schrodinger.application.msv.gui.msv_widget module

schrodinger.application.msv.gui.msv_widget.format_seq_name_with_chain(seq, include_chain)

Return a name identifying the sequence, with the chain name optionally in parentheses

Parameters

• seq (sequence.Sequence) – The sequence to format

• include_chain (bool) – Whether to include the chain in the name

Returns

A formatted name to identify the sequence

Return type

str

schrodinger.application.msv.gui.msv_widget.prompt_if_seqs_hidden(func, self, *args, **kwargs)

Decorator that shows a dialog and skips the function if the widget has hidden seqs

class schrodinger.application.msv.gui.msv_widget.MsvTaskQueue(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.tasks.queue.TaskQueue

description: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

AUTO_TASKDIR = 1

CMDLINE = 1

DEFAULT_TASKDIR_SETTING = None

DONE = 3

DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

FAILED = 2

GUI = 2

INTERRUPT_ENABLED = False

RUNNING = 1

TEMP_TASKDIR = 2

WAITING = 0

__init__(*args, **kwargs)

addFuncToGroup(func, group=None, order=None)

Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.

The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.

Parameters

• func – the function to add

• group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.

• order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.

addPostprocessor(func, order=0)

Adds a postproceessor function to this task instance. If the function has been decorated with @postprocessor, the order specified by the decorator will be used.

Parameters

• func (typing.Callable) – the function to add

• order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.

addPreprocessor(func, order=None)

Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.

Parameters

• func – the function to add

• order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.

classmethod addSubParam(name, param, update_owner=True)

addTask(task)

blockSignals(self, bool) → bool

block_signal_propagation()

calling_context

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

childEvent(self, QChildEvent)

children(self) → List[QObject]

classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue(*args, **kwargs)

deleteLater(self)

descriptionChanged

descriptionReplaced

destroyed

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

disconnect(QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

failure_info

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

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]

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

Return type

cls

classmethod fromJsonFilename(filename)

classmethod fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam(*args, **kwargs)

getAddedFuncs(group=None)

getDebugString()

getFuncGroup(group=None)

Retrieve the functions belonging to the specified group.

Parameters

group (FuncGroupMarker) – the group marker

Returns

the functions in the specified group, in order

Return type

list

classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(*args, **kwargs)

classmethod getParamValue(*args, **kwargs)

classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters

name (str) – The name of the subparam to get the value for.

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTaskDir()

Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file in the taskdir.

getTasks()

Return all tasks in the queue.

Return type

tuple[tasks.AbstractTask]

getTypeHint()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

guard()

Context manager that saves any Exception raised inside

static guard_method(func)

inherits(self, str) → bool

initAbstract()

initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: parameters.CompoundParam

input: parameters.CompoundParam

All CompoundParam instances are automatically serializable if their subparams are serializable. To serialize and deserialize, use the schrodinger json module:

from schrodinger.models import json
class Coord(parameters.CompoundParam):
    x: int
    y: int

c1 = Coord(x=1, y=2)
c1_string = json.dumps(c1)
c2 = json.loads(c1_string, DataClass=Coord)
assert c1 == c2

inputChanged

inputReplaced

installEventFilter(self, QObject)

classmethod isAbstract()

Whether the param is an “abstract” param.

isDebugEnabled()

isDefault(*args, **kwargs)

isInterruptionRequested()

isRunning()

isSignalConnected(self, QMetaMethod) → bool

isStartable()

isWidgetType(self) → bool

isWindowType(self) → bool

kill()

Implementations are responsible for immediately stopping the task. No threads or processes should be running after this method is complete.

This method should be called sparingly since in many contexts the task will be forced to terminate without a chance to clean up or free resources.

killTimer(self, int)

mainDone

max_progress: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

max_progressChanged

max_progressReplaced

max_running_tasks: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

max_running_tasksChanged

max_running_tasksReplaced

metaObject(self) → QMetaObject

moveToThread(self, QThread)

name: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

nameChanged

nameReplaced

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

output: parameters.CompoundParam

All CompoundParam instances are automatically serializable if their subparams are serializable. To serialize and deserialize, use the schrodinger json module:

from schrodinger.models import json
class Coord(parameters.CompoundParam):
    x: int
    y: int

c1 = Coord(x=1, y=2)
c1_string = json.dumps(c1)
c2 = json.loads(c1_string, DataClass=Coord)
assert c1 == c2

outputChanged

outputReplaced

classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'

parent(self) → QObject

postprocessors()

Returns

A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()

Return type

list[typing.Callable]

preprocessors()

Returns

A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)

printDebug(*args)

processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)

The return value of the result_callback determines whether processing will proceeed to the next function.

Parameters

• chain (FuncChainDecorator) – which chain to process

• result_callback – the callback that will get called with the result of each function in the chain

Returns

a list of the results from the functions

progress: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

progressChanged

progressReplaced

progress_string: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

progress_stringChanged

progress_stringReplaced

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.

queueDone

queuedTaskFinished

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

replicate()

Create a new task with the same input and settings (but no output)

requestInterruption()

Request the task to stop.

To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included, INTERRUPT_ENABLED should be set to True.

reset(*args, **kwargs)

run()

classmethod runFromCmdLine()

runPreprocessing(callback=None, calling_context=None)

Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.

This method is “final” so that all preprocessing logic will be enclosed in the try/finally block.

Parameters

• callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor

• calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.

sender(self) → QObject

senderSignalIndex(self) → int

setObjectName(self, str)

classmethod setParamValue(*args, **kwargs)

setParent(self, QObject)

setProperty(self, str, Any) → bool

classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6

Parameters

• param1 – The first abstract param to keep synced

• param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setUpMain()

setValue(*args, **kwargs)

signalsBlocked(self) → bool

skip_eq_check()

specifyTaskDir(taskdir_spec)

Specify the taskdir creation behavior. Use one of the following options:

A directory name (string). This may be a relative or absolute path

None - no taskdir is requested. The task will use the CWD as its taskdir

AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.

TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.

Parameters

taskdir_spec – one of the four options listed above

start(skip_preprocessing=False)

This is the main method for starting a task. Start will check if a task is not already running, run preprocessing, and then run the task.

Failures in preprocessing will interrupt the task start, and the task will never enter the RUNNING state.

Parameters

skip_preprocessing (bool) – whether to skip preprocessing. This can be useful if preprocessing was already performed prior to calling start.

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>

status: Status

statusChanged

statusReplaced

taskDirSetting()

Returns the taskdir spec. See specifyTaskDir() for details.

taskDone

taskFailed

taskStarted

thread(self) → QThread

timerEvent(self, QTimerEvent)

toDict(*args, **kwargs)

toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns

A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders

tr(self, str, disambiguation: str = None, n: int = - 1) → str

valueChanged

wait(timeout=None)

Block until the task is finished executing or timeout seconds have passed.

Warning

This should not be called directly from GUI code - see PANEL-18317. It is safe to call inside a subprocess or job. Run git grep "task.wait(" to see safe examples annotated with “# OK”.

Parameters

timeout (NoneType or int) – Amount of time in seconds to wait before timing out. If None or a negative number, this method will wait until the task is finished.

class schrodinger.application.msv.gui.msv_widget.AbstractMsvWidget(parent=None, struc_model=None, *, undo_stack)

Bases: schrodinger.models.mappers.MapperMixin, schrodinger.ui.qt.basewidgets.BaseWidget

Acts as a controller/container for a ProteinAlignment, the viewmodel proxy stacks that wrap it, and the views required to present these proxy stacks.

Each tab in the MSV contains a different instance of an MSV Widget.

Variables

• residueHovered – Signal emitted when a residue cell is hovered

• residueUnhovered – Signal emitted when a residue cell is unhovered

• resHighlightStatusChanged – Signal emitted when residue highlighting changes. Emitted with whether any residues are highlighted.

