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:
PyQt5.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__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
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.
-
AllDockWidgetFeatures
= 7¶
-
DockWidgetClosable
= 1¶
-
class
DockWidgetFeature
¶ Bases:
int
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
bit_length
() → int¶ Number of bits necessary to represent self in binary. >>> bin(37) ‘0b100101’ >>> (37).bit_length() 6
-
conjugate
()¶ Returns self, the complex conjugate of any int.
-
denominator
¶ the denominator of a rational number in lowest terms
-
from_bytes
(bytes, byteorder, *, signed=False) → int¶ Return the integer represented by the given array of bytes.
The bytes argument must be a bytes-like object (e.g. bytes or bytearray).
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument indicates whether two’s complement is used to represent the integer.
-
imag
¶ the imaginary part of a complex number
-
numerator
¶ the numerator of a rational number in lowest terms
-
real
¶ the real part of a complex number
-
to_bytes
(length, byteorder, *, signed=False) → bytes¶ Return an array of bytes representing an integer.
The integer is represented using length bytes. An OverflowError is raised if the integer is not representable with the given number of bytes.
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument determines whether two’s complement is used to represent the integer. If signed is False and a negative integer is given, an OverflowError is raised.
-
-
class
DockWidgetFeatures
¶ Bases:
sip.simplewrapper
QDockWidget.DockWidgetFeatures(Union[QDockWidget.DockWidgetFeatures, QDockWidget.DockWidgetFeature]) QDockWidget.DockWidgetFeatures(QDockWidget.DockWidgetFeatures)
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
-
DockWidgetFloatable
= 4¶
-
DockWidgetMovable
= 2¶
-
DockWidgetVerticalTitleBar
= 8¶
-
DrawChildren
= 2¶
-
DrawWindowBackground
= 1¶
-
IgnoreMask
= 4¶
-
NoDockWidgetFeatures
= 0¶
-
class
PaintDeviceMetric
¶ Bases:
int
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
bit_length
() → int¶ Number of bits necessary to represent self in binary. >>> bin(37) ‘0b100101’ >>> (37).bit_length() 6
-
conjugate
()¶ Returns self, the complex conjugate of any int.
-
denominator
¶ the denominator of a rational number in lowest terms
-
from_bytes
(bytes, byteorder, *, signed=False) → int¶ Return the integer represented by the given array of bytes.
The bytes argument must be a bytes-like object (e.g. bytes or bytearray).
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument indicates whether two’s complement is used to represent the integer.
-
imag
¶ the imaginary part of a complex number
-
numerator
¶ the numerator of a rational number in lowest terms
-
real
¶ the real part of a complex number
-
to_bytes
(length, byteorder, *, signed=False) → bytes¶ Return an array of bytes representing an integer.
The integer is represented using length bytes. An OverflowError is raised if the integer is not representable with the given number of bytes.
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument determines whether two’s complement is used to represent the integer. If signed is False and a negative integer is given, an OverflowError is raised.
-
-
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
¶ Bases:
int
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
bit_length
() → int¶ Number of bits necessary to represent self in binary. >>> bin(37) ‘0b100101’ >>> (37).bit_length() 6
-
conjugate
()¶ Returns self, the complex conjugate of any int.
-
denominator
¶ the denominator of a rational number in lowest terms
-
from_bytes
(bytes, byteorder, *, signed=False) → int¶ Return the integer represented by the given array of bytes.
The bytes argument must be a bytes-like object (e.g. bytes or bytearray).
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument indicates whether two’s complement is used to represent the integer.
-
imag
¶ the imaginary part of a complex number
-
numerator
¶ the numerator of a rational number in lowest terms
-
real
¶ the real part of a complex number
-
to_bytes
(length, byteorder, *, signed=False) → bytes¶ Return an array of bytes representing an integer.
The integer is represented using length bytes. An OverflowError is raised if the integer is not representable with the given number of bytes.
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument determines whether two’s complement is used to represent the integer. If signed is False and a negative integer is given, an OverflowError is raised.
-
-
class
RenderFlags
¶ Bases:
sip.simplewrapper
QWidget.RenderFlags(Union[QWidget.RenderFlags, QWidget.RenderFlag]) QWidget.RenderFlags(QWidget.RenderFlags)
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
-
acceptDrops
(self) → bool¶
-
accessibleDescription
(self) → str¶
-
accessibleName
(self) → str¶
-
actionEvent
(self, QActionEvent)¶
-
actions
(self) → List[QAction]¶
-
activateWindow
(self)¶
-
addAction
(self, QAction)¶
-
addActions
(self, object)¶
-
adjustSize
(self)¶
-
allowedAreas
(self) → Qt.DockWidgetAreas¶
-
autoFillBackground
(self) → bool¶
-
backgroundRole
(self) → QPalette.ColorRole¶
-
baseSize
(self) → QSize¶
-
blockSignals
(self, bool) → bool¶
-
changeEvent
(self, QEvent)¶
-
childAt
(self, QPoint) → QWidget¶ childAt(self, int, int) -> QWidget
-
childEvent
(self, QChildEvent)¶
-
children
(self) → object¶
-
childrenRect
(self) → QRect¶
-
childrenRegion
(self) → QRegion¶
-
clearFocus
(self)¶
-
clearMask
(self)¶
-
close
(self) → bool¶
-
colorCount
(self) → int¶
-
connectNotify
(self, QMetaMethod)¶
-
contentsMargins
(self) → QMargins¶
-
contentsRect
(self) → QRect¶
-
contextMenuEvent
(self, QContextMenuEvent)¶
-
contextMenuPolicy
(self) → Qt.ContextMenuPolicy¶
-
create
(self, window: sip.voidptr = 0, initializeWindow: bool = True, destroyOldWindow: bool = True)¶
-
createWindowContainer
(QWindow, parent: QWidget = None, flags: Union[Qt.WindowFlags, Qt.WindowType] = 0) → QWidget¶
-
cursor
(self) → QCursor¶
-
customContextMenuRequested
¶ customContextMenuRequested(self, QPoint) [signal]
-
customEvent
(self, QEvent)¶
-
deleteLater
(self)¶
-
depth
(self) → int¶
-
destroy
(self, destroyWindow: bool = True, destroySubWindows: bool = True)¶
-
destroyed
¶ destroyed(self, QObject = None) [signal]
-
devType
(self) → int¶
-
devicePixelRatio
(self) → int¶
-
devicePixelRatioF
(self) → float¶
-
devicePixelRatioFScale
() → float¶
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dragEnterEvent
(self, QDragEnterEvent)¶
-
dragLeaveEvent
(self, QDragLeaveEvent)¶
-
dragMoveEvent
(self, QDragMoveEvent)¶
-
dropEvent
(self, QDropEvent)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → object¶
-
effectiveWinId
(self) → sip.voidptr¶
-
ensurePolished
(self)¶
-
enterEvent
(self, QEvent)¶
-
event
(self, QEvent) → bool¶
-
eventFilter
(self, QObject, QEvent) → bool¶
-
features
(self) → QDockWidget.DockWidgetFeatures¶
-
featuresChanged
¶ featuresChanged(self, Union[QDockWidget.DockWidgetFeatures, QDockWidget.DockWidgetFeature]) [signal]
-
find
(sip.voidptr) → QWidget¶
-
findChild
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶ findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject
-
findChildren
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶ findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]
-
focusInEvent
(self, QFocusEvent)¶
-
focusNextChild
(self) → bool¶
-
focusNextPrevChild
(self, bool) → bool¶
-
focusOutEvent
(self, 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¶
-
getContentsMargins
(self) → Tuple[int, int, int, int]¶
-
grab
(self, rectangle: QRect = QRect(QPoint(0, 0), QSize(-1, -1))) → QPixmap¶
-
grabGesture
(self, Qt.GestureType, flags: Union[Qt.GestureFlags, Qt.GestureFlag] = Qt.GestureFlags())¶
-
grabKeyboard
(self)¶
-
grabMouse
(self)¶ grabMouse(self, Union[QCursor, Qt.CursorShape])
-
grabShortcut
(self, 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, int) → int¶
-
heightMM
(self) → int¶
-
hide
(self)¶
-
hideEvent
(self, QHideEvent)¶
-
inherits
(self, str) → bool¶
-
initPainter
(self, QPainter)¶
-
initStyleOption
(self, QStyleOptionDockWidget)¶
-
inputMethodEvent
(self, QInputMethodEvent)¶
-
inputMethodHints
(self) → Qt.InputMethodHints¶
-
inputMethodQuery
(self, Qt.InputMethodQuery) → Any¶
-
insertAction
(self, QAction, QAction)¶
-
insertActions
(self, QAction, Iterable[QAction])¶
-
installEventFilter
(self, QObject)¶
-
isActiveWindow
(self) → bool¶
-
isAncestorOf
(self, QWidget) → bool¶
-
isAreaAllowed
(self, Qt.DockWidgetArea) → bool¶
-
isEnabled
(self) → bool¶
-
isEnabledTo
(self, 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, QMetaMethod) → bool¶
-
isVisible
(self) → bool¶
-
isVisibleTo
(self, QWidget) → bool¶
-
isWidgetType
(self) → bool¶
-
isWindow
(self) → bool¶
-
isWindowModified
(self) → bool¶
-
isWindowType
(self) → bool¶
-
keyPressEvent
(self, QKeyEvent)¶
-
keyReleaseEvent
(self, QKeyEvent)¶
-
keyboardGrabber
() → QWidget¶
-
killTimer
(self, int)¶
-
layout
(self) → QLayout¶
-
layoutDirection
(self) → Qt.LayoutDirection¶
-
leaveEvent
(self, QEvent)¶
-
locale
(self) → QLocale¶
-
logicalDpiX
(self) → int¶
-
logicalDpiY
(self) → int¶
-
lower
(self)¶
-
mapFrom
(self, QWidget, QPoint) → QPoint¶
-
mapFromGlobal
(self, QPoint) → QPoint¶
-
mapFromParent
(self, QPoint) → QPoint¶
-
mapTo
(self, QWidget, QPoint) → QPoint¶
-
mapToGlobal
(self, QPoint) → QPoint¶
-
mapToParent
(self, QPoint) → QPoint¶
-
mask
(self) → QRegion¶
-
maximumHeight
(self) → int¶
-
maximumSize
(self) → QSize¶
-
maximumWidth
(self) → int¶
-
metaObject
(self) → QMetaObject¶
-
metric
(self, QPaintDevice.PaintDeviceMetric) → int¶
-
minimumHeight
(self) → int¶
-
minimumSize
(self) → QSize¶
-
minimumSizeHint
(self) → QSize¶
-
minimumWidth
(self) → int¶
-
mouseDoubleClickEvent
(self, QMouseEvent)¶
-
mouseGrabber
() → QWidget¶
-
mouseMoveEvent
(self, QMouseEvent)¶
-
mousePressEvent
(self, QMouseEvent)¶
-
mouseReleaseEvent
(self, QMouseEvent)¶
-
move
(self, QPoint)¶ move(self, int, int)
-
moveEvent
(self, QMoveEvent)¶
-
moveToThread
(self, QThread)¶
-
nativeEvent
(self, Union[QByteArray, bytes, bytearray], sip.voidptr) → Tuple[bool, int]¶
-
nativeParentWidget
(self) → QWidget¶
-
nextInFocusChain
(self) → QWidget¶
-
normalGeometry
(self) → QRect¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
overrideWindowFlags
(self, Union[Qt.WindowFlags, Qt.WindowType])¶
-
overrideWindowState
(self, Union[Qt.WindowStates, Qt.WindowState])¶
-
paintEngine
(self) → QPaintEngine¶
-
paintEvent
(self, 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, 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, PYQT_SIGNAL) → int¶
-
rect
(self) → QRect¶
-
releaseKeyboard
(self)¶
-
releaseMouse
(self)¶
-
releaseShortcut
(self, int)¶
-
removeAction
(self, QAction)¶
-
removeEventFilter
(self, QObject)¶
-
render
(self, QPaintDevice, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.DrawWindowBackground|QWidget.DrawChildren))¶ render(self, QPainter, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.DrawWindowBackground|QWidget.DrawChildren))
-
repaint
(self)¶ repaint(self, int, int, int, int) repaint(self, QRect) repaint(self, QRegion)
-
resize
(self, QSize)¶ resize(self, int, int)
-
resizeEvent
(self, QResizeEvent)¶
-
restoreGeometry
(self, Union[QByteArray, bytes, bytearray]) → bool¶
-
saveGeometry
(self) → QByteArray¶
-
scroll
(self, int, int)¶ scroll(self, int, int, QRect)
-
sender
(self) → QObject¶
-
senderSignalIndex
(self) → int¶
-
setAcceptDrops
(self, bool)¶
-
setAccessibleDescription
(self, str)¶
-
setAccessibleName
(self, str)¶
-
setAllowedAreas
(self, Union[Qt.DockWidgetAreas, Qt.DockWidgetArea])¶
-
setAttribute
(self, Qt.WidgetAttribute, on: bool = True)¶
-
setAutoFillBackground
(self, bool)¶
-
setBackgroundRole
(self, QPalette.ColorRole)¶
-
setBaseSize
(self, int, int)¶ setBaseSize(self, QSize)
-
setContentsMargins
(self, int, int, int, int)¶ setContentsMargins(self, QMargins)
-
setContextMenuPolicy
(self, Qt.ContextMenuPolicy)¶
-
setCursor
(self, Union[QCursor, Qt.CursorShape])¶
-
setDisabled
(self, bool)¶
-
setEnabled
(self, bool)¶
-
setFeatures
(self, Union[QDockWidget.DockWidgetFeatures, QDockWidget.DockWidgetFeature])¶
-
setFixedHeight
(self, int)¶
-
setFixedSize
(self, QSize)¶ setFixedSize(self, int, int)
-
setFixedWidth
(self, int)¶
-
setFloating
(self, bool)¶
-
setFocus
(self)¶ setFocus(self, Qt.FocusReason)
-
setFocusPolicy
(self, Qt.FocusPolicy)¶
-
setFocusProxy
(self, QWidget)¶
-
setFont
(self, QFont)¶
-
setForegroundRole
(self, QPalette.ColorRole)¶
-
setGeometry
(self, QRect)¶ setGeometry(self, int, int, int, int)
-
setGraphicsEffect
(self, QGraphicsEffect)¶
-
setHidden
(self, bool)¶
-
setInputMethodHints
(self, Union[Qt.InputMethodHints, Qt.InputMethodHint])¶
-
setLayout
(self, QLayout)¶
-
setLayoutDirection
(self, Qt.LayoutDirection)¶
-
setLocale
(self, QLocale)¶
-
setMask
(self, QBitmap)¶ setMask(self, QRegion)
-
setMaximumHeight
(self, int)¶
-
setMaximumSize
(self, int, int)¶ setMaximumSize(self, QSize)
-
setMaximumWidth
(self, int)¶
-
setMinimumHeight
(self, int)¶
-
setMinimumSize
(self, int, int)¶ setMinimumSize(self, QSize)
-
setMinimumWidth
(self, int)¶
-
setMouseTracking
(self, bool)¶
-
setObjectName
(self, str)¶
-
setPalette
(self, QPalette)¶
-
setParent
(self, QWidget)¶ setParent(self, QWidget, Union[Qt.WindowFlags, Qt.WindowType])
-
setProperty
(self, str, Any) → bool¶
-
setShortcutAutoRepeat
(self, int, enabled: bool = True)¶
-
setShortcutEnabled
(self, int, enabled: bool = True)¶
-
setSizeIncrement
(self, int, int)¶ setSizeIncrement(self, QSize)
-
setSizePolicy
(self, QSizePolicy)¶ setSizePolicy(self, QSizePolicy.Policy, QSizePolicy.Policy)
-
setStatusTip
(self, str)¶
-
setStyle
(self, QStyle)¶
-
setStyleSheet
(self, str)¶
-
setTabOrder
(QWidget, QWidget)¶
-
setTabletTracking
(self, bool)¶
-
setTitleBarWidget
(self, QWidget)¶
-
setToolTip
(self, str)¶
-
setToolTipDuration
(self, int)¶
-
setUpdatesEnabled
(self, bool)¶
-
setVisible
(self, bool)¶
-
setWhatsThis
(self, str)¶
-
setWidget
(self, QWidget)¶
-
setWindowFilePath
(self, str)¶
-
setWindowFlag
(self, Qt.WindowType, on: bool = True)¶
-
setWindowFlags
(self, Union[Qt.WindowFlags, Qt.WindowType])¶
-
setWindowIcon
(self, QIcon)¶
-
setWindowIconText
(self, str)¶
-
setWindowModality
(self, Qt.WindowModality)¶
-
setWindowModified
(self, bool)¶
-
setWindowOpacity
(self, float)¶
-
setWindowRole
(self, str)¶
-
setWindowState
(self, Union[Qt.WindowStates, Qt.WindowState])¶
-
setWindowTitle
