schrodinger.ui.sequencealignment.sequence_viewer module

This class implements a sequence viewer widget.

The sequence viewer widget is a QSplitter object that includes three child widgets: tree area, name area and sequence area.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.ui.sequencealignment.sequence_viewer.SequenceViewer(parent=None)

Bases: PyQt5.QtWidgets.QSplitter

The sequence viewer widget displays and manipulates sequences and associated data. The widget is a QSplitter that includes tree coupled areas: sequence area, name area and tree area.

__init__(parent=None)

tree_area

Create tree area widget

padded

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

undo_stack

State stack for undo/redo.

display_identity

Display percentange identity on a right side of the panel.

contents_changed

Update flags

cb_residue_selection_changed

Callbacks

job_settings

Global job settings

setPadded(padded)

Toggles alignment padding.

Parameters

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

setMouseAcross(enabled)

Toggles use mouse across rows mode.

Parameters

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

setBackgroundColor(color=(255, 255, 255))

Sets a background color.

Parameters

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

updateFontSize(size=None)

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

Parameters

size (int) – new font size

setWrapped(wrapped)

This method toggles sequence wrapping mode.

Parameters

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

hideSelectedSequences()

Hides all selected sequences.

deleteSelectedSequences()

Deletes all selected sequences.

Return type

bool

Returns

True if all sequences were removed

showAllSequences()

Shows all sequences.

fillGaps()

Fill a selected region with gaps.

removeGaps()

Removes all gaps.

deleteSelectedResidues()

Deletes all selected residues.

invertSelection()

Inverts residue selection.

deselectAll()

Deselects all residues.

selectAll()

Selects all residues.

minimizeAlignment()

Removes all gaps.

lockGaps()

Locks gaps.

unlockGaps()

Unlocks gaps.

selectAlignedBlocks()

Selects aligned blocks (the sequence regions without gaps).

selectStructureBlocks()

Selects blocks that have structure.

selectIdentities()

Selects identical residues in columns.

setHasTooltips(has_tooltips)

Toggles mouse hover tooltips.

Parameters

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

setHasHeaderRow(has_header_row)

Toggles header row.

Parameters

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

setHasRuler(has_ruler)

Toggles the ruler.

Parameters

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

deleteAnnotations()

Deletes all annotations.

deletePredictions()

Deletes all predictions.

loadFile(file_name, merge=False, replace=False, to_maestro=False, translate=False, new_list=None, maestro_include=True)

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

Note

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

Parameters

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

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

Saves sequences to a file.

Parameters

file_name (str) – name of the output file

Return type

bool

Returns

True if file successfully saved, False otherwise.

setColorMode(color_mode)

Colors sequences using a specified color mode.

Parameters

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

colorSequences(color=None)

Sets arbitrary color to the sequences.

propagateColors()

Propagates colors to Maestro workspace.

clearSequences()

Removes all sequences and updates the viewer.

expandAllSequences()

Expands all sequences.

collapseAllSequences()

Collapses all sequences.

addConsensus(toggle=False, update=True)

Adds a consensus annotation sequence.

addSymbols(toggle=False, update=True)

Adds a symbols sequence.

toggleHistory()

Toggles changes tracking feature.

resetHistory()

Toggles changes tracking feature.

addMeanHydrophobicity(toggle=False, update=True)

Adds a mean hydrophobicity annotation.

addMeanPI(toggle=False, update=True)

Adds a mean isoelectric point annotation.

addSequenceLogo(toggle=False, update=True)

Adds a sequence logo annotation.

zoomIn()

Increases zoom factor and updates sequence viewer contents.

zoomOut()

Decreases zoom factor and updates sequence viewer contents.

addAnnotation(annotation_type, remove=False)

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

Parameters

annotation_type (int) – Type of the annotation sequence.

addAllColorBlocks()

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

removeAllColorBlocks()

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

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

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

Note

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

Parameters

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

Type.update

bool

Param.update

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

updateStatusBar()

Updates bottom status bar.

setMode(mode)

Sets sequence viewer operation mode.