• renameSequenceRequested – A signal emitted to notify listeners to open the rename sequence dialog

• taskStarted – Signal emitted when a task is started. Task types should have a description defined in toolbar.TaskStatusBar.PRETTY_TASK_NAMES.

model_class

alias of schrodinger.application.msv.gui.gui_models.PageModel

duplicateIntoNewTabRequested

translateIntoNewTabRequested

residueHovered

residueUnhovered

openColorPanelRequested

resHighlightStatusChanged

editToolbarUpdateRequested

renameSequenceRequested

taskStarted

__init__(parent=None, struc_model=None, *, undo_stack)

Parameters

• parent (QtWidgets.QWidget) – The Qt parent

• struc_model (structure_model.StructureModel) – The structure model to use when interacting with sequences associated with three-dimensional structures. If None, a new structure model will be created.

• undo_stack (schrodinger.application.msv.command.UndoStack) – The undo stack to use.

initSetOptions()

Suggested subclass use: set instance variables, excluding layouts and subwidgets. Also use here to (optionally) apply the legacy stylesheet spacing settings (PANEL-19101).

initSetUp()

Creates widget from ui and stores it ui_widget.

Suggested subclass use: create and initialize subwidgets, and connect signals.

initLayOut()

@overrides: widgetmixins.InitMixin

onVScrollBarRangeChanged(_, max_)

When the vertical scrollbar is disabled, (i.e. the min and max are 0) style it to be mostly invisible.

setModel(model)

Sets the model object for the mapper. Disconnects the old model, if one is set, and connects the new model. Pass in None to have no model set.

Parameters

model – the model instance or None

getSignalsAndSlots(model)

Override this method to specify signal and slot pairs that need to be connected/disconnected whenever the model instance is switched using setModel. The model instance is provided as an argument so that instance-specific signals can be used, but any pairs of signals and slots may be returned from this method.

Returns

a list of 2-tuples where each tuple is a signal, slot pair

getValidIdMap()

Get the valid id map for the currently selected sequences.

Returns

Map of valid PDB IDs to their source sequence

Return type

dict(str: sequence.Sequence)

updateGetStructureLinkSeq()

Update if getting the structure from PDB action is enabled in the view.

property options_model

property image_export_dialog

Delay instantiation of the image export dialog until it is needed to prevent unnecessary file handles from being opened

Returns

the image export dialog

Return type

dialogs.MSVImageExportDialog

property seq_export_dialog

Delay instantiation of the image export dialog until it is needed to prevent unnecessary file handles from being opened

Returns

the image export dialog

Return type

dialogs.MSVSequenceExportDialog

openPropertyDialog()

Show the dialog that controls which properties are shown in the alignment metrics view

setStructureModel(model=None)

getShownSplitSequences()

Return the currently shown single-chain sequences in the order they appear in the alignment

Return type

tuple

getSelectedSequences()

Return a list of the currently selected sequences in the order they appear in the alignment

Returns

list of selected sequences

Return type

list of sequence.Sequence

setSelectedSequences(seqs)

Set sequence selection to the specified sequences.

Parameters

seqs (list of schrodinger.protein.sequence.Sequence) – List of sequences to select

selectAllSequences()

Select all sequences

deselectAllSequences()

Deselect all sequences

selectSequencesWithStructure()

Select all sequences with structures.

selectSequenceByIdentity()

Open a dialog to select sequences by identity.

invertSequenceSelection()

Invert sequence selection.

selectAntibodyHeavyChain()

selectAntibodyLightChain()

selectAllResidues()

Selects all residues

deselectAllResidues()

Deselects all residues

selectResiduesWithStructure()

Selects all residues with structure

selectAntibodyCDR()

Select residues with Antibody CDR.

selectColsWithStructure()

Select all columns that contain only structured residues.

selectBindingSites()

Select residues with binding site contacts.

selectProteinInterface()

Select the protein interface.

deselectGaps()

invertResSelection()

Invert the selection

deleteRedundantSeqs()

Show the dialog for defining and removing redundant sequences

deleteAllPredictions()

deleteAnnsFromAll()

Delete selected annotations from all sequences.

clearAnnotations()

Hide all selected annotations. Does not affect predicted annotations.

resetPick(pick_mode)

Set the default pick for the specified pick mode

clearConstraints()

updateCanUnlinkSequences()

updateDeleteSequencesEnabled()

updateMoveSequencesEnabled()

updateSetAsRefEnabled()

Enable/disable the menu model for Set As Reference Sequence

updateRenameSeqEnabled()

updateDuplicateSeqOptionsEnabled()

updateSelectMenuEnabled()

updateSelectProteinInterfaceMenuEnabled()

updateExpandEnabled()

updateAnchorSelectionEnabled()

updateRemoveHighlightsEnabled()

updateHideColumnsEnabled()

updateAlignSelectedSeqsEnabled()

generatePfam()

generatePredictionAnnotation(anno)

Generate predictions for the given prediction annotation. anno should be a key in PRED_ANNO_TO_PRED_FUNC.

generateAllPredictions()

undo()

Call undo on the undo stack

redo()

Call redo on the undo stack

resetUndoStack()

Reset the undo stack

This needs to be called when we perform an operation that gets tangled up with Maestro’s single step undo, so that permitting an undo from msv would result in data corruption.

anchorSelection()

Anchors all unanchored residues in the selection

clearAnchored()

Removes anchors from all anchored residues in the selection

getAlignment()

Returns the widget’s alignment instance

Return type

schrodinger.protein.alignment.BaseAlignment

Returns

The widget’s alignment

importSeq(seq, index=None)

Adds a given sequence to the widget’s alignment and align if the widget already had one or more sequences

Parameters

• seq (schrodinger.protein.sequence.ProteinSequence) – The sequence to add

• index (int or None) – Index to import the seq at

importSeqs(seqs, index=None, replace_selection=True)

Add sequences to the widget’s alignment and align if the widget already had one or more sequences.

Warning

Avoid calling this method from unittests as it adds a maestro test-time dependency

Parameters

• seqs (iterable(schrodinger.protein.sequence.ProteinSequence)) – Sequences to add

• index (int or None) – Index to import the seqs at (must be 1 or greater)

removeSelectedSeqs()

Remove the currently selected sequences from the alignment.

removeSequences(seqs)

Remove the specified sequences. Displays the new reference sequence in case it is hidden.

Parameters

seqs (list(sequence.Sequence)) – List of sequences to be removed

setSelectedSeqAsReference()

Set the selected sequence as the reference sequence. If more than one sequence is selected, no reference sequence will be set. Restore the expanded state of each sequence afterwards, because it will be reset after the reordering of the rows.

selectResForSeqs()

Select all residues in the alignment for the selected sequences

deselectResForSeqs()

Clears the selection of residues for the selected sequences.

blastSelectedSeq()

Set selected sequence as reference sequence and open BLAST search dialog.

expandSelectionAlongCols()

Expand selection based on current residue selection to include all residues in their columns.

expandSelectionReferenceOnly()

Select column residues for all columns that have a non-gap reference

selectIdentityColumns()

Select the residues in the identity columns of the alignment

selectAlignedResidues()

Selects residues in columns containing no gaps.

openBlastSearchDialog()

Implement sequence-type-specific BLAST dialog in child classes

moveSelectedSequences(direction)

Move the currently selected sequences in the specified direction.

Will prompt the user if there are hidden seqs and the direction is Up or Down.

Parameters

direction (viewconstants.Direction) – Direction to move items.

Raises

• ValueError – Invalid value of direction.

• IndexError – seq_list is not a subset of self.

classmethod moveItems(all_items, sel_items, direction)

Move the specified items in the specified direction.

Parameters

• all_items (list) – List of unique items.

• sel_items (list) – Items to move; must be a subset of all_items.

• direction (viewconstants.Direction) – Direction to move items.

