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

__abs__

abs(self)

__add__

Return self+value.

__and__

Return self&value.

__bool__

self != 0

__ceil__()

Ceiling of an Integral returns itself.

__class__

alias of sip.enumtype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'PyQt5.QtWidgets', '__or__': <slot wrapper '__or__' of 'DockWidgetFeature' objects>, '__ror__': <slot wrapper '__ror__' of 'DockWidgetFeature' objects>, '__dict__': <attribute '__dict__' of 'DockWidgetFeature' objects>, '__doc__': None, '__reduce__': <method '_pickle_enum' of 'DockWidgetFeature' objects>})
__dir__() → list

default dir() implementation

__divmod__

Return divmod(self, value).

__eq__

Return self==value.

__float__

float(self)

__floor__()

Flooring an Integral returns itself.

__floordiv__

Return self//value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getnewargs__()
__gt__

Return self>value.

__hash__

Return hash(self).

__index__

Return self converted to an integer, if self is suitable for use as an index into a list.

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__

int(self)

__invert__

~self

__le__

Return self<=value.

__lshift__

Return self<<value.

__lt__

Return self<value.

__mod__

Return self%value.

__module__ = 'PyQt5.QtWidgets'
__mul__

Return self*value.

__ne__

Return self!=value.

__neg__

-self

__new__()

Create and return a new object. See help(type) for accurate signature.

__or__

Return self|value.

__pos__

+self

__pow__

Return pow(self, value, mod).

__radd__

Return value+self.

__rand__

Return value&self.

__rdivmod__

Return divmod(value, self).

__reduce__()
__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__rfloordiv__

Return value//self.

__rlshift__

Return value<<self.

__rmod__

Return value%self.

__rmul__

Return value*self.

__ror__

Return value|self.

__round__()

Rounding an Integral returns itself. Rounding with an ndigits argument also returns an integer.

__rpow__

Return pow(value, self, mod).

__rrshift__

Return value>>self.

__rshift__

Return self>>value.

__rsub__

Return value-self.

__rtruediv__

Return value/self.

__rxor__

Return value^self.

__setattr__

Implement setattr(self, name, value).

__sizeof__()

Returns size in memory, in bytes

__str__

Return str(self).

__sub__

Return self-value.

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__truediv__

Return self/value.

__trunc__()

Truncating an Integral returns itself.

__xor__

Return self^value.

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)

__and__

Return self&value.

__bool__

self != 0

__class__

alias of sip.wrappertype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'PyQt5.QtWidgets', '__hash__': <slot wrapper '__hash__' of 'DockWidgetFeatures' objects>, '__lt__': <slot wrapper '__lt__' of 'DockWidgetFeatures' objects>, '__le__': <slot wrapper '__le__' of 'DockWidgetFeatures' objects>, '__eq__': <slot wrapper '__eq__' of 'DockWidgetFeatures' objects>, '__ne__': <slot wrapper '__ne__' of 'DockWidgetFeatures' objects>, '__gt__': <slot wrapper '__gt__' of 'DockWidgetFeatures' objects>, '__ge__': <slot wrapper '__ge__' of 'DockWidgetFeatures' objects>, '__bool__': <slot wrapper '__bool__' of 'DockWidgetFeatures' objects>, '__invert__': <slot wrapper '__invert__' of 'DockWidgetFeatures' objects>, '__and__': <slot wrapper '__and__' of 'DockWidgetFeatures' objects>, '__rand__': <slot wrapper '__rand__' of 'DockWidgetFeatures' objects>, '__xor__': <slot wrapper '__xor__' of 'DockWidgetFeatures' objects>, '__rxor__': <slot wrapper '__rxor__' of 'DockWidgetFeatures' objects>, '__or__': <slot wrapper '__or__' of 'DockWidgetFeatures' objects>, '__ror__': <slot wrapper '__ror__' of 'DockWidgetFeatures' objects>, '__int__': <slot wrapper '__int__' of 'DockWidgetFeatures' objects>, '__iand__': <slot wrapper '__iand__' of 'DockWidgetFeatures' objects>, '__ixor__': <slot wrapper '__ixor__' of 'DockWidgetFeatures' objects>, '__ior__': <slot wrapper '__ior__' of 'DockWidgetFeatures' objects>, '__weakref__': <attribute '__weakref__' of 'DockWidgetFeatures' objects>, '__doc__': 'QDockWidget.DockWidgetFeatures()\nQDockWidget.DockWidgetFeatures(Union[QDockWidget.DockWidgetFeatures, QDockWidget.DockWidgetFeature])\nQDockWidget.DockWidgetFeatures(QDockWidget.DockWidgetFeatures)'})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__iand__

Return self&=value.

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__

int(self)

__invert__

~self

__ior__

Return self|=value.

__ixor__

Return self^=value.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'PyQt5.QtWidgets'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__or__

Return self|value.

__rand__

Return value&self.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__ror__

Return value|self.

__rxor__

Return value^self.

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

__xor__

Return self^value.

DockWidgetFloatable = 4
DockWidgetMovable = 2
DockWidgetVerticalTitleBar = 8
DrawChildren = 2
DrawWindowBackground = 1
IgnoreMask = 4
NoDockWidgetFeatures = 0
class PaintDeviceMetric

Bases: int

__abs__

abs(self)

__add__

Return self+value.

__and__

Return self&value.

__bool__

self != 0

__ceil__()

Ceiling of an Integral returns itself.

__class__

alias of sip.enumtype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'PyQt5.QtGui', '__dict__': <attribute '__dict__' of 'PaintDeviceMetric' objects>, '__doc__': None, '__reduce__': <method '_pickle_enum' of 'PaintDeviceMetric' objects>})
__dir__() → list

default dir() implementation

__divmod__

Return divmod(self, value).

__eq__

Return self==value.