(self, str)¶
-
show
(self)¶
-
showEvent
(self, 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, QWidget)¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
statusTip
(self) → str¶
-
style
(self) → QStyle¶
-
styleSheet
(self) → str¶
-
tabletEvent
(self, QTabletEvent)¶
-
testAttribute
(self, Qt.WidgetAttribute) → bool¶
-
thread
(self) → QThread¶
-
timerEvent
(self, QTimerEvent)¶
-
titleBarWidget
(self) → QWidget¶
-
toggleViewAction
(self) → QAction¶
-
toolTip
(self) → str¶
-
toolTipDuration
(self) → int¶
-
topLevelChanged
¶ topLevelChanged(self, bool) [signal]
-
tr
(self, str, disambiguation: str = None, n: int = -1) → str¶
-
underMouse
(self) → bool¶
-
ungrabGesture
(self, Qt.GestureType)¶
-
unsetCursor
(self)¶
-
unsetLayoutDirection
(self)¶
-
unsetLocale
(self)¶
-
update
(self)¶ update(self, QRect) update(self, QRegion) update(self, int, int, int, int)
-
updateGeometry
(self)¶
-
updateMicroFocus
(self)¶
-
updatesEnabled
(self) → bool¶
-
visibilityChanged
¶ visibilityChanged(self, bool) [signal]
-
visibleRegion
(self) → QRegion¶
-
whatsThis
(self) → str¶
-
wheelEvent
(self, QWheelEvent)¶
-
widget
(self) → QWidget¶
-
width
(self) → int¶
-
widthMM
(self) → int¶
-
winId
(self) → sip.voidptr¶
-
window
(self) → QWidget¶
-
windowFilePath
(self) → str¶
-
windowFlags
(self) → Qt.WindowFlags¶
-
windowHandle
(self) → QWindow¶
-
windowIcon
(self) → QIcon¶
-
windowIconChanged
¶ windowIconChanged(self, QIcon) [signal]
-
windowIconText
(self) → str¶
-
windowIconTextChanged
¶ windowIconTextChanged(self, str) [signal]
-
windowModality
(self) → Qt.WindowModality¶
-
windowOpacity
(self) → float¶
-
windowRole
(self) → str¶
-
windowState
(self) → Qt.WindowStates¶
-
windowTitle
(self) → str¶
-
windowTitleChanged
¶ windowTitleChanged(self, str) [signal]
-
windowType
(self) → Qt.WindowType¶
-
x
(self) → int¶
-
y
(self) → int¶
-
-
class
schrodinger.application.bioluminate.ssv.viewer.
ViewerWindow
(parent)¶ Bases:
PyQt5.QtWidgets.QMainWindow
Provides the
SimplifiedSequenceViewer
with a window to occupy. This has the benefit of adding toolbars and allowing the sequence viewer (which is aQtWidgets.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 windowRaises: RuntimeError – If parent
is not correct type
-
action_factory
= None¶ 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, ifobjname
isNone
, 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 theViewerWindow
properties:
-
setToolBars
(toolbars)¶ Deletes all window toolbars and sets them to the new
toolbars
-
addImportToolBar
(area=4)¶ Adds an
ImportToolBar
widget to the area indicated (default: top).Parameters: area – The area to add the dock widget to
-
addUndoRedoToolBar
(area=4)¶ 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=4)¶ Adds a
FindToolBar
widget to the area indicated (default: top).Parameters: area – The area to add the dock widget to
-
addAlignToolBar
(area=8)¶ 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=8)¶ 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=8)¶ 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
¶ Bases:
int
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
bit_length
() → int¶ Number of bits necessary to represent self in binary. >>> bin(37) ‘0b100101’ >>> (37).bit_length() 6
-
conjugate
()¶ Returns self, the complex conjugate of any int.
-
denominator
¶ the denominator of a rational number in lowest terms
-
from_bytes
(bytes, byteorder, *, signed=False) → int¶ Return the integer represented by the given array of bytes.
The bytes argument must be a bytes-like object (e.g. bytes or bytearray).
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument indicates whether two’s complement is used to represent the integer.
-
imag
¶ the imaginary part of a complex number
-
numerator
¶ the numerator of a rational number in lowest terms
-
real
¶ the real part of a complex number
-
to_bytes
(length, byteorder, *, signed=False) → bytes¶ Return an array of bytes representing an integer.
The integer is represented using length bytes. An OverflowError is raised if the integer is not representable with the given number of bytes.
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument determines whether two’s complement is used to represent the integer. If signed is False and a negative integer is given, an OverflowError is raised.
-
-
class
DockOptions
¶ Bases:
sip.simplewrapper
QMainWindow.DockOptions(Union[QMainWindow.DockOptions, QMainWindow.DockOption]) QMainWindow.DockOptions(QMainWindow.DockOptions)
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
-
DrawChildren
= 2¶
-
DrawWindowBackground
= 1¶
-
ForceTabbedDocks
= 8¶
-
GroupedDragging
= 32¶
-
IgnoreMask
= 4¶
-
class
PaintDeviceMetric
¶ Bases:
int
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
bit_length
() → int¶ Number of bits necessary to represent self in binary. >>> bin(37) ‘0b100101’ >>> (37).bit_length() 6
-
conjugate
()¶ Returns self, the complex conjugate of any int.
-
denominator
¶ the denominator of a rational number in lowest terms
-
from_bytes
(bytes, byteorder, *, signed=False) → int¶ Return the integer represented by the given array of bytes.
The bytes argument must be a bytes-like object (e.g. bytes or bytearray).
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument indicates whether two’s complement is used to represent the integer.
-
imag
¶ the imaginary part of a complex number
-
numerator
¶ the numerator of a rational number in lowest terms
-
real
¶ the real part of a complex number
-
to_bytes
(length, byteorder, *, signed=False) → bytes¶ Return an array of bytes representing an integer.
The integer is represented using length bytes. An OverflowError is raised if the integer is not representable with the given number of bytes.
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument determines whether two’s complement is used to represent the integer. If signed is False and a negative integer is given, an OverflowError is raised.
-
-
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
¶ Bases:
int
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
bit_length
() → int¶ Number of bits necessary to represent self in binary. >>> bin(37) ‘0b100101’ >>> (37).bit_length() 6
-
conjugate
()¶ Returns self, the complex conjugate of any int.
-
denominator
¶ the denominator of a rational number in lowest terms
-
from_bytes
(bytes, byteorder, *, signed=False) → int¶ Return the integer represented by the given array of bytes.
The bytes argument must be a bytes-like object (e.g. bytes or bytearray).
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument indicates whether two’s complement is used to represent the integer.
-
imag
¶ the imaginary part of a complex number
-
numerator
¶ the numerator of a rational number in lowest terms
-
real
¶ the real part of a complex number
-
to_bytes
(length, byteorder, *, signed=False) → bytes¶ Return an array of bytes representing an integer.
The integer is represented using length bytes. An OverflowError is raised if the integer is not representable with the given number of bytes.
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument determines whether two’s complement is used to represent the integer. If signed is False and a negative integer is given, an OverflowError is raised.
