizeMode(value)

Bases: enum.Enum

An enumeration.

Fixed = 0

Adjust = 1

class ScrollHint(value)

Bases: enum.Enum

An enumeration.

EnsureVisible = 0

PositionAtTop = 1

PositionAtBottom = 2

PositionAtCenter = 3

class ScrollMode(value)

Bases: enum.Enum

An enumeration.

ScrollPerItem = 0

ScrollPerPixel = 1

ScrollPerItem = 0

ScrollPerPixel = 1

SelectColumns = 2

SelectItems = 0

SelectRows = 1

SelectedClicked = 4

class SelectionBehavior(value)

Bases: enum.Enum

An enumeration.

SelectItems = 0

SelectRows = 1

SelectColumns = 2

class SelectionMode(value)

Bases: enum.Enum

An enumeration.

NoSelection = 0

SingleSelection = 1

MultiSelection = 2

ExtendedSelection = 3

ContiguousSelection = 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

SinglePass = 0

SingleSelection = 1

class SizeAdjustPolicy(value)

Bases: enum.Enum

An enumeration.

AdjustIgnored = 0

AdjustToContentsOnFirstShow = 1

AdjustToContents = 2

Snap = 2

class State(value)

Bases: enum.Enum

An enumeration.

NoState = 0

DraggingState = 1

DragSelectingState = 2

EditingState = 3

ExpandingState = 4

CollapsingState = 5

AnimatingState = 6

Static = 0

class StyleMask(value)

Bases: enum.Enum

An enumeration.

Shadow_Mask = 240

Shape_Mask = 15

StyledPanel = 6

Sunken = 48

TopToBottom = 1

VLine = 5

class ViewMode(value)

Bases: enum.Enum

An enumeration.

ListMode = 0

IconMode = 1

WinPanel = 3

__init__(master, atomic_constraints=None)

Create a StructureListWidget instance

Parameters

• master (ReorderAtomFrame) – The mapping property of the master is used by some subclasses

• atomic_constraints (list or None) – list of atomic constraints for each atom or None

__len__()

Return len(self).

acceptDrops(self) → bool

accessibleDescription(self) → str

accessibleName(self) → str

actionEvent(self, a0: QActionEvent)

actions(self) → List[QAction]

activateWindow(self)

activated

activated(self, index: QModelIndex) [signal]

addAction(self, action: QAction)

addActions(self, actions: Iterable[QAction])

addItem(self, aitem: QListWidgetItem)

addItem(self, label: str) → None

addItems(self, labels: Iterable[str])

addScrollBarWidget(self, widget: QWidget, alignment: Qt.AlignmentFlag)

adjustSize(self)

allItems()

Return all the items in the list widget in order, including hidden ones

Return type

list

Returns

list of all QListWidgetItems in the list widget in order

allItemsIter(role=ItemDataRole.UserRole)

Return a generator over text and data of the list widget, inspired by .items() method of dict.

Parameters

role (int) – User role to pass do .data function

Return type

generator(tuple(str, type))

Returns

Generator over tupple of text and data of the list widget

allText()

Return the list of all text values, including hidden items

Return type

list

Returns

List of strings

alternatingRowColors(self) → bool

atom_clicked

autoFillBackground(self) → bool

autoScrollMargin(self) → int

backgroundRole(self) → QPalette.ColorRole

baseSize(self) → QSize

batchSize(self) → int

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(self)

clearFocus(self)

clearMask(self)

clearPropertyFlags(self)

clearSelection(self)

clicked

clicked(self, index: QModelIndex) [signal]

close(self) → bool

closeEditor(self, editor: QWidget, hint: QAbstractItemDelegate.EndEditHint)

closeEvent(self, a0: QCloseEvent)

closePersistentEditor(self, item: QListWidgetItem)

colorCount(self) → int

commitData(self, editor: QWidget)

connectNotify(self, signal: QMetaMethod)

contentsMargins(self) → QMargins

contentsRect(self) → QRect

contextMenuEvent(self, a0: QContextMenuEvent)

contextMenuPolicy(self) → Qt.ContextMenuPolicy

cornerWidget(self) → QWidget

count(self) → int

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

currentChanged(self, current: QModelIndex, previous: QModelIndex)

currentIndex(self) → QModelIndex

currentItem(self) → QListWidgetItem

currentItemChanged

currentItemChanged(self, current: QListWidgetItem, previous: QListWidgetItem) [signal]

currentRow(self) → int

currentRowChanged

currentRowChanged(self, currentRow: int) [signal]

currentTextChanged

currentTextChanged(self, currentText: str) [signal]

cursor(self) → QCursor

customContextMenuRequested

customContextMenuRequested(self, pos: QPoint) [signal]

customEvent(self, a0: QEvent)

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

defaultDropAction(self) → Qt.DropAction

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

dirtyRegionOffset(self) → QPoint

disconnect(a0: QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, signal: QMetaMethod)

doubleClicked

doubleClicked(self, index: QModelIndex) [signal]

dragDropMode(self) → QAbstractItemView.DragDropMode

dragDropOverwriteMode(self) → bool

dragEnabled(self) → bool

dragEnterEvent(self, e: QDragEnterEvent)

dragLeaveEvent(self, e: QDragLeaveEvent)

dragMoveEvent(self, e: QDragMoveEvent)

drawFrame(self, a0: QPainter)

dropEvent(self, event: QDropEvent)

dropIndicatorPosition(self) → QAbstractItemView.DropIndicatorPosition

dropMimeData(self, index: int, data: QMimeData, action: Qt.DropAction) → bool

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

edit(self, index: QModelIndex)

edit(self, index: QModelIndex, trigger: QAbstractItemView.EditTrigger, event: QEvent) → bool

editItem(self, item: QListWidgetItem)

editTriggers(self) → QAbstractItemView.EditTrigger

editorDestroyed(self, editor: QObject)

effectiveWinId(self) → PyQt6.sip.voidptr

ensurePolished(self)

enterEvent(self, event: QEnterEvent)

entered

entered(self, index: QModelIndex) [signal]

event(self, e: QEvent) → bool

eventFilter(self, object: QObject, event: QEvent) → bool

executeDelayedItemsLayout(self)

fill()

Fill the items in the ListWidget using the current structure

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]

findItems(self, text: str, flags: Qt.MatchFlag) → List[QListWidgetItem]

flow(self) → QListView.Flow

focusInEvent(self, e: QFocusEvent)

focusNextChild(self) → bool

focusNextPrevChild(self, next: bool) → bool

focusOutEvent(self, e: 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

getMarkedAtoms(guess=False)

Get atom indexes of marked atoms.

Parameters

guess (bool) – True if this mark results from a guess, False if not. The background color used depends on this parameter.

Return type

list(int)

Returns

Indexes of marked atoms

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

gridSize(self) → QSize

hasAutoScroll(self) → bool

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)

horizontalOffset(self) → int

horizontalScrollBar(self) → QScrollBar

horizontalScrollBarPolicy(self) → Qt.ScrollBarPolicy

horizontalScrollMode(self) → QAbstractItemView.ScrollMode

horizontalScrollbarAction(self, action: int)

horizontalScrollbarValueChanged(self, value: int)

iconSize(self) → QSize

iconSizeChanged

iconSizeChanged(self, size: QSize) [signal]

indexAt(self, p: QPoint) → QModelIndex

indexFromItem(self, item: QListWidgetItem) → QModelIndex

indexWidget(self, index: QModelIndex) → QWidget

indexesMoved

indexesMoved(self, indexes: Iterable[QModelIndex]) [signal]

inherits(self, classname: str) → bool

initPainter(self, painter: QPainter)

initStyleOption(self, option: QStyleOptionFrame)

initViewItemOption(self, option: QStyleOptionViewItem)

inputMethodEvent(self, event: QInputMethodEvent)

inputMethodHints(self) → Qt.InputMethodHint

inputMethodQuery(self, query: Qt.InputMethodQuery) → Any

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

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

insertItem(self, row: int, item: QListWidgetItem)

insertItem(self, row: int, label: str) → None

insertItems(self, row: int, labels: Iterable[str])

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

isIndexHidden(self, index: QModelIndex) → bool

isLeftToRight(self) → bool

isMaximized(self) → bool

isMinimized(self) → bool

isModal(self) → bool

isPersistentEditorOpen(self, item: QListWidgetItem) → bool

isRightToLeft(self) → bool

isRowHidden(self, row: int) → bool

isSelectionRectVisible(self) → bool

isSignalConnected(self, signal: QMetaMethod) → bool

isSortingEnabled(self) → bool

isVisible(self) → bool

isVisibleTo(self, a0: QWidget) → bool

isWidgetType(self) → bool

isWindow(self) → bool

isWindowModified(self) → bool

isWindowType(self) → bool

isWrapping(self) → bool

item(self, row: int) → QListWidgetItem

itemActivated

itemActivated(self, item: QListWidgetItem) [signal]

itemAlignment(self) → Qt.AlignmentFlag

itemAt(self, p: QPoint) → QListWidgetItem

itemAt(self, ax: int, ay: int) → QListWidgetItem

itemChanged

itemChanged(self, item: QListWidgetItem) [signal]

itemClicked

itemClicked(self, item: QListWidgetItem) [signal]

itemDelegate(self) → QAbstractItemDelegate

itemDelegateForColumn(self, column: int) → QAbstractItemDelegate

itemDelegateForIndex(self, index: QModelIndex) → QAbstractItemDelegate

itemDelegateForRow(self, row: int) → QAbstractItemDelegate

itemDoubleClicked

itemDoubleClicked(self, item: QListWidgetItem) [signal]

itemEntered

itemEntered(self, item: QListWidgetItem) [signal]

itemFromIndex(self, index: QModelIndex) → QListWidgetItem

itemPressed

itemPressed(self, item: QListWidgetItem) [signal]

itemSelected(row)

React to the user selecting an item in the ListWidget

Parameters

row (int) – The row of the item selected

itemSelectionChanged

itemSelectionChanged(self) [signal]

itemWidget(self, item: QListWidgetItem) → QWidget

items(self, data: QMimeData) → List[QListWidgetItem]

keyPressEvent(self, e: QKeyEvent)

keyReleaseEvent(self, a0: QKeyEvent)

keyboardGrabber() → QWidget

keyboardSearch(self, search: str)

killTimer(self, id: int)

layout(self) → QLayout

layoutDirection(self) → Qt.LayoutDirection

layoutMode(self) → QListView.LayoutMode

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

maximumViewportSize(self) → QSize

maximumWidth(self) → int

metaObject(self) → QMetaObject

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

midLineWidth(self) → int

mimeData(self, items: Iterable[QListWidgetItem]) → QMimeData

mimeTypes(self) → List[str]

minimumHeight(self) → int

minimumSize(self) → QSize

minimumSizeHint(self) → QSize

minimumWidth(self) → int

model(self) → QAbstractItemModel

modelColumn(self) → int

mouseDoubleClickEvent(self, e: QMouseEvent)

mouseGrabber() → QWidget

mouseMoveEvent(self, e: QMouseEvent)

mousePressEvent(self, e: QMouseEvent)

mouseReleaseEvent(self, e: QMouseEvent)

move(self, a0: QPoint)

move(self, ax: int, ay: int) → None

moveCursor(self, cursorAction: QAbstractItemView.CursorAction, modifiers: Qt.KeyboardModifier) → QModelIndex

moveEvent(self, a0: QMoveEvent)

moveToThread(self, thread: QThread)

movement(self) → QListView.Movement

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]

openPersistentEditor(self, item: QListWidgetItem)

overrideWindowFlags(self, type: Qt.WindowType)

overrideWindowState(self, state: Qt.WindowState)

paintEngine(self) → QPaintEngine

paintEvent(self, e: QPaintEvent)

paintingActive(self) → bool

palette(self) → QPalette

parent(self) → QObject

parentWidget(self) → QWidget

parseAtomText(text)

Parse the given text into an element and atom index

Parameters

text (str) – String describing the atom such as C 13, H 1, etc. Also accepts strings for mapped atoms such as “C 13 - C 12”

Return type

(str, int)

Returns

The element and atom index specified by text

physicalDpiX(self) → int

physicalDpiY(self) → int

pos(self) → QPoint

pressed

pressed(self, index: QModelIndex) [signal]

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

rectForIndex(self, index: QModelIndex) → QRect

releaseKeyboard(self)

releaseMouse(self)

releaseShortcut(self, id: int)

removeAction(self, action: QAction)

removeEventFilter(self, a0: QObject)

removeItem(item)

Removes and returns the given item

Parameters

item (QListWidgetItem or 0) – The item to be removed from the list widget or 0 if it is not found in the list widget

removeItemByText(text)

Removes and returns the item with the given text

Parameters

text (str) – the text of the item to be removed

Return type

QListWidgetItem or None

Returns

The removed item, or None if an item with the given text is not found.

removeItemWidget(self, aItem: QListWidgetItem)

removeSelectedItems()

Removes selected items.

