schrodinger.application.bioluminate.ssv.viewer module

The simplified version of the sequence viewer used in the MSV.

Also provides access to the viewer as a QtWidgets.QMainWindow and as a QtWidgets.QDockWidget.

schrodinger.application.bioluminate.ssv.viewer.catch_last_added(fn)

A decorator for action callbacks that deal with importing sequences into the sequence viewer. The decorator will add a last_sequences_added property to the class of the decorated method. This will store all sequences added to the viewer in the last import step.

This must decorate a class with a sequence_group property.

class schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget

Bases: PyQt6.QtWidgets.QDockWidget

The dock widget that can set a ViewerWindow as the main widget. This makes the ViewerWindow dockable.

WINDOW_TITLE = 'Sequence Viewer'
FLOATABLE = 4
MOVABLE = 2
CLOSABLE = 1
__init__()
floatChange(floating=False)

Slot for callback that is fired when the dock’s floating status changes. Currently this only set the dock’s window title is it is floating.

setFloatable()

Configure the dock widget to only be able to pop out, not be draggable.

setFloatableMovable()

Configure the dock widget to be draggable and be able to pop out.

setFloatableMovableClosable()

Configure the dock widget to be draggable, be able to pop out and be closable.

closeEvent(event)

Override the close event so that when the widget is floating clicking the close button will just dock it. This is a workaround since MacOSX does not have the float button when the panel is floating.

DockWidgetClosable = 1
class DockWidgetFeature(value)

Bases: enum.Flag

An enumeration.

DockWidgetClosable = 1
DockWidgetMovable = 2
DockWidgetFloatable = 4
DockWidgetVerticalTitleBar = 8
NoDockWidgetFeatures = 0
DockWidgetFloatable = 4
DockWidgetMovable = 2
DockWidgetVerticalTitleBar = 8
DrawChildren = 2
DrawWindowBackground = 1
IgnoreMask = 4
NoDockWidgetFeatures = 0
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
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)
allowedAreas(self) → Qt.DockWidgetArea
allowedAreasChanged

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

autoFillBackground(self) → bool
backgroundRole(self) → QPalette.ColorRole
baseSize(self) → QSize
blockSignals(self, b: bool) → bool
changeEvent(self, event: QEvent)
childAt(self, p: QPoint) → QWidget
childAt(self, ax: int, ay: int) → QWidget
childEvent(self, a0: QChildEvent)
children(self) → List[QObject]
childrenRect(self) → QRect
childrenRegion(self) → QRegion
clearFocus(self)
clearMask(self)
close(self) → bool
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)
dockLocationChanged

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

dragEnterEvent(self, a0: QDragEnterEvent)
dragLeaveEvent(self, a0: QDragLeaveEvent)
dragMoveEvent(self, a0: QDragMoveEvent)
dropEvent(self, a0: QDropEvent)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
effectiveWinId(self) → PyQt6.sip.voidptr
ensurePolished(self)
enterEvent(self, event: QEnterEvent)
event(self, event: QEvent) → bool
eventFilter(self, a0: QObject, a1: QEvent) → bool
features(self) → QDockWidget.DockWidgetFeature
featuresChanged

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

find(a0: PyQt6.sip.voidptr) → QWidget
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
focusInEvent(self, a0: QFocusEvent)
focusNextChild(self) → bool
focusNextPrevChild(self, next: bool) → bool
focusOutEvent(self, a0: QFocusEvent)
focusPolicy(self) → Qt.FocusPolicy
focusPreviousChild(self) → bool
focusProxy(self) → QWidget
focusWidget(self) → QWidget
font(self) → QFont
fontInfo(self) → QFontInfo
fontMetrics(self) → QFontMetrics
foregroundRole(self) → QPalette.ColorRole
frameGeometry(self) → QRect
frameSize(self) → QSize
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: QStyleOptionDockWidget)
inputMethodEvent(self, a0: QInputMethodEvent)
inputMethodHints(self) → Qt.InputMethodHint
inputMethodQuery(self, a0: Qt.InputMethodQuery) → Any
insertAction(self, before: QAction, action: QAction)
insertActions(self, before: QAction, actions: Iterable[QAction])
installEventFilter(self, a0: QObject)
isActiveWindow(self) → bool
isAncestorOf(self, child: QWidget) → bool
isAreaAllowed(self, area: Qt.DockWidgetArea) → bool
isEnabled(self) → bool
isEnabledTo(self, a0: QWidget) → bool
isFloating(self) → bool
isFullScreen(self) → bool
isHidden(self) → bool
isLeftToRight(self) → bool
isMaximized(self) → bool
isMinimized(self) → bool
isModal(self) → bool
isRightToLeft(self) → bool
isSignalConnected(self, signal: QMetaMethod) → bool
isVisible(self) → bool
isVisibleTo(self, a0: QWidget) → bool
isWidgetType(self) → bool
isWindow(self) → bool
isWindowModified(self) → bool
isWindowType(self) → bool
keyPressEvent(self, a0: QKeyEvent)
keyReleaseEvent(self, a0: QKeyEvent)
keyboardGrabber() → QWidget
killTimer(self, id: int)
layout(self) → QLayout
layoutDirection(self) → Qt.LayoutDirection
leaveEvent(self, a0: QEvent)
locale(self) → QLocale
logicalDpiX(self) → int
logicalDpiY(self) → int
lower(self)
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, 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, 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)
setAllowedAreas(self, areas: Qt.DockWidgetArea)
setAttribute(self, attribute: Qt.WidgetAttribute, on: bool = True)
setAutoFillBackground(self, enabled: bool)
setBackgroundRole(self, a0: QPalette.ColorRole)
setBaseSize(self, basew: int, baseh: int)
setBaseSize(self, s: QSize) → None
setContentsMargins(self, left: int, top: int, right: int, bottom: int)
setContentsMargins(self, margins: QMargins) → None
setContextMenuPolicy(self, policy: Qt.ContextMenuPolicy)
setCursor(self, a0: Union[QCursor, Qt.CursorShape])
setDisabled(self, a0: bool)
setEnabled(self, a0: bool)
setFeatures(self, features: QDockWidget.DockWidgetFeature)
setFixedHeight(self, h: int)
setFixedSize(self, a0: QSize)
setFixedSize(self, w: int, h: int) → None
setFixedWidth(self, w: int)
setFloating(self, floating: bool)
setFocus(self)
setFocus(self, reason: Qt.FocusReason) → None
setFocusPolicy(self, policy: Qt.FocusPolicy)
setFocusProxy(self, a0: QWidget)
setFont(self, a0: QFont)
setForegroundRole(self, a0: QPalette.ColorRole)
setGeometry(self, a0: QRect)
setGeometry(self, ax: int, ay: int, aw: int, ah: int) → None
setGraphicsEffect(self, effect: QGraphicsEffect)
setHidden(self, hidden: bool)
setInputMethodHints(self, hints: Qt.InputMethodHint)
setLayout(self, a0: QLayout)
setLayoutDirection(self, direction: Qt.LayoutDirection)
setLocale(self, locale: QLocale)
setMask(self, a0: QBitmap)
setMask(self, a0: QRegion) → None
setMaximumHeight(self, maxh: int)
setMaximumSize(self, maxw: int, maxh: int)
setMaximumSize(self, s: QSize) → None
setMaximumWidth(self, maxw: int)
setMinimumHeight(self, minh: int)
setMinimumSize(self, minw: int, minh: int)
setMinimumSize(self, s: QSize) → None
setMinimumWidth(self, minw: int)
setMouseTracking(self, enable: bool)
setObjectName(self, name: str)
setPalette(self, a0: QPalette)
setParent(self, parent: QWidget)
setParent(self, parent: QWidget, f: Qt.WindowType) → None
setProperty(self, name: str, value: Any) → bool
setScreen(self, a0: QScreen)
setShortcutAutoRepeat(self, id: int, enabled: bool = True)
setShortcutEnabled(self, id: int, enabled: bool = True)
setSizeIncrement(self, w: int, h: int)
setSizeIncrement(self, s: QSize) → None
setSizePolicy(self, a0: QSizePolicy)
setSizePolicy(self, hor: QSizePolicy.Policy, ver: QSizePolicy.Policy) → None
setStatusTip(self, a0: str)
setStyle(self, a0: QStyle)
setStyleSheet(self, styleSheet: str)
setTabOrder(a0: QWidget, a1: QWidget)
setTabletTracking(self, enable: bool)
setTitleBarWidget(self, widget: QWidget)
setToolTip(self, a0: str)
setToolTipDuration(self, msec: int)
setUpdatesEnabled(self, enable: bool)
setVisible(self, visible: bool)
setWhatsThis(self, a0: str)
setWidget(self, widget: QWidget)
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)
titleBarWidget(self) → QWidget
toggleViewAction(self) → QAction
toolTip(self) → str
toolTipDuration(self) → int
topLevelChanged

