schrodinger.ui.sequencealignment.prime_gui module¶

Implementation of Qt dialog boxes used by multiple sequence viewer.

class schrodinger.ui.sequencealignment.prime_gui.PrimeSettingsDialog(sequence_group, viewer=None)[source]¶

Bases: PyQt5.QtWidgets.QDockWidget

This class implements the “Prime Settings” dialog.

__init__(sequence_group, viewer=None)[source]¶

button_ok¶: “Build model” push button.

button_help¶: “Help” push button.

knowledge_based_rb¶: Knowledge-based mode radio button.

energy_based_rb¶: Energy-based mode radio button.

kb_models_le¶: Knowledge-based mode line edit.

kb_models_layout¶: Number of models layout

method_layout¶: Method layout

button_close¶: “Close” push button.

top_button_layout¶: Top button layout.

button_layout¶: Button layout.

contents¶: Main widget.

tabs¶: Settings tabs.

retain_numbers_cb¶: Retain residue numbers checkbox.

retain_rotamers_cb¶: Retain rotamers checkbox.

optimize_side_chains_cb¶: Optimize side chains checkbox.

minimize_residues_cb¶: Minimize residues not obtained from templates.

optimizeSideChainsChanged()[source]¶

toggleConstraints(visible)[source]¶: Toggles visibility of the query constraints.

tabChanged(index)[source]¶: Tab changed callback.

removeQueryLigands()[source]¶: Clears the list of query ligand annotations. Called when ligand tab is closed or the user exits the build mode.

addQueryLigands(ligand_name_list)[source]¶

Creates ligand annotations for the query sequence. The annotations are used to set ligand-query constraints.

Parameters: ligand_name_list (list(str)) – List of ligand names.

ligandListSelectionChanged()[source]¶: Called when ligand list selection changes.

templateListSelectionChanged()[source]¶: Called when template list selection changes.

refreshLigands()[source]¶: Refreshes contents of the ligand table

refreshTemplates()[source]¶: Rebuilds the list of templates.

getQueryList()[source]¶: Returns list of selected queries for heteromultimer modeling.

getTemplateList(selected_only=False)[source]¶

Returns a full list of templates for all queries.

If selected_only is True, returns only selected templates.

updateWidgets()[source]¶: Updates Prime settings dialog widget status based on current settings.

addConstraints()[source]¶: Enables query-query constraint mode.

clearConstraints()[source]¶: Clears all constraints.

buildHeteroMultimer()[source]¶: Enters heteromultimer building mode.

buildModeChanged()[source]¶: Called when build mode changes. Validates and updates GUI settings.

getParameters()[source]¶: Returns a dictionary of parameters for the Prime backend.

validateQuerySequences(group_list)[source]¶

Tests if all query sequences in the provided list of groups include only valid characters.

Parameters: group_list (list of SequenceGroup) – List of groups used to build the model.
Return type: bool
Returns: True if all sequences are valid, False otherwise.

buildModel()[source]¶: Actually launch the model building job.

previewModel()[source]¶: Launch the model building job in “preview” mode.

validateBuildMode()[source]¶: Validates current build mode and Sets ‘Build model’ button status.

helpCB()[source]¶: Invokes a Homology Modeling help page.

buttonImportCB()[source]¶: Callback for Import button.

buttonFindCB()[source]¶: Callback for Find button.

buttonGetCB()[source]¶: Callback for Get button.

AllDockWidgetFeatures = 7¶

DockWidgetClosable = 1¶

class DockWidgetFeature¶: Bases: int

class DockWidgetFeatures¶

class DockWidgetFeatures(Union[QDockWidget.DockWidgetFeatures, QDockWidget.DockWidgetFeature]) → None

class DockWidgetFeatures(QDockWidget.DockWidgetFeatures) → None

Bases: sip.simplewrapper

__init__(*args, **kwargs)¶

DockWidgetFloatable = 4¶

DockWidgetMovable = 2¶

DockWidgetVerticalTitleBar = 8¶

DrawChildren = 2¶

DrawWindowBackground = 1¶

IgnoreMask = 4¶

NoDockWidgetFeatures = 0¶

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)¶

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])¶

adjustSize(self)¶

allowedAreas(self) → Qt.DockWidgetAreas¶

allowedAreasChanged¶: allowedAreasChanged(self, Union[Qt.DockWidgetAreas, Qt.DockWidgetArea]) [signal]

autoFillBackground(self) → bool¶

backgroundRole(self) → QPalette.ColorRole¶

baseSize(self) → QSize¶

blockSignals(self, bool) → bool¶

changeEvent(self, QEvent)¶

childAt(self, QPoint) → QWidget¶
PrimeSettingsDialog.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(self, QCloseEvent)¶