-
-
class
RenderFlags
¶ Bases:
sip.simplewrapper
QWidget.RenderFlags(Union[QWidget.RenderFlags, QWidget.RenderFlag]) QWidget.RenderFlags(QWidget.RenderFlags)
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
-
VerticalTabs
= 16¶
-
acceptDrops
(self) → bool¶
-
accessibleDescription
(self) → str¶
-
accessibleName
(self) → str¶
-
actionEvent
(self, QActionEvent)¶
-
actions
(self) → List[QAction]¶
-
activateWindow
(self)¶
-
addAction
(self, QAction)¶
-
addActions
(self, object)¶
-
addDockWidget
(self, Qt.DockWidgetArea, QDockWidget)¶ addDockWidget(self, Qt.DockWidgetArea, QDockWidget, Qt.Orientation)
-
addToolBar
(self, Qt.ToolBarArea, QToolBar)¶ addToolBar(self, QToolBar) addToolBar(self, str) -> QToolBar
-
addToolBarBreak
(self, area: Qt.ToolBarArea = Qt.TopToolBarArea)¶
-
adjustSize
(self)¶
-
autoFillBackground
(self) → bool¶
-
backgroundRole
(self) → QPalette.ColorRole¶
-
baseSize
(self) → QSize¶
-
blockSignals
(self, bool) → bool¶
-
centralWidget
(self) → QWidget¶
-
changeEvent
(self, QEvent)¶
-
childAt
(self, QPoint) → QWidget¶ childAt(self, int, int) -> QWidget
-
childEvent
(self, QChildEvent)¶
-
children
(self) → object¶
-
childrenRect
(self) → QRect¶
-
childrenRegion
(self) → QRegion¶
-
clearFocus
(self)¶
-
clearMask
(self)¶
-
close
(self) → bool¶
-
closeEvent
(self, QCloseEvent)¶
-
colorCount
(self) → int¶
-
connectNotify
(self, QMetaMethod)¶
-
contentsMargins
(self) → QMargins¶
-
contentsRect
(self) → QRect¶
-
contextMenuEvent
(self, QContextMenuEvent)¶
-
contextMenuPolicy
(self) → Qt.ContextMenuPolicy¶
-
corner
(self, Qt.Corner) → Qt.DockWidgetArea¶
-
create
(self, window: sip.voidptr = 0, initializeWindow: bool = True, destroyOldWindow: bool = True)¶
-
createPopupMenu
(self) → QMenu¶
-
createWindowContainer
(QWindow, parent: QWidget = None, flags: Union[Qt.WindowFlags, Qt.WindowType] = 0) → QWidget¶
-
cursor
(self) → QCursor¶
-
customContextMenuRequested
¶ customContextMenuRequested(self, QPoint) [signal]
-
customEvent
(self, QEvent)¶
-
deleteLater
(self)¶
-
depth
(self) → int¶
-
destroy
(self, destroyWindow: bool = True, destroySubWindows: bool = True)¶
-
destroyed
¶ destroyed(self, QObject = None) [signal]
-
devType
(self) → int¶
-
devicePixelRatio
(self) → int¶
-
devicePixelRatioF
(self) → float¶
-
devicePixelRatioFScale
() → float¶
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dockOptions
(self) → QMainWindow.DockOptions¶
-
dockWidgetArea
(self, QDockWidget) → Qt.DockWidgetArea¶
-
documentMode
(self) → bool¶
-
dragEnterEvent
(self, QDragEnterEvent)¶
-
dragLeaveEvent
(self, QDragLeaveEvent)¶
-
dragMoveEvent
(self, QDragMoveEvent)¶
-
dropEvent
(self, QDropEvent)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → object¶
-
effectiveWinId
(self) → sip.voidptr¶
-
ensurePolished
(self)¶
-
enterEvent
(self, QEvent)¶
-
event
(self, QEvent) → bool¶
-
eventFilter
(self, QObject, QEvent) → bool¶
-
find
(sip.voidptr) → QWidget¶
-
findChild
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶ findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject
-
findChildren
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶ findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]
-
focusInEvent
(self, QFocusEvent)¶
-
focusNextChild
(self) → bool¶
-
focusNextPrevChild
(self, bool) → bool¶
-
focusOutEvent
(self, 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¶
-
getContentsMargins
(self) → Tuple[int, int, int, int]¶
-
grab
(self, rectangle: QRect = QRect(QPoint(0, 0), QSize(-1, -1))) → QPixmap¶
-
grabGesture
(self, Qt.GestureType, flags: Union[Qt.GestureFlags, Qt.GestureFlag] = Qt.GestureFlags())¶
-
grabKeyboard
(self)¶
-
grabMouse
(self)¶ grabMouse(self, Union[QCursor, Qt.CursorShape])
-
grabShortcut
(self, 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, int) → int¶
-
heightMM
(self) → int¶
-
hide
(self)¶
-
hideEvent
(self, QHideEvent)¶
-
iconSize
(self) → QSize¶
-
iconSizeChanged
¶ iconSizeChanged(self, QSize) [signal]
-
inherits
(self, str) → bool¶
-
initPainter
(self, QPainter)¶
-
inputMethodEvent
(self, QInputMethodEvent)¶
-
inputMethodHints
(self) → Qt.InputMethodHints¶
-
inputMethodQuery
(self, Qt.InputMethodQuery) → Any¶
-
insertAction
(self, QAction, QAction)¶
-
insertActions
(self, QAction, Iterable[QAction])¶
-
insertToolBar
(self, QToolBar, QToolBar)¶
-
insertToolBarBreak
(self, QToolBar)¶
-
installEventFilter
(self, QObject)¶
-
isActiveWindow
(self) → bool¶
-
isAncestorOf
(self, QWidget) → bool¶
-
isAnimated
(self) → bool¶
-
isDockNestingEnabled
(self) → bool¶
-
isEnabled
(self) → bool¶
-
isEnabledTo
(self, 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, QPoint) → bool¶
-
isSignalConnected
(self, QMetaMethod) → bool¶
-
isVisible
(self) → bool¶
-
isVisibleTo
(self, QWidget) → bool¶
-
isWidgetType
(self) → bool¶
-
isWindow
(self) → bool¶
-
isWindowModified
(self) → bool¶
-
isWindowType
(self) → bool¶
-
keyPressEvent
(self, QKeyEvent)¶
-
keyReleaseEvent
(self, QKeyEvent)¶
-
keyboardGrabber
() → QWidget¶
-
killTimer
(self, int)¶
-
layout
(self) → QLayout¶
-
layoutDirection
(self) → Qt.LayoutDirection¶
-
leaveEvent
(self, QEvent)¶
-
locale
(self) → QLocale¶
-
logicalDpiX
(self) → int¶
-
logicalDpiY
(self) → int¶
-
lower
(self)¶
-
mapFrom
(self, QWidget, QPoint) → QPoint¶
-
mapFromGlobal
(self, QPoint) → QPoint¶
-
mapFromParent
(self, QPoint) → QPoint¶
-
mapTo
(self, QWidget, QPoint) → QPoint¶
-
mapToGlobal
(self, QPoint) → QPoint¶
-
mapToParent
(self, QPoint) → QPoint¶
-
mask
(self) → QRegion¶
-
maximumHeight
(self) → int¶
-
maximumSize
(self) → QSize¶
-
maximumWidth
(self) → int¶
-
metaObject
(self) → QMetaObject¶
-
metric
(self, QPaintDevice.PaintDeviceMetric) → int¶
-
minimumHeight
(self) → int¶
-
minimumSize
(self) → QSize¶
-
minimumSizeHint
(self) → QSize¶
-
minimumWidth
(self) → int¶
-
mouseDoubleClickEvent
(self, QMouseEvent)¶
-
mouseGrabber
() → QWidget¶
-
mouseMoveEvent
(self, QMouseEvent)¶
-
mousePressEvent
(self, QMouseEvent)¶
-
mouseReleaseEvent
(self, QMouseEvent)¶
-
move
(self, QPoint)¶ move(self, int, int)
-
moveEvent
(self, QMoveEvent)¶
-
moveToThread
(self, QThread)¶
-
nativeEvent
(self, Union[QByteArray, bytes, bytearray], sip.voidptr) → Tuple[bool, int]¶
-
nativeParentWidget
(self) → QWidget¶
-
nextInFocusChain
(self) → QWidget¶
-
normalGeometry
(self) → QRect¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
overrideWindowFlags
(self, Union[Qt.WindowFlags, Qt.WindowType])¶
-
overrideWindowState
(self, Union[Qt.WindowStates, Qt.WindowState])¶
-
paintEngine
(self) → QPaintEngine¶
-
paintEvent
(self, 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, 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, PYQT_SIGNAL) → int¶
-
rect
(self) → QRect¶
-
releaseKeyboard
(self)¶
-
releaseMouse
(self)¶
-
releaseShortcut
(self, int)¶
-
removeAction
(self, QAction)¶
-
removeDockWidget
(self, QDockWidget)¶
-
removeEventFilter
(self, QObject)¶
-
removeToolBarBreak
(self, QToolBar)¶
-
render