topLevelChanged(self, topLevel: bool) [signal]

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str
underMouse(self) → bool
ungrabGesture(self, type: Qt.GestureType)
unsetCursor(self)
unsetLayoutDirection(self)
unsetLocale(self)
update(self)
update(self, a0: QRect) → None
update(self, a0: QRegion) → None
update(self, ax: int, ay: int, aw: int, ah: int) → None
updateGeometry(self)
updateMicroFocus(self, query: Qt.InputMethodQuery = Qt.ImQueryAll)
updatesEnabled(self) → bool
visibilityChanged

visibilityChanged(self, visible: bool) [signal]

visibleRegion(self) → QRegion
whatsThis(self) → str
wheelEvent(self, a0: QWheelEvent)
widget(self) → QWidget
width(self) → int
widthMM(self) → int
winId(self) → PyQt6.sip.voidptr
window(self) → QWidget
windowFilePath(self) → str
windowFlags(self) → Qt.WindowType
windowHandle(self) → QWindow
windowIcon(self) → QIcon
windowIconChanged

windowIconChanged(self, icon: QIcon) [signal]

windowIconText(self) → str
windowIconTextChanged

windowIconTextChanged(self, iconText: str) [signal]

windowModality(self) → Qt.WindowModality
windowOpacity(self) → float
windowRole(self) → str
windowState(self) → Qt.WindowState
windowTitle(self) → str
windowTitleChanged

windowTitleChanged(self, title: str) [signal]

windowType(self) → Qt.WindowType
x(self) → int
y(self) → int
class schrodinger.application.bioluminate.ssv.viewer.ViewerWindow(parent)

Bases: PyQt6.QtWidgets.QMainWindow

Provides the SimplifiedSequenceViewer with a window to occupy. This has the benefit of adding toolbars and allowing the sequence viewer (which is a QtWidgets.QSplitter) to be a stand-alone window.

WINDOW_TITLE = 'Sequence Viewer'
IMPORT_TOOLBAR = 'import_toolbar'
UNDO_REDO_TOOLBAR = 'undo_redo_toolbar'
FIND_TOOLBAR = 'find_toolbar'
ALIGN_TOOLBAR = 'align_toolbar'
CONSENSUS_TOOLBAR = 'consensus_toolbar'
ANTIBODY_NUM_TOOLBAR = 'antibody_numbering_toolbar'
BREAK_TOOLBAR = 'break_toolbar'
DEFAULT_TOOLBARS = ['import_toolbar', 'undo_redo_toolbar', 'find_toolbar', 'align_toolbar']
__init__(parent)
Parameters

parent (SimplifiedSequenceViewer) – The sequence viewer object that will use this window

Raises

RuntimeError – If parent is not correct type

action_factory

The factory to use when creating actions. We want to set all the action’s parent to the passed in parent, which is a SequenceViewer. All of the actions associated with the viewer are the module, schrodinger.ui.sequencealignment.sequence_viewer.

removeToolBar(objname=None)

Overrides the base class’s QtWidgets.QMainWindow.removeToolBar method to allow for removal of a single toolbar based on the toolbar’s object name or, if objname is None, removal of all the window’s toolbars.

addToolBars(toolbars)

Add toolbars to the sequence viewer. The toolbars arg should be a list of items taken from the ViewerWindow properties:

setToolBars(toolbars)

Deletes all window toolbars and sets them to the new toolbars

addImportToolBar(area=ToolBarArea.TopToolBarArea)

Adds an ImportToolBar widget to the area indicated (default: top).

Parameters

area – The area to add the dock widget to

addUndoRedoToolBar(area=ToolBarArea.TopToolBarArea)

Adds a widget that handles undo/redo operations to the area indicated (default: top).

Parameters

area – The area to add the dock widget to

addFindToolBar(area=ToolBarArea.TopToolBarArea)

Adds a FindToolBar widget to the area indicated (default: top).

Parameters

area – The area to add the dock widget to

addAlignToolBar(area=ToolBarArea.BottomToolBarArea)

Adds a toolbar to the area indicated (default: bottom) that contains all of the actions for alignment.

Parameters

area – The area to add the dock widget to

addConsensusToolBar(area=ToolBarArea.BottomToolBarArea)

Adds a ConsensusToolBar widget to the area indicated (default: bottom) that contains all of the actions for consensus visualization.

Parameters

area – The area to add the dock widget to

addAntibodyNumberingToolBar(area=ToolBarArea.BottomToolBarArea)

Add a AntibodyNumberingToolBar widget to the area indicated (default: bottom).

Parameters

area – The area to add the dock widget to

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

Bases: enum.Flag

An enumeration.

AnimatedDocks = 1
AllowNestedDocks = 2
AllowTabbedDocks = 4
ForceTabbedDocks = 8
VerticalTabs = 16
GroupedDragging = 32
DrawChildren = 2
DrawWindowBackground = 1
ForceTabbedDocks = 8
GroupedDragging = 32
IgnoreMask = 4
class PaintDeviceMetric(value)

Bases: enum.Enum

An enumeration.

PdmWidth = 1
PdmHeight = 2
PdmWidthMM = 3
PdmHeightMM = 4
PdmNumColors = 5
PdmDepth = 6
PdmDpiX = 7
PdmDpiY = 8
PdmPhysicalDpiX = 9
PdmPhysicalDpiY = 10
PdmDevicePixelRatio = 11
PdmDevicePixelRatioScaled = 12
PdmDepth = 6
PdmDevicePixelRatio = 11
PdmDevicePixelRatioScaled = 12
PdmDpiX = 7
PdmDpiY = 8
PdmHeight = 2
PdmHeightMM = 4
PdmNumColors = 5
PdmPhysicalDpiX = 9
PdmPhysicalDpiY = 10
PdmWidth = 1
PdmWidthMM = 3
class RenderFlag(value)

Bases: enum.Flag

An enumeration.