Note

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

Parameters

mode (int) – Sequence viewer mode.

getMode()

Gets current sequence viewer operational mode.

Return type

int

Returns

Current sequence viewer mode.

auxBorderWidth()

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

maxColumns(custom_width=None, custom_height=None, calculate_width=False)

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

Return type

int or tuple

Returns

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

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

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

runClustal(ignore_selection=False)

Runs Clustal alignment and updates self.

setPopupMenus(name_menu=None, sequence_menu=None, tree_menu=None)

Sets popup menu for name area widget.

Parameters

menu (QPopupMenu) – Name area popup menu.

findPattern(pattern)

Finds a specified PROSITE-like pattern in the sequences.

Parameters

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

undo()

Undoes the last operation.

redo()

Redoes previously undone operation.

runSSP()

Runs secondary structure prediction and incorporates the results.

runPfam()

Runs Pfam simulation and incorporates the results.

runBlast(failed_callback=None, ok_callback=None)

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

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

Parameters

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

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

• failed_callback – The callback to call when the job succeeds

See also failedBlastCallback and successBlastCallback.

blastFailedCallback(dialog, results_dialog, ok_callback)

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

blastOkCallback(results_dialog)

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

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

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

Parameters

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

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

Return type

string/bool

Returns

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

moveUp()

Moves selected sequences one level up.

moveDown()

Moves selected sequences one level down.

moveTop()

Moves selected sequences to the top of the group.

moveBottom()

Moves selected sequences to the bottom of the group.

synchronizeWithMaestro()

Synchronizes sequence viewer contents with Maestro workspace.

duplicateSequences()

Duplicates selected sequences.

setUndoRedoActions(undo_action, redo_action)

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

Parameters

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

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

setDisplayIdentity(value)

Turns on and off displaing sequence identity information.

Parameters

value (bool) – Display identity value.

setDisplaySimilarity(value)

Turns on and off displaing sequence similarity information.

Parameters

value (bool) – Display similarity value.

setDisplayHomology(value)

Turns on and off displaing sequence homology information.

Parameters

value (bool) – Display homology value.

setDisplayScore(value)

Turns on and off displaing sequence score information.

Parameters

value (bool) – display score value.

setBoundaries(value)

Turns on and off displaying sequence boundaries on the alignment.

Parameters

value (bool) – if True, display boundaries

saveProject(file_name, auto_save=False)

Saves current project to an external file.

loadProject(file_name)

Loads a MSV project from an external file.

removeRedundancy()

Removes redundant sequences.

weightColorsSettings()

Enables weighting by colors.

pairwiseAlignment()

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

alignByResidueNumbers()

Performs a sequence alignment using residue numbers as IDs.

alignMerge()

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

editSequence()

Edits a selected sequence.

createSequence()

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

pasteFasta()

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

setAsReference()

Sets a selected sequence as a reference.

selectAllSequences()

Selects all sequences in the group.

unselectAllSequences()

Deselects all sequences in the group.

invertSequenceSelection()

Inverts current sequence selection range.

findPrevious()

Scrolls to a previous occurence of a selected pattern.

findNext()

Scrolls to a next occurence of a selected pattern.

anchorSelection()

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

clearAnchors()

Clears the rectricted part of the alignment.

saveImage(file_name, save_all=True, format='PNG', custom_width=None, custom_height=None)

Saves current view to a PNG image file.

displayMessage(message)

Displays a message on a status bar.

setConsiderGaps(value)

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

Parameters

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

getConsiderGaps()

Gets value of consider gaps flag.

Rtype value

bool

Returns

Should we consider gaps for sequence identity calculations.

expandSelection()

Expands selection to include entire columns.

expandSelectionRef()

Expands selection from reference sequence to include entire columns.

setUseColors(use_colors)

Sets use colors flag.

