schrodinger.ui.sequencealignment.prime_gui module

Implementation of Qt dialog boxes used by multiple sequence viewer.

Copyright Schrodinger, LLC. All rights reserved.

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]

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

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

Bases: sip.simplewrapper

QDockWidget.DockWidgetFeatures(Union[QDockWidget.DockWidgetFeatures, QDockWidget.DockWidgetFeature]) QDockWidget.DockWidgetFeatures(QDockWidget.DockWidgetFeatures)

__init__(*args, **kwargs)

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

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

Bases: int

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

Bases: sip.simplewrapper

QWidget.RenderFlags(Union[QWidget.RenderFlags, QWidget.RenderFlag]) QWidget.RenderFlags(QWidget.RenderFlags)

__init__(*args, **kwargs)

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

acceptDrops(self) → bool
accessibleDescription(self) → str
accessibleName(self) → str
actionEvent(self, QActionEvent)
actions(self) → List[QAction]
activateWindow(self)
addAction(self, QAction)
addActions(self, 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

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: 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(self)
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) → sip.voidptr
ensurePolished(self)
enterEvent(self, QEvent)
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
features(self) → QDockWidget.DockWidgetFeatures
featuresChanged

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

find(sip.voidptr) → QWidget
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

focusInEvent(self, QFocusEvent)
focusNextChild(self) → bool
focusNextPrevChild(self, bool) → bool
focusOutEvent(self, QFocusEvent)
focusPolicy(self) → Qt.FocusPolicy
focusPreviousChild(self) → bool
focusProxy(self) → QWidget
focusWidget(self) → QWidget
font(self) → QFont
fontInfo(self) → QFontInfo
fontMetrics(self) → QFontMetrics
foregroundRole(self) → QPalette.ColorRole
frameGeometry(self) → QRect
frameSize(self) → QSize
geometry(self) → QRect
getContentsMargins(self) → Tuple[int, int, int, int]
grab(self, rectangle: QRect = QRect(QPoint(0, 0), QSize(- 1, - 1))) → QPixmap
grabGesture(self, Qt.GestureType, flags: Union[Qt.GestureFlags, Qt.GestureFlag] = Qt.GestureFlags())
grabKeyboard(self)
grabMouse(self)

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

grabShortcut(self, Union[QKeySequence, QKeySequence.StandardKey, str, int], context: Qt.ShortcutContext = Qt.WindowShortcut) → int
graphicsEffect(self) → QGraphicsEffect
graphicsProxyWidget(self) → QGraphicsProxyWidget
hasFocus(self) → bool
hasHeightForWidth(self) → bool
hasMouseTracking(self) → bool
hasTabletTracking(self) → bool
height(self) → int
heightForWidth(self, int) → int
heightMM(self) → int
hide(self)
hideEvent(self, QHideEvent)
inherits(self, str) → bool
initPainter(self, QPainter)
initStyleOption(self, QStyleOptionDockWidget)
inputMethodEvent(self, QInputMethodEvent)
inputMethodHints(self) → Qt.InputMethodHints
inputMethodQuery(self, Qt.InputMethodQuery) → Any
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)

move(self, int, int)

moveEvent(self, QMoveEvent)
moveToThread(self, QThread)
nativeEvent(self, Union[QByteArray, bytes, bytearray], sip.voidptr) → Tuple[bool, int]
nativeParentWidget(self) → QWidget
nextInFocusChain(self) → QWidget
normalGeometry(self) → QRect
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

overrideWindowFlags(self, Union[Qt.WindowFlags, Qt.WindowType])
overrideWindowState(self, Union[Qt.WindowStates, Qt.WindowState])
paintEngine(self) → QPaintEngine
paintEvent(self, QPaintEvent)
paintingActive(self) → bool
palette(self) → QPalette
parent(self) → QObject
parentWidget(self) → QWidget
physicalDpiX(self) → int
physicalDpiY(self) → int
pos(self) → QPoint
previousInFocusChain(self) → QWidget
property(self, str) → Any
pyqtConfigure(...)