DrawWindowBackground = 1
DrawChildren = 2
IgnoreMask = 4
VerticalTabs = 16
acceptDrops(self) → bool
accessibleDescription(self) → str
accessibleName(self) → str
actionEvent(self, a0: QActionEvent)
actions(self) → List[QAction]
activateWindow(self)
addAction(self, action: QAction)
addActions(self, actions: Iterable[QAction])
addDockWidget(self, area: Qt.DockWidgetArea, dockwidget: QDockWidget)
addDockWidget(self, area: Qt.DockWidgetArea, dockwidget: QDockWidget, orientation: Qt.Orientation) → None
addToolBar(self, area: Qt.ToolBarArea, toolbar: QToolBar)
addToolBar(self, toolbar: QToolBar) → None
addToolBar(self, title: str) → QToolBar
addToolBarBreak(self, area: Qt.ToolBarArea = Qt.TopToolBarArea)
adjustSize(self)
autoFillBackground(self) → bool
backgroundRole(self) → QPalette.ColorRole
baseSize(self) → QSize
blockSignals(self, b: bool) → bool
centralWidget(self) → QWidget
changeEvent(self, a0: QEvent)
childAt(self, p: QPoint) → QWidget
childAt(self, ax: int, ay: int) → QWidget
childEvent(self, a0: QChildEvent)
children(self) → List[QObject]
childrenRect(self) → QRect
childrenRegion(self) → QRegion
clearFocus(self)
clearMask(self)
close(self) → bool
closeEvent(self, a0: QCloseEvent)
colorCount(self) → int
connectNotify(self, signal: QMetaMethod)
contentsMargins(self) → QMargins
contentsRect(self) → QRect
contextMenuEvent(self, event: QContextMenuEvent)
contextMenuPolicy(self) → Qt.ContextMenuPolicy
corner(self, corner: Qt.Corner) → Qt.DockWidgetArea
create(self, window: PyQt6.sip.voidptr = 0, initializeWindow: bool = True, destroyOldWindow: bool = True)
createPopupMenu(self) → QMenu
createWindowContainer(window: QWindow, parent: typing.Optional[QWidget] = None, flags: Qt.WindowType = Qt.WindowFlags()) → QWidget
cursor(self) → QCursor
customContextMenuRequested

customContextMenuRequested(self, pos: QPoint) [signal]

customEvent(self, a0: QEvent)
deleteLater(self)
depth(self) → int
destroy(self, destroyWindow: bool = True, destroySubWindows: bool = True)
destroyed

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

devType(self) → int
devicePixelRatio(self) → float
devicePixelRatioF(self) → float
devicePixelRatioFScale() → float
disconnect(a0: QMetaObject.Connection) → bool
disconnect(self) → None
disconnectNotify(self, signal: QMetaMethod)
dockOptions(self) → QMainWindow.DockOption
dockWidgetArea(self, dockwidget: QDockWidget) → Qt.DockWidgetArea
documentMode(self) → bool
dragEnterEvent(self, a0: QDragEnterEvent)
dragLeaveEvent(self, a0: QDragLeaveEvent)
dragMoveEvent(self, a0: QDragMoveEvent)
dropEvent(self, a0: QDropEvent)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
effectiveWinId(self) → PyQt6.sip.voidptr
ensurePolished(self)
enterEvent(self, event: QEnterEvent)
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]
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
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)
iconSize(self) → QSize
iconSizeChanged

iconSizeChanged(self, iconSize: QSize) [signal]

inherits(self, classname: str) → bool
initPainter(self, painter: QPainter)
inputMethodEvent(self, a0: QInputMethodEvent)
inputMethodHints(self) → Qt.InputMethodHint
inputMethodQuery(self, a0: Qt.InputMethodQuery) → Any
insertAction(self, before: QAction, action: QAction)
insertActions(self, before: QAction, actions: Iterable[QAction])
insertToolBar(self, before: QToolBar, toolbar: QToolBar)
insertToolBarBreak(self, before: QToolBar)
installEventFilter(self, a0: QObject)
isActiveWindow(self) → bool
isAncestorOf(self, child: QWidget) → bool
isAnimated(self) → bool
isDockNestingEnabled(self) → 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
isSeparator(self, pos: QPoint) → bool
isSignalConnected(self, signal: QMetaMethod) → bool
isVisible(self) → bool
isVisibleTo(self, a0: QWidget) → bool
isWidgetType(self) → bool
isWindow(self) → bool
isWindowModified(self) → bool
isWindowType(self) → bool
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
menuBar(self) → QMenuBar
menuWidget(self) → QWidget
metaObject(self) → QMetaObject
metric(self, a0: QPaintDevice.PaintDeviceMetric) → int
minimumHeight(self) → int
minimumSize(self) → QSize
minimumSizeHint(self) → QSize
minimumWidth(self) → int
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)
removeDockWidget(self, dockwidget: QDockWidget)
removeEventFilter(self, a0: QObject)
removeToolBarBreak(self, before: QToolBar)
render(self, target: QPaintDevice, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: QWidget.RenderFlag = QWidget.RenderFlags(QWidget.DrawWindowBackground | QWidget.DrawChildren))
render(self, painter: QPainter, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: QWidget.RenderFlag = QWidget.RenderFlags(QWidget.DrawWindowBackground | QWidget.DrawChildren)) → None
repaint(self)
repaint(self, x: int, y: int, w: int, h: int) → None
repaint(self, a0: QRect) → None
repaint(self, a0: QRegion) → None
resize(self, a0: QSize)
resize(self, w: int, h: int) → None
resizeDocks(self, docks: Iterable[QDockWidget], sizes: Iterable[int], orientation: Qt.Orientation)
resizeEvent(self, a0: QResizeEvent)
restoreDockWidget(self, dockwidget: QDockWidget) → bool
restoreGeometry(self, geometry: QByteArray) → bool
restoreState(self, state: QByteArray, version: int = 0) → bool
saveGeometry(self) → QByteArray
saveState(self, version: int = 0) → QByteArray
screen(self) → QScreen
scroll(self, dx: int, dy: int)
scroll(self, dx: int, dy: int, a2: QRect) → None
sender(self) → QObject
senderSignalIndex(self) → int
setAcceptDrops(self, on: bool)
setAccessibleDescription(self, description: str)
setAccessibleName(self, name: str)
setAnimated(self, enabled: bool)
setAttribute(self, attribute: Qt.WidgetAttribute, on: bool = True)
setAutoFillBackground(self, enabled: bool)
setBackgroundRole(self, a0: QPalette.ColorRole)
setBaseSize(self, basew: int, baseh: int)
setBaseSize(self, s: QSize) → None
setCentralWidget(self, widget: QWidget)
setContentsMargins(self, left: int, top: int, right: int, bottom: int)
setContentsMargins(self, margins: QMargins) → None
setContextMenuPolicy(self, policy: Qt.ContextMenuPolicy)
setCorner(self, corner: Qt.Corner, area: Qt.DockWidgetArea)
setCursor(self, a0: Union[QCursor, Qt.CursorShape])
setDisabled(self, a0: bool)
setDockNestingEnabled(self, enabled: bool)
setDockOptions(self, options: QMainWindow.DockOption)
setDocumentMode(self, enabled: bool)
setEnabled(self, a0: bool)
setFixedHeight(self, h: int)
setFixedSize(self, a0: QSize)
setFixedSize(self, w: int, h: int) → None
setFixedWidth(self, w: int)
setFocus(self)
setFocus(self, reason: Qt.FocusReason) → None
setFocusPolicy(self, policy: Qt.FocusPolicy)
setFocusProxy(self, a0: QWidget)
setFont(self, a0: QFont)
setForegroundRole(self, a0: QPalette.ColorRole)
setGeometry(self, a0: QRect)
setGeometry(self, ax: int, ay: int, aw: int, ah: int) → None
setGraphicsEffect(self, effect: QGraphicsEffect)
setHidden(self, hidden: bool)
setIconSize(self, iconSize: QSize)
setInputMethodHints(self, hints: Qt.InputMethodHint)
setLayout(self, a0: QLayout)
setLayoutDirection(self, direction: Qt.LayoutDirection)
setLocale(self, locale: QLocale)
setMask(self, a0: QBitmap)
setMask(self, a0: QRegion) → None
setMaximumHeight(self, maxh: int)
setMaximumSize(self, maxw: int, maxh: int)
setMaximumSize(self, s: QSize) → None
setMaximumWidth(self, maxw: int)
setMenuBar(self, menubar: QMenuBar)
setMenuWidget(self, menubar: QWidget)
setMinimumHeight(self, minh: int)
setMinimumSize(self, minw: int, minh: int)
setMinimumSize(self, s: QSize) → None
setMinimumWidth(self, minw: int)
setMouseTracking(self, enable: bool)
setObjectName(self, name: str)
setPalette(self, a0: QPalette)
setParent(self, parent: QWidget)
setParent(self, parent: QWidget, f: Qt.WindowType) → None
setProperty(self, name: str, value: Any) → bool
setScreen(self, a0: QScreen)
setShortcutAutoRepeat(self, id: int, enabled: bool = True)
setShortcutEnabled(self, id: int, enabled: bool = True)
setSizeIncrement(self, w: int, h: int)
setSizeIncrement(self, s: QSize) → None
setSizePolicy(self, a0: QSizePolicy)
setSizePolicy(self, hor: QSizePolicy.Policy, ver: QSizePolicy.Policy) → None
setStatusBar(self, statusbar: QStatusBar)
setStatusTip(self, a0: str)
setStyle(self, a0: QStyle)
setStyleSheet(self, styleSheet: str)
setTabOrder(a0: QWidget, a1: QWidget)
setTabPosition(self, areas: Qt.DockWidgetArea, tabPosition: QTabWidget.TabPosition)
setTabShape(self, tabShape: QTabWidget.TabShape)
setTabletTracking(self, enable: bool)
setToolButtonStyle(self, toolButtonStyle: Qt.ToolButtonStyle)
setToolTip(self, a0: str)
setToolTipDuration(self, msec: int)
setUnifiedTitleAndToolBarOnMac(self, set: bool)
setUpdatesEnabled(self, enable: bool)
setVisible(self, visible: bool)
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
splitDockWidget(self, after: QDockWidget, dockwidget: QDockWidget, orientation: Qt.Orientation)
stackUnder(self, a0: QWidget)
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
statusBar(self) → QStatusBar
statusTip(self) → str
style(self) → QStyle
styleSheet(self) → str
tabPosition(self, area: Qt.DockWidgetArea) → QTabWidget.TabPosition
tabShape(self) → QTabWidget.TabShape
tabifiedDockWidgetActivated