(self, QPaintDevice, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.DrawWindowBackground|QWidget.DrawChildren))¶ render(self, QPainter, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.DrawWindowBackground|QWidget.DrawChildren))
-
repaint
(self)¶ repaint(self, int, int, int, int) repaint(self, QRect) repaint(self, QRegion)
-
resize
(self, QSize)¶ resize(self, int, int)
-
resizeDocks
(self, Iterable[QDockWidget], Iterable[int], Qt.Orientation)¶
-
resizeEvent
(self, QResizeEvent)¶
-
restoreDockWidget
(self, QDockWidget) → bool¶
-
restoreGeometry
(self, Union[QByteArray, bytes, bytearray]) → bool¶
-
restoreState
(self, Union[QByteArray, bytes, bytearray], version: int = 0) → bool¶
-
saveGeometry
(self) → QByteArray¶
-
saveState
(self, version: int = 0) → QByteArray¶
-
scroll
(self, int, int)¶ scroll(self, int, int, QRect)
-
sender
(self) → QObject¶
-
senderSignalIndex
(self) → int¶
-
setAcceptDrops
(self, bool)¶
-
setAccessibleDescription
(self, str)¶
-
setAccessibleName
(self, str)¶
-
setAnimated
(self, bool)¶
-
setAttribute
(self, Qt.WidgetAttribute, on: bool = True)¶
-
setAutoFillBackground
(self, bool)¶
-
setBackgroundRole
(self, QPalette.ColorRole)¶
-
setBaseSize
(self, int, int)¶ setBaseSize(self, QSize)
-
setCentralWidget
(self, QWidget)¶
-
setContentsMargins
(self, int, int, int, int)¶ setContentsMargins(self, QMargins)
-
setContextMenuPolicy
(self, Qt.ContextMenuPolicy)¶
-
setCorner
(self, Qt.Corner, Qt.DockWidgetArea)¶
-
setCursor
(self, Union[QCursor, Qt.CursorShape])¶
-
setDisabled
(self, bool)¶
-
setDockNestingEnabled
(self, bool)¶
-
setDockOptions
(self, Union[QMainWindow.DockOptions, QMainWindow.DockOption])¶
-
setDocumentMode
(self, bool)¶
-
setEnabled
(self, bool)¶
-
setFixedHeight
(self, int)¶
-
setFixedSize
(self, QSize)¶ setFixedSize(self, int, int)
-
setFixedWidth
(self, int)¶
-
setFocus
(self)¶ setFocus(self, Qt.FocusReason)
-
setFocusPolicy
(self, Qt.FocusPolicy)¶
-
setFocusProxy
(self, QWidget)¶
-
setFont
(self, QFont)¶
-
setForegroundRole
(self, QPalette.ColorRole)¶
-
setGeometry
(self, QRect)¶ setGeometry(self, int, int, int, int)
-
setGraphicsEffect
(self, QGraphicsEffect)¶
-
setHidden
(self, bool)¶
-
setIconSize
(self, QSize)¶
-
setInputMethodHints
(self, Union[Qt.InputMethodHints, Qt.InputMethodHint])¶
-
setLayout
(self, QLayout)¶
-
setLayoutDirection
(self, Qt.LayoutDirection)¶
-
setLocale
(self, QLocale)¶
-
setMask
(self, QBitmap)¶ setMask(self, QRegion)
-
setMaximumHeight
(self, int)¶
-
setMaximumSize
(self, int, int)¶ setMaximumSize(self, QSize)
-
setMaximumWidth
(self, int)¶
-
setMenuBar
(self, QMenuBar)¶
-
setMenuWidget
(self, QWidget)¶
-
setMinimumHeight
(self, int)¶
-
setMinimumSize
(self, int, int)¶ setMinimumSize(self, QSize)
-
setMinimumWidth
(self, int)¶
-
setMouseTracking
(self, bool)¶
-
setObjectName
(self, str)¶
-
setPalette
(self, QPalette)¶
-
setParent
(self, QWidget)¶ setParent(self, QWidget, Union[Qt.WindowFlags, Qt.WindowType])
-
setProperty
(self, str, Any) → bool¶
-
setShortcutAutoRepeat
(self, int, enabled: bool = True)¶
-
setShortcutEnabled
(self, int, enabled: bool = True)¶
-
setSizeIncrement
(self, int, int)¶ setSizeIncrement(self, QSize)
-
setSizePolicy
(self, QSizePolicy)¶ setSizePolicy(self, QSizePolicy.Policy, QSizePolicy.Policy)
-
setStatusBar
(self, QStatusBar)¶
-
setStatusTip
(self, str)¶
-
setStyle
(self, QStyle)¶
-
setStyleSheet
(self, str)¶
-
setTabOrder
(QWidget, QWidget)¶
-
setTabPosition
(self, Union[Qt.DockWidgetAreas, Qt.DockWidgetArea], QTabWidget.TabPosition)¶
-
setTabShape
(self, QTabWidget.TabShape)¶
-
setTabletTracking
(self, bool)¶
-
setToolButtonStyle
(self, Qt.ToolButtonStyle)¶
-
setToolTip
(self, str)¶
-
setToolTipDuration
(self, int)¶
-
setUnifiedTitleAndToolBarOnMac
(self, bool)¶
-
setUpdatesEnabled
(self, bool)¶
-
setVisible
(self, bool)¶
-
setWhatsThis
(self, str)¶
-
setWindowFilePath
(self, str)¶
-
setWindowFlag
(self, Qt.WindowType, on: bool = True)¶
-
setWindowFlags
(self, Union[Qt.WindowFlags, Qt.WindowType])¶
-
setWindowIcon
(self, QIcon)¶
-
setWindowIconText
(self, str)¶
-
setWindowModality
(self, Qt.WindowModality)¶
-
setWindowModified
(self, bool)¶
-
setWindowOpacity
(self, float)¶
-
setWindowRole
(self, str)¶
-
setWindowState
(self, Union[Qt.WindowStates, Qt.WindowState])¶
-
setWindowTitle
(self, str)¶
-
show
(self)¶
-
showEvent
(self, 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, QDockWidget, QDockWidget, Qt.Orientation)¶
-
stackUnder
(self, QWidget)¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
statusBar
(self) → QStatusBar¶
-
statusTip
(self) → str¶
-
style
(self) → QStyle¶
-
styleSheet
(self) → str¶
-
tabPosition
(self, Qt.DockWidgetArea) → QTabWidget.TabPosition¶
-
tabShape
(self) → QTabWidget.TabShape¶
-
tabifiedDockWidgetActivated
¶ tabifiedDockWidgetActivated(self, QDockWidget) [signal]
-
tabifiedDockWidgets
(self, QDockWidget) → object¶
-
tabifyDockWidget
(self, QDockWidget, QDockWidget)¶
-
tabletEvent
(self, QTabletEvent)¶
-
takeCentralWidget
(self) → QWidget¶
-
testAttribute
(self, Qt.WidgetAttribute) → bool¶
-
thread
(self) → QThread¶
-
timerEvent
(self, QTimerEvent)¶
-
toolBarArea
(self, QToolBar) → Qt.ToolBarArea¶
-
toolBarBreak
(self, QToolBar) → bool¶
-
toolButtonStyle
(self) → Qt.ToolButtonStyle¶
-
toolTip
(self) → str¶
-
toolTipDuration
(self) → int¶
-
tr
(self, str, disambiguation: str = None, n: int = -1) → str¶
-
underMouse
(self) → bool¶
-
ungrabGesture
(self, Qt.GestureType)¶
-
unifiedTitleAndToolBarOnMac
(self) → bool¶
-
unsetCursor
(self)¶
-
unsetLayoutDirection
(self)¶
-
unsetLocale
(self)¶
-
update
(self)¶ update(self, QRect) update(self, QRegion) update(self, int, int, int, int)
-
updateGeometry
(self)¶
-
updateMicroFocus
(self)¶
-
updatesEnabled
(self) → bool¶
-
visibleRegion
(self) → QRegion¶
-
whatsThis
(self) → str¶
-
wheelEvent
(self, QWheelEvent)¶
-
width
(self) → int¶
-
widthMM
(self) → int¶
-
winId
(self) → sip.voidptr¶
-
window
(self) → QWidget¶
-
windowFilePath
(self) → str¶
-
windowFlags
(self) → Qt.WindowFlags¶
-
windowHandle
(self) → QWindow¶
-
windowIcon
(self) → QIcon¶
-
windowIconChanged
¶ windowIconChanged(self, QIcon) [signal]
-
windowIconText
(self) → str¶
-
windowIconTextChanged
¶ windowIconTextChanged(self, str) [signal]
-
windowModality
(self) → Qt.WindowModality¶
-
windowOpacity
(self) → float¶
-
windowRole
(self) → str¶
-
windowState
(self) → Qt.WindowStates¶
-
windowTitle
(self) → str¶
-
windowTitleChanged
¶ windowTitleChanged(self, 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:
SimplifiedSequenceViewer.WORKSPACE
SimplifiedSequenceViewer.PROJECT_TABLE
SimplifiedSequenceViewer.PDB_STRING
SimplifiedSequenceViewer.FILES
-
__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:
-
window
(self) → QWidget¶
-
dock_widget
= None¶ Widget the allows
self.window
to be dockable
-
last_sequences_imported
= None¶ 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
-
protein_sequences
¶ Property for all sequences in the viewer that are valid proteins
Return type: list of sequences
-
structure_sequences
¶ Property for all sequences in the viewer that have structures.