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)¶

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)¶

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

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)¶

event(self, QEvent) → bool¶

eventFilter(self, QObject, QEvent) → bool¶

features(self) → QDockWidget.DockWidgetFeatures¶

featuresChanged¶: featuresChanged(self, Union[QDockWidget.DockWidgetFeatures, QDockWidget.DockWidgetFeature]) [signal]

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¶

frameSize(self) → QSize¶

geometry(self) → QRect¶

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

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

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

grabKeyboard(self)¶

grabMouse(self)¶
grabMouse(self, Union[QCursor, Qt.CursorShape]) → 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)¶

inherits(self, str) → bool¶

initPainter(self, QPainter)¶

initStyleOption(self, QStyleOptionDockWidget)¶

inputMethodEvent(self, QInputMethodEvent)¶

inputMethodHints(self) → Qt.InputMethodHints¶

inputMethodQuery(self, Qt.InputMethodQuery) → Any¶

PrimeSettingsDialog.insertAction(self, QAction, QAction)

insertActions(self, QAction, Iterable[QAction])¶

installEventFilter(self, QObject)¶

isActiveWindow(self) → bool¶

isAncestorOf(self, QWidget) → bool¶

isAreaAllowed(self, Qt.DockWidgetArea) → bool¶

isEnabled(self) → bool¶

isEnabledTo(self, QWidget) → bool¶

isFloating(self) → bool¶

isFullScreen(self) → bool¶

isHidden(self) → bool¶

isLeftToRight(self) → bool¶

isMaximized(self) → bool¶

isMinimized(self) → bool¶

isModal(self) → bool¶

isRightToLeft(self) → bool¶

isSignalConnected(self, QMetaMethod) → bool¶

isVisible(self) → bool¶

isVisibleTo(self, QWidget) → bool¶

isWidgetType(self) → bool¶

isWindow(self) → bool¶

isWindowModified(self) → bool¶

isWindowType(self) → bool¶

keyPressEvent(self, QKeyEvent)¶

keyReleaseEvent(self, QKeyEvent)¶

keyboardGrabber() → QWidget¶

killTimer(self, int)¶

layout(self) → QLayout¶

layoutDirection(self) → Qt.LayoutDirection¶

leaveEvent(self, QEvent)¶

locale(self) → QLocale¶

logicalDpiX(self) → int¶

logicalDpiY(self) → int¶

lower(self)¶

mapFrom(self, QWidget, QPoint) → QPoint¶

mapFromGlobal(self, QPoint) → QPoint¶

mapFromParent(self, QPoint) → QPoint¶

mapTo(self, QWidget, QPoint) → QPoint¶

mapToGlobal(self, QPoint) → QPoint¶

mapToParent(self, QPoint) → QPoint¶

mask(self) → QRegion¶

maximumHeight(self) → int¶

maximumSize(self) → QSize¶

maximumWidth(self) → int¶

metaObject(self) → QMetaObject¶

metric(self, QPaintDevice.PaintDeviceMetric) → int¶

minimumHeight(self) → int¶

minimumSize(self) → QSize¶

minimumSizeHint(self) → QSize¶

minimumWidth(self) → int¶

mouseDoubleClickEvent(self, QMouseEvent)¶

mouseGrabber() → QWidget¶

mouseMoveEvent(self, QMouseEvent)¶

mousePressEvent(self, QMouseEvent)¶

mouseReleaseEvent(self, QMouseEvent)¶

move(self, QPoint)¶
PrimeSettingsDialog.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.

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)¶
PrimeSettingsDialog.repaint(self, int, int, int, int) -> None
repaint(self, QRect) → None
repaint(self, QRegion) → None

resize(self, QSize)¶
PrimeSettingsDialog.resize(self, int, int) -> None

resizeEvent(self, QResizeEvent)¶

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

saveGeometry(self) → QByteArray¶

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

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setAcceptDrops(self, bool)¶

setAccessibleDescription(self, str)¶

setAccessibleName(self, str)¶

setAllowedAreas(self, Union[Qt.DockWidgetAreas, Qt.DockWidgetArea])¶

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

setAutoFillBackground(self, bool)¶

setBackgroundRole(self, QPalette.ColorRole)¶

PrimeSettingsDialog.setBaseSize(self, int, int)
setBaseSize(self, QSize) → None¶

PrimeSettingsDialog.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)¶

setFeatures(self, Union[QDockWidget.DockWidgetFeatures, QDockWidget.DockWidgetFeature])¶