tabifiedDockWidgetActivated(self, dockWidget: QDockWidget) [signal]

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

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

toolTip(self) → str
toolTipDuration(self) → int
tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str
underMouse(self) → bool
ungrabGesture(self, type: Qt.GestureType)
unifiedTitleAndToolBarOnMac(self) → bool
unsetCursor(self)
unsetLayoutDirection(self)
unsetLocale(self)
update(self)
update(self, a0: QRect) → None
update(self, a0: QRegion) → None
update(self, ax: int, ay: int, aw: int, ah: int) → None
updateGeometry(self)
updateMicroFocus(self, query: Qt.InputMethodQuery = Qt.ImQueryAll)
updatesEnabled(self) → bool
visibleRegion(self) → QRegion
whatsThis(self) → str
wheelEvent(self, a0: QWheelEvent)
width(self) → int
widthMM(self) → int
winId(self) → PyQt6.sip.voidptr
window(self) → QWidget
windowFilePath(self) → str
windowFlags(self) → Qt.WindowType
windowHandle(self) → QWindow
windowIcon(self) → QIcon
windowIconChanged

windowIconChanged(self, icon: QIcon) [signal]

windowIconText(self) → str
windowIconTextChanged

windowIconTextChanged(self, iconText: str) [signal]

windowModality(self) → Qt.WindowModality
windowOpacity(self) → float
windowRole(self) → str
windowState(self) → Qt.WindowState
windowTitle(self) → str
windowTitleChanged

windowTitleChanged(self, title: str) [signal]

windowType(self) → Qt.WindowType
x(self) → int
y(self) → int
class schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer(parent, toolbars=None, auto_align=False, require3d=True)

Bases: schrodinger.ui.sequencealignment.sequence_viewer.SequenceViewer

Creates a sequence viewer that can be opened by an action or added to a main window as a dockable item. Here is an example of how to add a dockable item to a QMainWindow, or AppFramework window:

from schrodinger.applications.bioluminate import sequence_viewer

self.sequence_viewer = sequence_viewer.SimplifiedSequenceViewer(<window>)
self.addDockWidget(
    QtCore.Qt.TopDockWidgetArea,
    self.sequence_viewer.asDock()
)

If you want to add a button that will open the viewer in a new window:

from schrodinger.applications.bioluminate import sequence_viewer

self.sequence_viewer = sequence_viewer.SimplifiedSequenceViewer(<window>)
self.viewer_button   = QtWidgets.QPushButton(self.tr('Open Model Viewer...'))
self.viewer_button.clicked.connect(self.openSequenceViewer)

then in the connected method (openSequenceViewer):

self.sequence_viewer.window.show()
self.sequence_viewer.window.setFocus()

If you want to simply add a sequence viewer frame to your app:

self.sequence_viewer = SimplifiedSequenceViewer(<window>)
<layout>.addWidget( self.sequence_viewer.asFrame() )
WORKSPACE = 'workspace'
PROJET_TABLE = 'projecttable'
PDB_STRING = 'pdb_string'
FILES = 'files'
MANUAL_SEQUENCE = 'manual_sequence'
sequencesImported

Signal emitted after any structures have been imported by any means into the viewer. The string passed in the emit will be one of:

__init__(parent, toolbars=None, auto_align=False, require3d=True)
Parameters

  • parent – Parent widget of the sequence viewer

  • toolbars (list of strings) – A list of toolbar flags to use (see ViewerWindow for available toolbars

  • auto_align (boolean) – Whether to auto-align sequences when a new one is imported

  • require3d (boolean) – Whether to allow fasta sequence files to be imported. If set to True (default) only structures with 3D coordinates are allowed.