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

reset(self)

resetHorizontalScrollMode(self)

resetVerticalScrollMode(self)

resize(self, a0: QSize)

resize(self, w: int, h: int) → None

resizeEvent(self, e: QResizeEvent)

resizeMode(self) → QListView.ResizeMode

restoreGeometry(self, geometry: QByteArray) → bool

rootIndex(self) → QModelIndex

row(self, item: QListWidgetItem) → int

rowByText(text, match=MatchFlag.MatchExactly)

Returns the row that a given text is in. Also accounts for hidden items.

Parameters

• text (str) – The text to find

• match (Qt.MatchFlag) – Type of match to search for - default is exact

Return type

int or False

Returns

Row that holds matched text (can be 0), if text is not matched, returns False

rowsAboutToBeRemoved(self, parent: QModelIndex, start: int, end: int)

rowsInserted(self, parent: QModelIndex, start: int, end: int)

saveGeometry(self) → QByteArray

scheduleDelayedItemsLayout(self)

screen(self) → QScreen

scroll(self, dx: int, dy: int)

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

scrollBarWidgets(self, alignment: Qt.AlignmentFlag) → List[QWidget]

scrollContentsBy(self, dx: int, dy: int)

scrollDirtyRegion(self, dx: int, dy: int)

scrollTo(self, index: QModelIndex, hint: QAbstractItemView.ScrollHint = QAbstractItemView.EnsureVisible)

scrollToBottom(self)

scrollToItem(self, item: QListWidgetItem, hint: QAbstractItemView.ScrollHint = QAbstractItemView.EnsureVisible)

scrollToTop(self)

selectAll(self)

selectAtom(index)

Select the item that corresponds to the atom index

Parameters

index (int) – The index of atom whose item should be selected

selectedIndexes(self) → List[QModelIndex]

selectedItems(self) → List[QListWidgetItem]

selectedText()

Return the list of selected text values, including those of hidden items

Return type

list

Returns

List of strings, each member is the text of a selected item

selectionBehavior(self) → QAbstractItemView.SelectionBehavior

selectionChanged(self, selected: QItemSelection, deselected: QItemSelection)

selectionCommand(self, index: QModelIndex, event: typing.Optional[QEvent] = None) → QItemSelectionModel.SelectionFlag

selectionMode(self) → QAbstractItemView.SelectionMode

selectionModel(self) → QItemSelectionModel

sender(self) → QObject

senderSignalIndex(self) → int

setAcceptDrops(self, on: bool)

setAccessibleDescription(self, description: str)

setAccessibleName(self, name: str)

setAlternatingRowColors(self, enable: bool)

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

setAutoFillBackground(self, enabled: bool)

setAutoScroll(self, enable: bool)

setAutoScrollMargin(self, margin: int)

setBackgroundRole(self, a0: QPalette.ColorRole)

setBaseSize(self, basew: int, baseh: int)

setBaseSize(self, s: QSize) → None

setBatchSize(self, batchSize: int)

setContentsMargins(self, left: int, top: int, right: int, bottom: int)

setContentsMargins(self, margins: QMargins) → None

setContextMenuPolicy(self, policy: Qt.ContextMenuPolicy)

setCornerWidget(self, widget: QWidget)

setCurrentIndex(self, index: QModelIndex)

setCurrentItem(self, item: QListWidgetItem)

setCurrentItem(self, item: QListWidgetItem, command: QItemSelectionModel.SelectionFlag) → None

setCurrentRow(self, row: int)

setCurrentRow(self, row: int, command: QItemSelectionModel.SelectionFlag) → None

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

setDefaultDropAction(self, dropAction: Qt.DropAction)

setDirtyRegion(self, region: QRegion)

setDisabled(self, a0: bool)

setDragDropMode(self, behavior: QAbstractItemView.DragDropMode)

setDragDropOverwriteMode(self, overwrite: bool)

setDragEnabled(self, enable: bool)

setDropIndicatorShown(self, enable: bool)

setEditTriggers(self, triggers: QAbstractItemView.EditTrigger)

setEnabled(self, a0: bool)

setFixedHeight(self, h: int)

setFixedSize(self, a0: QSize)

setFixedSize(self, w: int, h: int) → None

setFixedWidth(self, w: int)

setFlow(self, flow: QListView.Flow)

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)

setGridSize(self, size: QSize)

setHidden(self, hidden: bool)

setHorizontalScrollBar(self, scrollbar: QScrollBar)

setHorizontalScrollBarPolicy(self, a0: Qt.ScrollBarPolicy)

setHorizontalScrollMode(self, mode: QAbstractItemView.ScrollMode)

setIconSize(self, size: QSize)

setIndexWidget(self, index: QModelIndex, widget: QWidget)

setInputMethodHints(self, hints: Qt.InputMethodHint)

setItemAlignment(self, alignment: Qt.AlignmentFlag)

setItemDelegate(self, delegate: QAbstractItemDelegate)

setItemDelegateForColumn(self, column: int, delegate: QAbstractItemDelegate)

setItemDelegateForRow(self, row: int, delegate: QAbstractItemDelegate)

setItemWidget(self, item: QListWidgetItem, widget: QWidget)

setLayout(self, a0: QLayout)

setLayoutDirection(self, direction: Qt.LayoutDirection)

setLayoutMode(self, mode: QListView.LayoutMode)

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)

setModel(self, model: QAbstractItemModel)

setModelColumn(self, column: int)

setMouseTracking(self, enable: bool)

setMovement(self, movement: QListView.Movement)

setObjectName(self, name: str)

setPalette(self, a0: QPalette)

setParent(self, parent: QWidget)

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

setPositionForIndex(self, position: QPoint, index: QModelIndex)

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

setResizeMode(self, mode: QListView.ResizeMode)

setRootIndex(self, index: QModelIndex)

setRowHidden(self, row: int, hide: bool)

setScreen(self, a0: QScreen)

setSelection(self, rect: QRect, command: QItemSelectionModel.SelectionFlag)

setSelectionBehavior(self, behavior: QAbstractItemView.SelectionBehavior)

setSelectionMode(self, mode: QAbstractItemView.SelectionMode)

setSelectionModel(self, selectionModel: QItemSelectionModel)

setSelectionRectVisible(self, show: bool)

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

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

setSizeAdjustPolicy(self, policy: QAbstractScrollArea.SizeAdjustPolicy)

setSizeIncrement(self, w: int, h: int)

setSizeIncrement(self, s: QSize) → None

setSizePolicy(self, a0: QSizePolicy)

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

setSortingEnabled(self, enable: bool)

setSpacing(self, space: int)

setState(self, state: QAbstractItemView.State)

setStatusTip(self, a0: str)

setStructure(struct)

Set the structure object for this widget and fill the widget

Parameters

struct (schrodinger.structure.Structure) – The structure object containing the data for this ListWidget

setStyle(self, a0: QStyle)

setStyleSheet(self, styleSheet: str)

setTabKeyNavigation(self, enable: bool)

setTabOrder(a0: QWidget, a1: QWidget)

setTabletTracking(self, enable: bool)

setTextElideMode(self, mode: Qt.TextElideMode)

setTextSelected(text, selected=True)

Selects the item with the given text. Will select hidden items too.

Parameters

• text (str) – the text of the item to be selected

• selected (bool) – True if the item should be selected, False if it should be deselected.

Return type

bool

Returns

True if an item with the given text is found, False if not

setToolTip(self, a0: str)

setToolTipDuration(self, msec: int)

setUniformItemSizes(self, enable: bool)

setUpdatesEnabled(self, enable: bool)

setVerticalScrollBar(self, scrollbar: QScrollBar)

setVerticalScrollBarPolicy(self, a0: Qt.ScrollBarPolicy)

setVerticalScrollMode(self, mode: QAbstractItemView.ScrollMode)

setViewMode(self, mode: QListView.ViewMode)

setViewport(self, widget: QWidget)

setViewportMargins(self, left: int, top: int, right: int, bottom: int)

setViewportMargins(self, margins: QMargins) → None

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)

setWordWrap(self, on: bool)

setWrapping(self, enable: bool)

setupViewport(self, viewport: QWidget)

sharedPainter(self) → QPainter

show(self)

showDropIndicator(self) → bool

showEvent(self, a0: QShowEvent)

showFullScreen(self)

showMaximized(self)

showMinimized(self)

showNormal(self)

signalsBlocked(self) → bool

size(self) → QSize

sizeAdjustPolicy(self) → QAbstractScrollArea.SizeAdjustPolicy

sizeHint(self) → QSize

sizeHintForColumn(self, column: int) → int

sizeHintForIndex(self, index: QModelIndex) → QSize

sizeHintForRow(self, row: int) → int

sizeIncrement(self) → QSize

sizePolicy(self) → QSizePolicy

sortItems(self, order: Qt.SortOrder = Qt.AscendingOrder)

spacing(self) → int

stackUnder(self, a0: QWidget)

startDrag(self, supportedActions: Qt.DropAction)

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

state(self) → QAbstractItemView.State

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

statusTip(self) → str

style(self) → QStyle

styleSheet(self) → str

supportedDropActions(self) → Qt.DropAction

tabKeyNavigation(self) → bool

tabletEvent(self, a0: QTabletEvent)

takeItem(self, row: int) → QListWidgetItem

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

textElideMode(self) → Qt.TextElideMode

thread(self) → QThread

timerEvent(self, e: 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)

uniformItemSizes(self) → bool

unsetCursor(self)

unsetLayoutDirection(self)

unsetLocale(self)

update(self)

update(self, index: QModelIndex) → None

updateEditorData(self)

updateEditorGeometries(self)

updateGeometries(self)

updateGeometry(self)

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

updatesEnabled(self) → bool

verticalOffset(self) → int

verticalScrollBar(self) → QScrollBar

verticalScrollBarPolicy(self) → Qt.ScrollBarPolicy

verticalScrollMode(self) → QAbstractItemView.ScrollMode

verticalScrollbarAction(self, action: int)

verticalScrollbarValueChanged(self, value: int)

viewMode(self) → QListView.ViewMode

viewport(self) → QWidget

viewportEntered

viewportEntered(self) [signal]

viewportEvent(self, e: QEvent) → bool

viewportMargins(self) → QMargins

viewportSizeHint(self) → QSize

visibleRegion(self) → QRegion

visualItemRect(self, item: QListWidgetItem) → QRect

visualRect(self, index: QModelIndex) → QRect

visualRegionForSelection(self, selection: QItemSelection) → QRegion

whatsThis(self) → str

wheelEvent(self, e: 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

wordWrap(self) → bool

x(self) → int

y(self) → int

class schrodinger.application.matsci.reordergui.StructureView(scene)

Bases: schrodinger.ui.qt.structure2d.structure_view

View which holds a structure_item object

atom_highlighted

AdjustIgnored = 0

AdjustToContents = 2

AdjustToContentsOnFirstShow = 1

AnchorUnderMouse = 2

AnchorViewCenter = 1

BoundingRectViewportUpdate = 4

Box = 1

CacheBackground = 1

class CacheModeFlag(value)

Bases: enum.Flag

An enumeration.

CacheNone = 0

CacheBackground = 1

CacheNone = 0

DontAdjustForAntialiasing = 2

DontSavePainterState = 1

class DragMode(value)

Bases: enum.Enum

An enumeration.

NoDrag = 0

ScrollHandDrag = 1

RubberBandDrag = 2

DrawChildren = 2

DrawWindowBackground = 1

FullViewportUpdate = 0

HLine = 4

IgnoreMask = 4

MinimalViewportUpdate = 1

NoAnchor = 0

NoDrag = 0

NoFrame = 0

NoViewportUpdate = 3

class OptimizationFlag(value)

Bases: enum.Flag

An enumeration.

DontSavePainterState = 1

DontAdjustForAntialiasing = 2

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

RubberBandDrag = 2

ScrollHandDrag = 1

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 SizeAdjustPolicy(value)

Bases: enum.Enum

An enumeration.

AdjustIgnored = 0

AdjustToContentsOnFirstShow = 1

AdjustToContents = 2

SmartViewportUpdate = 2

class StyleMask(value)

Bases: enum.Enum

An enumeration.

Shadow_Mask = 240

Shape_Mask = 15

StyledPanel = 6

Sunken = 48

VLine = 5

class ViewportAnchor(value)

Bases: enum.Enum

An enumeration.

NoAnchor = 0

AnchorViewCenter = 1

AnchorUnderMouse = 2

class ViewportUpdateMode(value)

Bases: enum.Enum

An enumeration.