__float__

float(self)

__floor__()

Flooring an Integral returns itself.

__floordiv__

Return self//value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getnewargs__()
__gt__

Return self>value.

__hash__

Return hash(self).

__index__

Return self converted to an integer, if self is suitable for use as an index into a list.

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__

int(self)

__invert__

~self

__le__

Return self<=value.

__lshift__

Return self<<value.

__lt__

Return self<value.

__mod__

Return self%value.

__module__ = 'PyQt5.QtGui'
__mul__

Return self*value.

__ne__

Return self!=value.

__neg__

-self

__new__()

Create and return a new object. See help(type) for accurate signature.

__or__

Return self|value.

__pos__

+self

__pow__

Return pow(self, value, mod).

__radd__

Return value+self.

__rand__

Return value&self.

__rdivmod__

Return divmod(value, self).

__reduce__()
__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__rfloordiv__

Return value//self.

__rlshift__

Return value<<self.

__rmod__

Return value%self.

__rmul__

Return value*self.

__ror__

Return value|self.

__round__()

Rounding an Integral returns itself. Rounding with an ndigits argument also returns an integer.

__rpow__

Return pow(value, self, mod).

__rrshift__

Return value>>self.

__rshift__

Return self>>value.

__rsub__

Return value-self.

__rtruediv__

Return value/self.

__rxor__

Return value^self.

__setattr__

Implement setattr(self, name, value).

__sizeof__()

Returns size in memory, in bytes

__str__

Return str(self).

__sub__

Return self-value.

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__truediv__

Return self/value.

__trunc__()

Truncating an Integral returns itself.

__xor__

Return self^value.

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

__abs__

abs(self)

__add__

Return self+value.

__and__

Return self&value.

__bool__

self != 0

__ceil__()

Ceiling of an Integral returns itself.

__class__

alias of sip.enumtype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'PyQt5.QtWidgets', '__or__': <slot wrapper '__or__' of 'RenderFlag' objects>, '__ror__': <slot wrapper '__ror__' of 'RenderFlag' objects>, '__dict__': <attribute '__dict__' of 'RenderFlag' objects>, '__doc__': None, '__reduce__': <method '_pickle_enum' of 'RenderFlag' objects>})
__dir__() → list

default dir() implementation

__divmod__

Return divmod(self, value).

__eq__

Return self==value.

__float__

float(self)

__floor__()

Flooring an Integral returns itself.

__floordiv__

Return self//value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getnewargs__()
__gt__

Return self>value.

__hash__

Return hash(self).

__index__

Return self converted to an integer, if self is suitable for use as an index into a list.

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__

int(self)

__invert__

~self

__le__

Return self<=value.

__lshift__

Return self<<value.

__lt__

Return self<value.

__mod__

Return self%value.

__module__ = 'PyQt5.QtWidgets'
__mul__

Return self*value.

__ne__

Return self!=value.

__neg__

-self

__new__()

Create and return a new object. See help(type) for accurate signature.

__or__

Return self|value.

__pos__

+self

__pow__

Return pow(self, value, mod).

__radd__

Return value+self.

__rand__

Return value&self.

__rdivmod__

Return divmod(value, self).

__reduce__()
__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__rfloordiv__

Return value//self.

__rlshift__

Return value<<self.

__rmod__

Return value%self.

__rmul__

Return value*self.

__ror__

Return value|self.

__round__()

Rounding an Integral returns itself. Rounding with an ndigits argument also returns an integer.

__rpow__

Return pow(value, self, mod).

__rrshift__

Return value>>self.

__rshift__

Return self>>value.

__rsub__

Return value-self.

__rtruediv__

Return value/self.

__rxor__

Return value^self.

__setattr__

Implement setattr(self, name, value).

__sizeof__()

Returns size in memory, in bytes

__str__

Return str(self).

__sub__

Return self-value.

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__truediv__

Return self/value.

__trunc__()

Truncating an Integral returns itself.

__xor__

Return self^value.

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)

__and__

Return self&value.

__bool__

self != 0

__class__

alias of sip.wrappertype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'PyQt5.QtWidgets', '__hash__': <slot wrapper '__hash__' of 'RenderFlags' objects>, '__lt__': <slot wrapper '__lt__' of 'RenderFlags' objects>, '__le__': <slot wrapper '__le__' of 'RenderFlags' objects>, '__eq__': <slot wrapper '__eq__' of 'RenderFlags' objects>, '__ne__': <slot wrapper '__ne__' of 'RenderFlags' objects>, '__gt__': <slot wrapper '__gt__' of 'RenderFlags' objects>, '__ge__': <slot wrapper '__ge__' of 'RenderFlags' objects>, '__bool__': <slot wrapper '__bool__' of 'RenderFlags' objects>, '__invert__': <slot wrapper '__invert__' of 'RenderFlags' objects>, '__and__': <slot wrapper '__and__' of 'RenderFlags' objects>, '__rand__': <slot wrapper '__rand__' of 'RenderFlags' objects>, '__xor__': <slot wrapper '__xor__' of 'RenderFlags' objects>, '__rxor__': <slot wrapper '__rxor__' of 'RenderFlags' objects>, '__or__': <slot wrapper '__or__' of 'RenderFlags' objects>, '__ror__': <slot wrapper '__ror__' of 'RenderFlags' objects>, '__int__': <slot wrapper '__int__' of 'RenderFlags' objects>, '__iand__': <slot wrapper '__iand__' of 'RenderFlags' objects>, '__ixor__': <slot wrapper '__ixor__' of 'RenderFlags' objects>, '__ior__': <slot wrapper '__ior__' of 'RenderFlags' objects>, '__weakref__': <attribute '__weakref__' of 'RenderFlags' objects>, '__doc__': 'QWidget.RenderFlags()\nQWidget.RenderFlags(Union[QWidget.RenderFlags, QWidget.RenderFlag])\nQWidget.RenderFlags(QWidget.RenderFlags)'})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__iand__

Return self&=value.