See

ViewerWindow

window(self) → QWidget
dock_widget

Widget the allows self.window to be dockable

last_sequences_imported

Stores the last sequences added to the viewer.

setupViewer()

Sets up the viewer’s window and context menus

enableMaestroSync()

Enables selection and color synchronization with Maestro

asDock()

Returns the viewer as a dock widget.

asFrame()

Returns the viewer as a frame widget

property protein_sequences

Property for all sequences in the viewer that are valid proteins

Return type

list of sequences

property structure_sequences

Property for all sequences in the viewer that have structures.

Return type

list of sequences

property selected_sequences

Property returning all selected sequences in the viewer. This does not include a child sequence.

Return type

list of sequences

getReferenceStructure()

Gets the structure associated with the reference sequence from maestro’s PT. If there is no structure for the reference None is returned.

Return type

schrodinger.structure.Structure

generateSeqProjectRows(include_reference=True)

Create a generator for all sequences that have a project table row associated with them. Yields each sequence’s row from the PT.

Parameters

include_reference (bool) – Whether to include the reference seq

Returns

A generator that yields a schrodinger.project.ProjectRow

Return type

generator

generateSeqStructures(include_reference=True)

Create a generator for all sequences that have a project table row associated with them. Yields each sequence’s structure from the PT.

Parameters

include_reference (bool) – Whether to include the reference structure

Returns

A generator that yields a schrodinger.structure.Structure

Return type

generator

getSeqStructure(sequence)

Get the structure associated with a Sequence.

Returns

A structure object if found otherwise None

Return type

None or structure

importFromPDB(*args, **kwargs)
importFromFile(*args, **kwargs)
importFromFilePaths(filenames, to_maestro=True)

Import a list of filesnames into the sequence viewer.

Parameters

filenames (list of strings) – Filenames to be imported

importFromWorkspace(*args, **kwargs)
importFromProjectTable(*args, **kwargs)
createSequence(*args, **kwargs)

Creates a new sequence and adds it to the sequence group.

addAnnotationAction()
setColorModeAction()
focusFinder()

Switch focus to Find Pattern input box.

nameContextCallback(position, seq=None)

Callback used when context menus called for the view with the pdb name.

sequenceContextCallback(position, res=None)

Callback used when context menus called for the view with the sequences in it.

treeContextCallback(position, tree=None)

Callback used when context menus called for the tree view

selectOnlyByEntry(entry_ids)

Selects rows in the sequence viewer that are associated with the passed in entry ids.

selectOnlyBySeqs(sequences)

Selects rows in the sequence viewer that are associated with the passed in sequences.

Parameters

sequences (schrodinger.ui.sequencealignment.sequence.Sequence or list of them.) – Sequence or sequences to select in viewer

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
__len__()

Return len(self).

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])
addAllColorBlocks()

Adds all available color blocks annotations to selected or all sequences in the sequence group.

addAnnotation(annotation_type, remove=False)

Adds a new annotation sequence to selected sequences or to all sequences if no sequence is selected.

Parameters

annotation_type (int) – Type of the annotation sequence.

addConsensus(toggle=False, update=True)

Adds a consensus annotation sequence.

addGlobalAnnotations()

Add global annotations action callback.

addMeanHydrophobicity(toggle=False, update=True)

Adds a mean hydrophobicity annotation.

addMeanPI(toggle=False, update=True)

Adds a mean isoelectric point annotation.

Adds a sequence logo annotation.

addSymbols(toggle=False, update=True)

Adds a symbols sequence.

addUserAnnotation(annotation_type='region')
addWidget(self, widget: QWidget)
adjustSize(self)
alignByResidueNumbers()

Performs a sequence alignment using residue numbers as IDs.

alignMerge()

Performs a pariwise alignment using dynamic programming (Smith-Waterman algorithm). Sequentially merges the aligned sequences with the existing alignment.

alignStructures()

Aligns available structures.

alignmentSettingsDialog()

Opens alignment settings dialog.

analyzeBindingSite()

Performs binding site analysis.

anchorSelection()

Freezes the selected part of the alignment so it is not possible to move residues outside of the restricted part.

assignAntibodyScheme(scheme='Chothia', display_annotation=True, annotation_color=(255, 0, 0), remove=False, renumber_entry=True, renumber=True, annotate=True, select=False)

Assigns a specified antibody numbering scheme.

Parameters

  • scheme – Numbering scheme type. ‘Chothia’, ‘EnhancedChothia’ ‘IMGT’, ‘AHo’ or ‘Kabat’ are valid choices. Please refer to psp.antibody docs for more details.

  • display_annotation – Displays a custom annotation for the assigned loops (default: True)

  • annotation_color – R,G,B color uses for annotation (default: red)

  • remove (bool) – If True, instead of creating new annotations, the function removes any existing CDR annotations and quits.

  • renumber (bool) – When True, the function will assign new residue numbers according to the selected scheme.

  • renumber_entry (bool) – When True the function will renumber corresponding Maestro entry.

  • annotate (bool) – When True, the function will create new CDR annotations (note: the ‘remove’ paarameter will override this).

  • select (bool) – When True, the function will select residues belonging to the CDRs.

Return type

int

Returns

Number of successfully re-numbered sequences.

associateMaestroEntries()

Displays ‘Associate Maestro Entries’ dialog.

autoFillBackground(self) → bool
auxBorderWidth()

Calculates a width of sequence area border that includes auxiliary information (sequence similarity, borders, etc).

backgroundRole(self) → QPalette.ColorRole
baseSize(self) → QSize
blastFailedCallback(dialog, results_dialog, ok_callback)

The default callback to call when a BLAST search job fails. This will retry the job if it was a locally run job and try to use the a remote job to succeed.

blastOkCallback(results_dialog)

The default callback to call when a BLAST search job succeeds. This will show the BLAST results panel which allows users to choose which sequences to import into the sequence viewer, with the best 10 highlighted.

blockSignals(self, b: bool) → bool
buildModel()

Builds 3D model of reference sequence.

changeEvent(self, a0: QEvent)
changeQuery(index)
childAt(self, p: QPoint) → QWidget
childAt(self, ax: int, ay: int) → QWidget
childEvent(self, a0: QChildEvent)
children(self) → List[QObject]
childrenCollapsible(self) → bool
childrenRect(self) → QRect
childrenRegion(self) → QRegion
clearAnchors()

Clears the rectricted part of the alignment.

clearConstraints()

Clears pairwise alignment constraints.

clearFocus(self)
clearMarkedResidues()

Clears residues that are marked by custom color.

clearMask(self)
clearQueryConstraints()

Toggles a query sequence constraints.

clearSequences()

Removes all sequences and updates the viewer.

clearSet()
close(self) → bool
closeEvent(event)

Called on window close request. Will attempt to save MSV state in current Maestro project directory.

closestLegalPosition(self, a0: int, a1: int) → int
collapseAllSequences()

Collapses all sequences.

colorCount(self) → int
colorEntrySurface()
colorSequenceNames(color)
colorSequences(color=None)

Sets arbitrary color to the sequences.

colorToRGB(color)

Converts a color name string to RGB tuple.

computeSequenceProfile()

Computes internal sequence profile and updates self.

connectNotify(self, signal: QMetaMethod)
contentsMargins(self) → QMargins
contentsRect(self) → QRect
contextMenuEvent(self, a0: QContextMenuEvent)
contextMenuPolicy(self) → Qt.ContextMenuPolicy
copySequences(group)

Copies all or selected sequences from group to self.sequence_group.

count(self) → int
create(self, window: PyQt6.sip.voidptr = 0, initializeWindow: bool = True, destroyOldWindow: bool = True)
createCommandDict()

Creates an external command dictionary.