FullViewportUpdate = 0

MinimalViewportUpdate = 1

SmartViewportUpdate = 2

BoundingRectViewportUpdate = 4

NoViewportUpdate = 3

WinPanel = 3

__init__(scene)

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])

addScrollBarWidget(self, widget: QWidget, alignment: Qt.AlignmentFlag)

adjustSize(self)

alignment(self) → Qt.AlignmentFlag

atom_clicked

autoFillBackground(self) → bool

backgroundBrush(self) → QBrush

backgroundRole(self) → QPalette.ColorRole

baseSize(self) → QSize

blockSignals(self, b: bool) → bool

bond_clicked

cacheMode(self) → QGraphicsView.CacheModeFlag

centerOn(self, pos: QPointF)

centerOn(self, item: QGraphicsItem) → None

centerOn(self, ax: float, ay: float) → None

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(self, a0: QCloseEvent)

colorCount(self) → int

connectNotify(self, signal: QMetaMethod)

contentsMargins(self) → QMargins

contentsRect(self) → QRect

contextMenuEvent(self, event: QContextMenuEvent)

contextMenuPolicy(self) → Qt.ContextMenuPolicy

cornerWidget(self) → QWidget

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, event: QDragEnterEvent)

dragLeaveEvent(self, event: QDragLeaveEvent)

dragMode(self) → QGraphicsView.DragMode

dragMoveEvent(self, event: QDragMoveEvent)

drawBackground(self, painter: QPainter, rect: QRectF)

drawForeground(self, painter: QPainter, rect: QRectF)

drawFrame(self, a0: QPainter)

dropEvent(self, event: QDropEvent)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

effectiveWinId(self) → PyQt6.sip.voidptr

ensurePolished(self)

ensureVisible(self, rect: QRectF, xMargin: int = 50, yMargin: int = 50)

ensureVisible(self, item: QGraphicsItem, xMargin: int = 50, yMargin: int = 50) → None

ensureVisible(self, x: float, y: float, w: float, h: float, xMargin: int = 50, yMargin: int = 50) → None

enterEvent(self, event: QEnterEvent)

event(self, event: 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]

fitInView(self, rect: QRectF, mode: Qt.AspectRatioMode = Qt.IgnoreAspectRatio)

fitInView(self, item: QGraphicsItem, mode: Qt.AspectRatioMode = Qt.IgnoreAspectRatio) → None

fitInView(self, x: float, y: float, w: float, h: float, mode: Qt.AspectRatioMode = Qt.IgnoreAspectRatio) → None

focusInEvent(self, event: QFocusEvent)

focusNextChild(self) → bool

focusNextPrevChild(self, next: bool) → bool

focusOutEvent(self, event: QFocusEvent)

focusPolicy(self) → Qt.FocusPolicy

focusPreviousChild(self) → bool

focusProxy(self) → QWidget

focusWidget(self) → QWidget

font(self) → QFont

fontInfo(self) → QFontInfo

fontMetrics(self) → QFontMetrics

foregroundBrush(self) → QBrush

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

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)

horizontalScrollBar(self) → QScrollBar

horizontalScrollBarPolicy(self) → Qt.ScrollBarPolicy

inherits(self, classname: str) → bool

initPainter(self, painter: QPainter)

initStyleOption(self, option: QStyleOptionFrame)

inputMethodEvent(self, event: QInputMethodEvent)

inputMethodHints(self) → Qt.InputMethodHint

inputMethodQuery(self, query: Qt.InputMethodQuery) → Any

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

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

installEventFilter(self, a0: QObject)

invalidateScene(self, rect: QRectF = QRectF(), layers: QGraphicsScene.SceneLayer = QGraphicsScene.AllLayers)

isActiveWindow(self) → bool

isAncestorOf(self, child: QWidget) → bool

isEnabled(self) → bool

isEnabledTo(self, a0: QWidget) → bool

isFullScreen(self) → bool

isHidden(self) → bool

isInteractive(self) → bool

isLeftToRight(self) → bool

isMaximized(self) → bool

isMinimized(self) → bool

isModal(self) → bool

isRightToLeft(self) → bool

isSignalConnected(self, signal: QMetaMethod) → bool

isTransformed(self) → bool

isVisible(self) → bool

isVisibleTo(self, a0: QWidget) → bool

isWidgetType(self) → bool

isWindow(self) → bool

isWindowModified(self) → bool

isWindowType(self) → bool

itemAt(self, pos: QPoint) → QGraphicsItem

itemAt(self, ax: int, ay: int) → QGraphicsItem

items(self) → List[QGraphicsItem]

items(self, pos: QPoint) → List[QGraphicsItem]

items(self, x: int, y: int) → List[QGraphicsItem]

items(self, x: int, y: int, w: int, h: int, mode: Qt.ItemSelectionMode = Qt.IntersectsItemShape) → List[QGraphicsItem]

items(self, rect: QRect, mode: Qt.ItemSelectionMode = Qt.IntersectsItemShape) → List[QGraphicsItem]

items(self, polygon: QPolygon, mode: Qt.ItemSelectionMode = Qt.IntersectsItemShape) → List[QGraphicsItem]

items(self, path: QPainterPath, mode: Qt.ItemSelectionMode = Qt.IntersectsItemShape) → List[QGraphicsItem]

keyPressEvent(self, event: QKeyEvent)

keyReleaseEvent(self, event: 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

mapFromScene(self, point: QPointF) → QPoint

mapFromScene(self, rect: QRectF) → QPolygon

mapFromScene(self, polygon: QPolygonF) → QPolygon

mapFromScene(self, path: QPainterPath) → QPainterPath

mapFromScene(self, ax: float, ay: float) → QPoint

mapFromScene(self, ax: float, ay: float, w: float, h: float) → QPolygon

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

mapToScene(self, point: QPoint) → QPointF

mapToScene(self, rect: QRect) → QPolygonF

mapToScene(self, polygon: QPolygon) → QPolygonF

mapToScene(self, path: QPainterPath) → QPainterPath

mapToScene(self, ax: int, ay: int) → QPointF

mapToScene(self, ax: int, ay: int, w: int, h: int) → QPolygonF

mask(self) → QRegion

maximumHeight(self) → int

maximumSize(self) → QSize

maximumViewportSize(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, event: QMouseEvent)

mouseGrabber() → QWidget

mouseMoveEvent(self, event: QMouseEvent)

mousePressEvent(self, event: QMouseEvent)

mouseReleaseEvent(self, event: 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]

optimizationFlags(self) → QGraphicsView.OptimizationFlag

overrideWindowFlags(self, type: Qt.WindowType)

overrideWindowState(self, state: Qt.WindowState)

paintEngine(self) → QPaintEngine

paintEvent(self, event: 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, painter: QPainter, target: QRectF = QRectF(), source: QRect = QRect(), mode: Qt.AspectRatioMode = Qt.KeepAspectRatio)

renderHints(self) → QPainter.RenderHint

repaint(self)

repaint(self, x: int, y: int, w: int, h: int) → None

repaint(self, a0: QRect) → None

repaint(self, a0: QRegion) → None

resetCachedContent(self)

resetTransform(self)

resize(self, a0: QSize)

resize(self, w: int, h: int) → None

resizeAnchor(self) → QGraphicsView.ViewportAnchor

resizeEvent(self, event: QResizeEvent)

restoreGeometry(self, geometry: QByteArray) → bool

rotate(self, angle: float)

rubberBandChanged

rubberBandChanged(self, viewportRect: QRect, fromScenePoint: QPointF, toScenePoint: QPointF) [signal]

rubberBandRect(self) → QRect

rubberBandSelectionMode(self) → Qt.ItemSelectionMode

saveGeometry(self) → QByteArray

scale(self, sx: float, sy: float)

scene(self) → QGraphicsScene

sceneRect(self) → QRectF

screen(self) → QScreen

scroll(self, dx: int, dy: int)

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

scrollBarWidgets(self, alignment: Qt.AlignmentFlag) → List[QWidget]

scrollContentsBy(self, dx: int, dy: int)

sender(self) → QObject

senderSignalIndex(self) → int

setAcceptDrops(self, on: bool)

setAccessibleDescription(self, description: str)

setAccessibleName(self, name: str)

setAlignment(self, alignment: Qt.AlignmentFlag)

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

setAutoFillBackground(self, enabled: bool)

setBackgroundBrush(self, brush: Union[QBrush, QColor, Qt.GlobalColor, int, QGradient])

setBackgroundRole(self, a0: QPalette.ColorRole)

setBaseSize(self, basew: int, baseh: int)

setBaseSize(self, s: QSize) → None

setCacheMode(self, mode: QGraphicsView.CacheModeFlag)

setContentsMargins(self, left: int, top: int, right: int, bottom: int)

setContentsMargins(self, margins: QMargins) → None

setContextMenuPolicy(self, policy: Qt.ContextMenuPolicy)

setCornerWidget(self, widget: QWidget)

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

setDisabled(self, a0: bool)

setDragMode(self, mode: QGraphicsView.DragMode)

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)

setForegroundBrush(self, brush: Union[QBrush, QColor, Qt.GlobalColor, int, QGradient])

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)

setHorizontalScrollBar(self, scrollbar: QScrollBar)

setHorizontalScrollBarPolicy(self, a0: Qt.ScrollBarPolicy)

setInputMethodHints(self, hints: Qt.InputMethodHint)

setInteractive(self, allowed: bool)

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)

setOptimizationFlag(self, flag: QGraphicsView.OptimizationFlag, enabled: bool = True)

setOptimizationFlags(self, flags: QGraphicsView.OptimizationFlag)

setPalette(self, a0: QPalette)

setParent(self, parent: QWidget)

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

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

setRenderHint(self, hint: QPainter.RenderHint, on: bool = True)

setRenderHints(self, hints: QPainter.RenderHint)

setResizeAnchor(self, anchor: QGraphicsView.ViewportAnchor)

setRubberBandSelectionMode(self, mode: Qt.ItemSelectionMode)

setScene(self, scene: QGraphicsScene)

setSceneRect(self, rect: QRectF)

setSceneRect(self, ax: float, ay: float, aw: float, ah: float) → None

setScreen(self, a0: QScreen)

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

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

setSizeAdjustPolicy(self, policy: QAbstractScrollArea.SizeAdjustPolicy)

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)

setTransform(self, matrix: QTransform, combine: bool = False)

setTransformationAnchor(self, anchor: QGraphicsView.ViewportAnchor)

setUpdatesEnabled(self, enable: bool)

setVerticalScrollBar(self, scrollbar: QScrollBar)

setVerticalScrollBarPolicy(self, a0: Qt.ScrollBarPolicy)

setViewport(self, widget: QWidget)

setViewportMargins(self, left: int, top: int, right: int, bottom: int)

setViewportMargins(self, margins: QMargins) → None

setViewportUpdateMode(self, mode: QGraphicsView.ViewportUpdateMode)

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)

setupViewport(self, widget: QWidget)

sharedPainter(self) → QPainter

shear(self, sh: float, sv: float)

show(self)

showEvent(self, event: QShowEvent)

showFullScreen(self)

showMaximized(self)

showMinimized(self)

showNormal(self)

signalsBlocked(self) → bool

size(self) → QSize

sizeAdjustPolicy(self) → QAbstractScrollArea.SizeAdjustPolicy

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

transform(self) → QTransform

transformationAnchor(self) → QGraphicsView.ViewportAnchor

translate(self, dx: float, dy: float)

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)

updateScene(self, rects: Iterable[QRectF])

updateSceneRect(self, rect: QRectF)

updatesEnabled(self) → bool

verticalScrollBar(self) → QScrollBar

verticalScrollBarPolicy(self) → Qt.ScrollBarPolicy

viewport(self) → QWidget

viewportEvent(self, event: QEvent) → bool

viewportMargins(self) → QMargins

viewportSizeHint(self) → QSize

viewportTransform(self) → QTransform

viewportUpdateMode(self) → QGraphicsView.ViewportUpdateMode

visibleRegion(self) → QRegion

whatsThis(self) → str

wheelEvent(self, event: 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.matsci.reordergui.StructurePic(scene)

Bases: schrodinger.ui.qt.structure2d.structure_item

The QGraphicsItem that holds a 2D image of a structure

__init__(scene)

Create a StructurePic instance

Parameters

scene (QGraphicsScene) – The Scene this image is placed in

reset()

Clear all the annotators and remove the picture

hoverMoveEvent(event)

Track when the mouse is over an atom - emit a signal when it enters a new atom or leaves an atom. An index of 0 is emitted when the mouse is not over any atom.

setStructure(struct)

Set the structure - create a new image of it

Parameters

struct (schrodinger.structure.Structure) – The structure object for this picture

selectAtom(index)

Select an atom in the image and regenerate the picture

Parameters

index (int) – The atom index to select

markAtomMapped(index, guess=False, generate=True)

Mark an atom as mapped (either by guess or manually) and regenerate the picture.

Parameters

• index (int) – The atom index to mark

• guess (bool) – True if this mark results from a guess, False if not. The background color used depends on this parameter.

• generate (bool) – Whether to regenerate the 2D picture

markAtomUnmapped(index)

Mark an atom as unmapped and regenerate the picture.

Parameters

index (int) – The atom index to mark

highlightAtom(index, guess=False)

Highlight an atom

Parameters

• index (int) – The atom index to highlight

• guess (bool) – True if this atom is marked by a guess, False if it was marked by the user. The background color used depends on this parameter.

highlightSuggestedAtom(index)

Highlight suggested atom

Parameters

index (int) – The atom index to highlight

class CacheMode(value)

Bases: enum.Enum

An enumeration.

NoCache = 0

ItemCoordinateCache = 1

DeviceCoordinateCache = 2

DeviceCoordinateCache = 2

class GraphicsItemChange(value)

Bases: enum.Enum

An enumeration.