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__

int(self)

__invert__

~self

__ior__

Return self|=value.

__ixor__

Return self^=value.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'PyQt5.QtWidgets'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__or__

Return self|value.

__rand__

Return value&self.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__ror__

Return value|self.

__rxor__

Return value^self.

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

__xor__

Return self^value.

__class__

alias of sip.wrappertype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.bioluminate.ssv.viewer', '__doc__': '\n The dock widget that can set a `ViewerWindow` as the main\n widget. This makes the ViewerWindow dockable.\n\n ', 'WINDOW_TITLE': 'Sequence Viewer', 'FLOATABLE': 4, 'MOVABLE': 2, 'CLOSABLE': 1, '__init__': <function SequenceDockWidget.__init__>, 'floatChange': <function SequenceDockWidget.floatChange>, 'setFloatable': <function SequenceDockWidget.setFloatable>, 'setFloatableMovable': <function SequenceDockWidget.setFloatableMovable>, 'setFloatableMovableClosable': <function SequenceDockWidget.setFloatableMovableClosable>, 'closeEvent': <function SequenceDockWidget.closeEvent>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattr__(self, str) → object
__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.bioluminate.ssv.viewer'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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)
sharedPainter(self) → QPainter
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 a QtWidgets.QSplitter) to be a stand-alone window.

WINDOW_TITLE = 'Sequence Viewer'
IMPORT_TOOLBAR = 'import_toolbar'
UNDO_REDO_TOOLBAR = 'undo_redo_toolbar'
FIND_TOOLBAR = 'find_toolbar'
ALIGN_TOOLBAR = 'align_toolbar'
CONSENSUS_TOOLBAR = 'consensus_toolbar'
ANTIBODY_NUM_TOOLBAR = 'antibody_numbering_toolbar'
BREAK_TOOLBAR = 'break_toolbar'
DEFAULT_TOOLBARS = ['import_toolbar', 'undo_redo_toolbar', 'find_toolbar', 'align_toolbar']
__init__(parent)
Parameters:parent (SimplifiedSequenceViewer) – The sequence viewer object that will use this window
Raises:RuntimeError – If parent is not correct type
action_factory = 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, if objname is None, removal of all the window’s toolbars.

addToolBars(toolbars)

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

setToolBars(toolbars)

Deletes all window toolbars and sets them to the new toolbars

addImportToolBar(area=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

__abs__

abs(self)

__add__

Return self+value.

__and__

Return self&value.

__bool__

self != 0

__ceil__()

Ceiling of an Integral returns itself.

__class__

alias of sip.enumtype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'PyQt5.QtWidgets', '__or__': <slot wrapper '__or__' of 'DockOption' objects>, '__ror__': <slot wrapper '__ror__' of 'DockOption' objects>, '__dict__': <attribute '__dict__' of 'DockOption' objects>, '__doc__': None, '__reduce__': <method '_pickle_enum' of 'DockOption' objects>})
__dir__() → list

default dir() implementation

__divmod__

Return divmod(self, value).

__eq__

Return self==value.

__float__

float(self)

__floor__()

Flooring an Integral returns itself.

__floordiv__

Return self//value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getnewargs__()
__gt__

Return self>value.

__hash__

Return hash(self).

__index__

Return self converted to an integer, if self is suitable for use as an index into a list.

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__

int(self)

__invert__

~self

__le__

Return self<=value.

__lshift__

Return self<<value.

__lt__

Return self<value.

__mod__

Return self%value.

__module__ = 'PyQt5.QtWidgets'
__mul__

Return self*value.

__ne__

Return self!=value.

__neg__

-self

__new__()

Create and return a new object. See help(type) for accurate signature.

__or__

Return self|value.

__pos__

+self

__pow__

Return pow(self, value, mod).

__radd__

Return value+self.

__rand__

Return value&self.

__rdivmod__

Return divmod(value, self).

__reduce__()
__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__rfloordiv__

Return value//self.

__rlshift__

Return value<<self.

__rmod__

Return value%self.

__rmul__

Return value*self.

__ror__

Return value|self.

__round__()

Rounding an Integral returns itself. Rounding with an ndigits argument also returns an integer.

__rpow__

Return pow(value, self, mod).

__rrshift__

Return value>>self.

__rshift__

Return self>>value.

__rsub__

Return value-self.

__rtruediv__

Return value/self.

__rxor__

Return value^self.

__setattr__

Implement setattr(self, name, value).

__sizeof__()

Returns size in memory, in bytes

__str__

Return str(self).

__sub__

Return self-value.

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__truediv__

Return self/value.

__trunc__()

Truncating an Integral returns itself.

__xor__

Return self^value.

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)

__and__

Return self&value.

__bool__

self != 0

__class__

alias of sip.wrappertype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'PyQt5.QtWidgets', '__hash__': <slot wrapper '__hash__' of 'DockOptions' objects>, '__lt__': <slot wrapper '__lt__' of 'DockOptions' objects>, '__le__': <slot wrapper '__le__' of 'DockOptions' objects>, '__eq__': <slot wrapper '__eq__' of 'DockOptions' objects>, '__ne__': <slot wrapper '__ne__' of 'DockOptions' objects>, '__gt__': <slot wrapper '__gt__' of 'DockOptions' objects>, '__ge__': <slot wrapper '__ge__' of 'DockOptions' objects>, '__bool__': <slot wrapper '__bool__' of 'DockOptions' objects>, '__invert__': <slot wrapper '__invert__' of 'DockOptions' objects>, '__and__': <slot wrapper '__and__' of 'DockOptions' objects>, '__rand__': <slot wrapper '__rand__' of 'DockOptions' objects>, '__xor__': <slot wrapper '__xor__' of 'DockOptions' objects>, '__rxor__': <slot wrapper '__rxor__' of 'DockOptions' objects>, '__or__': <slot wrapper '__or__' of 'DockOptions' objects>, '__ror__': <slot wrapper '__ror__' of 'DockOptions' objects>, '__int__': <slot wrapper '__int__' of 'DockOptions' objects>, '__iand__': <slot wrapper '__iand__' of 'DockOptions' objects>, '__ixor__': <slot wrapper '__ixor__' of 'DockOptions' objects>, '__ior__': <slot wrapper '__ior__' of 'DockOptions' objects>, '__weakref__': <attribute '__weakref__' of 'DockOptions' objects>, '__doc__': 'QMainWindow.DockOptions()\nQMainWindow.DockOptions(Union[QMainWindow.DockOptions, QMainWindow.DockOption])\nQMainWindow.DockOptions(QMainWindow.DockOptions)'})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__iand__