Parameters

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

toggleConstraints()

Toggles a pairwise alignment constraints.

clearConstraints()

Clears pairwise alignment constraints.

enableQueryConstraints()

Toggles a query sequence constraints.

disableQueryConstraints(remove_if_empty=True)

Toggles a query sequence constraints.

clearQueryConstraints()

Toggles a query sequence constraints.

setIdentityInColumns(value)

Sets “Calculate identity in columns” setting.

showBlastResults()

Displays BLAST results dialog.

addGlobalAnnotations()

Add global annotations action callback.

removeGlobalAnnotations()

Removes global annotations.

hideColumns(unselected=False)

Hides selected columns.

showColumns()

Shows all hidden columns.

computeSequenceProfile()

Computes internal sequence profile and updates self.

alignmentSettingsDialog()

Opens alignment settings dialog.

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

Downloads a corresponding PDB structure.

Returns

True if the download was successful, otherwise False.

Return type

boolean

showJobLog()

Displays a job log window.

showJobSettings()

Displays a job settings dialog.

buildModel()

Builds 3D model of reference sequence.

alignStructures()

Aligns available structures.

markResidues(rgb)

Marks selected residues using a specified RGB color.

Parameters

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

clearMarkedResidues()

Clears residues that are marked by custom color.

cropSelectedResidues()

Crops residues in a selected area.

displayLigands()

Displays Maestro ligand interaction fingerprints.

newSet(name=None)

Creates a new query set

clearSet()

changeQuery(index)

excludeSelected()

excludeQueryEntries()

includeQueryEntries()

deleteSet(index)

Remove a sequence viewer tab.

emphasizeArea(area)

colorSequenceNames(color)

incorporateIncludedEntries(incorporate_scratch_entry=None)

Incorporates included entries into the SV.

incorporateSelectedEntries()

Incorporates selected entries into the SV.

colorEntrySurface()

runPredictors(predictor_list)

Runs a specified residue-level property predictors.

renameSequence()

Renames a selected sequence.

copySequences(group)

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

makeTabsFromGroupList()

Create named query tabs based on self sequence group list.

passSelectionToMaestro()

closeEvent(event)

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

showEvent(event)

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

resizeEvent(event)

Resize event handler. Update font face and size here.

createCommandDict()

Creates an external command dictionary.

colorToRGB(color)

Converts a color name string to RGB tuple.

selectSequencesByName(name_list)

executeCommandFile(cmd_file_name)

Executes an external command file.

setCallback(callback, event_type='residue_selection_changed')

Sets a sequence viewer callback.

Parameters

• event_type (string) – Type of callback event.

• callback – Callback function to be called.

getContents(all_sequences=False)

Returns contents of the current sequence group (tab).

Parameters

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

Return type

list of tuples

Returns

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

selectColumns(column_list)

Selects specified columns in the viewer.

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

Parameters

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

selectResidues(sequence_list)

Selects specified residues in the viewer.

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

Parameters

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

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

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

Parameters

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

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

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

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

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

The following numerical values are possible:

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

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

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

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

Parameters

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

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

Return type

dictionary of lists of floats

Returns

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

getSASA(sequences=[], selected_only=False, ignore_gaps=False, normalize=True, percentage=False)

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

Param

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

Type

ignore_gaps

Param

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

Parameters

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

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

Return type

list of tuples

Returns

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

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

Assigns a specified antibody numbering scheme.

Parameters

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

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

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

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

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

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

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

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

Return type

int

Returns

Number of successfully re-numbered sequences.

analyzeBindingSite()

Performs binding site analysis.

maestroWorkspaceChanged(what_changed)

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

maestroProjectChanged()

This method is invoked whenever Maestro project changes.

maestroProjectClose()

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

maestroProjectOpen()

This function is invoked whenever Maestro project is opened.

initMaestro()

Initializes Maestro callbacks.

removeMaestroCallbacks()

Removes registered Maestro callbacks.

maestroCommandCallback(command)

Called when Maestro executes a command.

translate()

Translates DNA / RNA to amino acids.

addUserAnnotation(annotation_type='region')

removeUserAnnotations()

updateAnnotationsMenu()