Return type: list of sequences
-
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
orstructure
-
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)¶
-
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
¶ Bases:
int
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
bit_length
() → int¶ Number of bits necessary to represent self in binary. >>> bin(37) ‘0b100101’ >>> (37).bit_length() 6
-
conjugate
()¶ Returns self, the complex conjugate of any int.
-
denominator
¶ the denominator of a rational number in lowest terms
-
from_bytes
(bytes, byteorder, *, signed=False) → int¶ Return the integer represented by the given array of bytes.
The bytes argument must be a bytes-like object (e.g. bytes or bytearray).
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument indicates whether two’s complement is used to represent the integer.
-
imag
¶ the imaginary part of a complex number
-
numerator
¶ the numerator of a rational number in lowest terms
-
real
¶ the real part of a complex number
-
to_bytes
(length, byteorder, *, signed=False) → bytes¶ Return an array of bytes representing an integer.
The integer is represented using length bytes. An OverflowError is raised if the integer is not representable with the given number of bytes.
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument determines whether two’s complement is used to represent the integer. If signed is False and a negative integer is given, an OverflowError is raised.
-
-
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
¶ Bases:
int
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
bit_length
() → int¶ Number of bits necessary to represent self in binary. >>> bin(37) ‘0b100101’ >>> (37).bit_length() 6
-
conjugate
()¶ Returns self, the complex conjugate of any int.
-
denominator
¶ the denominator of a rational number in lowest terms
-
from_bytes
(bytes, byteorder, *, signed=False) → int¶ Return the integer represented by the given array of bytes.
The bytes argument must be a bytes-like object (e.g. bytes or bytearray).
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument indicates whether two’s complement is used to represent the integer.
-
imag
¶ the imaginary part of a complex number
-
numerator
¶ the numerator of a rational number in lowest terms
-
real
¶ the real part of a complex number
-
to_bytes
(length, byteorder, *, signed=False) → bytes¶ Return an array of bytes representing an integer.
The integer is represented using length bytes. An OverflowError is raised if the integer is not representable with the given number of bytes.
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument determines whether two’s complement is used to represent the integer. If signed is False and a negative integer is given, an OverflowError is raised.
-
-
class
RenderFlags
¶ Bases:
sip.simplewrapper
QWidget.RenderFlags(Union[QWidget.RenderFlags, QWidget.RenderFlag]) QWidget.RenderFlags(QWidget.RenderFlags)
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
-
class
Shadow
¶ Bases:
int
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
bit_length
() → int¶ Number of bits necessary to represent self in binary. >>> bin(37) ‘0b100101’ >>> (37).bit_length() 6
-
conjugate
()¶ Returns self, the complex conjugate of any int.
-
denominator
¶ the denominator of a rational number in lowest terms
-
from_bytes
(bytes, byteorder, *, signed=False) → int¶ Return the integer represented by the given array of bytes.
The bytes argument must be a bytes-like object (e.g. bytes or bytearray).
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument indicates whether two’s complement is used to represent the integer.
-
imag
¶ the imaginary part of a complex number
-
numerator
¶ the numerator of a rational number in lowest terms
-
real
¶ the real part of a complex number
-
to_bytes
(length, byteorder, *, signed=False) → bytes¶ Return an array of bytes representing an integer.
The integer is represented using length bytes. An OverflowError is raised if the integer is not representable with the given number of bytes.
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument determines whether two’s complement is used to represent the integer. If signed is False and a negative integer is given, an OverflowError is raised.
-
-
Shadow_Mask
= 240¶
-
class
Shape
¶ Bases:
int
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
bit_length
() → int¶ Number of bits necessary to represent self in binary. >>> bin(37) ‘0b100101’ >>> (37).bit_length() 6
-
conjugate
()¶ Returns self, the complex conjugate of any int.
-
denominator
¶ the denominator of a rational number in lowest terms
-
from_bytes
(bytes, byteorder, *, signed=False) → int¶ Return the integer represented by the given array of bytes.
The bytes argument must be a bytes-like object (e.g. bytes or bytearray).
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument indicates whether two’s complement is used to represent the integer.
-
imag
¶ the imaginary part of a complex number
-
numerator
¶ the numerator of a rational number in lowest terms
-
real
¶ the real part of a complex number
-
to_bytes
(length, byteorder, *, signed=False) → bytes¶ Return an array of bytes representing an integer.
The integer is represented using length bytes. An OverflowError is raised if the integer is not representable with the given number of bytes.
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument determines whether two’s complement is used to represent the integer. If signed is False and a negative integer is given, an OverflowError is raised.
-
-
Shape_Mask
= 15¶
-
class
StyleMask
¶ Bases:
int
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
bit_length
() → int¶ Number of bits necessary to represent self in binary. >>> bin(37) ‘0b100101’ >>> (37).bit_length() 6
-
conjugate
()¶ Returns self, the complex conjugate of any int.
-
denominator
¶ the denominator of a rational number in lowest terms
-
from_bytes
(bytes, byteorder, *, signed=False) → int¶ Return the integer represented by the given array of bytes.
The bytes argument must be a bytes-like object (e.g. bytes or bytearray).
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument indicates whether two’s complement is used to represent the integer.
-
imag
¶ the imaginary part of a complex number
-
numerator
¶ the numerator of a rational number in lowest terms
-
real
¶ the real part of a complex number
-
to_bytes
(length, byteorder, *, signed=False) → bytes¶ Return an array of bytes representing an integer.
The integer is represented using length bytes. An OverflowError is raised if the integer is not representable with the given number of bytes.
The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.
The signed keyword-only argument determines whether two’s complement is used to represent the integer. If signed is False and a negative integer is given, an OverflowError is raised.
-
-
StyledPanel
= 6¶
-
Sunken
= 48¶
-
VLine
= 5¶
-
WinPanel
= 3¶
-
__len__
¶ Return len(self).
-
acceptDrops
(self) → bool¶
-
accessibleDescription
(self) → str¶
-
accessibleName
(self) → str¶
-
actionEvent
(self, QActionEvent)¶
-
actions
(self) → List[QAction]¶
-
activateWindow
(self)¶
-
addAction
(self, QAction)¶
-
addActions
(self, object)¶
-
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.
-
addSequenceLogo
(toggle=False, update=True)¶ Adds a sequence logo annotation.
-
addSymbols
(toggle=False, update=True)¶ Adds a symbols sequence.
-
addUserAnnotation
(annotation_type='region')¶
-
addWidget
(self, 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, bool) → bool¶
-
buildModel
()¶ Builds 3D model of reference sequence.