Return self&=value.

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__

int(self)

__invert__

~self

__ior__

Return self|=value.

__ixor__

Return self^=value.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'PyQt5.QtWidgets'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__or__

Return self|value.

__rand__

Return value&self.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__ror__

Return value|self.

__rxor__

Return value^self.

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

__xor__

Return self^value.

DrawChildren = 2
DrawWindowBackground = 1
ForceTabbedDocks = 8
GroupedDragging = 32
IgnoreMask = 4
class PaintDeviceMetric

Bases: int

__abs__

abs(self)

__add__

Return self+value.

__and__

Return self&value.

__bool__

self != 0

__ceil__()

Ceiling of an Integral returns itself.

__class__

alias of sip.enumtype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'PyQt5.QtGui', '__dict__': <attribute '__dict__' of 'PaintDeviceMetric' objects>, '__doc__': None, '__reduce__': <method '_pickle_enum' of 'PaintDeviceMetric' objects>})
__dir__() → list

default dir() implementation

__divmod__

Return divmod(self, value).

__eq__

Return self==value.

__float__

float(self)

__floor__()

Flooring an Integral returns itself.

__floordiv__

Return self//value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getnewargs__()
__gt__

Return self>value.

__hash__

Return hash(self).

__index__

Return self converted to an integer, if self is suitable for use as an index into a list.

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__

int(self)

__invert__

~self

__le__

Return self<=value.

__lshift__

Return self<<value.

__lt__

Return self<value.

__mod__

Return self%value.

__module__ = 'PyQt5.QtGui'
__mul__

Return self*value.

__ne__

Return self!=value.

__neg__

-self

__new__()

Create and return a new object. See help(type) for accurate signature.

__or__

Return self|value.

__pos__

+self

__pow__

Return pow(self, value, mod).

__radd__

Return value+self.

__rand__

Return value&self.

__rdivmod__

Return divmod(value, self).

__reduce__()
__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__rfloordiv__

Return value//self.

__rlshift__

Return value<<self.

__rmod__

Return value%self.

__rmul__

Return value*self.

__ror__

Return value|self.

__round__()

Rounding an Integral returns itself. Rounding with an ndigits argument also returns an integer.

__rpow__

Return pow(value, self, mod).

__rrshift__

Return value>>self.

__rshift__

Return self>>value.

__rsub__

Return value-self.

__rtruediv__

Return value/self.

__rxor__

Return value^self.

__setattr__

Implement setattr(self, name, value).

__sizeof__()

Returns size in memory, in bytes

__str__

Return str(self).

__sub__

Return self-value.

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__truediv__

Return self/value.

__trunc__()

Truncating an Integral returns itself.

__xor__

Return self^value.

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

__abs__

abs(self)

__add__

Return self+value.

__and__

Return self&value.

__bool__

self != 0

__ceil__()

Ceiling of an Integral returns itself.

__class__

alias of sip.enumtype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'PyQt5.QtWidgets', '__or__': <slot wrapper '__or__' of 'RenderFlag' objects>, '__ror__': <slot wrapper '__ror__' of 'RenderFlag' objects>, '__dict__': <attribute '__dict__' of 'RenderFlag' objects>, '__doc__': None, '__reduce__': <method '_pickle_enum' of 'RenderFlag' objects>})
__dir__() → list

default dir() implementation

__divmod__

Return divmod(self, value).

__eq__

Return self==value.

__float__

float(self)

__floor__()

Flooring an Integral returns itself.

__floordiv__

Return self//value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getnewargs__()
__gt__

Return self>value.

__hash__

Return hash(self).

__index__

Return self converted to an integer, if self is suitable for use as an index into a list.

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__

int(self)

__invert__

~self

__le__

Return self<=value.

__lshift__

Return self<<value.

__lt__

Return self<value.

__mod__

Return self%value.

__module__ = 'PyQt5.QtWidgets'
__mul__

Return self*value.

__ne__

Return self!=value.

__neg__

-self

__new__()

Create and return a new object. See help(type) for accurate signature.

__or__

Return self|value.

__pos__

+self

__pow__

Return pow(self, value, mod).

__radd__

Return value+self.

__rand__

Return value&self.

__rdivmod__

Return divmod(value, self).

__reduce__()
__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__rfloordiv__

Return value//self.

__rlshift__

Return value<<self.

__rmod__

Return value%self.

__rmul__

Return value*self.

__ror__

Return value|self.

__round__()

Rounding an Integral returns itself. Rounding with an ndigits argument also returns an integer.

__rpow__

Return pow(value, self, mod).

__rrshift__

Return value>>self.

__rshift__

Return self>>value.

__rsub__

Return value-self.

__rtruediv__

Return value/self.

__rxor__

Return value^self.

__setattr__

Implement setattr(self, name, value).

__sizeof__()

Returns size in memory, in bytes

__str__

Return str(self).

__sub__

Return self-value.

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__truediv__

Return self/value.

__trunc__()

Truncating an Integral returns itself.