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

Crops residues in a selected area.

cursor(self) → QCursor
customContextMenuRequested

customContextMenuRequested(self, pos: QPoint) [signal]

customEvent(self, a0: QEvent)
deleteAnnotations()

Deletes all annotations.

deleteByEntry(entry_ids)

Deletes rows in the sequence viewer that are associated with the passed in entry ids. If any rows are selected before this is called, they are retained.

deleteLater(self)
deletePredictions()

Deletes all predictions.

deleteSelectedResidues()

Deletes all selected residues.

deleteSelectedSequences()

Deletes all selected sequences.

Return type

bool

Returns

True if all sequences were removed

deleteSet(index)

Remove a sequence viewer tab.

depth(self) → int
deselectAll()

Deselects all residues.

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
disableQueryConstraints(remove_if_empty=True)

Toggles a query sequence constraints.

disconnect(a0: QMetaObject.Connection) → bool
disconnect(self) → None
disconnectNotify(self, signal: QMetaMethod)
displayLigands()

Displays Maestro ligand interaction fingerprints.

displayMessage(message)

Displays a message on a status bar.

downloadPDB(maestro_include=True, maestro_incorporate=True, remote_query=True)

Downloads a corresponding PDB structure.

Returns

True if the download was successful, otherwise False.

Return type

boolean

dragEnterEvent(self, a0: QDragEnterEvent)
dragLeaveEvent(self, a0: QDragLeaveEvent)
dragMoveEvent(self, a0: QDragMoveEvent)
drawFrame(self, a0: QPainter)
dropEvent(self, a0: QDropEvent)
dumpObjectInfo(self)
dumpObjectTree(self)
duplicateSequences()

Duplicates selected sequences.

dynamicPropertyNames(self) → List[QByteArray]
editSequence()

Edits a selected sequence.

effectiveWinId(self) → PyQt6.sip.voidptr
emphasizeArea(area)
enableQueryConstraints()

Toggles a query sequence constraints.

ensurePolished(self)
enterEvent(self, event: QEnterEvent)
event(self, a0: QEvent) → bool
eventFilter(self, a0: QObject, a1: QEvent) → bool
excludeQueryEntries()
excludeSelected()
executeCommandFile(cmd_file_name)

Executes an external command file.

expandAllSequences()

Expands all sequences.

expandSelection()

Expands selection to include entire columns.

expandSelectionRef()

Expands selection from reference sequence to include entire columns.

fetchSequence(ids, replace=None, progress=None, maestro_include=False, maestro_incorporate=True, remote_query=True)

Fetches sequences from online repositories based on entry ID. This method attempts to automatically recognize the repository by looking on the specified entry ID format.

Parameters

  • entry_id (str) – Entry ID in the online database.

  • replace (Sequence) – Sequence to be replaced by a matching PDB sequence.

Return type

string/bool

Returns

On success “ok” or True, on error “error”, “cancelled” or “invalid”

fillGaps()

Fill a selected region with gaps.

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]
findNext()

Scrolls to a next occurence of a selected pattern.

findPattern(pattern)

Finds a specified PROSITE-like pattern in the sequences.

Parameters

pattern (str) – Pattern to find in the sequence group.

findPrevious()

Scrolls to a previous occurence of a selected pattern.

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
generateRows(use_max_length=False, custom_width=None, custom_height=None)

Generate rows that can be directly displayed by the sequence area widget. This method is relatively fast, because it doesn’t generate actual sequence chunks, but rather calculates pointers.

geometry(self) → QRect
getConsiderGaps()

Gets value of consider gaps flag.

Rtype value

bool

Returns

Should we consider gaps for sequence identity calculations.

getContents(all_sequences=False)

Returns contents of the current sequence group (tab).

Parameters

all_sequences (boolean) – If False (default), return only protein sequences. If True, return all sequences including ruler, annotations, spacers, etc.

Return type

list of tuples

Returns

Returns a list of following tuples: (sequence_index, sequence_short_name, sequence_full_name, maestro_entry_id, maestro_chain_name, sequence_string)

getGlobalAnnotations(annotation_types=['all'], ignore_query=False, ignore_gaps=False)

Returns global annotations for calculate for each position of the alignment.

Parameters

annotation_types (list of strings) – List of global annotation types to be calculated. The following types are allowed:

“all” (default value): All available annotations.

“variability_percentage”: sequence variability (normalized Shannon entropy) calculated for each alignment position.

“variability_count”: Number of different residue types for each alignment position.

“group_conservation”: Classification based on pre-defined conservation groups: ‘strong’ or ‘weak’ conservations.

The following numerical values are possible:

3: identity 2: strong conservation 1: weak conservation 0: no conservation -1: gap in query

“query_match_percentage”: Percentage of sequences that match the corresponding residue of the query sequence.

“sasa”: Solvent-accessible surface area. It is not used by default and it has to be explicitly specified.

“sasa_percentage”: Percentage of solvent-accessible surface area. It is not used by default and it has to be explicitly specified.

Parameters

  • query (ignore) – Determines if query (parent) sequence should be included in calculations.

  • ignore_gaps (boolean) – Determines if gaps in query sequence should be included in calculations. If False, only values calculated for ungapped positions will be returned.

Return type

dictionary of lists of floats

Returns

Returns a dictionary with annotation names as keys and lists of numbers including calculated annotations for each alignment position.

getMode()

Gets current sequence viewer operational mode.

Return type

int

Returns

Current sequence viewer mode.

getRange(self, index: int) → Tuple[int, int]
getSASA(sequences=[], selected_only=False, ignore_gaps=False, normalize=True, percentage=False)

Calculates residue sequence accessible surface area for each sequence. The calculated area is not normalized.

Param

List of sequences to calculate SASA. When multiple sequences come from a single entry, the calculation will be optimized (performed once per entry).

Type

ignore_gaps

Param

If True the gaps will not be included in the output list.

Parameters

  • normalize (bool) – Should we normalize the SASA area by area of amino acid in default conformation.

  • percentage (bool) – If True return percentage SASA instead of absolute values.

Return type

list of tuples

Returns

Each tuple includes (sequence_index, list_residue_sasa) If SASA could not be calculated (e.g. no structural information), the list_residue_sasa is empty.

getStructureAlignment()
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
handle(self, index: int) → QSplitterHandle
handleWidth(self) → int
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)
hideColumns(unselected=False)

Hides selected columns.

hideEvent(self, a0: QHideEvent)
hideSelectedSequences()

Hides all selected sequences.

includeQueryEntries()
incorporateIncludedEntries(incorporate_scratch_entry=None)

Incorporates included entries into the SV.

incorporateSelectedEntries()

Incorporates selected entries into the SV.

incorporateStructure(st)

Incorporates a structure passed as a Structure object.

indexOf(self, w: QWidget) → int
inherits(self, classname: str) → bool
initMaestro()

Initializes Maestro callbacks.