Box = 1

DrawChildren = 2

DrawWindowBackground = 1

HLine = 4

IgnoreMask = 4

NoFrame = 0

class PaintDeviceMetric

Bases: int

Panel = 2

PdmDepth = 6

PdmDevicePixelRatio = 11

PdmDevicePixelRatioScaled = 12

PdmDpiX = 7

PdmDpiY = 8

PdmHeight = 2

PdmHeightMM = 4

PdmNumColors = 5

PdmPhysicalDpiX = 9

PdmPhysicalDpiY = 10

PdmWidth = 1

PdmWidthMM = 3

Plain = 16

Raised = 32

class RenderFlag

Bases: int

class RenderFlags

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

class RenderFlags(QWidget.RenderFlags) → None

Bases: sip.simplewrapper

__init__(*args, **kwargs)

class Shadow

Bases: int

Shadow_Mask = 240

class Shape

Bases: int

Shape_Mask = 15

class StyleMask

Bases: int

StyledPanel = 6

Sunken = 48

VLine = 5

WinPanel = 3

__len__()

Return len(self).

acceptDrops(self) → bool

accessibleDescription(self) → str

accessibleName(self) → str

actionEvent(self, QActionEvent)

actions(self) → List[QAction]

activateWindow(self)

addAction(self, QAction)

addActions(self, Iterable[QAction])

addWidget(self, QWidget)

adjustSize(self)

autoFillBackground(self) → bool

backgroundRole(self) → QPalette.ColorRole

baseSize(self) → QSize

blockSignals(self, bool) → bool

changeEvent(self, QEvent)

childAt(self, QPoint) → QWidget

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

childEvent(self, QChildEvent)

children(self) → List[QObject]

childrenCollapsible(self) → bool

childrenRect(self) → QRect

childrenRegion(self) → QRegion

clearFocus(self)

clearMask(self)

close(self) → bool

SequenceViewer.closestLegalPosition(self, int, int) -> int

colorCount(self) → int

connectNotify(self, QMetaMethod)

contentsMargins(self) → QMargins

contentsRect(self) → QRect

contextMenuEvent(self, QContextMenuEvent)

contextMenuPolicy(self) → Qt.ContextMenuPolicy

count(self) → int

create(self, window: PyQt5.sip.voidptr = 0, initializeWindow: bool = True, destroyOldWindow: bool = True)

createHandle(self) → QSplitterHandle

createWindowContainer(QWindow, parent: QWidget = None, flags: Union[Qt.WindowFlags, Qt.WindowType] = 0) → QWidget

cursor(self) → QCursor

customContextMenuRequested

customContextMenuRequested(self, QPoint) [signal]

customEvent(self, QEvent)

deleteLater(self)

depth(self) → int

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

destroyed

destroyed(self, 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)

drawFrame(self, QPainter)

dropEvent(self, QDropEvent)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

effectiveWinId(self) → PyQt5.sip.voidptr

ensurePolished(self)

enterEvent(self, QEvent)

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

frameGeometry(self) → QRect

frameRect(self) → QRect

frameShadow(self) → QFrame.Shadow

frameShape(self) → QFrame.Shape

frameSize(self) → QSize

frameStyle(self) → int

frameWidth(self) → int

geometry(self) → QRect

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

getRange(self, int) → Tuple[int, int]

grab(self, rectangle: QRect = QRect(QPoint(0, 0), QSize(- 1, - 1))) → QPixmap

grabGesture(self, Qt.GestureType, flags: Union[Qt.GestureFlags, Qt.GestureFlag] = Qt.GestureFlags())

grabKeyboard(self)

grabMouse(self)

grabMouse(self, Union[QCursor, Qt.CursorShape]) → None

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

graphicsEffect(self) → QGraphicsEffect

graphicsProxyWidget(self) → QGraphicsProxyWidget

handle(self, int) → QSplitterHandle

handleWidth(self) → int

hasFocus(self) → bool

hasHeightForWidth(self) → bool

hasMouseTracking(self) → bool

hasTabletTracking(self) → bool

height(self) → int

heightForWidth(self, int) → int

heightMM(self) → int

hide(self)