ItemPositionChange = 0

ItemVisibleChange = 2

ItemEnabledChange = 3

ItemSelectedChange = 4

ItemParentChange = 5

ItemChildAddedChange = 6

ItemChildRemovedChange = 7

ItemTransformChange = 8

ItemPositionHasChanged = 9

ItemTransformHasChanged = 10

ItemSceneChange = 11

ItemVisibleHasChanged = 12

ItemEnabledHasChanged = 13

ItemSelectedHasChanged = 14

ItemParentHasChanged = 15

ItemSceneHasChanged = 16

ItemCursorChange = 17

ItemCursorHasChanged = 18

ItemToolTipChange = 19

ItemToolTipHasChanged = 20

ItemFlagsChange = 21

ItemFlagsHaveChanged = 22

ItemZValueChange = 23

ItemZValueHasChanged = 24

ItemOpacityChange = 25

ItemOpacityHasChanged = 26

ItemScenePositionHasChanged = 27

ItemRotationChange = 28

ItemRotationHasChanged = 29

ItemScaleChange = 30

ItemScaleHasChanged = 31

ItemTransformOriginPointChange = 32

ItemTransformOriginPointHasChanged = 33

class GraphicsItemFlag(value)

Bases: enum.Flag

An enumeration.

ItemIsMovable = 1

ItemIsSelectable = 2

ItemIsFocusable = 4

ItemClipsToShape = 8

ItemClipsChildrenToShape = 16

ItemIgnoresTransformations = 32

ItemIgnoresParentOpacity = 64

ItemDoesntPropagateOpacityToChildren = 128

ItemStacksBehindParent = 256

ItemUsesExtendedStyleOption = 512

ItemHasNoContents = 1024

ItemSendsGeometryChanges = 2048

ItemAcceptsInputMethod = 4096

ItemNegativeZStacksBehindParent = 8192

ItemIsPanel = 16384

ItemSendsScenePositionChanges = 65536

ItemContainsChildrenInShape = 524288

ItemAcceptsInputMethod = 4096

ItemChildAddedChange = 6

ItemChildRemovedChange = 7

ItemClipsChildrenToShape = 16

ItemClipsToShape = 8

ItemContainsChildrenInShape = 524288

ItemCoordinateCache = 1

ItemCursorChange = 17

ItemCursorHasChanged = 18

ItemDoesntPropagateOpacityToChildren = 128

ItemEnabledChange = 3

ItemEnabledHasChanged = 13

ItemFlagsChange = 21

ItemFlagsHaveChanged = 22

ItemHasNoContents = 1024

ItemIgnoresParentOpacity = 64

ItemIgnoresTransformations = 32

ItemIsFocusable = 4

ItemIsMovable = 1

ItemIsPanel = 16384

ItemIsSelectable = 2

ItemNegativeZStacksBehindParent = 8192

ItemOpacityChange = 25

ItemOpacityHasChanged = 26

ItemParentChange = 5

ItemParentHasChanged = 15

ItemPositionChange = 0

ItemPositionHasChanged = 9

ItemRotationChange = 28

ItemRotationHasChanged = 29

ItemScaleChange = 30

ItemScaleHasChanged = 31

ItemSceneChange = 11

ItemSceneHasChanged = 16

ItemScenePositionHasChanged = 27

ItemSelectedChange = 4

ItemSelectedHasChanged = 14

ItemSendsGeometryChanges = 2048

ItemSendsScenePositionChanges = 65536

ItemStacksBehindParent = 256

ItemToolTipChange = 19

ItemToolTipHasChanged = 20

ItemTransformChange = 8

ItemTransformHasChanged = 10

ItemTransformOriginPointChange = 32

ItemTransformOriginPointHasChanged = 33

ItemUsesExtendedStyleOption = 512

ItemVisibleChange = 2

ItemVisibleHasChanged = 12

ItemZValueChange = 23

ItemZValueHasChanged = 24

NoCache = 0

NonModal = 0

PanelModal = 1

class PanelModality(value)

Bases: enum.Enum

An enumeration.

NonModal = 0

PanelModal = 1

SceneModal = 2

SceneModal = 2

Type = 1

UserType = 65536

acceptDrops(self) → bool

acceptHoverEvents(self) → bool

acceptTouchEvents(self) → bool

acceptedMouseButtons(self) → Qt.MouseButton

add_annotator(annotator)

Adds annotator to stack. The order that these functions get added is the order that they will be applied to the picture.

Parameters

annotator (schrodinger.infra.canvas2d.ChemViewAnnotator) – Annotator which draws on top an image

add_annotator_function_return(function)

Add functions that need to get returned after the structure is rendered on the screen. An example of this would be a function that returns drawmol coordinates.

advance(self, phase: int)

boundingRect(self) → QRectF

boundingRegion(self, itemToDeviceTransform: QTransform) → QRegion

boundingRegionGranularity(self) → float

cacheMode(self) → QGraphicsItem.CacheMode

childItems(self) → List[QGraphicsItem]

childrenBoundingRect(self) → QRectF

clear()

Clear picture from item.

clearFocus(self)

clear_annotators()

Clears all annotators

clipPath(self) → QPainterPath

collidesWithItem(self, other: QGraphicsItem, mode: Qt.ItemSelectionMode = Qt.IntersectsItemShape) → bool

collidesWithPath(self, path: QPainterPath, mode: Qt.ItemSelectionMode = Qt.IntersectsItemShape) → bool

collidingItems(self, mode: Qt.ItemSelectionMode = Qt.IntersectsItemShape) → List[QGraphicsItem]

commonAncestorItem(self, other: QGraphicsItem) → QGraphicsItem

contains(self, point: QPointF) → bool

contextMenuEvent(self, event: QGraphicsSceneContextMenuEvent)

cursor(self) → QCursor

data(self, key: int) → Any

deviceTransform(self, viewportTransform: QTransform) → QTransform

dragEnterEvent(self, event: QGraphicsSceneDragDropEvent)

dragLeaveEvent(self, event: QGraphicsSceneDragDropEvent)

dragMoveEvent(self, event: QGraphicsSceneDragDropEvent)

dropEvent(self, event: QGraphicsSceneDragDropEvent)

effectiveOpacity(self) → float

ensureVisible(self, rect: QRectF = QRectF(), xMargin: int = 50, yMargin: int = 50)

ensureVisible(self, x: float, y: float, w: float, h: float, xMargin: int = 50, yMargin: int = 50) → None

filtersChildEvents(self) → bool

flags(self) → QGraphicsItem.GraphicsItemFlag

focusInEvent(self, event: QFocusEvent)

focusItem(self) → QGraphicsItem

focusOutEvent(self, event: QFocusEvent)

focusProxy(self) → QGraphicsItem

generate_picture(gen_coord=True)

Generates a QPicture of the structure. This should be called after setting the structure and the accompaning annotators.

Parameters

gen_coord (bool) – if True generate coordinates.

getBondAtLocation(pos)

Return the bond at the specified coordinates

Parameters

pos (PyQt5.QtCore.QPoint) – The specified coordinates

Returns

If there is a bond at the specified coordinates, return a list of the chmmol atom indices for the two bound atoms. (Note that the chmmol atom indices are zero-indexed, so you should add one to each index if you want the schrodinger.structure.Structure atom indices). If there is no bond at the specified coordinates, return an empty list.

Return type

list

grabKeyboard(self)

grabMouse(self)

graphicsEffect(self) → QGraphicsEffect

group(self) → QGraphicsItemGroup

hasCursor(self) → bool

hasFocus(self) → bool

hide(self)

hoverEnterEvent(self, event: QGraphicsSceneHoverEvent)

hoverLeaveEvent(self, event: QGraphicsSceneHoverEvent)

inputMethodEvent(self, event: QInputMethodEvent)

inputMethodHints(self) → Qt.InputMethodHint

inputMethodQuery(self, query: Qt.InputMethodQuery) → Any

installSceneEventFilter(self, filterItem: QGraphicsItem)

isActive(self) → bool

isAncestorOf(self, child: QGraphicsItem) → bool

isBlockedByModalPanel(self) → Tuple[bool, QGraphicsItem]

isClipped(self) → bool

isEnabled(self) → bool

isObscured(self, rect: QRectF = QRectF()) → bool

isObscured(self, ax: float, ay: float, w: float, h: float) → bool

isObscuredBy(self, item: QGraphicsItem) → bool

isPanel(self) → bool

isSelected(self) → bool

isUnderMouse(self) → bool

isVisible(self) → bool

isVisibleTo(self, parent: QGraphicsItem) → bool

isWidget(self) → bool

isWindow(self) → bool

itemChange(self, change: QGraphicsItem.GraphicsItemChange, value: Any) → Any

itemTransform(self, other: QGraphicsItem) → Tuple[QTransform, bool]

keyPressEvent(self, event: QKeyEvent)

keyReleaseEvent(self, event: QKeyEvent)

mapFromItem(self, item: QGraphicsItem, point: QPointF) → QPointF

mapFromItem(self, item: QGraphicsItem, rect: QRectF) → QPolygonF

mapFromItem(self, item: QGraphicsItem, polygon: QPolygonF) → QPolygonF

mapFromItem(self, item: QGraphicsItem, path: QPainterPath) → QPainterPath

mapFromItem(self, item: QGraphicsItem, ax: float, ay: float) → QPointF

mapFromItem(self, item: QGraphicsItem, ax: float, ay: float, w: float, h: float) → QPolygonF

mapFromParent(self, point: QPointF) → QPointF

mapFromParent(self, rect: QRectF) → QPolygonF

mapFromParent(self, polygon: QPolygonF) → QPolygonF

mapFromParent(self, path: QPainterPath) → QPainterPath

mapFromParent(self, ax: float, ay: float) → QPointF

mapFromParent(self, ax: float, ay: float, w: float, h: float) → QPolygonF

mapFromScene(self, point: QPointF) → QPointF

mapFromScene(self, rect: QRectF) → QPolygonF

mapFromScene(self, polygon: QPolygonF) → QPolygonF

mapFromScene(self, path: QPainterPath) → QPainterPath

mapFromScene(self, ax: float, ay: float) → QPointF

mapFromScene(self, ax: float, ay: float, w: float, h: float) → QPolygonF

mapRectFromItem(self, item: QGraphicsItem, rect: QRectF) → QRectF

mapRectFromItem(self, item: QGraphicsItem, ax: float, ay: float, w: float, h: float) → QRectF

mapRectFromParent(self, rect: QRectF) → QRectF

mapRectFromParent(self, ax: float, ay: float, w: float, h: float) → QRectF

mapRectFromScene(self, rect: QRectF) → QRectF

mapRectFromScene(self, ax: float, ay: float, w: float, h: float) → QRectF

mapRectToItem(self, item: QGraphicsItem, rect: QRectF) → QRectF

mapRectToItem(self, item: QGraphicsItem, ax: float, ay: float, w: float, h: float) → QRectF

mapRectToParent(self, rect: QRectF) → QRectF

mapRectToParent(self, ax: float, ay: float, w: float, h: float) → QRectF

mapRectToScene(self, rect: QRectF) → QRectF

mapRectToScene(self, ax: float, ay: float, w: float, h: float) → QRectF

mapToItem(self, item: QGraphicsItem, point: QPointF) → QPointF

mapToItem(self, item: QGraphicsItem, rect: QRectF) → QPolygonF

mapToItem(self, item: QGraphicsItem, polygon: QPolygonF) → QPolygonF

mapToItem(self, item: QGraphicsItem, path: QPainterPath) → QPainterPath

mapToItem(self, item: QGraphicsItem, ax: float, ay: float) → QPointF

mapToItem(self, item: QGraphicsItem, ax: float, ay: float, w: float, h: float) → QPolygonF

mapToParent(self, point: QPointF) → QPointF

mapToParent(self, rect: QRectF) → QPolygonF

mapToParent(self, polygon: QPolygonF) → QPolygonF

mapToParent(self, path: QPainterPath) → QPainterPath

mapToParent(self, ax: float, ay: float) → QPointF

mapToParent(self, ax: float, ay: float, w: float, h: float) → QPolygonF

mapToScene(self, point: QPointF) → QPointF

mapToScene(self, rect: QRectF) → QPolygonF

mapToScene(self, polygon: QPolygonF) → QPolygonF

mapToScene(self, path: QPainterPath) → QPainterPath

mapToScene(self, ax: float, ay: float) → QPointF

mapToScene(self, ax: float, ay: float, w: float, h: float) → QPolygonF

mouseDoubleClickEvent(self, event: QGraphicsSceneMouseEvent)

mouseMoveEvent(self, event: QGraphicsSceneMouseEvent)

mousePressEvent(event)

Emit a signal if the user left-clicked on an atom or a bond

mouseReleaseEvent(self, event: QGraphicsSceneMouseEvent)

moveBy(self, dx: float, dy: float)

opacity(self) → float

opaqueArea(self) → QPainterPath

paint(painter, option, widget=0)

Overrides the paint function to draw the picture that has already been generated. This should never be called manually.