setFixedHeight(self, int)¶

setFixedSize(self, QSize)¶
PrimeSettingsDialog.setFixedSize(self, int, int) -> None

setFixedWidth(self, int)¶

setFloating(self, bool)¶

setFocus(self)¶
setFocus(self, Qt.FocusReason) → None

setFocusPolicy(self, Qt.FocusPolicy)¶

setFocusProxy(self, QWidget)¶

setFont(self, QFont)¶

setForegroundRole(self, QPalette.ColorRole)¶

setGeometry(self, QRect)¶
PrimeSettingsDialog.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)¶

PrimeSettingsDialog.setMaximumSize(self, int, int)
setMaximumSize(self, QSize) → None¶

setMaximumWidth(self, int)¶

setMinimumHeight(self, int)¶

PrimeSettingsDialog.setMinimumSize(self, int, int)
setMinimumSize(self, QSize) → None¶

setMinimumWidth(self, int)¶

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)¶

PrimeSettingsDialog.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)¶

PrimeSettingsDialog.setTabOrder(QWidget, QWidget)

setTabletTracking(self, bool)¶

setTitleBarWidget(self, QWidget)¶

setToolTip(self, str)¶

setToolTipDuration(self, int)¶

setUpdatesEnabled(self, bool)¶

setVisible(self, bool)¶

setWhatsThis(self, str)¶

setWidget(self, QWidget)¶

setWindowFilePath(self, str)¶

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

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

setWindowIcon(self, QIcon)¶

setWindowIconText(self, str)¶

setWindowModality(self, Qt.WindowModality)¶

setWindowModified(self, bool)¶

setWindowOpacity(self, float)¶

setWindowRole(self, str)¶

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

setWindowTitle(self, str)¶

sharedPainter(self) → QPainter¶

show(self)¶

showEvent(self, QShowEvent)¶

showFullScreen(self)¶

showMaximized(self)¶

showMinimized(self)¶

showNormal(self)¶

signalsBlocked(self) → bool¶

size(self) → QSize¶

sizeHint(self) → QSize¶

sizeIncrement(self) → QSize¶

sizePolicy(self) → QSizePolicy¶

stackUnder(self, QWidget)¶

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>¶

statusTip(self) → str¶

style(self) → QStyle¶

styleSheet(self) → str¶

tabletEvent(self, QTabletEvent)¶

testAttribute(self, Qt.WidgetAttribute) → bool¶

thread(self) → QThread¶

timerEvent(self, QTimerEvent)¶

titleBarWidget(self) → QWidget¶

toggleViewAction(self) → QAction¶

toolTip(self) → str¶

toolTipDuration(self) → int¶

topLevelChanged¶: topLevelChanged(self, bool) [signal]

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

underMouse(self) → bool¶

ungrabGesture(self, Qt.GestureType)¶

unsetCursor(self)¶

unsetLayoutDirection(self)¶

unsetLocale(self)¶

update(self)¶
update(self, QRect) → None
update(self, QRegion) → None
PrimeSettingsDialog.update(self, int, int, int, int) -> None

updateGeometry(self)¶

updateMicroFocus(self)¶

updatesEnabled(self) → bool¶

visibilityChanged¶: visibilityChanged(self, bool) [signal]

visibleRegion(self) → QRegion¶

whatsThis(self) → str¶

wheelEvent(self, QWheelEvent)¶

widget(self) → QWidget¶

width(self) → int¶

widthMM(self) → int¶

winId(self) → 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.ui.sequencealignment.prime_gui.showPrimeSettingsDialog(viewer, sequence_group, build_model_func, progress_dialog)[source]¶: Opens Prime settings dialog and returns a parameter tuple.

schrodinger.ui.sequencealignment.prime_gui.setPrimeSequenceGroup(sequence_group)[source]¶

schrodinger.ui.sequencealignment.prime_gui.getPrimeLigandsForEntryID(entry_id)[source]¶

schrodinger.ui.sequencealignment.prime_gui.updatePrimeQueryList(refresh_templates=True, refresh_ligands=False)[source]¶

schrodinger.ui.sequencealignment.prime_gui.primeValidateBuildMode()[source]¶