hideEvent(self, QHideEvent)

indexOf(self, QWidget) → int

inherits(self, str) → bool

initPainter(self, QPainter)

initStyleOption(self, QStyleOptionFrame)

inputMethodEvent(self, QInputMethodEvent)

inputMethodHints(self) → Qt.InputMethodHints

inputMethodQuery(self, Qt.InputMethodQuery) → Any

SequenceViewer.insertAction(self, QAction, QAction)

insertActions(self, QAction, Iterable[QAction])

insertWidget(self, int, QWidget)

installEventFilter(self, QObject)

isActiveWindow(self) → bool

isAncestorOf(self, QWidget) → bool

isCollapsible(self, int) → bool

isEnabled(self) → bool

isEnabledTo(self, QWidget) → bool

isFullScreen(self) → bool

isHidden(self) → bool

isLeftToRight(self) → bool

isMaximized(self) → bool

isMinimized(self) → bool

isModal(self) → bool

isRightToLeft(self) → bool

isSignalConnected(self, QMetaMethod) → bool

isVisible(self) → bool

isVisibleTo(self, QWidget) → bool

isWidgetType(self) → bool

isWindow(self) → bool

isWindowModified(self) → bool

isWindowType(self) → bool

keyPressEvent(self, QKeyEvent)

keyReleaseEvent(self, QKeyEvent)

keyboardGrabber() → QWidget

killTimer(self, int)

layout(self) → QLayout

layoutDirection(self) → Qt.LayoutDirection

leaveEvent(self, QEvent)

lineWidth(self) → int

locale(self) → QLocale

logicalDpiX(self) → int

logicalDpiY(self) → int

lower(self)

mapFrom(self, QWidget, QPoint) → QPoint

mapFromGlobal(self, QPoint) → QPoint

mapFromParent(self, QPoint) → QPoint

mapTo(self, QWidget, QPoint) → QPoint

mapToGlobal(self, QPoint) → QPoint

mapToParent(self, QPoint) → QPoint

mask(self) → QRegion

maximumHeight(self) → int

maximumSize(self) → QSize

maximumWidth(self) → int

metaObject(self) → QMetaObject

metric(self, QPaintDevice.PaintDeviceMetric) → int

midLineWidth(self) → int

minimumHeight(self) → int

minimumSize(self) → QSize

minimumSizeHint(self) → QSize

minimumWidth(self) → int

mouseDoubleClickEvent(self, QMouseEvent)

mouseGrabber() → QWidget

mouseMoveEvent(self, QMouseEvent)

mousePressEvent(self, QMouseEvent)

mouseReleaseEvent(self, QMouseEvent)

move(self, QPoint)

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

moveEvent(self, QMoveEvent)

SequenceViewer.moveSplitter(self, int, int)

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]

opaqueResize(self) → bool

orientation(self) → Qt.Orientation

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

overrideWindowState(self, Union[Qt.WindowStates, Qt.WindowState])

paintEngine(self) → QPaintEngine

paintEvent(self, QPaintEvent)

paintingActive(self) → bool

palette(self) → QPalette

parent(self) → QObject

parentWidget(self) → QWidget

physicalDpiX(self) → int

physicalDpiY(self) → int

pos(self) → QPoint

previousInFocusChain(self) → QWidget

property(self, str) → Any

pyqtConfigure(...)

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

raise_(self)

receivers(self, PYQT_SIGNAL) → int

rect(self) → QRect

refresh(self)

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

renumberResidues()

Executes ‘Renumber Residues’ command.

repaint(self)

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

repaint(self, QRect) → None

repaint(self, QRegion) → None

replaceWidget(self, int, QWidget) → QWidget

resize(self, QSize)

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

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

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

saveGeometry(self) → QByteArray

saveState(self) → QByteArray

SequenceViewer.scroll(self, int, int)

SequenceViewer.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)