panel(self) → QGraphicsItem

panelModality(self) → QGraphicsItem.PanelModality

parentItem(self) → QGraphicsItem

parentObject(self) → QGraphicsObject

parentWidget(self) → QGraphicsWidget

pos(self) → QPointF

prepareGeometryChange(self)

removeSceneEventFilter(self, filterItem: QGraphicsItem)

resetTransform(self)

rotation(self) → float

scale(self) → float

scene(self) → QGraphicsScene

sceneBoundingRect(self) → QRectF

sceneEvent(self, event: QEvent) → bool

sceneEventFilter(self, watched: QGraphicsItem, event: QEvent) → bool

scenePos(self) → QPointF

sceneTransform(self) → QTransform

scroll(self, dx: float, dy: float, rect: QRectF = QRectF())

setAcceptDrops(self, on: bool)

setAcceptHoverEvents(self, enabled: bool)

setAcceptTouchEvents(self, enabled: bool)

setAcceptedMouseButtons(self, buttons: Qt.MouseButton)

setActive(self, active: bool)

setBoundingRegionGranularity(self, granularity: float)

setCacheMode(self, mode: QGraphicsItem.CacheMode, logicalCacheSize: QSize = QSize())

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

setData(self, key: int, value: Any)

setEnabled(self, enabled: bool)

setFiltersChildEvents(self, enabled: bool)

setFlag(self, flag: QGraphicsItem.GraphicsItemFlag, enabled: bool = True)

setFlags(self, flags: QGraphicsItem.GraphicsItemFlag)

setFocus(self, focusReason: Qt.FocusReason = Qt.OtherFocusReason)

setFocusProxy(self, item: QGraphicsItem)

setGraphicsEffect(self, effect: QGraphicsEffect)

setGroup(self, group: QGraphicsItemGroup)

setInputMethodHints(self, hints: Qt.InputMethodHint)

setOpacity(self, opacity: float)

setPanelModality(self, panelModality: QGraphicsItem.PanelModality)

setParentItem(self, parent: QGraphicsItem)

setPos(self, pos: QPointF)

setPos(self, ax: float, ay: float) → None

setRotation(self, angle: float)

setScale(self, scale: float)

setSelected(self, selected: bool)

setToolTip(self, toolTip: str)

setTransform(self, matrix: QTransform, combine: bool = False)

setTransformOriginPoint(self, origin: QPointF)

setTransformOriginPoint(self, ax: float, ay: float) → None

setTransformations(self, transformations: Iterable[QGraphicsTransform])

setVisible(self, visible: bool)

setX(self, x: float)

setY(self, y: float)

setZValue(self, z: float)

set_colormap(colormap)

Sets the colormap for the atom and bond coloring. Otherwise, the coloring used will be that coming from the ct and/or chmmol.

set_rect(rect)

Parameters

rect (QRect) – size of bounding box

set_structure(struct, StereoType=StereoType.StereoFromAnnotationAndGeometry_Safe, hydrogenTreatment=H.H_ExplicitOnly, wantProperties=True, wantMMStereoProps=True, readAtomBondProperties=True, allowRadicals=False)

Set the structure to the given Structure object.

Parameters

• struct (schrodinger.structure.Structure class object) – structure to be drawn on the canvas

• StereoType (ChmMmctAdaptor.StereoType) – Stereochemistry option to use. Avialable options: # Does not include stereochemistry info: canvas2d.ChmMmctAdaptor.NoStereo # Ignores mmstereo annotations: canvas2d.ChmMmctAdaptor.StereoFromGeometry # Silently ignores stereo information that Canvas doesn’t agree with: canvas2d.ChmMmctAdaptor.StereoFromGeometry_Safe # Ignores 3d geometry: canvas2d.ChmMmctAdaptor.StereoFromAnnotation # Silently ignores stereo information that Canvas doesn’t agree with: canvas2d.ChmMmctAdaptor.StereoFromAnnotation_Safe # Uses mmstereo annotaions with 3D geometry as a backup: canvas2d.ChmMmctAdaptor.StereoFromAnnotationAndGeometry # Silently ignores stereo information that Canvas doesn’t agree with: canvas2d.ChmMmctAdaptor.StereoFromAnnotationAndGeometry_Safe

• hydrogenTreatment (canvas2d.ChmAtomOption.H) – Hydrogen treatment method. canvas2d.ChmAtomOption.H_Never canvas2d.ChmAtomOption.H_ExplicitOnly canvas2d.ChmAtomOption.H_Polar canvas2d.ChmAtomOption.H_ExplicitPolar canvas2d.ChmAtomOption.H_Chiral canvas2d.ChmAtomOption.H_ExplicitChiral canvas2d.ChmAtomOption.H_ExplicitPolarAndChiral canvas2d.ChmAtomOption.H_All

• wantProperties (bool) – Whether properties should be copied.

• wantMMStereoProps (bool) – Whether to copy mmstereo properties.

• readAtomBondProperties (bool) – Whether to copy atom and bond-level properties.

• allowRadicals (bool) – Whether to assume that valence deficiencies represent unpaired electrons.

set_text(text, alignment=None)

Sets text in the view. This is useful if you display text in place of a structure, in places where no structure is available.

Parameters

• text (string) – text to be displayed

• alignment (Qt.AlignmentFlags) – alignment flags of text, defaults to QtCore.Qt.AlignVCenter|QtCore.Qt.AlignCenter

shape(self) → QPainterPath

show(self)

stackBefore(self, sibling: QGraphicsItem)

toGraphicsObject(self) → QGraphicsObject

toolTip(self) → str

topLevelItem(self) → QGraphicsItem

topLevelWidget(self) → QGraphicsWidget

transform(self) → QTransform

transformOriginPoint(self) → QPointF

transformations(self) → List[QGraphicsTransform]

type(self) → int

ungrabKeyboard(self)

ungrabMouse(self)

unsetCursor(self)

update(self, rect: QRectF = QRectF())

update(self, ax: float, ay: float, width: float, height: float) → None

updateMicroFocus(self)

wheelEvent(self, event: QGraphicsSceneWheelEvent)

window(self) → QGraphicsWidget

x(self) → float

y(self) → float

zValue(self) → float

class schrodinger.application.matsci.reordergui.StructureFrame(master, label_layout, structure_layout, list_layout, struct=None, mytype='Comparison', atomic_constraints=None, enable_2d_structure=True)

Bases: PyQt6.QtWidgets.QFrame

A QFrame that contains a 2D image of a structure. This also creates a QListWidget that is coordinated with the 2D image. This is the base class for both the Reference and Comparison structures.

__init__(master, label_layout, structure_layout, list_layout, struct=None, mytype='Comparison', atomic_constraints=None, enable_2d_structure=True)

Create a StructureFrame instance

Parameters

• master (ReorderAtomFrame) – The master Frame for this widget

• label_layout (QBoxLayout) – The layout to add the label.

• structure_layout (QBoxLayout) – The layout to add this widget to.

• list_layout (QBoxLayout) – The layout to add the associated ListWidget to.

• struct (schrodinger.structure.Structure) – The structure for this frame

• mytype (str) – Either REFERENCE or COMPARISON, the type of structure this Frame applies to.

• atomic_constraints (list or None) – list of atomic constraints for each atom or None

• enable_2d_structure (bool) – If True, enable/show 2D structure. Can be slow for inorganic materials

generatePicture()

Regenerate the 2D picture to show any changes

setLabel(guessing=False)

Set the label that describes what the user should do

Parameters

guessing (bool) – True if there is currently a guess in place, False if not.

setStructure(struct)

Set the structure for this frame. Updates the image and the list widget

Parameters

struct (schrodinger.structure.Structure) – The structure for this frame

highlightAtom(index, guess=False)

Highlight the given atom

Parameters

• index (int) – The atom index to highlight

• guess (bool) – True if this atom is marked by a guess, False if it was marked by the user. The background color used depends on this parameter.

unmapAtom(index)

Mark an atom as unmapped

Parameters

index (int) – The atom index to mark

reset(reset_structure=True)

Reset to a blank frame, or remove any mapping but keep the structure

Parameters

reset_structure – True if the structure should be reset, False if it should be kept

isValidAtomIndex(index)

Check if this index is a valid atom index for the loaded structure

Parameters

index (int) – The atom index to check

Return type

bool

Returns

True 0 < index <= atom_total, False otherwise

selectAtom(index)

Select an atom in both the image and listwidget

Parameters

index (int) – The atom index to select

Return type

structure._StructureAtom

Returns

selected atom

mapAtom(index, guess=False, generate=True)

Mark an atom as mapped

Parameters

• index (int) – The atom index to mark

• guess (bool) – True if this atom is marked by a guess, False if it was marked by the user. The background color used depends on this parameter.

• generate (bool) – Whether to regenerate the 2D picture

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

clearFocus(self)

clearMask(self)

close(self) → bool

closeEvent(self, a0: QCloseEvent)

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

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

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]

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

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)

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.matsci.reordergui.ComparisonFrame(master, label_layout, structure_layout, list_layout, struct=None, mytype='Comparison', atomic_constraints=None, enable_2d_structure=True)

Bases: schrodinger.application.matsci.reordergui.StructureFrame

The StructureFrame for the Comparison structure

suggestCloseAtom(xyz)

Highlight and return index of the closest atom from the XYZ location taking into account PBCs.

Param

Coordinates

Return type

int

Returns

Closest atom index

suggestedIndex()

Get last suggested index.

Return type

int or None

Returns

last suggested index

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

__init__(master, label_layout, structure_layout, list_layout, struct=None, mytype='Comparison', atomic_constraints=None, enable_2d_structure=True)

Create a StructureFrame instance

Parameters

• master (ReorderAtomFrame) – The master Frame for this widget

• label_layout (QBoxLayout) – The layout to add the label.

• structure_layout (QBoxLayout) – The layout to add this widget to.

• list_layout (QBoxLayout) – The layout to add the associated ListWidget to.

• struct (schrodinger.structure.Structure) – The structure for this frame

• mytype (str) – Either REFERENCE or COMPARISON, the type of structure this Frame applies to.

• atomic_constraints (list or None) – list of atomic constraints for each atom or None

• enable_2d_structure (bool) – If True, enable/show 2D structure. Can be slow for inorganic materials

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

clearFocus(self)

clearMask(self)

close(self) → bool

closeEvent(self, a0: QCloseEvent)

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

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

generatePicture()

Regenerate the 2D picture to show any changes

geometry(self) → QRect

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)

highlightAtom(index, guess=False)

Highlight the given atom

Parameters

• index (int) – The atom index to highlight

• guess (bool) – True if this atom is marked by a guess, False if it was marked by the user. The background color used depends on this parameter.

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

isValidAtomIndex(index)

Check if this index is a valid atom index for the loaded structure

Parameters

index (int) – The atom index to check

Return type

bool

Returns

True 0 < index <= atom_total, False otherwise

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)

mapAtom(index, guess=False, generate=True)

Mark an atom as mapped

Parameters

• index (int) – The atom index to mark

• guess (bool) – True if this atom is marked by a guess, False if it was marked by the user. The background color used depends on this parameter.

• generate (bool) – Whether to regenerate the 2D picture

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]

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

reset(reset_structure=True)

Reset to a blank frame, or remove any mapping but keep the structure

Parameters

reset_structure – True if the structure should be reset, False if it should be kept

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

selectAtom(index)

Select an atom in both the image and listwidget

Parameters

index (int) – The atom index to select

Return type

structure._StructureAtom

Returns

selected atom

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)

setLabel(guessing=False)

Set the label that describes what the user should do

Parameters

guessing (bool) – True if there is currently a guess in place, False if not.

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)

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)

setStructure(struct)

Set the structure for this frame. Updates the image and the list widget

Parameters

struct (schrodinger.structure.Structure) – The structure for this frame

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)

unmapAtom(index)

Mark an atom as unmapped

Parameters

index (int) – The atom index to mark

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.matsci.reordergui.ReferenceFrame(*args, **kwargs)

Bases: schrodinger.application.matsci.reordergui.StructureFrame

The StructureFrame for the Reference structure

__init__(*args, **kwargs)

Create a ReferenceFrame object. Parameters are described in the StructureFrame class

mapAtom(ref_index, advance=True, **kwargs)

Map the given atom index in the comparison structure to the given atom index in the reference structure.

Parameters

• ref_index (int) – The atom index of the reference molecule

• advance (bool) – Whether to advance the selected atom or not. The selection will automatically be advanced if ref_index is the currently selected atom regardless of this setting.

advanceSelection(index)

Move the selection to the next unmapped atom with a higher index. If none exist, start checking again at atom 1.

Parameters

index (int) – Start search for unmapped atoms with indexes higher than this number

selectedIndex()

Get the index of the currently selected atom

Return type

int

Returns

The index of the selected Reference atom

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

clearFocus(self)

clearMask(self)

close(self) → bool

closeEvent(self, a0: QCloseEvent)

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

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

generatePicture()

Regenerate the 2D picture to show any changes

geometry(self) → QRect

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)

highlightAtom(index, guess=False)

Highlight the given atom

Parameters

• index (int) – The atom index to highlight

• guess (bool) – True if this atom is marked by a guess, False if it was marked by the user. The background color used depends on this parameter.