-
changeEvent
(self, QEvent)¶
-
changeQuery
(index)¶
-
childAt
(self, QPoint) → QWidget¶ childAt(self, int, int) -> QWidget
-
childEvent
(self, QChildEvent)¶
-
children
(self) → object¶
-
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, int, 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, QMetaMethod)¶
-
contentsMargins
(self) → QMargins¶
-
contentsRect
(self) → QRect¶
-
contextMenuEvent
(self, QContextMenuEvent)¶
-
contextMenuPolicy
(self) → Qt.ContextMenuPolicy¶
-
copySequences
(group)¶ Copies all or selected sequences from group to self.sequence_group.
-
count
(self) → int¶
-
create
(self, window: sip.voidptr = 0, initializeWindow: bool = True, destroyOldWindow: bool = True)¶
-
createCommandDict
()¶ Creates an external command dictionary.
-
createHandle
(self) → QSplitterHandle¶
-
createWindowContainer
(QWindow, parent: QWidget = None, flags: Union[Qt.WindowFlags, Qt.WindowType] = 0) → QWidget¶
-
cropSelectedResidues
()¶ Crops residues in a selected area.
-
cursor
(self) → QCursor¶
-
customContextMenuRequested
¶ customContextMenuRequested(self, QPoint) [signal]
-
customEvent
(self, 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, QObject = None) [signal]
-
devType
(self) → int¶
-
devicePixelRatio
(self) → int¶
-
devicePixelRatioF
(self) → float¶
-
devicePixelRatioFScale
() → float¶
-
disableQueryConstraints
(remove_if_empty=True)¶ Toggles a query sequence constraints.
-
disconnect
(self)¶
-
disconnectNotify
(self, 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, QDragEnterEvent)¶
-
dragLeaveEvent
(self, QDragLeaveEvent)¶
-
dragMoveEvent
(self, QDragMoveEvent)¶
-
drawFrame
(self, QPainter)¶
-
dropEvent
(self, QDropEvent)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
duplicateSequences
()¶ Duplicates selected sequences.
-
dynamicPropertyNames
(self) → object¶
-
editSequence
()¶ Edits a selected sequence.
-
effectiveWinId
(self) → sip.voidptr¶
-
emphasizeArea
(area)¶
-
enableQueryConstraints
()¶ Toggles a query sequence constraints.
-
ensurePolished
(self)¶
-
enterEvent
(self, QEvent)¶
-
event
(self, QEvent) → bool¶
-
eventFilter
(self, QObject, 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
(sip.voidptr) → QWidget¶
-
findChild
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶ findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject
-
findChildren
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶ findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, 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, QFocusEvent)¶
-
focusNextChild
(self) → bool¶
-
focusNextPrevChild
(self, bool) → bool¶
-
focusOutEvent
(self, 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)
-
getContentsMargins
(self) → Tuple[int, int, int, int]¶
-
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, 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, Qt.GestureType, flags: Union[Qt.GestureFlags, Qt.GestureFlag] = Qt.GestureFlags())¶
-
grabKeyboard
(self)¶
-
grabMouse
(self)¶ grabMouse(self, Union[QCursor, Qt.CursorShape])
-
grabShortcut
(self, Union[QKeySequence, QKeySequence.StandardKey, str, int], context: Qt.ShortcutContext = Qt.WindowShortcut) → int¶
-
graphicsEffect
(self) → QGraphicsEffect¶
-
graphicsProxyWidget
(self) → QGraphicsProxyWidget¶
-
handle
(self, int) → QSplitterHandle¶
-
handleWidth
(self) → int¶
-
hasFocus
(self) → bool¶
-
hasHeightForWidth
(self) → bool¶
-
hasMouseTracking
(self) → bool¶
-
hasTabletTracking
(self) → bool¶
-
height
(self) → int¶
-
heightForWidth
(self, int) → int¶
-
heightMM
(self) → int¶
-
hide
(self)¶
-
hideColumns
(unselected=False)¶ Hides selected columns.
-
hideEvent
(self, 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, QWidget) → int¶
-
inherits
(self, str) → bool¶
-
initMaestro
()¶ Initializes Maestro callbacks.
-
initPainter
(self, QPainter)¶
-
initStyleOption
(self, QStyleOptionFrame)¶
-
inputMethodEvent
(self, QInputMethodEvent)¶
-
inputMethodHints
(self) → Qt.InputMethodHints¶
-
inputMethodQuery
(self, Qt.InputMethodQuery) → Any¶
-
insertAction
(self, QAction, QAction)¶
-
insertActions
(self, QAction, Iterable[QAction])¶
-
insertWidget
(self, int, QWidget)¶
-
installEventFilter
(self, QObject)¶
-
invertSelection
()¶ Inverts residue selection.
-
invertSequenceSelection
()¶ Inverts current sequence selection range.
-
isActiveWindow
(self) → bool¶
-
isAncestorOf
(self, QWidget) → bool¶
-
isCollapsible
(self, int) → bool¶
-
isEnabled
(self) → bool¶
-
isEnabledTo
(self, 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, QMetaMethod) → bool¶
-
isVisible
(self) → bool¶
-
isVisibleTo
(self, QWidget) → bool¶
-
isWidgetType
(self) → bool¶
-
isWindow
(self) → bool¶
-
isWindowModified
(self) → bool¶
-
isWindowType
(self) → bool¶
-
keyPressEvent
(self, QKeyEvent)¶
-
keyReleaseEvent
(self, QKeyEvent)¶
-
keyboardGrabber
() → QWidget¶
-
killTimer
(self, int)¶
-
layout
(self) → QLayout¶
-
layoutDirection
(self) → Qt.LayoutDirection¶
-
leaveEvent
(self, 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, QWidget, QPoint) → QPoint¶
-
mapFromGlobal
(self, QPoint) → QPoint¶
-
mapFromParent
(self, QPoint) → QPoint¶
-
mapTo
(self, QWidget, QPoint) → QPoint¶
-
mapToGlobal
(self, QPoint) → QPoint¶
-
mapToParent
(self, QPoint) → QPoint¶
-
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, QPaintDevice.PaintDeviceMetric) → int¶
-
midLineWidth
(self) → int¶
-
minimizeAlignment
()¶ Removes all gaps.
-
minimumHeight
(self) → int¶
-
minimumSize
(self) → QSize¶
-
minimumSizeHint
(self) → QSize¶
-
minimumWidth
(self) → int¶
-
mouseDoubleClickEvent
(self, QMouseEvent)¶
-
mouseGrabber
() → QWidget¶
-
mouseMoveEvent
(self, QMouseEvent)¶
-
mousePressEvent
(self, QMouseEvent)¶
-
mouseReleaseEvent
(self, QMouseEvent)¶
-
move
(self, QPoint)¶ move(self, int, int)
-
moveBottom
()¶ Moves selected sequences to the bottom of the group.
-
moveDown
()¶ Moves selected sequences one level down.
-
moveEvent
(self, QMoveEvent)¶
-
moveSplitter
(self, int, int)¶
-
moveToThread
(self, QThread)¶
-
moveTop
()¶ Moves selected sequences to the top of the group.
-
moveUp
()¶ Moves selected sequences one level up.
-
nativeEvent
(self, Union[QByteArray, bytes, bytearray], sip.voidptr) → Tuple[bool, int]¶
-
nativeParentWidget
(self) → QWidget¶
-
newSet
(name=None)¶ Creates a new query set
-
nextInFocusChain
(self) → QWidget¶
-
normalGeometry
(self) → QRect¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
opaqueResize
(self) → bool¶
-
orientation
(self) → Qt.Orientation¶
-
overrideWindowFlags
(self, Union[Qt.WindowFlags, Qt.WindowType])¶
-
overrideWindowState
(self, Union[Qt.WindowStates, Qt.WindowState])¶
-
paintEngine
(self) → QPaintEngine¶
-
paintEvent
(self, 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, 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, PYQT_SIGNAL) → int¶
-
rect
(self) → QRect¶
-
redo
()¶ Redoes previously undone operation.
-
refresh
(self)¶
-
releaseKeyboard
(self)¶
-
releaseMouse
(self)¶
-
releaseShortcut
(self, int)¶
-
removeAction
(self, QAction)¶
-
removeAllColorBlocks
()¶ Removes all color blocks annotations from selected or all sequences in the sequence group.
-
removeEventFilter
(self, 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, QPaintDevice, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.DrawWindowBackground|QWidget.DrawChildren))¶ render(self, QPainter, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.DrawWindowBackground|QWidget.DrawChildren))
-
renumberResidues
()¶ Executes ‘Renumber Residues’ command.