SequenceViewer.setBaseSize(self, int, int)

setBaseSize(self, QSize) → None

setChildrenCollapsible(self, bool)

setCollapsible(self, int, bool)

SequenceViewer.setContentsMargins(self, int, int, int, int)

setContentsMargins(self, QMargins) → None

setContextMenuPolicy(self, Qt.ContextMenuPolicy)

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

setDisabled(self, bool)

setEnabled(self, bool)

setFixedHeight(self, int)

setFixedSize(self, QSize)

SequenceViewer.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)

setFrameRect(self, QRect)

setFrameShadow(self, QFrame.Shadow)

setFrameShape(self, QFrame.Shape)

setFrameStyle(self, int)

setGeometry(self, QRect)

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

setGraphicsEffect(self, QGraphicsEffect)

setHandleWidth(self, int)

setHidden(self, bool)

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

setLayout(self, QLayout)

setLayoutDirection(self, Qt.LayoutDirection)

setLineWidth(self, int)

setLocale(self, QLocale)

setMask(self, QBitmap)

setMask(self, QRegion) → None

setMaximumHeight(self, int)

SequenceViewer.setMaximumSize(self, int, int)

setMaximumSize(self, QSize) → None

setMaximumWidth(self, int)

setMidLineWidth(self, int)

setMinimumHeight(self, int)

SequenceViewer.setMinimumSize(self, int, int)

setMinimumSize(self, QSize) → None

setMinimumWidth(self, int)

setMouseTracking(self, bool)

setObjectName(self, str)

setOpaqueResize(self, opaque: bool = True)

setOrientation(self, Qt.Orientation)

setPalette(self, QPalette)

setParent(self, QWidget)

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

setProperty(self, str, Any) → bool

setRubberBand(self, int)

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

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

SequenceViewer.setSizeIncrement(self, int, int)

setSizeIncrement(self, QSize) → None

setSizePolicy(self, QSizePolicy)

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

setSizes(self, Iterable[int])

setStatusTip(self, str)

SequenceViewer.setStretchFactor(self, int, int)

setStyle(self, QStyle)

setStyleSheet(self, str)

SequenceViewer.setTabOrder(QWidget, QWidget)

setTabletTracking(self, bool)

setToolTip(self, str)

setToolTipDuration(self, int)

setUpdatesEnabled(self, bool)

setVisible(self, bool)

setWhatsThis(self, str)

setWindowFilePath(self, str)

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

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

setWindowIcon(self, QIcon)

setWindowIconText(self, str)

setWindowModality(self, Qt.WindowModality)

setWindowModified(self, bool)

setWindowOpacity(self, float)

setWindowRole(self, str)

setWindowState(self, Union[Qt.WindowStates, Qt.WindowState])

setWindowTitle(self, str)

sharedPainter(self) → QPainter

show(self)

showFullScreen(self)

showMaximized(self)

showMinimized(self)

showNormal(self)

signalsBlocked(self) → bool

size(self) → QSize

sizeHint(self) → QSize

sizeIncrement(self) → QSize

sizePolicy(self) → QSizePolicy

sizes(self) → List[int]

splitterMoved

splitterMoved(self, int, int) [signal]

stackUnder(self, QWidget)

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>

statusTip(self) → str

style(self) → QStyle

styleSheet(self) → str

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

underMouse(self) → bool

ungrabGesture(self, Qt.GestureType)

unsetCursor(self)

unsetLayoutDirection(self)

unsetLocale(self)

update(self)

update(self, QRect) → None

update(self, QRegion) → None

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

updateGeometry(self)

updateMicroFocus(self)

updatesEnabled(self) → bool

visibleRegion(self) → QRegion

whatsThis(self) → str

wheelEvent(self, QWheelEvent)

widget(self, int) → QWidget

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

getStructureAlignment()

associateMaestroEntries()

Displays ‘Associate Maestro Entries’ dialog.

selectLigandContacts(ligand=None)

Selects residues in ligand proximity in selected ligand sequence.

incorporateStructure(st)

Incorporates a structure passed as a Structure object.

showCompareSequencesDialog()

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