Returns

Reordered items

Return type

list

Raises

ValueError – Invalid value of direction or sel_items is not a subset of all_items.

getColorScheme()

getShownRowTypes()

Returns a list of enums representing the shown row types

Return type

list

Returns

A list of enums

rowWrap()

Indicates whether rows are currently wrapped

Return type

bool

Returns

Whether the rows are currently wrapped

groupedByType()

Indicates whether rows are grouped by type

Return type

bool

Returns

Whether the rows are currently grouped by type

updateColorsEnabled()

Set whether to color all sequences from the options model

updateSeqColorScheme()

Set the sequence color scheme from the options model.

showColorSchemeEditor()

setSequenceExpansionState(sequences=None, expand=True)

Set the expansion state for the given (or all shown) sequences.

Parameters

• sequences (list(Sequence)) – Sequences to expand or collapse. If None, use all shown sequences.

• expand (bool) – Whether to expand the sequences

translateSelectedSequences()

Translate the selected nucleic acid sequences

translateSeqsInPlace(seqs)

Translate the given sequences in place.

Parameters

seqs (iterable[sequence.NucleicAcidSequence]) – The sequencs to translate

applyColorScheme(scheme)

Set the sequence row color scheme.

Parameters

scheme – The color scheme to be applied.

Type

color.AbstractRowColorScheme

setSelectedResColor(color)

Set the highlight color of the selected residues and enable colors

clearAllHighlights()

updateRowWrap()

Set the row wrapping on the widget

sortBy(sort_by, reverse=False)

Sort the alignment by the specified criteria.

Parameters

• sort_by (viewconstants.SortTypes) – The criterion to sort on

• reverse – Whether to sort in reverse (descending) order.

saveImage()

Saves multiple sequence alignment as an image file, by default, exports image of the entire alignment.

getLogoView()

Return an alignment view which contains the rulers and sequence logo.

Returns

the logo view

Return type

view.LogoAlignmentView

timeScrolling(only_horizontal=False, print_to_stdout=True)

Scroll the alignment and print how long it takes to the terminal.

Parameters

• only_horizontal (bool) – If True, the alignment will only be scrolled horizontally. If False, the alignment will be scrolled both vertically and horizontally.

• print_to_stdout (bool) – Whether to print a message when scrolling is starting and ending.

Returns

The time (in seconds) to scroll the alignment.

Return type

float

timeScrollingByPage()

Scroll the alignment and print how long it takes to the terminal. Scrolling is only done downwards and rightwards so that no cached data is used.

profileScrolling()

Scroll the alignment while recording profiling data. Returns immediately.

profileScrollingBlocking(only_horizontal=False, print_to_stdout=True, filename=None)

Scroll the alignment while recording profiling data. Returns when scrolling is complete.

Parameters

• only_horizontal (bool) – If True, the alignment will only be scrolled horizontally. If False, the alignment will be scrolled both vertically and horizontally.

• print_to_stdout (bool) – Whether to print the filename, the measured time, and a message when scrolling is starting and ending.

• filename (str or None) – The file to save profiling data to. If not given, a filename will be generated using the current date and time.

Returns

The time (in seconds) to scroll the alignment.

Return type

float

profileScrollingByPage()

Scroll the alignment while recording profiling data. Scrolling is only done downwards and rightwards so that no cached data is used.

onWorkspaceColorsChanged()

pullWorkspaceColors()

Update the current color scheme with colors from the workspace. This does not modify the options model.

applyColorsToWorkspace(all_atoms=False)

Update the colors in the workspace with colors from the MSV.

Parameters

all_atoms (bool) – Whether to color all atoms or just carbons

loadPdbs(pdb_paths, index=None)

Loads a pdb file into the widget. This will load the PDB into the workspace for all widgets. (See comments on MSV-1326.) If an index is specified, sequences will be loaded at that index. Index cannot be specified for Workspace tab.

Parameters

• pdb_path (str) – Path to the pdb file

• index (int or None) – Index to insert the sequences at. Cannot be specified for Workspace widget.

Raise

ValueError if index is specified for Workspace widget.

importIncluded(replace_selection=True)

Import all sequences that are included in the Maestro workspace.

importSelected()

Import all sequences that are selected in the Maestro project table.

getReferenceSeq()

Helper function that returns the reference sequence.

Returns

reference sequence of the underlying alignment

Return type

Sequence

isWorkspace()

Returns

Whether this widget contains an alignment that is always kept in sync with the Maestro workspace.

Return type

bool

setLightMode(enable)

Enable or disable lightmode on the widget’s views and model

setEditMode(enable)

Enable or disable edit mode.

Parameters

enable (bool) – Whether to enable edit mode.

insertGapsToLeftOfSelection()

deleteSelectedGaps()

copySelectedSeqs()

Returns a dictionary of new copies of each selected sequence mapped to the sequence it was copied from.

Returns

Dictionary of new sequence copies mapped to their source sequence

Return type

dict

duplicateAtBottom()

Duplicate selected sequences and add at bottom

duplicateAtTop()

Duplicate selected sequences and add at top

duplicateAsRef()

Duplicate selected sequence and make reference seq

duplicateInPlace()

Duplicate selected sequences and add in place

insertResidues()

deleteGapOnlyColumns()

Delete all columns in the alignment comprised of only gaps

copySelection()

deleteSelection()

changeResidues()

replaceSelection()

replaceSelectionWithGaps()

hideSelectedSeqs()

showWorkspaceSequences()

showAllSeqs()

enableFindSequence()

Enable sequence filtering on the model

APPLY_LEGACY_STYLESHEET = True

APPLY_PANELX_STYLESHEET = False

class BtnPos(value)

Bases: enum.IntEnum

An enumeration.

Left = 0

Middle = 1

Right = 2

DrawChildren = 2

DrawWindowBackground = 1

IgnoreMask = 4

class PaintDeviceMetric

Bases: int

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

class RenderFlags

class RenderFlags(Union[QWidget.RenderFlags, QWidget.RenderFlag]) → None

class RenderFlags(QWidget.RenderFlags) → None

Bases: sip.simplewrapper

__init__(*args, **kwargs)

SHOW_AS_WINDOW = False

class StdBtn(value)

Bases: enum.IntEnum

An enumeration.

Ok = 0

Cancel = 1

Reset = 2

Help = 3

acceptDrops(self) → bool

property accepted

accessibleDescription(self) → str

accessibleName(self) → str

actionEvent(self, QActionEvent)

actions(self) → List[QAction]

activateWindow(self)

addAction(self, QAction)

addActions(self, Iterable[QAction])

adjustSize(self)

autoFillBackground(self) → bool

backgroundRole(self) → QPalette.ColorRole

baseSize(self) → QSize

blockSignals(self, bool) → bool

changeEvent(self, QEvent)

childAt(self, QPoint) → QWidget

AbstractMsvWidget.childAt(self, int, int) -> QWidget

childEvent(self, QChildEvent)

children(self) → List[QObject]

childrenRect(self) → QRect

childrenRegion(self) → QRegion

clearFocus(self)

clearMask(self)

close(self) → bool

closeEvent(event)

Ensures proper handling of OK, Cancel, and [X] button clicks

colorCount(self) → int

connectNotify(self, QMetaMethod)

contentsMargins(self) → QMargins

contentsRect(self) → QRect

contextMenuEvent(self, QContextMenuEvent)

contextMenuPolicy(self) → Qt.ContextMenuPolicy

create(self, window: PyQt5.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)

debug()

defineMappings()

Override this in the subclass to define mappings. Should return a list of tuples [(<target>, <param>)]. Targets can be:

1. a basic widget, like QLineEdit or QComboBox

2. a custom object that inherits MapperMixin or TargetMixin

3. a TargetSpec instance

4. a slot

For common widgets, standard signals and getter/setter methods will be used, as defined in mappers._get_default_access_names().

For more fine-grained custom control, instantiate a TargetSpec object, which allows custom setters, getters, and signals to be specified.

Supplying a slot as the first element of the tuple is equivalent to providing TargetSpec(slot=my_slot).

Note that all target slots are triggered on setModel() as well as in response to the specified signal.

The param is an abstract param reference, e.g. MyModel.my_param.