__xor__

Return self^value.

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)

__and__

Return self&value.

__bool__

self != 0

__class__

alias of sip.wrappertype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'PyQt5.QtWidgets', '__hash__': <slot wrapper '__hash__' of 'RenderFlags' objects>, '__lt__': <slot wrapper '__lt__' of 'RenderFlags' objects>, '__le__': <slot wrapper '__le__' of 'RenderFlags' objects>, '__eq__': <slot wrapper '__eq__' of 'RenderFlags' objects>, '__ne__': <slot wrapper '__ne__' of 'RenderFlags' objects>, '__gt__': <slot wrapper '__gt__' of 'RenderFlags' objects>, '__ge__': <slot wrapper '__ge__' of 'RenderFlags' objects>, '__bool__': <slot wrapper '__bool__' of 'RenderFlags' objects>, '__invert__': <slot wrapper '__invert__' of 'RenderFlags' objects>, '__and__': <slot wrapper '__and__' of 'RenderFlags' objects>, '__rand__': <slot wrapper '__rand__' of 'RenderFlags' objects>, '__xor__': <slot wrapper '__xor__' of 'RenderFlags' objects>, '__rxor__': <slot wrapper '__rxor__' of 'RenderFlags' objects>, '__or__': <slot wrapper '__or__' of 'RenderFlags' objects>, '__ror__': <slot wrapper '__ror__' of 'RenderFlags' objects>, '__int__': <slot wrapper '__int__' of 'RenderFlags' objects>, '__iand__': <slot wrapper '__iand__' of 'RenderFlags' objects>, '__ixor__': <slot wrapper '__ixor__' of 'RenderFlags' objects>, '__ior__': <slot wrapper '__ior__' of 'RenderFlags' objects>, '__weakref__': <attribute '__weakref__' of 'RenderFlags' objects>, '__doc__': 'QWidget.RenderFlags()\nQWidget.RenderFlags(Union[QWidget.RenderFlags, QWidget.RenderFlag])\nQWidget.RenderFlags(QWidget.RenderFlags)'})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__iand__

Return self&=value.

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__

int(self)

__invert__

~self

__ior__

Return self|=value.

__ixor__

Return self^=value.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'PyQt5.QtWidgets'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__or__

Return self|value.

__rand__

Return value&self.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__ror__

Return value|self.

__rxor__

Return value^self.

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

__xor__

Return self^value.

VerticalTabs = 16
__class__

alias of sip.wrappertype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.bioluminate.ssv.viewer', '__doc__': '\n Provides the `SimplifiedSequenceViewer` with a window to occupy.\n This has the benefit of adding toolbars and allowing the sequence\n viewer (which is a `QtWidgets.QSplitter`) to be a stand-alone window.\n\n ', '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__': <function ViewerWindow.__init__>, 'removeToolBar': <function ViewerWindow.removeToolBar>, 'addToolBars': <function ViewerWindow.addToolBars>, 'setToolBars': <function ViewerWindow.setToolBars>, 'addImportToolBar': <function ViewerWindow.addImportToolBar>, 'addUndoRedoToolBar': <function ViewerWindow.addUndoRedoToolBar>, 'addFindToolBar': <function ViewerWindow.addFindToolBar>, 'addAlignToolBar': <function ViewerWindow.addAlignToolBar>, 'addConsensusToolBar': <function ViewerWindow.addConsensusToolBar>, 'addAntibodyNumberingToolBar': <function ViewerWindow.addAntibodyNumberingToolBar>, 'setAntibodyNumberingToolBarVisible': <function ViewerWindow.setAntibodyNumberingToolBarVisible>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattr__(self, str) → object
__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.bioluminate.ssv.viewer'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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
menuBar(self) → QMenuBar
menuWidget(self) → QWidget
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)
sharedPainter(self) → QPainter
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:

__init__(parent, toolbars=None, auto_align=False, require3d=True)
Parameters:
  • parent – Parent widget of the sequence viewer
  • toolbars (list of strings) – A list of toolbar flags to use (see ViewerWindow for available toolbars
  • auto_align (boolean) – Whether to auto-align sequences when a new one is imported
  • require3d (boolean) – Whether to allow fasta sequence files to be imported. If set to True (default) only structures with 3D coordinates are allowed.
See:

ViewerWindow

window(self) → QWidget
dock_widget = 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 or structure
importFromPDB(*args, **kwargs)
importFromFile(*args, **kwargs)
importFromFilePaths(filenames, to_maestro=True)

Import a list of filesnames into the sequence viewer.

Parameters:filenames (list of strings) – Filenames to be imported
importFromWorkspace(*args, **kwargs)
importFromProjectTable(*args, **kwargs)
createSequence(*args, **kwargs)
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

__abs__

abs(self)

__add__

Return self+value.

__and__

Return self&value.

__bool__

self != 0

__ceil__()

Ceiling of an Integral returns itself.

__class__

alias of sip.enumtype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'PyQt5.QtGui', '__dict__': <attribute '__dict__' of 'PaintDeviceMetric' objects>, '__doc__': None, '__reduce__': <method '_pickle_enum' of 'PaintDeviceMetric' objects>})
__dir__() → list

default dir() implementation

__divmod__

Return divmod(self, value).

__eq__

Return self==value.

__float__

float(self)

__floor__()

Flooring an Integral returns itself.

__floordiv__

Return self//value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getnewargs__()
__gt__

Return self>value.

__hash__

Return hash(self).

__index__

Return self converted to an integer, if self is suitable for use as an index into a list.

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__

int(self)

__invert__

~self

__le__

Return self<=value.

__lshift__

Return self<<value.

__lt__

Return self<value.

__mod__

Return self%value.

__module__ = 'PyQt5.QtGui'
__mul__

Return self*value.

__ne__

Return self!=value.