-
repaint
(self)¶ repaint(self, int, int, int, int) repaint(self, QRect) repaint(self, QRegion)
-
replaceWidget
(self, int, QWidget) → QWidget¶
-
resetHistory
()¶ Toggles changes tracking feature.
-
resize
(self, QSize)¶ resize(self, int, int)
-
resizeEvent
(event)¶ Resize event handler. Update font face and size here.
-
restoreGeometry
(self, Union[QByteArray, bytes, bytearray]) → bool¶
-
restoreState
(self, Union[QByteArray, bytes, bytearray]) → 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
andsuccessBlastCallback
.
-
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¶
-
scroll
(self, int, int)¶ scroll(self, int, int, QRect)
-
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, bool)¶
-
setAccessibleDescription
(self, str)¶
-
setAccessibleName
(self, str)¶
-
setAsReference
()¶ Sets a selected sequence as a reference.
-
setAttribute
(self, Qt.WidgetAttribute, on: bool = True)¶
-
setAutoFillBackground
(self, bool)¶
-
setBackgroundColor
(color=(255, 255, 255))¶ Sets a background color.
Parameters: color ((int, int, int)) – Background color RGB tuple.
-
setBackgroundRole
(self, QPalette.ColorRole)¶
-
setBaseSize
(self, int, int)¶ setBaseSize(self, QSize)
-
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, bool)¶
-
setCollapsible
(self, int, 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, int, int, int, int)¶ setContentsMargins(self, QMargins)
-
setContextMenuPolicy
(self, Qt.ContextMenuPolicy)¶
-
setCursor
(self, Union[QCursor, Qt.CursorShape])¶
-
setDisabled
(self, 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, bool)¶
-
setFixedHeight
(self, int)¶
-
setFixedSize
(self, QSize)¶ setFixedSize(self, int, int)
-
setFixedWidth
(self, int)¶
-
setFocus
(self)¶ setFocus(self, Qt.FocusReason)
-
setFocusPolicy
(self, Qt.FocusPolicy)¶
-
setFocusProxy
(self, QWidget)¶
-
setFont
(self, QFont)¶
-
setForegroundRole
(self, QPalette.ColorRole)¶
-
setFrameRect
(self, QRect)¶
-
setFrameShadow
(self, QFrame.Shadow)¶
-
setFrameShape
(self, QFrame.Shape)¶
-
setFrameStyle
(self, int)¶
-
setGeometry
(self, QRect)¶ setGeometry(self, int, int, int, int)
-
setGraphicsEffect
(self, QGraphicsEffect)¶
-
setHandleWidth
(self, 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, bool)¶
-
setIdentityInColumns
(value)¶ Sets “Calculate identity in columns” setting.
-
setInputMethodHints
(self, Union[Qt.InputMethodHints, Qt.InputMethodHint])¶
-
setLayout
(self, QLayout)¶
-
setLayoutDirection
(self, Qt.LayoutDirection)¶
-
setLineWidth
(self, int)¶
-
setLocale
(self, QLocale)¶
-
setMask
(self, QBitmap)¶ setMask(self, QRegion)
-
setMaximumHeight
(self, int)¶
-
setMaximumSize
(self, int, int)¶ setMaximumSize(self, QSize)
-
setMaximumWidth
(self, int)¶
-
setMidLineWidth
(self, int)¶
-
setMinimumHeight
(self, int)¶
-
setMinimumSize
(self, int, int)¶ setMinimumSize(self, QSize)
-
setMinimumWidth
(self, 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, bool)¶
-
setObjectName
(self, str)¶
-
setOpaqueResize
(self, opaque: bool = True)¶
-
setOrientation
(self, Qt.Orientation)¶
-
setPadded
(padded)¶ Toggles alignment padding.
Parameters: padded (bool) – If True, enable padded mode, False - disable it.
-
setPalette
(self, QPalette)¶
-
setParent
(self, QWidget)¶ setParent(self, QWidget, Union[Qt.WindowFlags, Qt.WindowType])
-
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, str, Any) → bool¶
-
setRubberBand
(self, int)¶
-
setShortcutAutoRepeat
(self, int, enabled: bool = True)¶
-
setShortcutEnabled
(self, int, enabled: bool = True)¶
-
setSizeIncrement
(self, int, int)¶ setSizeIncrement(self, QSize)
-
setSizePolicy
(self, QSizePolicy)¶ setSizePolicy(self, QSizePolicy.Policy, QSizePolicy.Policy)
-
setSizes
(self, Iterable[int])¶
-
setStatusTip
(self, str)¶
-
setStretchFactor
(self, int, int)¶
-
setStyle
(self, QStyle)¶
-
setStyleSheet
(self, str)¶
-
setTabOrder
(QWidget, QWidget)¶
-
setTabletTracking
(self, bool)¶
-
setToolTip
(self, str)¶
-
setToolTipDuration
(self, 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, bool)¶
-
setUseColors
(use_colors)¶ Sets use colors flag.
Parameters: use_colors (bool) – If True, colors will be used to draw the sequences.
-
setVisible
(self, bool)¶
-
setWhatsThis
(self, str)¶
-
setWindowFilePath
(self, str)¶
-
setWindowFlag
(self, Qt.WindowType, on: bool = True)¶
-
setWindowFlags
(self, Union[Qt.WindowFlags, Qt.WindowType])¶
-
setWindowIcon
(self, QIcon)¶
-
setWindowIconText
(self, str)¶
-
setWindowModality
(self, Qt.WindowModality)¶
-
setWindowModified
(self, bool)¶
-
setWindowOpacity
(self, float)¶
-
setWindowRole
(self, str)¶
-
setWindowState
(self, Union[Qt.WindowStates, Qt.WindowState])¶
-
setWindowTitle
(self, str)¶
-
setWrapped
(wrapped)¶ This method toggles sequence wrapping mode.
Parameters: wrapped (bool) – if True, enable wrapped mode, otherwise - disable it
-
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, int, int) [signal]
-
stackUnder
(self, QWidget)¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
statusTip
(self) → str¶
-
style
(self) → QStyle¶
-
styleSheet
(self) → str¶
-
synchronizeWithMaestro
()¶ Synchronizes sequence viewer contents with Maestro workspace.
-
tabletEvent
(self, QTabletEvent)¶
-
testAttribute
(self, Qt.WidgetAttribute) → bool¶
-
thread
(self) → QThread¶
-
timerEvent
(self, QTimerEvent)¶
-
toggleConstraints
()¶ Toggles a pairwise alignment constraints.
-
toggleHistory
()¶ Toggles changes tracking feature.
-
toolTip
(self) → str¶
-
toolTipDuration
(self) → int¶
-
tr
(self, str, disambiguation: str = None, n: int = -1) → str¶
-
translate
()¶ Translates DNA / RNA to amino acids.
-
underMouse
(self) → bool¶
-
undo
()¶ Undoes the last operation.
-
ungrabGesture
(self, Qt.GestureType)¶
-
unlockGaps
()¶ Unlocks gaps.
-
unselectAllSequences
()¶ Deselects all sequences in the group.
-
unsetCursor
(self)¶
-
unsetLayoutDirection
(self)¶
-
unsetLocale
(self)¶
-
update
(self)¶ update(self, QRect) update(self, QRegion) update(self, int, int, int, int)
-
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)¶
-
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, QWheelEvent)¶
-
widget
(self, int) → QWidget¶
-
width
(self) → int¶
-
widthMM
(self) → int¶
-
winId
(self) → sip.voidptr¶
-
windowFilePath
(self) → str¶
-
windowFlags
(self) → Qt.WindowFlags¶
-
windowHandle
(self) → QWindow¶
-
windowIcon
(self) → QIcon¶
-
windowIconChanged
¶ windowIconChanged(self, QIcon) [signal]
-
windowIconText
(self) → str¶
-
windowIconTextChanged
¶ windowIconTextChanged(self, str) [signal]
-
windowModality
(self) → Qt.WindowModality¶
-
windowOpacity
(self) → float¶
-
windowRole
(self) → str¶
-
windowState
(self) → Qt.WindowStates¶
-
windowTitle
(self) → str¶
-
windowTitleChanged
¶ windowTitleChanged(self, 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.
-
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
-