Example:

def defineMappings(self):
    combo = self.style_combo
    return [(self.name_le, MyModel.name),
            (TargetSpec(combo,
                    getter=combo.currentText,
                    setter=combo.setCurrentText), MyModel.style),
            (self.coord_widget, MyModel.coord),
            (self._onASLTextChanged, MyModel.asl_text)]

deleteLater(self)

depth(self) → int

destroy(self, destroyWindow: bool = True, destroySubWindows: bool = True)

destroyed

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

devType(self) → int

devicePixelRatio(self) → int

devicePixelRatioF(self) → float

devicePixelRatioFScale() → float

disconnect(QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, QMetaMethod)

dragEnterEvent(self, QDragEnterEvent)

dragLeaveEvent(self, QDragLeaveEvent)

dragMoveEvent(self, QDragMoveEvent)

dropEvent(self, QDropEvent)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

effectiveWinId(self) → PyQt5.sip.voidptr

ensurePolished(self)

enterEvent(self, QEvent)

error(*args, **kwargs)

Shows a popup error message box. For parameter documentation see messagebox.MessageBox.

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

find(PyQt5.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

forgetMessageBoxResponse(key)

Forgets any previously saved response that was stored via a save_response_key.

Parameters

key – the key for the response to forget

frameGeometry(self) → QRect

frameSize(self) → QSize

geometry(self) → QRect

getContentsMargins(self) → Tuple[int, int, int, int]

getModel()

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]) → None

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)

info(*args, **kwargs)

Shows a popup information message box. For parameter documentation see messagebox.MessageBox.

inherits(self, str) → bool

initFinalize()

Suggested subclass use: perform any remaining initialization.

initPainter(self, QPainter)

initSetDefaults()

@overrides: widgetmixins.InitMixin

inputMethodEvent(self, QInputMethodEvent)

inputMethodHints(self) → Qt.InputMethodHints

inputMethodQuery(self, Qt.InputMethodQuery) → Any

AbstractMsvWidget.insertAction(self, QAction, QAction)

insertActions(self, QAction, Iterable[QAction])

installEventFilter(self, QObject)

isActiveWindow(self) → bool

isAncestorOf(self, QWidget) → 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)

locale(self) → QLocale

logicalDpiX(self) → int

logicalDpiY(self) → int

lower(self)

makeInitialModel()

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

mappedParams()

Return a list of the abstract params that are mapped to.

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

property model

mouseDoubleClickEvent(self, QMouseEvent)

mouseGrabber() → QWidget

mouseMoveEvent(self, QMouseEvent)

mousePressEvent(self, QMouseEvent)

mouseReleaseEvent(self, QMouseEvent)

move(self, QPoint)

AbstractMsvWidget.move(self, int, int) -> None

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.

question(*args, **kwargs)

Shows a popup question message box. For parameter documentation see messagebox.QuestionMessageBox.

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.RenderFlag.DrawWindowBackground | QWidget.RenderFlag.DrawChildren))

render(self, QPainter, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.RenderFlag.DrawWindowBackground | QWidget.RenderFlag.DrawChildren)) → None

repaint(self)

AbstractMsvWidget.repaint(self, int, int, int, int) -> None

repaint(self, QRect) → None

repaint(self, QRegion) → None

reportValidation(results)

Present validation messages to the user. This is an implmentation of the ValidationMixin interface and does not need to be called directly.

This method assumes that error and question methods have been defined in the subclass, as in e.g. widget_mixins.MessageBoxMixin.

Parameters

results (validation.ValidationResults) – Set of validation results generated by validate

Returns

if True, there were no validation errors and the user decided to continue despite any warnings. If False, there was at least one validation error or the user decided to abort when faced with a warning.

resetMappedParams()

resize(self, QSize)

AbstractMsvWidget.resize(self, int, int) -> None

resizeEvent(self, QResizeEvent)

restoreGeometry(self, Union[QByteArray, bytes, bytearray]) → bool

run(blocking=False, modal=False, finished_callback=None)

Show this widget, while optionally blocking, making the widget window modal, and registering a callback for when the widget is closed again.

Parameters

• blocking (bool) – if True, block progress in the calling method until the widget is closed again.

• modal (bool) – if True, open this widget as window modal. Otherwise, open this widget as nonmodal.

• finished_callback (a callable object) – an object that will be called with no arguments when this widget is closed.

runAllSlots()

runValidation(silent=False, validate_children=True, stop_on_fail=True)

Runs validation and reports the results (unless run silently).

Parameters

• silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.

• validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.

• stop_on_fail (bool) – stop validation when first failure is encountered

Returns

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type

ValidationResults or bool

saveGeometry(self) → QByteArray

AbstractMsvWidget.scroll(self, int, int)

AbstractMsvWidget.scroll(self, int, int, QRect) -> None

sender(self) → QObject

senderSignalIndex(self) → int

setAcceptDrops(self, bool)

setAccessibleDescription(self, str)

setAccessibleName(self, str)

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

setAutoFillBackground(self, bool)

setBackgroundRole(self, QPalette.ColorRole)

AbstractMsvWidget.setBaseSize(self, int, int)

setBaseSize(self, QSize) → None

AbstractMsvWidget.setContentsMargins(self, int, int, int, int)

setContentsMargins(self, QMargins) → None

setContextMenuPolicy(self, Qt.ContextMenuPolicy)

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

setDefaults()

@overrides: af2.App

setDisabled(self, bool)

setEnabled(self, bool)

setFixedHeight(self, int)

setFixedSize(self, QSize)

AbstractMsvWidget.setFixedSize(self, int, int) -> None

setFixedWidth(self, int)

setFocus(self)

setFocus(self, Qt.FocusReason) → None

setFocusPolicy(self, Qt.FocusPolicy)

setFocusProxy(self, QWidget)

setFont(self, QFont)

setForegroundRole(self, QPalette.ColorRole)

setGeometry(self, QRect)

AbstractMsvWidget.setGeometry(self, int, int, int, int) -> None

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) → None

setMaximumHeight(self, int)

AbstractMsvWidget.setMaximumSize(self, int, int)

setMaximumSize(self, QSize) → None

setMaximumWidth(self, int)

setMinimumHeight(self, int)

AbstractMsvWidget.setMinimumSize(self, int, int)

setMinimumSize(self, QSize) → None

setMinimumWidth(self, int)

setModelWithoutSlots(model)

This is called when this MapperMixin is a sub-widget of a parent MapperMixin. Since the slots will all be called at the end of the parent setModel, they shouldn’t be called during the sub-widget’s setModel.

setMouseTracking(self, bool)

setObjectName(self, str)

setPalette(self, QPalette)

setParent(self, QWidget)

setParent(self, QWidget, Union[Qt.WindowFlags, Qt.WindowType]) → None

setProperty(self, str, Any) → bool

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

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

AbstractMsvWidget.setSizeIncrement(self, int, int)

setSizeIncrement(self, QSize) → None

setSizePolicy(self, QSizePolicy)

setSizePolicy(self, QSizePolicy.Policy, QSizePolicy.Policy) → None

setStatusTip(self, str)

setStyle(self, QStyle)

setStyleSheet(self, str)

AbstractMsvWidget.setTabOrder(QWidget, QWidget)

setTabletTracking(self, bool)

setToolTip(self, str)

setToolTipDuration(self, int)

setUpdatesEnabled(self, bool)

setVisible(self, bool)

setWhatsThis(self, str)

setWidgetLayout()

Set the widget layout

setWindowFilePath(self, str)

setWindowFlag(self, Qt.WindowType, on: bool = True)

setWindowFlags(self, Union[Qt.WindowFlags, Qt.WindowType])

setWindowFlagsForRun()

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)

setting_model()

sharedPainter(self) → QPainter

show()

Override the show method to clear and previous value of self.accepted

showEvent(self, QShowEvent)

showFullScreen(self)

showMaximized(self)

showMessageBox(*args, **kwargs)

Shows a popup message box. For parameter documentation see messagebox.MessageBox.