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

raise_(self)
receivers(self, PYQT_SIGNAL) → int
rect(self) → QRect
releaseKeyboard(self)
releaseMouse(self)
releaseShortcut(self, int)
removeAction(self, QAction)
removeEventFilter(self, QObject)
render(self, QPaintDevice, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.DrawWindowBackground | QWidget.DrawChildren))

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

repaint(self)

repaint(self, int, int, int, int) repaint(self, QRect) repaint(self, QRegion)

resize(self, QSize)

resize(self, int, int)

resizeEvent(self, QResizeEvent)
restoreGeometry(self, Union[QByteArray, bytes, bytearray]) → bool
saveGeometry(self) → QByteArray
PrimeSettingsDialog.scroll(self, int, int)

scroll(self, int, int, QRect)

sender(self) → QObject
senderSignalIndex(self) → int
setAcceptDrops(self, bool)
setAccessibleDescription(self, str)
setAccessibleName(self, str)
setAllowedAreas(self, Union[Qt.DockWidgetAreas, Qt.DockWidgetArea])
setAttribute(self, Qt.WidgetAttribute, on: bool = True)
setAutoFillBackground(self, bool)
setBackgroundRole(self, QPalette.ColorRole)
PrimeSettingsDialog.setBaseSize(self, int, int)

setBaseSize(self, QSize)

PrimeSettingsDialog.setContentsMargins(self, int, int, int, int)

setContentsMargins(self, QMargins)

setContextMenuPolicy(self, Qt.ContextMenuPolicy)
setCursor(self, Union[QCursor, Qt.CursorShape])
setDisabled(self, bool)
setEnabled(self, bool)
setFeatures(self, Union[QDockWidget.DockWidgetFeatures, QDockWidget.DockWidgetFeature])
setFixedHeight(self, int)
setFixedSize(self, QSize)

setFixedSize(self, int, int)

setFixedWidth(self, int)
setFloating(self, bool)
setFocus(self)

setFocus(self, Qt.FocusReason)

setFocusPolicy(self, Qt.FocusPolicy)
setFocusProxy(self, QWidget)
setFont(self, QFont)
setForegroundRole(self, QPalette.ColorRole)
setGeometry(self, QRect)

setGeometry(self, int, int, int, int)

setGraphicsEffect(self, QGraphicsEffect)
setHidden(self, bool)
setInputMethodHints(self, Union[Qt.InputMethodHints, Qt.InputMethodHint])
setLayout(self, QLayout)
setLayoutDirection(self, Qt.LayoutDirection)
setLocale(self, QLocale)
setMask(self, QBitmap)

setMask(self, QRegion)

setMaximumHeight(self, int)
PrimeSettingsDialog.setMaximumSize(self, int, int)

setMaximumSize(self, QSize)

setMaximumWidth(self, int)
setMinimumHeight(self, int)
PrimeSettingsDialog.setMinimumSize(self, int, int)

setMinimumSize(self, QSize)

setMinimumWidth(self, int)
setMouseTracking(self, bool)
setObjectName(self, str)
setPalette(self, QPalette)
setParent(self, QWidget)

setParent(self, QWidget, Union[Qt.WindowFlags, Qt.WindowType])

setProperty(self, str, Any) → bool
setShortcutAutoRepeat(self, int, enabled: bool = True)
setShortcutEnabled(self, int, enabled: bool = True)
PrimeSettingsDialog.setSizeIncrement(self, int, int)

setSizeIncrement(self, QSize)

setSizePolicy(self, QSizePolicy)

setSizePolicy(self, QSizePolicy.Policy, QSizePolicy.Policy)

setStatusTip(self, str)
setStyle(self, QStyle)
setStyleSheet(self, str)
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) update(self, QRegion) update(self, int, int, int, int)

updateGeometry(self)
updateMicroFocus(self)
updatesEnabled(self) → bool
visibilityChanged

visibilityChanged(self, bool) [signal]

visibleRegion(self) → QRegion
whatsThis(self) → str
wheelEvent(self, QWheelEvent)
widget(self) → QWidget
width(self) → int
widthMM(self) → int
winId(self) → sip.voidptr
window(self) → QWidget
windowFilePath(self) → str
windowFlags(self) → Qt.WindowFlags
windowHandle(self) → QWindow
windowIcon(self) → QIcon
windowIconChanged

windowIconChanged(self, QIcon) [signal]

windowIconText(self) → str
windowIconTextChanged

windowIconTextChanged(self, str) [signal]

windowModality(self) → Qt.WindowModality
windowOpacity(self) → float
windowRole(self) → str
windowState(self) → Qt.WindowStates
windowTitle(self) → str
windowTitleChanged

windowTitleChanged(self, str) [signal]

windowType(self) → Qt.WindowType
x(self) → int
y(self) → int
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]