__neg__

-self

__new__()

Create and return a new object. See help(type) for accurate signature.

__or__

Return self|value.

__pos__

+self

__pow__

Return pow(self, value, mod).

__radd__

Return value+self.

__rand__

Return value&self.

__rdivmod__

Return divmod(value, self).

__reduce__()
__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__rfloordiv__

Return value//self.

__rlshift__

Return value<<self.

__rmod__

Return value%self.

__rmul__

Return value*self.

__ror__

Return value|self.

__round__()

Rounding an Integral returns itself. Rounding with an ndigits argument also returns an integer.

__rpow__

Return pow(value, self, mod).

__rrshift__

Return value>>self.

__rshift__

Return self>>value.

__rsub__

Return value-self.

__rtruediv__

Return value/self.

__rxor__

Return value^self.

__setattr__

Implement setattr(self, name, value).

__sizeof__()

Returns size in memory, in bytes

__str__

Return str(self).

__sub__

Return self-value.

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__truediv__

Return self/value.

__trunc__()

Truncating an Integral returns itself.

__xor__

Return self^value.

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

__abs__

abs(self)

__add__

Return self+value.

__and__

Return self&value.

__bool__

self != 0

__ceil__()

Ceiling of an Integral returns itself.

__class__

alias of sip.enumtype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'PyQt5.QtWidgets', '__or__': <slot wrapper '__or__' of 'RenderFlag' objects>, '__ror__': <slot wrapper '__ror__' of 'RenderFlag' objects>, '__dict__': <attribute '__dict__' of 'RenderFlag' objects>, '__doc__': None, '__reduce__': <method '_pickle_enum' of 'RenderFlag' objects>})
__dir__() → list

default dir() implementation

__divmod__

Return divmod(self, value).

__eq__

Return self==value.

__float__

float(self)

__floor__()

Flooring an Integral returns itself.

__floordiv__

Return self//value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getnewargs__()
__gt__

Return self>value.

__hash__

Return hash(self).

__index__

Return self converted to an integer, if self is suitable for use as an index into a list.

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__

int(self)

__invert__

~self

__le__

Return self<=value.

__lshift__

Return self<<value.

__lt__

Return self<value.

__mod__

Return self%value.

__module__ = 'PyQt5.QtWidgets'
__mul__

Return self*value.

__ne__

Return self!=value.

__neg__

-self

__new__()

Create and return a new object. See help(type) for accurate signature.

__or__

Return self|value.

__pos__

+self

__pow__

Return pow(self, value, mod).

__radd__

Return value+self.

__rand__

Return value&self.

__rdivmod__

Return divmod(value, self).

__reduce__()
__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__rfloordiv__

Return value//self.

__rlshift__

Return value<<self.

__rmod__

Return value%self.

__rmul__

Return value*self.

__ror__

Return value|self.

__round__()

Rounding an Integral returns itself. Rounding with an ndigits argument also returns an integer.

__rpow__

Return pow(value, self, mod).

__rrshift__

Return value>>self.

__rshift__

Return self>>value.

__rsub__

Return value-self.

__rtruediv__

Return value/self.

__rxor__

Return value^self.

__setattr__

Implement setattr(self, name, value).

__sizeof__()

Returns size in memory, in bytes

__str__

Return str(self).

__sub__

Return self-value.

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__truediv__

Return self/value.

__trunc__()

Truncating an Integral returns itself.

__xor__

Return self^value.

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)

__and__

Return self&value.

__bool__

self != 0

__class__

alias of sip.wrappertype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'PyQt5.QtWidgets', '__hash__': <slot wrapper '__hash__' of 'RenderFlags' objects>, '__lt__': <slot wrapper '__lt__' of 'RenderFlags' objects>, '__le__': <slot wrapper '__le__' of 'RenderFlags' objects>, '__eq__': <slot wrapper '__eq__' of 'RenderFlags' objects>, '__ne__': <slot wrapper '__ne__' of 'RenderFlags' objects>, '__gt__': <slot wrapper '__gt__' of 'RenderFlags' objects>, '__ge__': <slot wrapper '__ge__' of 'RenderFlags' objects>, '__bool__': <slot wrapper '__bool__' of 'RenderFlags' objects>, '__invert__': <slot wrapper '__invert__' of 'RenderFlags' objects>, '__and__': <slot wrapper '__and__' of 'RenderFlags' objects>, '__rand__': <slot wrapper '__rand__' of 'RenderFlags' objects>, '__xor__': <slot wrapper '__xor__' of 'RenderFlags' objects>, '__rxor__': <slot wrapper '__rxor__' of 'RenderFlags' objects>, '__or__': <slot wrapper '__or__' of 'RenderFlags' objects>, '__ror__': <slot wrapper '__ror__' of 'RenderFlags' objects>, '__int__': <slot wrapper '__int__' of 'RenderFlags' objects>, '__iand__': <slot wrapper '__iand__' of 'RenderFlags' objects>, '__ixor__': <slot wrapper '__ixor__' of 'RenderFlags' objects>, '__ior__': <slot wrapper '__ior__' of 'RenderFlags' objects>, '__weakref__': <attribute '__weakref__' of 'RenderFlags' objects>, '__doc__': 'QWidget.RenderFlags()\nQWidget.RenderFlags(Union[QWidget.RenderFlags, QWidget.RenderFlag])\nQWidget.RenderFlags(QWidget.RenderFlags)'})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__iand__

Return self&=value.

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__

int(self)

__invert__

~self

__ior__

Return self|=value.

__ixor__

Return self^=value.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'PyQt5.QtWidgets'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__or__

Return self|value.

__rand__

Return value&self.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__ror__

Return value|self.

__rxor__

Return value^self.

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

__xor__

Return self^value.

class Shadow

Bases: int

__abs__

abs(self)

__add__

Return self+value.

__and__

Return self&value.