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)

toolTip(self) → str

toolTipDuration(self) → int

tr(self, str, disambiguation: str = None, n: int = - 1) → str

ui_module = None

underMouse(self) → bool

ungrabGesture(self, Qt.GestureType)

unsetCursor(self)

unsetLayoutDirection(self)

unsetLocale(self)

update(self)

update(self, QRect) → None

update(self, QRegion) → None

AbstractMsvWidget.update(self, int, int, int, int) -> None

updateGeometry(self)

updateMicroFocus(self)

updatesEnabled(self) → bool

visibleRegion(self) → QRegion

warning(*args, **kwargs)

Shows a popup warning message box. For parameter documentation see messagebox.MessageBox.

whatsThis(self) → str

wheelEvent(self, QWheelEvent)

width(self) → int

widthMM(self) → int

winId(self) → PyQt5.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.msv.gui.msv_widget.ProteinAlignmentMsvWidget(parent=None, struc_model=None, *, undo_stack)

Bases: schrodinger.application.msv.gui.msv_widget.AbstractMsvWidget

Variables

• startBlastTaskRequested – Signal emitted to request running a blast task. The widget doesn’t start the task itself to avoid problems if the widget is deleted while the task is running.

• startPredictorBlastTaskRequested – Signal emitted to request running a blast task for predictors.

• proteinStructAlignResultsReady – Signal emitted when protein structure alignment results are ready. Emitted with a list of align.AbstractStructureAligner.Result namedtuples.

alignmentFinished

startBlastTaskRequested

startPredictorBlastTaskRequested

proteinStructAlignResultsReady

initSetUp()

Creates widget from ui and stores it ui_widget.

Suggested subclass use: create and initialize subwidgets, and connect signals.

initSetOptions()

Suggested subclass use: set instance variables, excluding layouts and subwidgets. Also use here to (optionally) apply the legacy stylesheet spacing settings (PANEL-19101).

defineMappings()

Override this in the subclass to define mappings. Should return a list of tuples [(<target>, <param>)]. Targets can be:

1. a basic widget, like QLineEdit or QComboBox

2. a custom object that inherits MapperMixin or TargetMixin

3. a TargetSpec instance

4. a slot

For common widgets, standard signals and getter/setter methods will be used, as defined in mappers._get_default_access_names().

For more fine-grained custom control, instantiate a TargetSpec object, which allows custom setters, getters, and signals to be specified.

Supplying a slot as the first element of the tuple is equivalent to providing TargetSpec(slot=my_slot).

Note that all target slots are triggered on setModel() as well as in response to the specified signal.

The param is an abstract param reference, e.g. MyModel.my_param.

Example:

def defineMappings(self):
    combo = self.style_combo
    return [(self.name_le, MyModel.name),
            (TargetSpec(combo,
                    getter=combo.currentText,
                    setter=combo.setCurrentText), MyModel.style),
            (self.coord_widget, MyModel.coord),
            (self._onASLTextChanged, MyModel.asl_text)]

getSignalsAndSlots(model)

Override this method to specify signal and slot pairs that need to be connected/disconnected whenever the model instance is switched using setModel. The model instance is provided as an argument so that instance-specific signals can be used, but any pairs of signals and slots may be returned from this method.

Returns

a list of 2-tuples where each tuple is a signal, slot pair

onQuickAlignRequested()

Align based on model settings

callAlignMethod(align_mode: schrodinger.infra.util.StructAlnMode)

Call appropriate Align method based the alignment mode.

invokeProfileAlignment()

runProfileAlignment()

multipleAlignment(*, _start=None, _end=None)

Run multiple sequence alignment.

_start and _end are private implementation params and not part of the public API (will be ignored if passed)

optimizeAlignment(target_seq, template_seq, ligand_asl=None, residue_asl=None, radius=None)

updateWorkspaceSelection()

Apply residue selection from this widget to the Maestro workspace. This will remove residue selection for any workspace entries without a linked sequence and will update residue selection for any entries awaiting delayed sync. (Residue selection is not automatically synchronized for newly included entries until selection is changed in either the workspace or the MSV. This method will force that synchronization.)

invokePairwiseAlignment()

pairwiseAlignment(*, _start=None, _end=None)

Run pairwise sequence alignment using modified Needleman-Wunsch algorithm.

If residues are anchored, pairwise alignment with locked reference gaps will be performed instead. If no sequences are selected, the first non-reference sequence will be aligned to the reference sequence. If one or more sequences are selected, each selected non-reference sequence will be aligned to the reference sequence.

_start and _end are private implementation params and not part of the public API (will be ignored if passed)

mergedPairwiseAlignment(*, _start=None, _end=None)

Runs a pairwise alignment while preserving reference gaps.

_start and _end are private implementation params and not part of the public API (will be ignored if passed)

pairwiseAlignmentSecondaryStructure()

alignBySuperposition()

Align sequences by structure superposition.

The pairwise residue C-alpha distances are converted to a scoring matrix where a short distance is a high score and vice versa.

alignByResidueNumbers(*, _start=None, _end=None)

Align by residue numbers.

_start and _end are private implementation params and not part of the public API (will be ignored if passed)

superimposeStructures(show_panel=True)

Superimposes the workspace structures according to their sequence alignment in the MSV.

Parameters

show_panel (bool) – Whether to show the superimpose ASL panel

runStructureAlignment()

Runs protein structure alignment.

runBindingSiteAlignment()

Runs binding site alignment

exportSequences()

Exports sequences in FASTA format.

openBlastSearchDialog()

Opens Blast Search dialog.

hasBlastResults(for_ref_seq=False)

Return whether the blast task is done.

Parameters

for_ref_seq – Whether to require that the results are for the current reference seq

downloadBlastPDBs(pdb_ids)

movePattern(forward=True)

Scroll view to next or previous pattern instance.

Parameters

forward (bool) – whether to move pattern view forward

APPLY_LEGACY_STYLESHEET = True

APPLY_PANELX_STYLESHEET = False

class BtnPos(value)

Bases: enum.IntEnum

An enumeration.

Left = 0

Middle = 1

Right = 2

DrawChildren = 2

DrawWindowBackground = 1

IgnoreMask = 4

class PaintDeviceMetric

Bases: int

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

class RenderFlags

class RenderFlags(Union[QWidget.RenderFlags, QWidget.RenderFlag]) → None

class RenderFlags(QWidget.RenderFlags) → None

Bases: sip.simplewrapper

__init__(*args, **kwargs)

SHOW_AS_WINDOW = False

class StdBtn(value)

Bases: enum.IntEnum

An enumeration.

Ok = 0

Cancel = 1

Reset = 2

Help = 3

__init__(parent=None, struc_model=None, *, undo_stack)

Parameters

• parent (QtWidgets.QWidget) – The Qt parent

• struc_model (structure_model.StructureModel) – The structure model to use when interacting with sequences associated with three-dimensional structures. If None, a new structure model will be created.

• undo_stack (schrodinger.application.msv.command.UndoStack) – The undo stack to use.

acceptDrops(self) → bool

property accepted

accessibleDescription(self) → str

accessibleName(self) → str

actionEvent(self, QActionEvent)

actions(self) → List[QAction]

activateWindow(self)

addAction(self, QAction)

addActions(self, Iterable[QAction])

adjustSize(self)

anchorSelection()

Anchors all unanchored residues in the selection

applyColorScheme(scheme)

Set the sequence row color scheme.

Parameters

scheme – The color scheme to be applied.

Type

color.AbstractRowColorScheme

applyColorsToWorkspace(all_atoms=False)

Update the colors in the workspace with colors from the MSV.