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

isValidAtomIndex(index)

Check if this index is a valid atom index for the loaded structure

Parameters

index (int) – The atom index to check

Return type

bool

Returns

True 0 < index <= atom_total, False otherwise

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]

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

reset(reset_structure=True)

Reset to a blank frame, or remove any mapping but keep the structure

Parameters

reset_structure – True if the structure should be reset, False if it should be kept

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

selectAtom(index)

Select an atom in both the image and listwidget

Parameters

index (int) – The atom index to select

Return type

structure._StructureAtom

Returns

selected atom

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)

setLabel(guessing=False)

Set the label that describes what the user should do

Parameters

guessing (bool) – True if there is currently a guess in place, False if not.

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)

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)

setStructure(struct)

Set the structure for this frame. Updates the image and the list widget

Parameters

struct (schrodinger.structure.Structure) – The structure for this frame

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)

unmapAtom(index)

Mark an atom as unmapped

Parameters

index (int) – The atom index to mark

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.matsci.reordergui.PickPairToggleIntermediate(checkbox, pick_function, pick_text='Pick 2 atoms to define a pair', allow_locked_entries=False)

Bases: schrodinger.ui.picking.PickPairToggle

Class that allows: to call pick function in the intermediate picking state (only one atom is picked out of two); to prevent calling pick function at all if desired.

setStructures(reference, comparison)

Set the reference and comparison structures

Parameters

• reference (schrodinger.structure.Structure) – The structure to use as the reference

• comparison (schrodinger.structure.Structure) – The structure to use as the comparison

__init__(checkbox, pick_function, pick_text='Pick 2 atoms to define a pair', allow_locked_entries=False)

See parent class for argument documentation.

Parameters

natoms (int or None) – the number of atoms in the group or None to allow any number of picks

callPickFunction()

Call the pick function with the current selection

fullCommand(toggled)

Gets called when the checkbutton is toggled. Manages settings of all pick toggles, and then calls the user-specified command (if it exists).

Parameters

toggled (bool) – indicates whether check box is toggled on or off

on()

reset()

Unpick all atoms and update markers

setPickText(new_text)

Set’s the text that is shown in the workspace banner

Parameters

new_text (str) – The text to show in the banner

start()

stop()

property workspace_ct

Get a copy of the workspace structure

(lazily and cached)

class schrodinger.application.matsci.reordergui.ReorderAtomFrame(parent=None, by_element=True, by_smiles=True, by_smarts=True, by_superposition=True, default_method='SMARTS patterns of whole molecule or unique atoms', layout=None, reference_structure=None, comparison_structure=None, reference_structure_constraints=None, enable_2d_structure=True)

Bases: schrodinger.ui.qt.swidgets.SFrame

A frame which allows the user to reorder the atoms of a comparison structure based on the atom order of a reference structure. The widgets provide the ability to guess at atom order based on multiple algorithms and also manually specify order using 2D images of the structures.

MAP_COUNTER_LABEL = '{num_mapped_atoms} of {atom_total}\natoms mapped'

__init__(parent=None, by_element=True, by_smiles=True, by_smarts=True, by_superposition=True, default_method='SMARTS patterns of whole molecule or unique atoms', layout=None, reference_structure=None, comparison_structure=None, reference_structure_constraints=None, enable_2d_structure=True)

Create a ReorderAtomFrame widget

Parameters

• parent (QWidget) – The parent widget with a .warning(str) method

• by_element (bool) – Provide widgets to allow a guess based on lone elements

• by_smiles (bool) – Provide widgets to allow a guess based on unique SMILES order

• by_smarts (bool) – Provide widgets to allow a guess based on SMARTS patterns

• by_superposition (bool) – Provide widgets to allow a guess based on 3D superposition of the structures

• default_method (str) – Default guess method

• layout (QBoxLayout) – The layout to place this frame into

• reference_structure (schrodinger.structure.Structure) – The structure to use as the reference

• comparison_structure (schrodinger.structure.Structure) – The structure to use as the comparison

• enable_2d_structure (bool) – If True, enable/show 2D structure. Can be slow for inorganic materials

updateMapCounter()

Updates the label indicating the number of atoms mapped

Return type

None

show2DStructures(state)

Show or hide 2D structure pictures

Parameters

state (bool) – If True, show 2D structure picture, otherwise hide

setStructures(reference, comparison)

Set the reference and comparison structures

Parameters

• reference (schrodinger.structure.Structure) – The structure to use as the reference

• comparison (schrodinger.structure.Structure) – The structure to use as the comparison

guessMode(guessmode)

Set the current guess mode - affects label texts and enabling/disabling widgets and user interaction signals.

Parameters

guessmode (bool) – True if a guess is currently taking place and has not yet been Accepted/Rejected, False if any other situation

selectRefAtom(index)

Select the current atom in the reference structure

Parameters

index (int) – The index of the atom to select

mapPair(ref_index, comp_index, advance=True, guess=False, generate=True)

Create a mapping between an atom in the Comparison structure to an atom in the Reference structure.

Parameters

• ref_index (int) – The atom index of the reference atom to map

• comp_index (int) – The atom index of the comparison atom to map

• advance (bool) – True if the Reference atom selection should be advanced, False if not

• guess (bool) – True if this mark results from a guess, False if not. The background color used depends on this parameter.

• generate (bool) – Whether to regenerate the 2D picture

unmapPair(ref_index, comp_index)

Create a mapping between an atom in the Comparison structure to an atom in the Reference structure.

Parameters

• ref_index (int) – The atom index of the reference atom to map

• comp_index (int) – The atom index of the comparison atom to map

mapCompAtom(comp_index, ref_index=None, auto=True, advance=True)

Map an atom in the Comparison structure to an atom in the Reference structure

Parameters

• comp_index (int) – The atom index of the comparison atom to map

• ref_index (int or None) – If an int, the index of the reference atom to map to. If not given, the selected reference atom will be used

• auto (bool) – Whether to Auto guess additional atoms based on this mapping. Default is True - but autoguessing will only occur if the user has checked the Auto guess box.

• advance (bool) – True if the Reference atom selection should be advanced, False if not

markAtomsInWS()

Mark selected atoms for guess in the WS.

markSuggestedAtomsInWS(ref_idx, comp_idx)

Pick reference atom in the WS and mark suggested comparison atom.

Parameters

• ref_idx (int) – Index of the atom to pick in the reference WS

• comp_idx (int or None) – If int, mark atom in the comparison WS structure

autoMap()

Automatically map no-brainer atoms based on the current mapping. No-brainer atoms are atoms that are the only atoms remaining of a given element, or hydrogens bound to mapped atoms that can be uniquely identified.

compAtomFromRefAtom(index)

Get the atom in the Comparison structure that is mapped to the given index in the Reference structure

Parameters

index (int) – The index of the Reference atom to check

Return type

int

Returns

The index of the Comparison atom mapped to the given Reference atom

refAtomFromCompAtom(index)

Get the atom in the Reference structure that is mapped to the given index in the Comparison structure

Parameters

index (int) – The index of the Comparison atom to check

Return type

int

Returns

The index of the Reference atom mapped to the given Comparison atom

highlightCompAtom(comp_index)

Highlight an atom in the Comparision structure

Parameters

comp_index (int) – The index of the comparison atom to highlight

highlightRefAtom(ref_index)

Highlight an atom in the Reference structure

Parameters

ref_index (int) – The index of the reference atom to highlight

highlightMapPair(ref_index, comp_index)

Highlight the mapped pair of atoms

Parameters

• ref_index (int) – The index of the reference atom to highlight

• comp_index (int) – The index of the comparison atom to highlight

guessOrder()

Make a guess at the new order of the Comparison atoms

guessAccepted()

User has accepted the guess, make the atoms truly mapped

guessRejected()

User has rejected the guess remove it

isInGuessMode()

Is the panel currently in guess mode?

Return type

bool

Returns

True if the panel is in guess mode, False if not

finishGuess()

Finish guess mode after the user has accepted or rejected the guess.

Note - this method should be callable even if not currently in a guess.

doneReordering()

Check if the reordering process is done

Return type

bool

Returns

True if all the atoms in one of the structures are mapped

getReorderedStructure()

Get a reordered version of the comparison structure

Return type

schrodinger.structure.Structure, list or (None, None)

Returns

The comparison structure with the atoms reordered as specified in the mapping, and the list used to reorder the structure. The first element of the list is the original index of the atom that is first in the reordered structure, the second is the original index of the atom that is second in the reordered structure, etc. (None, None) is returned if the structure is not ready for reordering.

resetMap()

Reset only the map, keeping the structures

reset(reset_structures=True)

Reset the frame

Parameters

reset_structures (bool) – True if structures should be reset, False if they should be kept

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])

addStretch()

Add stretch to the frame layout.

addWidget(widget)

Add widget to the frame layout.

Parameters

widget (QWidget) – Widget to place on the layout

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(self, a0: QCloseEvent)

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

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

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]

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

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)

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.matsci.reordergui.ReorderAtomPanel(**kwargs)

Bases: schrodinger.ui.qt.appframework2.af2.JobApp

A simple panel that takes two selected entries and allows one of them to be reordered - this is mainly for testing and example purposes.

setPanelOptions()

Override the generic parent class to set panel options

layOut()

Lay out the widgets for this panel

loadStructures()

Load in the two structures. The first selected entry will be the reference.

createReorderedEntry()

Create a new, reordered version of the second selected entry. If run from maestro, this will be created as a new project entry and included in the workspace.

DrawChildren = 2

DrawWindowBackground = 1

IGNORE_DELAYED_CALLBACKS = False

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

__init__(**kwargs)

Parameters

• stop_before (int) – Exit the constructor before specified step.

• parent (QWidget) – Parent widget, if any.

• in_knime (bool) – Whether we are currently running under KNIME - a mode in which input selector is hidden, optionally a custom Workspace Structure is specified, and buttom bar has OK & Cancel buttons.

• workspace_st_file (bool) – Structure to be returned by getWorkspaceStructure() when in_knime is True.

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])

addJaguarMarker(atoms, color=None, icon=None, text='', alt_color=None, highlight=False)

Add a marker to the specified atom(s)

Parameters

• atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to mark. A list may contain between one and four atoms (inclusive).

• color (tuple, str, int, or schrodinger.structutils.color) – The color of the marker and icon. May be an RGB tuple, color name, color index, or schrodinger.structutils.color instance. If not given, white will be used.

• icon (int) – The icon to draw next to the marker. Should be one the self.MARKER_ICONS constants. If not given, no icon will be drawn.

• text (str) – The text to display next to the marker. If not given, no text will be displayed. Note that this argument will be ignored when marking a single atom.

• alt_color (tuple, str, int, or schrodinger.structutils.color) – The alternate marker color. This color is always used for text, and is used for the marker and icon when highlight is True. If not given, color will be used.

• highlight (bool) – Whether the marker should be highlighted. A highlighted marker is indicated with thicker lines and is colored using alt_color instead of color.

Returns

The newly created marker

Return type

schrodinger.maestro.markers._BaseMarker

Raises

ValueError – If a marker already exists for the specified atoms

Note

Either an icon or text may be displayed on a marker, but not both. If both are given, only the text will be shown.

addMainTaskRunner(runner, taskwidget)

A “main” task runner is a runner that is operated by a task widget (generally a job bar) at the very bottom of the panel. A panel may have more than one main task, but there is always one that is the “current” task. This is useful for panels that have multiple modes, with each mode launching a different job.

The related method, self.setCurrentTask(), is used to switch between main runners that have been added via this function.

Parameters

• runner (tasks.AbstractTaskRuner) – the task runner

• taskwidget (taskwidgets.TaskUIMixin) – the associated task widget

addMarker(atoms, color=(1.0, 1.0, 1.0), group_name=None)

Generates a set of simple, dot-styled markers for a group of atoms.

Parameters

• atoms (list or schrodinger.structure._StructureAtom) – List of atoms to be marked

• color (tuple of 3 floats) – The amount of red, green and blue to use, each ranging from 0.0 to 1.0. Default is white (1., 1., 1.).

@group_name: Optional string to set as the name of this group of markers in Maestro. If not set, a unique identifier will be generated.

addMarkerFromAsl(asl, color=(1.0, 1.0, 1.0), group_name=None)

Generates a set of simple, dot-styled markers for group of Workspace atoms that match the given ASL. Same atoms continue to be marked even if the Workspace is later modified such that ASL matching changes.

Parameters

• asl – ASL for the atoms to mark.

• color (tuple of 3 floats) – The amount of red, green and blue to use, each ranging from 0.0 to 1.0. Default is white (1., 1., 1.).

@group_name: Optional string to set as the name of this group of markers in Maestro. If not set, a unique identifier will be generated.

Returns

Marker object

Return type

markers.Marker

addProjectJobNote(job_id, jobname)

Adds a note to the project annotation file. :param job_id: The ID of the job, as assigned by Maestro :type job_id: string :param jobname: The name of the job, as shown in the job panel :type jobname: string

adjustSize(self)

applyAliasedSettings(settings)

Applies any aliased settings with new values from the dictionary. Any aliases not present in the settings dictionary will be left unchanged.

Parameters

settings (dict) – a dictionary mapping aliases to new values to apply

applySettings(settings, target=None)

autoFillBackground(self) → bool

backgroundRole(self) → QPalette.ColorRole

baseSize(self) → QSize

blockSignals(self, b: bool) → bool

buildCallbackDicts()

Create a dictionary of all methods that have a maestro_callback decorator.