__bool__

self != 0

__ceil__()

Ceiling of an Integral returns itself.

__class__

alias of sip.enumtype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'PyQt5.QtWidgets', '__dict__': <attribute '__dict__' of 'Shadow' objects>, '__doc__': None, '__reduce__': <method '_pickle_enum' of 'Shadow' objects>})
__dir__() → list

default dir() implementation

__divmod__

Return divmod(self, value).

__eq__

Return self==value.

__float__

float(self)

__floor__()

Flooring an Integral returns itself.

__floordiv__

Return self//value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getnewargs__()
__gt__

Return self>value.

__hash__

Return hash(self).

__index__

Return self converted to an integer, if self is suitable for use as an index into a list.

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__

int(self)

__invert__

~self

__le__

Return self<=value.

__lshift__

Return self<<value.

__lt__

Return self<value.

__mod__

Return self%value.

__module__ = 'PyQt5.QtWidgets'
__mul__

Return self*value.

__ne__

Return self!=value.

__neg__

-self

__new__()

Create and return a new object. See help(type) for accurate signature.

__or__

Return self|value.

__pos__

+self

__pow__

Return pow(self, value, mod).

__radd__

Return value+self.

__rand__

Return value&self.

__rdivmod__

Return divmod(value, self).

__reduce__()
__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__rfloordiv__

Return value//self.

__rlshift__

Return value<<self.

__rmod__

Return value%self.

__rmul__

Return value*self.

__ror__

Return value|self.

__round__()

Rounding an Integral returns itself. Rounding with an ndigits argument also returns an integer.

__rpow__

Return pow(value, self, mod).

__rrshift__

Return value>>self.

__rshift__

Return self>>value.

__rsub__

Return value-self.

__rtruediv__

Return value/self.

__rxor__

Return value^self.

__setattr__

Implement setattr(self, name, value).

__sizeof__()

Returns size in memory, in bytes

__str__

Return str(self).

__sub__

Return self-value.

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__truediv__

Return self/value.

__trunc__()

Truncating an Integral returns itself.

__xor__

Return self^value.

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

__abs__

abs(self)

__add__

Return self+value.

__and__

Return self&value.

__bool__

self != 0

__ceil__()

Ceiling of an Integral returns itself.

__class__

alias of sip.enumtype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'PyQt5.QtWidgets', '__dict__': <attribute '__dict__' of 'Shape' objects>, '__doc__': None, '__reduce__': <method '_pickle_enum' of 'Shape' objects>})
__dir__() → list

default dir() implementation

__divmod__

Return divmod(self, value).

__eq__

Return self==value.

__float__

float(self)

__floor__()

Flooring an Integral returns itself.

__floordiv__

Return self//value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getnewargs__()
__gt__

Return self>value.

__hash__

Return hash(self).

__index__

Return self converted to an integer, if self is suitable for use as an index into a list.

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__

int(self)

__invert__

~self

__le__

Return self<=value.

__lshift__

Return self<<value.

__lt__

Return self<value.

__mod__

Return self%value.

__module__ = 'PyQt5.QtWidgets'
__mul__

Return self*value.

__ne__

Return self!=value.

__neg__

-self

__new__()

Create and return a new object. See help(type) for accurate signature.

__or__

Return self|value.

__pos__

+self

__pow__

Return pow(self, value, mod).

__radd__

Return value+self.

__rand__

Return value&self.

__rdivmod__

Return divmod(value, self).

__reduce__()
__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__rfloordiv__

Return value//self.

__rlshift__

Return value<<self.

__rmod__

Return value%self.

__rmul__

Return value*self.

__ror__

Return value|self.

__round__()

Rounding an Integral returns itself. Rounding with an ndigits argument also returns an integer.

__rpow__

Return pow(value, self, mod).

__rrshift__

Return value>>self.

__rshift__

Return self>>value.

__rsub__

Return value-self.

__rtruediv__

Return value/self.

__rxor__

Return value^self.

__setattr__

Implement setattr(self, name, value).

__sizeof__()

Returns size in memory, in bytes

__str__

Return str(self).

__sub__

Return self-value.

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__truediv__

Return self/value.

__trunc__()

Truncating an Integral returns itself.

__xor__

Return self^value.

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

__abs__

abs(self)

__add__

Return self+value.

__and__

Return self&value.

__bool__

self != 0

__ceil__()

Ceiling of an Integral returns itself.

__class__

alias of sip.enumtype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'PyQt5.QtWidgets', '__dict__': <attribute '__dict__' of 'StyleMask' objects>, '__doc__': None, '__reduce__': <method '_pickle_enum' of 'StyleMask' objects>})
__dir__() → list

default dir() implementation

__divmod__

Return divmod(self, value).

__eq__

Return self==value.

__float__

float(self)

__floor__()

Flooring an Integral returns itself.

__floordiv__

Return self//value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getnewargs__()
__gt__

Return self>value.

__hash__

Return hash(self).

__index__

Return self converted to an integer, if self is suitable for use as an index into a list.

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__

int(self)

__invert__

~self

__le__

Return self<=value.

__lshift__

Return self<<value.

__lt__

Return self<value.

__mod__

Return self%value.

__module__ = 'PyQt5.QtWidgets'
__mul__

Return self*value.

__ne__

Return self!=value.

__neg__

-self

__new__()

Create and return a new object. See help(type) for accurate signature.

__or__

Return self|value.

__pos__

+self

__pow__

Return pow(self, value, mod).

__radd__

Return value+self.

__rand__

Return value&self.

__rdivmod__

Return divmod(value, self).

__reduce__()
__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__rfloordiv__

Return value//self.

__rlshift__

Return value<<self.

__rmod__

Return value%self.

__rmul__

Return value*self.

__ror__

Return value|self.

__round__()

Rounding an Integral returns itself. Rounding with an ndigits argument also returns an integer.