Parameters

all_atoms (bool) – Whether to color all atoms or just carbons

autoFillBackground(self) → bool

backgroundRole(self) → QPalette.ColorRole

baseSize(self) → QSize

blastSelectedSeq()

Set selected sequence as reference sequence and open BLAST search dialog.

blockSignals(self, bool) → bool

changeEvent(self, QEvent)

changeResidues()

childAt(self, QPoint) → QWidget

ProteinAlignmentMsvWidget.childAt(self, int, int) -> QWidget

childEvent(self, QChildEvent)

children(self) → List[QObject]

childrenRect(self) → QRect

childrenRegion(self) → QRegion

clearAllHighlights()

clearAnchored()

Removes anchors from all anchored residues in the selection

clearAnnotations()

Hide all selected annotations. Does not affect predicted annotations.

clearConstraints()

clearFocus(self)

clearMask(self)

close(self) → bool

closeEvent(event)

Ensures proper handling of OK, Cancel, and [X] button clicks

colorCount(self) → int

connectNotify(self, QMetaMethod)

contentsMargins(self) → QMargins

contentsRect(self) → QRect

contextMenuEvent(self, QContextMenuEvent)

contextMenuPolicy(self) → Qt.ContextMenuPolicy

copySelectedSeqs()

Returns a dictionary of new copies of each selected sequence mapped to the sequence it was copied from.

Returns

Dictionary of new sequence copies mapped to their source sequence

Return type

dict

copySelection()

create(self, window: PyQt5.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)

debug()

deleteAllPredictions()

deleteAnnsFromAll()

Delete selected annotations from all sequences.

deleteGapOnlyColumns()

Delete all columns in the alignment comprised of only gaps

deleteLater(self)

deleteRedundantSeqs()

Show the dialog for defining and removing redundant sequences

deleteSelectedGaps()

deleteSelection()

depth(self) → int

deselectAllResidues()

Deselects all residues

deselectAllSequences()

Deselect all sequences

deselectGaps()

deselectResForSeqs()

Clears the selection of residues for the selected sequences.

destroy(self, destroyWindow: bool = True, destroySubWindows: bool = True)

destroyed

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

devType(self) → int

devicePixelRatio(self) → int

devicePixelRatioF(self) → float

devicePixelRatioFScale() → float

disconnect(QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, QMetaMethod)

dragEnterEvent(self, QDragEnterEvent)

dragLeaveEvent(self, QDragLeaveEvent)

dragMoveEvent(self, QDragMoveEvent)

dropEvent(self, QDropEvent)

dumpObjectInfo(self)

dumpObjectTree(self)

duplicateAsRef()

Duplicate selected sequence and make reference seq

duplicateAtBottom()

Duplicate selected sequences and add at bottom

duplicateAtTop()

Duplicate selected sequences and add at top

duplicateInPlace()

Duplicate selected sequences and add in place

duplicateIntoNewTabRequested

dynamicPropertyNames(self) → List[QByteArray]

editToolbarUpdateRequested

effectiveWinId(self) → PyQt5.sip.voidptr

enableFindSequence()

Enable sequence filtering on the model

ensurePolished(self)

enterEvent(self, QEvent)

error(*args, **kwargs)

Shows a popup error message box. For parameter documentation see messagebox.MessageBox.

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

expandSelectionAlongCols()

Expand selection based on current residue selection to include all residues in their columns.

expandSelectionReferenceOnly()

Select column residues for all columns that have a non-gap reference

find(PyQt5.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

forgetMessageBoxResponse(key)

Forgets any previously saved response that was stored via a save_response_key.

Parameters

key – the key for the response to forget

frameGeometry(self) → QRect

frameSize(self) → QSize

generateAllPredictions()

generatePfam()

generatePredictionAnnotation(anno)

Generate predictions for the given prediction annotation. anno should be a key in PRED_ANNO_TO_PRED_FUNC.

geometry(self) → QRect

getAlignment()

Returns the widget’s alignment instance

Return type

schrodinger.protein.alignment.BaseAlignment

Returns

The widget’s alignment

getColorScheme()

getContentsMargins(self) → Tuple[int, int, int, int]

getLogoView()

Return an alignment view which contains the rulers and sequence logo.

Returns

the logo view

Return type

view.LogoAlignmentView

getModel()

getReferenceSeq()

Helper function that returns the reference sequence.

Returns

reference sequence of the underlying alignment

Return type

Sequence

getSelectedSequences()

Return a list of the currently selected sequences in the order they appear in the alignment

Returns

list of selected sequences

Return type

list of sequence.Sequence

getShownRowTypes()

Returns a list of enums representing the shown row types

Return type

list

Returns

A list of enums

getShownSplitSequences()

Return the currently shown single-chain sequences in the order they appear in the alignment

Return type

tuple

getValidIdMap()

Get the valid id map for the currently selected sequences.

Returns

Map of valid PDB IDs to their source sequence

Return type

dict(str: sequence.Sequence)

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]) → None

grabShortcut(self, Union[QKeySequence, QKeySequence.StandardKey, str, int], context: Qt.ShortcutContext = Qt.WindowShortcut) → int

graphicsEffect(self) → QGraphicsEffect

graphicsProxyWidget(self) → QGraphicsProxyWidget

groupedByType()

Indicates whether rows are grouped by type

Return type

bool

Returns

Whether the rows are currently grouped by type

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)

hideSelectedSeqs()

property image_export_dialog

Delay instantiation of the image export dialog until it is needed to prevent unnecessary file handles from being opened

Returns

the image export dialog

Return type

dialogs.MSVImageExportDialog

importIncluded(replace_selection=True)

Import all sequences that are included in the Maestro workspace.

importSelected()

Import all sequences that are selected in the Maestro project table.

importSeq(seq, index=None)

Adds a given sequence to the widget’s alignment and align if the widget already had one or more sequences

Parameters

• seq (schrodinger.protein.sequence.ProteinSequence) – The sequence to add

• index (int or None) – Index to import the seq at

importSeqs(seqs, index=None, replace_selection=True)

Add sequences to the widget’s alignment and align if the widget already had one or more sequences.

Warning

Avoid calling this method from unittests as it adds a maestro test-time dependency

Parameters

• seqs (iterable(schrodinger.protein.sequence.ProteinSequence)) – Sequences to add

• index (int or None) – Index to import the seqs at (must be 1 or greater)

info(*args, **kwargs)

Shows a popup information message box. For parameter documentation see messagebox.MessageBox.

inherits(self, str) → bool

initFinalize()

Suggested subclass use: perform any remaining initialization.

initLayOut()

@overrides: widgetmixins.InitMixin

initPainter(self, QPainter)

initSetDefaults()

@overrides: widgetmixins.InitMixin

inputMethodEvent(self, QInputMethodEvent)

inputMethodHints(self) → Qt.InputMethodHints

inputMethodQuery(self, Qt.InputMethodQuery) → Any

ProteinAlignmentMsvWidget.insertAction(self, QAction, QAction)

insertActions(self, QAction, Iterable[QAction])

insertGapsToLeftOfSelection()

insertResidues()

installEventFilter(self, QObject)

invertResSelection()

Invert the selection

invertSequenceSelection()

Invert sequence selection.

isActiveWindow(self) → bool

isAncestorOf(self, QWidget) → 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

isWorkspace()

Returns

Whether this widget contains an alignment that is always kept in sync with the Maestro workspace.

Return type

bool

keyPressEvent(self, QKeyEvent)

keyReleaseEvent(self, QKeyEvent)

keyboardGrabber() → QWidget

killTimer(self, int)

layout(self) → QLayout

layoutDirection(self) → Qt.LayoutDirection

leaveEvent(self, QEvent)

loadPdbs(pdb_paths, index=None)

Loads a pdb file into the widget. This will load the PDB into the workspace for all widgets. (See comments on MSV-1326.) If an index is specified, sequences will be loaded at that index. Index cannot be specified for Workspace tab.

Parameters

• pdb_path (str) – Path to the pdb file

• index (int or None) – Index to insert the sequences at. Cannot be specified for Workspace widget.

Raise

ValueError if index is specified for Workspace widget.

locale(self) → QLocale

logicalDpiX(self) → int

logicalDpiY(self) → int

lower(self)

makeInitialModel()

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

mappedParams()

Return a list of the abstract params that are mapped to.