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

cleanup()

clearFocus(self)

clearMask(self)

close(self) → bool

closeEvent(event)

Receives the close event and calls the panel’s ‘close’-decorated appmethod. If the appmethod specifically returns False, the close event will be ignored and the panel will remain open. All other return values (including None) will allow the panel to proceed with closing.

This is a PyQT slot method and should not be explicitly called.

colorCount(self) → int

configDialogSettings()

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)

createBottomBar()

createInputSelector()

createJobDir()

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

currentTaskRunner()

cursor(self) → QCursor

customContextMenuRequested

customContextMenuRequested(self, pos: QPoint) [signal]

customEvent(self, a0: QEvent)

definePanelSettings()

Override this method to define the settings for the panel. The aliased settings provide an interface for saving/restoring panel state as well as for interacting with task/job runners that need to access the panel state in a way that is agnostic to the specifics of widget names and types.

Each panel setting is defined by a tuple that specifies the mapping of alias to panel setting. An optional third element in the tuple can be used to group settings by category. This allows multiple settings to share the same alias.

Each setting can either point to a specific object (usually a qt widget), or a pair of setter/getter functions.

If the mapped object is a string, this will be interpreted by af2 as referring to an attribute on the panel, and a AttributeSettingWrapper instance will automatically be created. For example, specifying the string ‘num_atoms’ will create a mapping to self.num_atoms which will simply get and set the value of that instance member.

Custom setter and getter functions should take the form getter(), returning a value that can be encoded/decoded by JSON, and setter(value), where the type of value is the same as the return type of the getter.

Commonly used objects/widgets should be handled automatically in settings.py. It’s worth considering whether it makes more sense to use a custom setter/getter here or add support for the widget in settings.py.

Returns

a list of tuples defining the custom settings.

Return type

list of tuples. Each tuple can be of type (str, object, str) or (str, (callable, callable), str) where the final str is optional.

Custom settings tuples consists of up to three elements:

1. alias - a string identier for the setting. Ex. “box_centroid”

2. either:

   1. an object of a type that is supported by settings.py or

   2. the string name of an existing panel attribute (i.e. member variable), or

   3. a (getter, setter) tuple. The getter should take no arguments, and the setter should take a single value.

3. optionally, a group identifier. This can be useful if the panel runs two different jobs that both have a parameter with the same name but that needs to map to different widgets. If a setting has a group name, it will be ignored by runners unless the runner name matches the group name.

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(text, preferences=None, key='', detailed_text=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.

• detailed_text (str) – Detailed (selectable) error text if any.

Return type

None

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

frameGeometry(self) → QRect

frameSize(self) → QSize

generateStatus()

Generate the text to put into the status bar

Returns

The text to put into the status bar

Return type

str

geometry(self) → QRect

getAliasedSettings()

getAliasedValue(alias)

getAllJaguarMarkers()

Get all markers._BaseMarker currently loaded into the panel

Returns

An iterator of markers._BaseMarker

Return type

iterator

getAllMarkers()

Get all markers.Marker loaded into the panel

Returns

list(markers.Marker)

Return type

list

getCmdListArgValue(cmdlist, arg)

getConfigDialog()

getJaguarMarker(atoms)

Retrieve a marker for the specified atom(s)

Parameters

atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to retrieve the marker for. A list may contain between one and four atoms (inclusive).

Returns

The requested marker

Return type

schrodinger.maestro.markers._BaseMarker

Raises

ValueError – If no marker exists for the specified atoms

Note

As indicated by the return type, this function only returns schrodinger.maestro.markers._BaseMarker derived markers. Multi atom schrodinger.maestro.markers.Marker type markers are not accessible in this way.

getJobSpec()

getObjValue(obj)

getPanelState()

Gets the current state of the panel in the form of a serializable dict. The state consists of the settings specified in definePanelSettings() as well as the automatically harvested settings.

getPersistenceKey(alias)

Return a unique identifier for saving/restoring a setting in the preferences. Override this method to change the key scheme (this is necessary if creating a common resource which is shared by multiple panels).

Parameters

alias (str) – the alias for which we are generating a key

getSettings(target=None, ignore_list=None)

getWorkspaceStructure()

If panel is open in Maestro session, returns the current workspace schrodinger.strucutre.Structure.

If panel is open from outside of Maestro, returns the self.workspace_st if self.workspace_st_file is available. Used while running from command line or starting the panel from KNIME.

Returns None otherwise.

Return type

schrodinger.structure.Structure or None

Returns

Maestro workspace structure or None

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

gui_closed

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)

hideAllJaguarMarkers()

Hide all schrodinger.maestro.markers._BaseMarker markers for this panel

hideAllMarkers()

Hide all schrodinger.maestro.markers.Marker markers for this panel.

hideEvent(self, a0: QHideEvent)

hideLayoutElements(layout)

Hide all elements from the given layout. Used for customizing KNIME panel wrappers.

ignoreMaestroCallbacks()

A context manager for temporarily disabling Maestro callbacks created using the decorators above. (Note that callbacks that have been manually added using maestro.*_callback_add() will not be disabled.)

Example:

def includeEntry(self, entry_id):
    proj = maestro.project_table_get()
    with self.ignoreMaestroCallbacks():
        proj[entry_id].in_workspace = project.IN_WORKSPACE

@maestro_callback.project_changed
def onProjectChanged(self):
    print "This method will not be called during includeEntry."

@maestro_callback.workspace_changed
def onWorkspaceChanged(self):
    print "Neither will this one."

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

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])

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

jobCompleted

jobDir()

jobname()

Return the job name currently set for the current task.

jobnameData()

Provides panel settings that are to be incorporated into job names. If self.default_jobname includes string formatting characters (i.e. %s, {0}, etc.), then this method must be implemented. It should return a tuple or a dictionary to be interpolated into the job name.

jobnameDataChanged()

If the job name includes panel settings, then this method should be called whenever the relevant panel settings are modified

keyPressEvent(self, a0: QKeyEvent)

keyReleaseEvent(self, a0: QKeyEvent)

keyboardGrabber() → QWidget

killTimer(self, id: int)

lastJobCompleted

launchFromJobSpec(oplsdir=None)

Call this function in start method if the calling script implements the launch api. This function requires implementation of getJobSpec to return the job specification.

Parameters

oplsdir (None, False or str) – If None (default), search widgets on the panel for a ffselector.ForceFieldSelector (or subclass thereof) and get any custom OPLS directory information from that widget. If False, do not use a custom OPLS directory. If a str, this is the path to use for the custom OPLS directory. Note that the OPLSDIR setting found by oplsdir=None is ambiguous if there is more than one ForceFieldSelector child widget, and that ForceFieldSelector widgets that are NOT child widgets of this panel - such as a widget on a dialog - will not be found. Setting this parameter to False for a panel that does not use a ForceFieldSelector widget avoids the widget search but will only shave a few thousandths of a second off job startup time even for very complex panels.

launchJobCmd(cmdlist, show_progress_bar=False, auto_add_host=True, use_parallel_flag=True, jobdir=None)

Launches a job control command. Use this to launch scripts that accept the standard job control options arguments like -HOST, -DISP, etc. By default, automatically populates standard arguments from the config dialog, but will not overwrite if they are already found in cmdlist. For example, if -HOST is found in cmdlist, launchJobCmd will ignore the host specified in the config dialog.

This method honors self.start_mode; it can either launch the script or write out a job file to the job directory.

Parameters

• cmdlist (list) – the command list

• show_progress_bar (bool) – Whether or not to show a progress bar tracking the job’s status.

• auto_add_host (bool) – Whether or not to automatically add -HOST flag to command when it is not already included.

• use_parallel_flag (bool) – Whether requesting CPUs > 1 without specifying threads > 1 should be represented by the use of the -PARALLEL X flag (True, default) or -HOST host:X (False). -PARALLEL is a Jaguar flag and may not be appropriate for other programs.

• jobdir (str) – launch the job from this dir, if provided.

Returns

Job object for started job, or None if job start failed or if writing instead of starting. Panels should in general ignore the return value.

launchLauncher(slauncher, show_progress_bar=False)

Either launches a launcher instance or writes the job invocation command, depending on the state of self.start_mode. This allows the panel’s start method to double as a write method.

Calling launchLauncher() is only necessary if creating a customized launcher using makeLauncher().

Parameters

show_progress_bar (int) – Whether or not to show a progress bar tracking the job’s status.

launchScript(script, script_args=None, input_files=[], structure_output_file=None, output_files=[], aux_modules=[], show_progress_bar=False, **kwargs)

DEPRECATED, add get_job_spec_from_args() to the backend script and launch it using launchJobCmd() or also add getJobSpec() to the panel and launch using launchFromJobSpec().

Creates and launches a script using makeLauncher. For documentation on method parameters, see makeLauncher below. Use this method for scripts that do not themselves integrate with job control.

This method honors self.start_mode; it can either launch the script or write out a job file to the job directory.

Parameters

show_progress_bar (bool) – Whether or not to show a progress bar tracking the job’s status.

launcherToCmdList(slauncher)

layout(self) → QLayout

layoutDirection(self) → Qt.LayoutDirection

leaveEvent(self, a0: QEvent)

loadPanelState(filename=None)

Load the panel state from a JSON file

Parameters

filename (str) – the JSON filename. Defaults to “panelstate.json”

loadPersistentOptions()

Load all persistent options from the preferences.

loadSettings(jobname)

Load the GUI state for the job in the CWD with the given name. Default implementation will return False. Each KNIME panel will need to implement a custom version. For example, the panel may want to read the <jobname.sh> file, parse the list of command-line options, and populate the GUI accordintly. If a panel writes key/value file, then it would need to read it here.

Returns

True if panel state was restored, False if saved state was not found.

Return type

bool

locale(self) → QLocale

logicalDpiX(self) → int

logicalDpiY(self) → int

lower(self)

makeLauncher(script, script_args=[], input_files=[], structure_output_file=None, output_files=[], aux_modules=[], **kwargs)

DEPRECATED, add get_job_spec_from_args() to the backend script and launch it using launchJobCmd() or also add getJobSpec() to the panel and launch using launchFromJobSpec().

Create a launcher.Launcher instance using the settings defined by the panel, its config dialog, and specified arguments. Returns a launcher instance ready to be launched or further modified. Use this method for scripts that do not themselves integrate with job control.

Only use this method if you need to modify the launcher before launching it. Otherwise, the method launchScript() is preferred to create the launcher and launch it.

Parameters

• script (str) – Remote path to the script to be launched. See Launcher documentation for more info. If only launching to localhost is desired, then a local path can be specified.

• script_args (list of str) – arguments to be added to the script’s command line

• input_files (list of str) – input files that will be copied to the temporary job directory.

• structure_output_file (str) – this is the file that will be registered with job control to incorporate at the end of the job

• output_files (list of str) – additional output files to be copied back from the temporary job directory

• aux_modules (list of modules) – Additional modules required by the script

Returns

A prepped launcher

Return type

Launcher

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

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]

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(run=True)

Launch a singleton instance of this class. If the panel has already been instantiated, the existing panel instance will be re-opened and brought to the front.

Parameters

run (bool) – Whether to launch the panel

Returns

The singleton panel instance

Return type

App

parent(self) → QObject

parentWidget(self) → QWidget

physicalDpiX(self) → int

physicalDpiY(self) → int

pos(self) → QPoint

previousInFocusChain(self) → QWidget

processSettings(settings=None, runner=None)

This method is meant to be used as a callback to a task runner. If it is called with no arguments, it returns a dictionary of all the alieased settings. If settings are passed, the settings are first applied to self, and then the newly modified settings are returned.

Parameters

• settings (dict or None) – a settings dictionary to apply to this object

• runner (tasks.AbstractTaskRuner) – the task runner that is invoking this callback. This optional argument is necessary for per-runner grouping of settings

processTaskMessage(message_type, text, options=None, runner=None)

This method is meant to be used as a callback to a task runner, and provides a single point of interaction from the runner to the user.

Parameters

• message_type (int) – the type of message being sent

• text (str) – the main text to show the user

• options – extra options

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.

raise_(self)

readShFile(jobname)

Reads the jobname.sh file (written by _write()) and returns the list of command line arguments

receivers(self, signal: PYQT_SIGNAL) → int

rect(self) → QRect

registerJob(job, show_progress_bar=False)

Registers a job with the periodic job check callback and starts timer.

Parameters

• job (jobcontrol.Job) – job to register

• show_progress_bar (bool) – Whether or not to show a progress bar tracking the job’s status.

releaseKeyboard(self)

releaseMouse(self)

releaseShortcut(self, id: int)

removeAction(self, action: QAction)

removeAllJaguarMarkers()

Remove all markers schrodinger.maestro.markers._BaseMarker markers from this panel

removeAllJaguarMarkersForEntry(eid)

Remove all markers for the specified entry id from this panel

Parameters

eid (str) – The entry id to remove markers for

removeAllMarkers()

Remove all schrodinger.maestro.markers.Marker markers from this panel.

removeEventFilter(self, a0: QObject)

removeJaguarMarker(marker)

Removes the specified marker

Parameters

marker (schrodinger.maestro.markers._BaseMarker) – The marker to remove

Raises

ValueError – If there is no marker on the specified atoms

removeJaguarMarkerForAtoms(atoms)

Removes the marker for specified atom(s)

Parameters

atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to retrieve the marker for. A list may contain between one and four atoms (inclusive).