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])
insertWidget(self, index: int, widget: QWidget)
installEventFilter(self, a0: QObject)
invertSelection()

Inverts residue selection.

invertSequenceSelection()

Inverts current sequence selection range.

isActiveWindow(self) → bool
isAncestorOf(self, child: QWidget) → bool
isCollapsible(self, index: int) → 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
loadFile(file_name, merge=False, replace=False, to_maestro=False, translate=False, new_list=None, maestro_include=True)

Loads a sequence file and merges the read sequences with current sequence viewer contents.

Note

This is a default behavior. To replace current contents with new sequences, clear the sequence viewer contents and then load the file.

Parameters

file_name (str) – name of the file to be read.

loadProject(file_name)

Loads a MSV project from an external file.

locale(self) → QLocale
lockGaps()

Locks gaps.

logicalDpiX(self) → int
logicalDpiY(self) → int
lower(self)
maestroCommandCallback(command)

Called when Maestro executes a command.

maestroProjectChanged()

This method is invoked whenever Maestro project changes.

maestroProjectClose()

This function is invoked whenever Maestro project is about to be closed.

maestroProjectOpen()

This function is invoked whenever Maestro project is opened.

maestroWorkspaceChanged(what_changed)

This function is invoked whenever Maestro colors change. It updates colors and selection state of the sequences associated with Maestro.

makeTabsFromGroupList()

Create named query tabs based on self sequence group list.

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
markResidues(rgb)

Marks selected residues using a specified RGB color.

Parameters

rgb ((int, int, int)) – RGB color tuple.

mask(self) → QRegion
maxColumns(custom_width=None, custom_height=None, calculate_width=False)

Calculates a maximum number of sequence columns that can fit into the viewer.

Return type

int or tuple

Returns

maximum number of columns or max number of columns and calculated width when calculate_width == True

maximumHeight(self) → int
maximumSize(self) → QSize
maximumWidth(self) → int
metaObject(self) → QMetaObject
metric(self, a0: QPaintDevice.PaintDeviceMetric) → int
midLineWidth(self) → int
minimizeAlignment()

Removes all gaps.

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
moveBottom()

Moves selected sequences to the bottom of the group.

moveDown()

Moves selected sequences one level down.

moveEvent(self, a0: QMoveEvent)
moveSplitter(self, pos: int, index: int)
moveToThread(self, thread: QThread)
moveTop()

Moves selected sequences to the top of the group.

moveUp()

Moves selected sequences one level up.

nativeEvent(self, eventType: QByteArray, message: PyQt6.sip.voidptr) → Tuple[bool, PyQt6.sip.voidptr]
nativeParentWidget(self) → QWidget
newSet(name=None)

Creates a new query set

nextInFocusChain(self) → QWidget
normalGeometry(self) → QRect
objectName(self) → str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

opaqueResize(self) → bool
orientation(self) → Qt.Orientation
overrideWindowFlags(self, type: Qt.WindowType)
overrideWindowState(self, state: Qt.WindowState)
paintEngine(self) → QPaintEngine
paintEvent(self, a0: QPaintEvent)
paintingActive(self) → bool
pairwiseAlignment()

Performs a pariwise alignment using dynamic programming (Smith-Waterman algorithm).

palette(self) → QPalette
parent(self) → QObject
parentWidget(self) → QWidget
passSelectionToMaestro()
pasteFasta()

Pastes an alignment in text FASTA format into the MSV window.

physicalDpiX(self) → int
physicalDpiY(self) → int
pos(self) → QPoint
previousInFocusChain(self) → QWidget
propagateColors()

Propagates colors to Maestro workspace.

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
redo()

Redoes previously undone operation.

refresh(self)
releaseKeyboard(self)
releaseMouse(self)
releaseShortcut(self, id: int)
removeAction(self, action: QAction)
removeAllColorBlocks()

Removes all color blocks annotations from selected or all sequences in the sequence group.

removeEventFilter(self, a0: QObject)
removeGaps()

Removes all gaps.

removeGlobalAnnotations()

Removes global annotations.

removeMaestroCallbacks()

Removes registered Maestro callbacks.

removeRedundancy()

Removes redundant sequences.

removeUserAnnotations()
renameSequence()

Renames a selected sequence.

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
renumberResidues()

Executes ‘Renumber Residues’ command.

repaint(self)
repaint(self, x: int, y: int, w: int, h: int) → None
repaint(self, a0: QRect) → None
repaint(self, a0: QRegion) → None
replaceWidget(self, index: int, widget: QWidget) → QWidget
resetHistory()

Toggles changes tracking feature.

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

Resize event handler. Update font face and size here.

restoreGeometry(self, geometry: QByteArray) → bool
restoreState(self, state: QByteArray) → bool
runBlast(failed_callback=None, ok_callback=None)

Takes a schrodinger.ui.sequencealignment.sequence.Sequence and runs a Blast simulation to determine the best matches. The status callbacks can be set.

This method will return None if the run dialog was cancelled, ‘failed’ if the job failed and ‘ok’ if the job succeeded.

Parameters

  • ref_sequence (schrodinger.ui.sequencealignment.sequence.Sequence) – The sequence to run the BLAST search against

  • failed_callback (callable) – The callback to call when the job fails

  • failed_callback – The callback to call when the job succeeds

See also failedBlastCallback and successBlastCallback.

runClustal(ignore_selection=False)

Runs Clustal alignment and updates self.

runPfam()

Runs Pfam simulation and incorporates the results.

runPredictors(predictor_list)

Runs a specified residue-level property predictors.

runSSP()

Runs secondary structure prediction and incorporates the results.

saveFile(file_name, save_annotations=False, selected_only=False, save_similarity=False, format='FASTA')

Saves sequences to a file.

Parameters

file_name (str) – name of the output file

Return type

bool

Returns

True if file successfully saved, False otherwise.

saveGeometry(self) → QByteArray
saveImage(file_name, save_all=True, format='PNG', custom_width=None, custom_height=None)

Saves current view to a PNG image file.

saveProject(file_name, auto_save=False)

Saves current project to an external file.

saveState(self) → QByteArray
screen(self) → QScreen
scroll(self, dx: int, dy: int)
scroll(self, dx: int, dy: int, a2: QRect) → None
selectAlignedBlocks()

Selects aligned blocks (the sequence regions without gaps).

selectAll()

Selects all residues.

selectAllSequences()

Selects all sequences in the group.

selectColumns(column_list)

Selects specified columns in the viewer.

First, the function deselects all contents, then selects columns specified by the provided list of alignment indices.

Parameters

column_list (list of integers) – List of colums to select.

selectIdentities()

Selects identical residues in columns.

selectLigandContacts(ligand=None)

Selects residues in ligand proximity in selected ligand sequence.

selectResidues(sequence_list)

Selects specified residues in the viewer.

The function deselects all contents, then selects residues specified by the alignment indices for each sequence.

Parameters

sequence_list (list of tuples) – Each tuple includes (sequence_index, list_of_alignment_indices)

selectSequencesByName(name_list)
selectStructureBlocks()

Selects blocks that have structure.

sender(self) → QObject
senderSignalIndex(self) → int
setAcceptDrops(self, on: bool)
setAccessibleDescription(self, description: str)
setAccessibleName(self, name: str)
setAsReference()

Sets a selected sequence as a reference.

setAttribute(self, attribute: Qt.WidgetAttribute, on: bool = True)
setAutoFillBackground(self, enabled: bool)
setBackgroundColor(color=(255, 255, 255))

Sets a background color.