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

property model

model_class

alias of schrodinger.application.msv.gui.gui_models.PageModel

mouseDoubleClickEvent(self, QMouseEvent)

mouseGrabber() → QWidget

mouseMoveEvent(self, QMouseEvent)

mousePressEvent(self, QMouseEvent)

mouseReleaseEvent(self, QMouseEvent)

move(self, QPoint)

ProteinAlignmentMsvWidget.move(self, int, int) -> None

moveEvent(self, QMoveEvent)

classmethod moveItems(all_items, sel_items, direction)

Move the specified items in the specified direction.

Parameters

• all_items (list) – List of unique items.

• sel_items (list) – Items to move; must be a subset of all_items.

• direction (viewconstants.Direction) – Direction to move items.

Returns

Reordered items

Return type

list

Raises

ValueError – Invalid value of direction or sel_items is not a subset of all_items.

moveSelectedSequences(direction)

Move the currently selected sequences in the specified direction.

Will prompt the user if there are hidden seqs and the direction is Up or Down.

Parameters

direction (viewconstants.Direction) – Direction to move items.

Raises

• ValueError – Invalid value of direction.

• IndexError – seq_list is not a subset of self.

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]

onVScrollBarRangeChanged(_, max_)

When the vertical scrollbar is disabled, (i.e. the min and max are 0) style it to be mostly invisible.

onWorkspaceColorsChanged()

openColorPanelRequested

openPropertyDialog()

Show the dialog that controls which properties are shown in the alignment metrics view

property options_model

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

profileScrolling()

Scroll the alignment while recording profiling data. Returns immediately.

profileScrollingBlocking(only_horizontal=False, print_to_stdout=True, filename=None)

Scroll the alignment while recording profiling data. Returns when scrolling is complete.

Parameters

• only_horizontal (bool) – If True, the alignment will only be scrolled horizontally. If False, the alignment will be scrolled both vertically and horizontally.

• print_to_stdout (bool) – Whether to print the filename, the measured time, and a message when scrolling is starting and ending.

• filename (str or None) – The file to save profiling data to. If not given, a filename will be generated using the current date and time.

Returns

The time (in seconds) to scroll the alignment.

Return type

float

profileScrollingByPage()

Scroll the alignment while recording profiling data. Scrolling is only done downwards and rightwards so that no cached data is used.

property(self, str) → Any

pullWorkspaceColors()

Update the current color scheme with colors from the workspace. This does not modify the options model.

pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

question(*args, **kwargs)

Shows a popup question message box. For parameter documentation see messagebox.QuestionMessageBox.

raise_(self)

receivers(self, PYQT_SIGNAL) → int

rect(self) → QRect

redo()

Call redo on the undo stack

releaseKeyboard(self)

releaseMouse(self)

releaseShortcut(self, int)

removeAction(self, QAction)

removeEventFilter(self, QObject)

removeSelectedSeqs()

Remove the currently selected sequences from the alignment.

removeSequences(seqs)

Remove the specified sequences. Displays the new reference sequence in case it is hidden.

Parameters

seqs (list(sequence.Sequence)) – List of sequences to be removed

renameSequenceRequested

render(self, QPaintDevice, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.RenderFlag.DrawWindowBackground | QWidget.RenderFlag.DrawChildren))

render(self, QPainter, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.RenderFlag.DrawWindowBackground | QWidget.RenderFlag.DrawChildren)) → None

repaint(self)

ProteinAlignmentMsvWidget.repaint(self, int, int, int, int) -> None

repaint(self, QRect) → None

repaint(self, QRegion) → None

replaceSelection()

replaceSelectionWithGaps()

reportValidation(results)

Present validation messages to the user. This is an implmentation of the ValidationMixin interface and does not need to be called directly.

This method assumes that error and question methods have been defined in the subclass, as in e.g. widget_mixins.MessageBoxMixin.

Parameters

results (validation.ValidationResults) – Set of validation results generated by validate

Returns

if True, there were no validation errors and the user decided to continue despite any warnings. If False, there was at least one validation error or the user decided to abort when faced with a warning.

resHighlightStatusChanged

resetMappedParams()

resetPick(pick_mode)

Set the default pick for the specified pick mode

resetUndoStack()

Reset the undo stack

This needs to be called when we perform an operation that gets tangled up with Maestro’s single step undo, so that permitting an undo from msv would result in data corruption.

residueHovered

residueUnhovered

resize(self, QSize)

ProteinAlignmentMsvWidget.resize(self, int, int) -> None

resizeEvent(self, QResizeEvent)

restoreGeometry(self, Union[QByteArray, bytes, bytearray]) → bool

rowWrap()

Indicates whether rows are currently wrapped

Return type

bool

Returns

Whether the rows are currently wrapped

run(blocking=False, modal=False, finished_callback=None)

Show this widget, while optionally blocking, making the widget window modal, and registering a callback for when the widget is closed again.

Parameters

• blocking (bool) – if True, block progress in the calling method until the widget is closed again.

• modal (bool) – if True, open this widget as window modal. Otherwise, open this widget as nonmodal.

• finished_callback (a callable object) – an object that will be called with no arguments when this widget is closed.

runAllSlots()

runValidation(silent=False, validate_children=True, stop_on_fail=True)

Runs validation and reports the results (unless run silently).

Parameters

• silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.

• validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.

• stop_on_fail (bool) – stop validation when first failure is encountered

Returns

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type

ValidationResults or bool

saveGeometry(self) → QByteArray

saveImage()

Saves multiple sequence alignment as an image file, by default, exports image of the entire alignment.

ProteinAlignmentMsvWidget.scroll(self, int, int)

ProteinAlignmentMsvWidget.scroll(self, int, int, QRect) -> None

selectAlignedResidues()

Selects residues in columns containing no gaps.

selectAllResidues()

Selects all residues

selectAllSequences()

Select all sequences

selectAntibodyCDR()

Select residues with Antibody CDR.

selectAntibodyHeavyChain()

selectAntibodyLightChain()

selectBindingSites()

Select residues with binding site contacts.

selectColsWithStructure()

Select all columns that contain only structured residues.

selectIdentityColumns()

Select the residues in the identity columns of the alignment

selectProteinInterface()

Select the protein interface.

selectResForSeqs()

Select all residues in the alignment for the selected sequences

selectResiduesWithStructure()

Selects all residues with structure

selectSequenceByIdentity()

Open a dialog to select sequences by identity.

selectSequencesWithStructure()

Select all sequences with structures.

sender(self) → QObject

senderSignalIndex(self) → int

property seq_export_dialog

Delay instantiation of the image export dialog until it is needed to prevent unnecessary file handles from being opened

Returns

the image export dialog

Return type

dialogs.MSVSequenceExportDialog

setAcceptDrops(self, bool)

setAccessibleDescription(self, str)

setAccessibleName(self, str)

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

setAutoFillBackground(self, bool)

setBackgroundRole(self, QPalette.ColorRole)

ProteinAlignmentMsvWidget.setBaseSize(self, int, int)

setBaseSize(self, QSize) → None

ProteinAlignmentMsvWidget.setContentsMargins(self, int, int, int, int)

setContentsMargins(self, QMargins) → None

setContextMenuPolicy(self, Qt.ContextMenuPolicy)

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

setDefaults()

@overrides: af2.App

setDisabled(self, bool)

setEditMode(enable)

Enable or disable edit mode.