Raises

ValueError – If no marker exists for the specified atoms

removeMarker(marker)

Remove the schrodinger.maestro.markers.Marker

Parameters

marker (schrodinger.maestro.markers.Marker) – Marker to remove

Raises

ValueError – If marker is the wrong type or is not associated with the panel.

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.

resetAllRunners()

Resets all task runners associated with this panel (main tasks and other tasks added via setupTaskRunner). This is called from _reset() and normally does not need to be called directly.

resize(self, a0: QSize)

resize(self, w: int, h: int) → None

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.

Parameters

app_wide (bool) – If True then this will restore the cursor for the entire application (including Maestro if running there). If False then this will apply only to this panel.

restoreGeometry(self, geometry: QByteArray) → bool

run()

runCanvas()

This handles Canvas-specific logic

classmethod runKnime(input_selector_file=None, workspace_st_file=None, jobname=None, run=True, load_settings=True, panel_state_file=None)

Call this static method to instantiate this panel in KNIME mode - where OK & Cancel buttons are shown at the bottom. Pressing OK button cases the job files to be written to the CWD.

Parameters

• input_selector_file (str) – the filename to be fed into the input selector, replacing interactive input from the user. Required if the panel contains an input selector.

• workspace_st_file (str) – the filename containing the schrodinger.structure.Structure that replaces the workspace structure in a Maestro session.

• jobname (str) – Jobname for the panel

• run (bool) – Whether to launch the panel. If False, just returns the panel instance without starting the event loop.

• load_settings (bool) – Whether to load previous settings for the given jobname from the CWD.

• panel_state_file – Unused (added for backwards compatability)

runMaestro()

This can be extended in derived classes to perform maestro-only tasks such as setting up the mini-monitor or connecting maestro callbacks

runMode()

runStandalone()

runSubpanel()

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

sanitizeJobnameText(text)

Modify the given text so it can be used in a job name. White space is replaced with underscores and all other disallowed characters are removed.

Parameters

text (basestring) – The text to sanitize

Returns

The sanitized text

Return type

basestring

saveGeometry(self) → QByteArray

savePersistentOptions()

Store all persistent options to the preferences.

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)

setAlias(alias, obj, persistent=False)

Sets an alias to conveniently access an object.

Parameters

• alias (hashable) – any hashable, but typically a string name

• obj (object) – the actual object to be referenced

• persistent (bool) – whether to make the setting persistent

setAliasedValue(alias, value)

setAliases(alias_dict, persistent=False)

Sets multiple aliases at once. Already used aliases are overwritten; other existing aliases are not affected.

Parameters

• alias_dict (dict) – map of aliases to objects

• persistent (bool) – whether to make the settings persistent

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

setConfigDialogSettings(new_values)

setContentsMargins(self, left: int, top: int, right: int, bottom: int)

setContentsMargins(self, margins: QMargins) → None

setContextMenuPolicy(self, policy: Qt.ContextMenuPolicy)

setCurrentTask(index)

Selects the current main task for the panel. Switching to a new task involves several steps. These are 1) saving the current panel state to the task runner, 2) hiding the current task widget (and all others), 3) showing the widget for the new task, and 4) setting the panel state to correspond to the new task runner’s settings.

Parameters

index (int) – the index of the task to be selected. The index for each main task is set sequentially from 0 as each task as added using self.addMainTaskRunner()

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

setDefaults()

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)

setJobname(jobname)

Set the job name for the current task.

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)

setMouseTracking(self, enable: bool)

setObjValue(obj, value)

setObjectName(self, name: str)

setPalette(self, a0: QPalette)

setPanelState(state)

Resets the panel and then sets the panel to the specified state

Parameters

state (PanelState) – the panel state to set. This object should originate from a call to getPanelState()

setParent(self, parent: QWidget)

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

setPersistent(alias=None)

Set options to be persistent. Any options to be made persistent must be aliased, since the alias is used to form the preference key. If no alias is specified, all aliased settings will be made persistent.

Parameters

alias (str or None) – the alias to save, or 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)

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.

Parameters

app_wide (bool) – If True then this will apply to the entire application (including Maestro if running there). If False then this 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)

setup()

setupJobCmd(cmdlist, auto_add_host=True, use_parallel_flag=True)

Adds standard arguments HOST, NJOBS, PROJ, DISP, VIEWNAME to the cmdlist if they are set in the config dialog. Settings pre-existing in the cmdlist take precedence over the config dialog settings.

Parameters

• cmdlist (list) – the command list

• auto_add_host (bool) – Whether or not to automatically add -HOST flat to command when it is not already included.

• use_parallel_flag (bool) – Whether requesting CPUs > 1 without specifying threads > 1 should be represented by the use of the -PARALLEL X flag (True, default) or -HOST host:X (False). -PARALLEL is a Jaguar flag and may not be appropriate for other programs.

setupTaskRunner(runner, taskwidget)

Connects a task widget to a task runner and associates the runner with this af2 panel via the panel callbacks.

This method is called by self.addMainTaskRunner() and does not need to be called for main tasks; however, it is useful for setting up other tasks that are not main tasks - for example, if there is a smaller job that gets launched from a button in the middle of the panel somewhere.

Parameters

• runner (tasks.AbstractTaskRuner) – the task runner

• taskwidget (taskwidgets.TaskUIMixin) – the associated task widget

sharedPainter(self) → QPainter

show()

Re-show all panel markers when the panel is re-shown. This separate method is needed for QDialog instances.

showAllJaguarMarkers()

Show all schrodinger.maestro.markers._BaseMarker markers for which all marked atoms are in the workspace. Hide all other markers.

showAllMarkers()

Set all schrodinger.maestro.markers.Marker markers to be shown if the relevant atoms are in the workspace. These markers are hidden automatically by Maestro when atoms are excluded.

showEvent(event)

When the panel is shown, call the panel’s ‘show’-decorated methods. Note that restoring a minimized panel will not trigger the ‘show’ methods.

showFullScreen(self)

showMaximized(self)

showMinimized(self)

showNormal(self)

showProgressBarForJob(job, show_lbl=True, start_timer=True)

Show a progress bar that tracks the progress of the specified job

Parameters

• job (schrodinger.job.jobcontrol.Job) – The job to track

• show_lbl (bool) – If True, the job progress text description will be shown above the progress bar. If False, the text description will not be shown.

• start_timer (bool) – If True, the progress bar will automatically be updated and removed when the job is complete. If False, it is the caller’s responsibility to periodically call self.progress_bar.readJobAndUpdateProgress() and to call self.status_bar.hideProgress() when the job is complete.

showSTUDialog(sh_txt, jobname)

Shows dialog with information necessary to start a STU test, including a label that links to the test suite.

Parameters

sh_txt (str) – Text contained within the .sh file

signalsBlocked(self) → bool

size(self) → QSize

sizeHint(self) → QSize

sizeIncrement(self) → QSize

sizePolicy(self) → QSizePolicy

stackUnder(self, a0: QWidget)

startDebug()

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

startUp()

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

statusTip(self) → str

style(self) → QStyle

styleSheet(self) → str

syncConfigDialog()

tabletEvent(self, a0: QTabletEvent)

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

thread(self) → QThread

timerEvent(self, a0: QTimerEvent)

property title

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)

updateJobname(uniquify_custom=True)

Generate a new job name based on the current panel settings

Parameters

uniquify_custom (bool) – Whether we should uniquify custom job name by adding integers to the end. If False, only standard and modified job names will be uniquified. (See JobnameType for an explanation of job name types.)

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

updateStatusBar()

Updates the status bar.

updatesEnabled(self) → bool

validForceFieldSelectorCustomOPLSDir()

Check whether a force field selector exists and if so whether it is set to use a custom OPLS directory that is valid. :return: whether OPLS directory has issues :rtype: bool

validateOPLSDir(opls_dir=None)

See forcefield.validate_opls_dir()

Parameters

opls_dir (str or None) – the opls dir to validate

Returns

the validation result

Return type

forcefield.OPLSDirResult

visibleRegion(self) → QRegion

warning(text, preferences=None, key='')

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

writeJobCmd(cmdlist, job_spec=None, launch_params=None)

Writes the job invocation command to a file named “<jobname>.sh” Removes options from the command that are maestro-specific.

Note this may modify the contents of cmdlist

Parameters

• job_spec (schrodinger.job.launchapi.JobSpecification) – The job specification for the command you want to write. This is NOT used to write the command that is run; it is used to write a commented-out, un-hashed, human-readable command in the sh file. If None (which is also the default), then the human-readable comment is not written. If it is present, launch_params must be present too.

• launch_params (job.launchparams.LaunchParameters) – Job launch params

writePanelState(filename=None)

Write the panel state to a JSON file

Parameters

filename (str) – the JSON filename. Defaults to “panelstate.json”

writeReadableCmdComment(cmdlist)

Append a readable and portable command (something that starts with $SCHRODINGER/run <script.py>) to the shell run file.

Parameters

cmdlist (list) – Commands to launch/submit the job

writeStateAndClose()

Will “write” the job files and close the panel.

x(self) → int

y(self) → int

class schrodinger.application.matsci.reordergui.ReorderAtomsDialog(master, struct1, struct2, modality=WindowModality.NonModal, struct1_atomic_constraints=None, default_guess_method='SMARTS patterns of whole molecule or unique atoms', enable_2d_structure=True, **kwargs)

Bases: schrodinger.ui.qt.swidgets.SDialog

A Window-Modal dialog that allows the user to reorder atoms in a comparison structure based on a reference structure.

__init__(master, struct1, struct2, modality=WindowModality.NonModal, struct1_atomic_constraints=None, default_guess_method='SMARTS patterns of whole molecule or unique atoms', enable_2d_structure=True, **kwargs)

Create a ReorderAtomDialog instance. See parent for **kwargs docs.

Parameters

• master (QWidget) – The parent widget

• struct1 (schrodinger.structure.Structure) – The reference structure. This structure will not be reordered.

• struct2 (schrodinger.structure.Structure) – The comparison structure. A copy of this structure will be reordered when the user clicks OK

• modality (int) – The modality of the dialog. Default is Qt.NonModal, other options may be Qt.WindowModal or Qt.ApplicationModal.

• struct1_atomic_constraints (list) – List of constraints in text format

• default_guess_method (str) – Default guess method

layOut()

Lay out the custom widgets in this dialog.

accept()

User has clicked accept, get the reordered structure, call the accept_command with it and close the dialog.

Return type

int or None

Returns

QDialog.Accepted if a structure has been reordered, or None if the reordering was incomplete and the dialog not closed

reject()

User has clicked reject - do nothing but call custom reject method

Return type

int

Returns

QDialog.Reject

Accepted = 1

class DialogCode(value)

Bases: enum.IntEnum

An enumeration.

Rejected = 0

Accepted = 1

DrawChildren = 2

DrawWindowBackground = 1

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

Rejected = 0

class RenderFlag(value)

Bases: enum.Flag

An enumeration.

DrawWindowBackground = 1

DrawChildren = 2

IgnoreMask = 4

acceptDrops(self) → bool

accepted

accepted(self) [signal]

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(self, a0: QCloseEvent)

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)

done(self, a0: int)

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(msg)

Display an error dialog with a message

Parameters

msg (str) – The message to display in the error dialog

event(self, a0: QEvent) → bool

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

exec(self) → int

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]

finished

finished(self, result: int) [signal]

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

giveHelp()

Display the help topic for this dialog

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(msg)

Display an information dialog with a message

Parameters

msg (str) – The message to display in the information dialog

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])

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

isSizeGripEnabled(self) → 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)

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

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]

open(self)

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.

question(msg, button1='OK', button2='Cancel')

Display a question dialog with a message Returns True if first button (default OK) is pressed, False otherwise.

Parameters

• msg (str) – The message to display in the question dialog

• button1 (str) – The text to display on first button

• button2 (str) – The text to display on second button

raise_(self)

receivers(self, signal: PYQT_SIGNAL) → int

rect(self) → QRect

rejected

rejected(self) [signal]

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

reset()

Reset the panel when the Reset button is pressed. Must be re-implemented in a subclass

resize(self, a0: QSize)

resize(self, w: int, h: int) → None

resizeEvent(self, a0: QResizeEvent)

restoreGeometry(self, geometry: QByteArray) → bool

result(self) → int

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])

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)

setModal(self, modal: bool)

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

setResult(self, r: int)

setScreen(self, a0: QScreen)

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

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

setSizeGripEnabled(self, a0: bool)

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

warning(msg)

Display a warning dialog with a message

Parameters

msg (str) – The message to display in the warning dialog

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

schrodinger.application.matsci.reordergui.panel()

Top-level function for bringing up the panel.

schrodinger.application.matsci.reordergui.main(*args)