Parameters

color ((int, int, int)) – Background color RGB tuple.

setBackgroundRole(self, a0: QPalette.ColorRole)
setBaseSize(self, basew: int, baseh: int)
setBaseSize(self, s: QSize) → None
setBoundaries(value)

Turns on and off displaying sequence boundaries on the alignment.

Parameters

value (bool) – if True, display boundaries

setCallback(callback, event_type='residue_selection_changed')

Sets a sequence viewer callback.

Parameters

  • event_type (string) – Type of callback event.

  • callback – Callback function to be called.

setChildrenCollapsible(self, a0: bool)
setCollapsible(self, index: int, a1: bool)
setColorMode(color_mode)

Colors sequences using a specified color mode.

Parameters

color_mode (int) – Color mode used to color the sequences.

setConsiderGaps(value)

Sets value of consider gaps flag. If set to True, gaps will be included in calculation of local sequence similarity measures.

Parameters

value (bool) – Should we consider gaps for sequence identity calculations.

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)
setDisplayHomology(value)

Turns on and off displaing sequence homology information.

Parameters

value (bool) – Display homology value.

setDisplayIdentity(value)

Turns on and off displaing sequence identity information.

Parameters

value (bool) – Display identity value.

setDisplayScore(value)

Turns on and off displaing sequence score information.

Parameters

value (bool) – display score value.

setDisplaySimilarity(value)

Turns on and off displaing sequence similarity information.

Parameters

value (bool) – Display similarity value.

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)
setHandleWidth(self, a0: int)
setHasHeaderRow(has_header_row)

Toggles header row.

Parameters

has_tooltips (bool) – If True, enable the header row, if False - disable it

setHasRuler(has_ruler)

Toggles the ruler.

Parameters

has_ruler (bool) – if True - enable the ruler, otherwise - disable it.

setHasTooltips(has_tooltips)

Toggles mouse hover tooltips.

Parameters

has_tooltips (bool) – if True, enable tooltips, if False -disable them

setHidden(self, hidden: bool)
setIdentityInColumns(value)

Sets “Calculate identity in columns” setting.

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)
setMode(mode)

Sets sequence viewer operation mode.

Note

See constants.py for more details on what modes are available.

Parameters

mode (int) – Sequence viewer mode.

setMouseAcross(enabled)

Toggles use mouse across rows mode.

Parameters

enabled (bool) – if True, enable “mouse across rows” mode, otherwise disable it

setMouseTracking(self, enable: bool)
setObjectName(self, name: str)
setOpaqueResize(self, opaque: bool = True)
setOrientation(self, a0: Qt.Orientation)
setPadded(padded)

Toggles alignment padding.

Parameters

padded (bool) – If True, enable padded mode, False - disable it.

setPalette(self, a0: QPalette)
setParent(self, parent: QWidget)
setParent(self, parent: QWidget, f: Qt.WindowType) → None
setPopupMenus(name_menu=None, sequence_menu=None, tree_menu=None)

Sets popup menu for name area widget.

Parameters

menu (QPopupMenu) – Name area popup menu.

setProperty(self, name: str, value: Any) → bool
setRubberBand(self, position: int)
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
setSizes(self, list: Iterable[int])
setStatusTip(self, a0: str)
setStretchFactor(self, index: int, stretch: int)
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)
setUndoRedoActions(undo_action, redo_action)

Sets Qt undo/redo actions, so that the undo/redo mechanism can change the corresponding menu items appropriately.

Parameters

  • undo_action (QAction) – Qt action for undo operation.

  • redo_action (QAction) – Qt action for redo operation.

setUpdatesEnabled(self, enable: bool)
setUseColors(use_colors)

Sets use colors flag.

Parameters

use_colors (bool) – If True, colors will be used to draw the sequences.

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)
setWrapped(wrapped)

This method toggles sequence wrapping mode.

Parameters

wrapped (bool) – if True, enable wrapped mode, otherwise - disable it

sharedPainter(self) → QPainter
show(self)
showAllSequences()

Shows all sequences.

showBlastResults()

Displays BLAST results dialog.

showColumns()

Shows all hidden columns.

showCompareSequencesDialog()

Create an instance of ‘Compare sequences’ dialog (if necessary) and open the dialog.

showEvent(event)

Called on window show request. Will attempt to restore MSV state from current Maestro project directory.

showFullScreen(self)
showJobLog()

Displays a job log window.

showJobSettings()

Displays a job settings dialog.

showMaximized(self)
showMinimized(self)
showNormal(self)
signalsBlocked(self) → bool
size(self) → QSize
sizeHint(self) → QSize
sizeIncrement(self) → QSize
sizePolicy(self) → QSizePolicy
sizes(self) → List[int]
splitterMoved

splitterMoved(self, pos: int, index: int) [signal]

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
synchronizeWithMaestro()

Synchronizes sequence viewer contents with Maestro workspace.

tabletEvent(self, a0: QTabletEvent)
testAttribute(self, attribute: Qt.WidgetAttribute) → bool
thread(self) → QThread
timerEvent(self, a0: QTimerEvent)
toggleConstraints()

Toggles a pairwise alignment constraints.

toggleHistory()

Toggles changes tracking feature.

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

Translates DNA / RNA to amino acids.

underMouse(self) → bool
undo()

Undoes the last operation.

ungrabGesture(self, type: Qt.GestureType)
unlockGaps()

Unlocks gaps.

unselectAllSequences()

Deselects all sequences in the group.

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
updateAnnotationsMenu()
updateFontSize(size=None)

Updates sequence viewer font size in all child widgets. Recomputes all font size dependent variables.

Parameters

size (int) – new font size

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

Updates bottom status bar.

updateView(generate_rows=True, update_colors=False, repaint=True, immediately=False)

Updates the sequence viewer, re-generates profile and re-colors the sequences. This should be called every time sequence group contents changes.

Note

This method may take a long time to execute if there are many sequences in the group. Consider making profile generation optional.

Parameters

generate_rows (bool) – Optional parameter. If False, the method will not re-generate rows (default=True).

Type.update

bool

Param.update

Optional parameter. If False, the method will not update the viewer contents (default=True).

updatesEnabled(self) → bool
visibleRegion(self) → QRegion
weightColorsSettings()

Enables weighting by colors.

whatsThis(self) → str
wheelEvent(self, a0: QWheelEvent)
widget(self, index: int) → QWidget
width(self) → int
widthMM(self) → int
winId(self) → PyQt6.sip.voidptr
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
zoomIn()

Increases zoom factor and updates sequence viewer contents.

zoomOut()

Decreases zoom factor and updates sequence viewer contents.

tree_area

Create tree area widget

padded

Pad alignment with gaps. If enabled, all sequences will be padded with gaps so that they all have identical lengths.

undo_stack

State stack for undo/redo.

display_identity

Display percentange identity on a right side of the panel.

contents_changed

Update flags

cb_residue_selection_changed

Callbacks

job_settings

Global job settings

deleteBySequences(sequences)

Deletes rows in the sequence viewer that are associated with the passed in sequences. If any rows are selected before this is called, they are retained.

importFromMaestro(method)
closeWindow()

Action for the “Close” button