Parameters

enable (bool) – Whether to enable edit mode.

setEnabled(self, bool)

setFixedHeight(self, int)

setFixedSize(self, QSize)

ProteinAlignmentMsvWidget.setFixedSize(self, int, int) -> None

setFixedWidth(self, int)

setFocus(self)

setFocus(self, Qt.FocusReason) → None

setFocusPolicy(self, Qt.FocusPolicy)

setFocusProxy(self, QWidget)

setFont(self, QFont)

setForegroundRole(self, QPalette.ColorRole)

setGeometry(self, QRect)

ProteinAlignmentMsvWidget.setGeometry(self, int, int, int, int) -> None

setGraphicsEffect(self, QGraphicsEffect)

setHidden(self, bool)

setInputMethodHints(self, Union[Qt.InputMethodHints, Qt.InputMethodHint])

setLayout(self, QLayout)

setLayoutDirection(self, Qt.LayoutDirection)

setLightMode(enable)

Enable or disable lightmode on the widget’s views and model

setLocale(self, QLocale)

setMask(self, QBitmap)

setMask(self, QRegion) → None

setMaximumHeight(self, int)

ProteinAlignmentMsvWidget.setMaximumSize(self, int, int)

setMaximumSize(self, QSize) → None

setMaximumWidth(self, int)

setMinimumHeight(self, int)

ProteinAlignmentMsvWidget.setMinimumSize(self, int, int)

setMinimumSize(self, QSize) → None

setMinimumWidth(self, int)

setModel(model)

Sets the model object for the mapper. Disconnects the old model, if one is set, and connects the new model. Pass in None to have no model set.

Parameters

model – the model instance or None

setModelWithoutSlots(model)

This is called when this MapperMixin is a sub-widget of a parent MapperMixin. Since the slots will all be called at the end of the parent setModel, they shouldn’t be called during the sub-widget’s setModel.

setMouseTracking(self, bool)

setObjectName(self, str)

setPalette(self, QPalette)

setParent(self, QWidget)

setParent(self, QWidget, Union[Qt.WindowFlags, Qt.WindowType]) → None

setProperty(self, str, Any) → bool

setSelectedResColor(color)

Set the highlight color of the selected residues and enable colors

setSelectedSeqAsReference()

Set the selected sequence as the reference sequence. If more than one sequence is selected, no reference sequence will be set. Restore the expanded state of each sequence afterwards, because it will be reset after the reordering of the rows.

setSelectedSequences(seqs)

Set sequence selection to the specified sequences.

Parameters

seqs (list of schrodinger.protein.sequence.Sequence) – List of sequences to select

setSequenceExpansionState(sequences=None, expand=True)

Set the expansion state for the given (or all shown) sequences.

Parameters

• sequences (list(Sequence)) – Sequences to expand or collapse. If None, use all shown sequences.

• expand (bool) – Whether to expand the sequences

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

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

ProteinAlignmentMsvWidget.setSizeIncrement(self, int, int)

setSizeIncrement(self, QSize) → None

setSizePolicy(self, QSizePolicy)

setSizePolicy(self, QSizePolicy.Policy, QSizePolicy.Policy) → None

setStatusTip(self, str)

setStructureModel(model=None)

setStyle(self, QStyle)

setStyleSheet(self, str)

ProteinAlignmentMsvWidget.setTabOrder(QWidget, QWidget)

setTabletTracking(self, bool)

setToolTip(self, str)

setToolTipDuration(self, int)

setUpdatesEnabled(self, bool)

setVisible(self, bool)

setWhatsThis(self, str)

setWidgetLayout()

Set the widget layout

setWindowFilePath(self, str)

setWindowFlag(self, Qt.WindowType, on: bool = True)

setWindowFlags(self, Union[Qt.WindowFlags, Qt.WindowType])

setWindowFlagsForRun()

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)

setting_model()

sharedPainter(self) → QPainter

show()

Override the show method to clear and previous value of self.accepted

showAllSeqs()

showColorSchemeEditor()

showEvent(self, QShowEvent)

showFullScreen(self)

showMaximized(self)

showMessageBox(*args, **kwargs)

Shows a popup message box. For parameter documentation see messagebox.MessageBox.

showMinimized(self)

showNormal(self)

showWorkspaceSequences()

signalsBlocked(self) → bool

size(self) → QSize

sizeHint(self) → QSize

sizeIncrement(self) → QSize

sizePolicy(self) → QSizePolicy

sortBy(sort_by, reverse=False)

Sort the alignment by the specified criteria.

Parameters

• sort_by (viewconstants.SortTypes) – The criterion to sort on

• reverse – Whether to sort in reverse (descending) order.

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)

taskStarted

testAttribute(self, Qt.WidgetAttribute) → bool

thread(self) → QThread

timeScrolling(only_horizontal=False, print_to_stdout=True)

Scroll the alignment and print how long it takes to the terminal.

Parameters

• only_horizontal (bool) – If True, the alignment will only be scrolled horizontally. If False, the alignment will be scrolled both vertically and horizontally.

• print_to_stdout (bool) – Whether to print a message when scrolling is starting and ending.

Returns

The time (in seconds) to scroll the alignment.

Return type

float

timeScrollingByPage()

Scroll the alignment and print how long it takes to the terminal. Scrolling is only done downwards and rightwards so that no cached data is used.

timerEvent(self, QTimerEvent)

toolTip(self) → str

toolTipDuration(self) → int

tr(self, str, disambiguation: str = None, n: int = - 1) → str

translateIntoNewTabRequested

translateSelectedSequences()

Translate the selected nucleic acid sequences

translateSeqsInPlace(seqs)

Translate the given sequences in place.

Parameters

seqs (iterable[sequence.NucleicAcidSequence]) – The sequencs to translate

ui_module = None

underMouse(self) → bool

undo()

Call undo on the undo stack

ungrabGesture(self, Qt.GestureType)

unsetCursor(self)

unsetLayoutDirection(self)

unsetLocale(self)

update(self)

update(self, QRect) → None

update(self, QRegion) → None

ProteinAlignmentMsvWidget.update(self, int, int, int, int) -> None

updateAlignSelectedSeqsEnabled()

updateAnchorSelectionEnabled()

updateCanUnlinkSequences()

updateColorsEnabled()

Set whether to color all sequences from the options model

updateDeleteSequencesEnabled()

updateDuplicateSeqOptionsEnabled()

updateExpandEnabled()

updateGeometry(self)

updateGetStructureLinkSeq()

Update if getting the structure from PDB action is enabled in the view.

updateHideColumnsEnabled()

updateMicroFocus(self)

updateMoveSequencesEnabled()

updateRemoveHighlightsEnabled()

updateRenameSeqEnabled()

updateRowWrap()

Set the row wrapping on the widget

updateSelectMenuEnabled()

updateSelectProteinInterfaceMenuEnabled()

updateSeqColorScheme()

Set the sequence color scheme from the options model.

updateSetAsRefEnabled()

Enable/disable the menu model for Set As Reference Sequence

updatesEnabled(self) → bool

visibleRegion(self) → QRegion

warning(*args, **kwargs)

Shows a popup warning message box. For parameter documentation see messagebox.MessageBox.

whatsThis(self) → str

wheelEvent(self, QWheelEvent)

width(self) → int

widthMM(self) → int

winId(self) → PyQt5.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

schrodinger.application.msv.gui.msv_widget.check_if_can_retry_blast(dialog_parent, task, blast_local_only)

For a failed BLAST task, show the appropriate dialog.

• If the task was run remote, show “Remote BLAST failed” error

• If tasks can only run locally, show “Local BLAST failed error”

• If the task was run locally, ask whether to try Remote BLAST

Returns

Whether the task should be retried remote

Return type

bool

schrodinger.application.msv.gui.msv_widget.get_svg_renderer(widget)

Get a renderer that can paint a widget by means of svg onto a paint devices. This effectively vectorizes the image, allowing for very high resolutions to be used when drawing on the paint device.

Parameters

widget (QtWidgets.QWidget) – a widget that can be converted into an svg. This needs a render method

Returns

the svg renderer

Return type

QtSvg.QSvgRenderer

schrodinger.application.msv.gui.msv_widget.save_pdf(renderer, file_name)

Draw an image from the renderer to the given file name as a pdf

Parameters

• renderer (QtSvg.QSvgRenderer) – the renderer that will draw the image

• file_name (str) – the name of the file to write to

schrodinger.application.msv.gui.msv_widget.save_png(renderer, file_name, dpi)

Draw an image from the renderer to the given file name as a png

Parameters

• renderer (QtSvg.QSvgRenderer) – the renderer that will draw the image

• file_name (str) – the name of the file to write to

• dpi (int) – how many dpi to export to PNG