__rpow__

Return pow(value, self, mod).

__rrshift__

Return value>>self.

__rshift__

Return self>>value.

__rsub__

Return value-self.

__rtruediv__

Return value/self.

__rxor__

Return value^self.

__setattr__

Implement setattr(self, name, value).

__sizeof__()

Returns size in memory, in bytes

__str__

Return str(self).

__sub__

Return self-value.

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__truediv__

Return self/value.

__trunc__()

Truncating an Integral returns itself.

__xor__

Return self^value.

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
__class__

alias of sip.wrappertype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.bioluminate.ssv.viewer', '__doc__': "\n Creates a sequence viewer that can be opened by an action or added to a main\n window as a dockable item. Here is an example of how to add a dockable item\n to a QMainWindow, or AppFramework window::\n\n from schrodinger.applications.bioluminate import sequence_viewer\n\n self.sequence_viewer = sequence_viewer.SimplifiedSequenceViewer(<window>)\n self.addDockWidget(\n QtCore.Qt.TopDockWidgetArea,\n self.sequence_viewer.asDock()\n )\n\n\n If you want to add a button that will open the viewer in a new window::\n\n from schrodinger.applications.bioluminate import sequence_viewer\n\n self.sequence_viewer = sequence_viewer.SimplifiedSequenceViewer(<window>)\n self.viewer_button = QtWidgets.QPushButton(self.tr('Open Model Viewer...'))\n self.viewer_button.clicked.connect(self.openSequenceViewer)\n\n then in the connected method (openSequenceViewer)::\n\n self.sequence_viewer.window.show()\n self.sequence_viewer.window.setFocus()\n\n\n If you want to simply add a sequence viewer frame to your app::\n\n self.sequence_viewer = SimplifiedSequenceViewer(<window>)\n <layout>.addWidget( self.sequence_viewer.asFrame() )\n\n\n ", 'WORKSPACE': 'workspace', 'PROJET_TABLE': 'projecttable', 'PDB_STRING': 'pdb_string', 'FILES': 'files', 'MANUAL_SEQUENCE': 'manual_sequence', 'sequencesImported': <unbound PYQT_SIGNAL SimplifiedSequenceViewer.sequencesImported[str]>, '__init__': <function SimplifiedSequenceViewer.__init__>, '_setContextMenus': <function SimplifiedSequenceViewer._setContextMenus>, 'setupViewer': <function SimplifiedSequenceViewer.setupViewer>, 'enableMaestroSync': <function SimplifiedSequenceViewer.enableMaestroSync>, 'asDock': <function SimplifiedSequenceViewer.asDock>, 'asFrame': <function SimplifiedSequenceViewer.asFrame>, 'protein_sequences': <property object>, 'structure_sequences': <property object>, 'selected_sequences': <property object>, 'getReferenceStructure': <function SimplifiedSequenceViewer.getReferenceStructure>, 'generateSeqProjectRows': <function SimplifiedSequenceViewer.generateSeqProjectRows>, 'generateSeqStructures': <function SimplifiedSequenceViewer.generateSeqStructures>, 'getSeqStructure': <function SimplifiedSequenceViewer.getSeqStructure>, 'importFromPDB': <function catch_last_added.<locals>.dec>, 'importFromFile': <function catch_last_added.<locals>.dec>, 'importFromFilePaths': <function SimplifiedSequenceViewer.importFromFilePaths>, 'importFromWorkspace': <function catch_last_added.<locals>.dec>, 'importFromProjectTable': <function catch_last_added.<locals>.dec>, 'createSequence': <function catch_last_added.<locals>.dec>, 'addAnnotationAction': <function SimplifiedSequenceViewer.addAnnotationAction>, 'setColorModeAction': <function SimplifiedSequenceViewer.setColorModeAction>, 'focusFinder': <function SimplifiedSequenceViewer.focusFinder>, 'nameContextCallback': <function SimplifiedSequenceViewer.nameContextCallback>, 'sequenceContextCallback': <function SimplifiedSequenceViewer.sequenceContextCallback>, 'treeContextCallback': <function SimplifiedSequenceViewer.treeContextCallback>, 'selectOnlyByEntry': <function SimplifiedSequenceViewer.selectOnlyByEntry>, 'selectOnlyBySeqs': <function SimplifiedSequenceViewer.selectOnlyBySeqs>, 'deleteByEntry': <function SimplifiedSequenceViewer.deleteByEntry>, 'deleteBySequences': <function SimplifiedSequenceViewer.deleteBySequences>, 'importFromMaestro': <function SimplifiedSequenceViewer.importFromMaestro>, 'closeWindow': <function SimplifiedSequenceViewer.closeWindow>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattr__(self, str) → object
__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__len__

Return len(self).

__lt__

Return self<value.

__module__ = 'schrodinger.application.bioluminate.ssv.viewer'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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.

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 and successBlastCallback.

runClustal(ignore_selection=False)

Runs Clustal alignment and updates self.

runPfam()

Runs Pfam simulation and incorporates the results.

runPredictors(predictor_list)

Runs a specified residue-level property predictors.

runSSP()

Runs secondary structure prediction and incorporates the results.

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

Saves sequences to a file.

Parameters:file_name (str) – name of the output file
Return type:bool
Returns:True if file successfully saved, False otherwise.
saveGeometry(self) → QByteArray
saveImage(file_name, save_all=True, format='PNG', custom_width=None, custom_height=None)

Saves current view to a PNG image file.

saveProject(file_name, auto_save=False)

Saves current project to an external file.

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

Shows all sequences.

showBlastResults()

Displays BLAST results dialog.

showColumns()

Shows all hidden columns.

showCompareSequencesDialog()

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

showEvent(event)

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

showFullScreen(self)
showJobLog()

Displays a job log window.

showJobSettings()

Displays a job settings dialog.

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

splitterMoved(self, 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