schrodinger.application.jaguar.gui.tabs.transition_state_tab module

class schrodinger.application.jaguar.gui.tabs.transition_state_tab.PerAtomBasisPopUp(parent)

Bases: schrodinger.ui.qt.pop_up_widgets.PopUp

Pop-up to select per-atom basis set

setup()

Subclass-specific initialization. Subclasses must implement this function.

Box = 1

DrawChildren = 2

DrawWindowBackground = 1

HLine = 4

IgnoreMask = 4

NoFrame = 0

class PaintDeviceMetric(value)

Bases: enum.Enum

An enumeration.

PdmWidth = 1

PdmHeight = 2

PdmWidthMM = 3

PdmHeightMM = 4

PdmNumColors = 5

PdmDepth = 6

PdmDpiX = 7

PdmDpiY = 8

PdmPhysicalDpiX = 9

PdmPhysicalDpiY = 10

PdmDevicePixelRatio = 11

PdmDevicePixelRatioScaled = 12

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(value)

Bases: enum.Flag

An enumeration.

DrawWindowBackground = 1

DrawChildren = 2

IgnoreMask = 4

class Shadow(value)

Bases: enum.IntEnum

An enumeration.

Plain = 16

Raised = 32

Sunken = 48

Shadow_Mask = 240

class Shape(value)

Bases: enum.IntEnum

An enumeration.

NoFrame = 0

Box = 1

Panel = 2

WinPanel = 3

HLine = 4

VLine = 5

StyledPanel = 6

Shape_Mask = 15

class StyleMask(value)

Bases: enum.Enum

An enumeration.

Shadow_Mask = 240

Shape_Mask = 15

StyledPanel = 6

Sunken = 48

VLine = 5

WinPanel = 3

__init__(parent)

acceptDrops(self) → bool

accessibleDescription(self) → str

accessibleName(self) → str

actionEvent(self, a0: QActionEvent)

actions(self) → List[QAction]

activateWindow(self)

addAction(self, action: QAction)

addActions(self, actions: Iterable[QAction])

adjustSize(self)

autoFillBackground(self) → bool

backgroundRole(self) → QPalette.ColorRole

baseSize(self) → QSize

blockSignals(self, b: bool) → bool

changeEvent(self, a0: QEvent)

childAt(self, p: QPoint) → QWidget

childAt(self, ax: int, ay: int) → QWidget

childEvent(self, a0: QChildEvent)

children(self) → List[QObject]

childrenRect(self) → QRect

childrenRegion(self) → QRegion

clearFocus(self)

clearMask(self)

close(self) → bool

closeEvent(self, a0: QCloseEvent)

colorCount(self) → int

connectNotify(self, signal: QMetaMethod)

contentsMargins(self) → QMargins

contentsRect(self) → QRect

contextMenuEvent(self, a0: QContextMenuEvent)

contextMenuPolicy(self) → Qt.ContextMenuPolicy

create(self, window: PyQt6.sip.voidptr = 0, initializeWindow: bool = True, destroyOldWindow: bool = True)

createWindowContainer(window: QWindow, parent: typing.Optional[QWidget] = None, flags: Qt.WindowType = Qt.WindowFlags()) → QWidget

cursor(self) → QCursor

customContextMenuRequested

customContextMenuRequested(self, pos: QPoint) [signal]

customEvent(self, a0: QEvent)

dataChanged

deleteLater(self)

depth(self) → int

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

destroyed

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

devType(self) → int

devicePixelRatio(self) → float

devicePixelRatioF(self) → float

devicePixelRatioFScale() → float

disconnect(a0: QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, signal: QMetaMethod)

dragEnterEvent(self, a0: QDragEnterEvent)

dragLeaveEvent(self, a0: QDragLeaveEvent)

dragMoveEvent(self, a0: QDragMoveEvent)

drawFrame(self, a0: QPainter)

dropEvent(self, a0: QDropEvent)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

effectiveWinId(self) → PyQt6.sip.voidptr

ensurePolished(self)

enterEvent(self, event: QEnterEvent)

estimateMaxHeight()

Return an estimate of the maximum allowable height of this pop up. This estimate is used to ensure that the pop up is positioned within the window. The default implementation uses the current size hint. Subclasses can reimplement this function if they can calculate a more accurate allowable height. This is typically only applicable if the pop up is likely to change size.

Returns

The maximum allowable height

Return type

int

estimateMaxWidth()

Return an estimate of the maximum allowable width of this pop up. This estimate is used to ensure that the pop up is positioned within the window. The default implementation uses the current size hint. Subclasses can reimplement this function if they can calculate a more accurate allowable width. This is typically only applicable if the pop up is likely to change size.

Returns

The maximum allowable width

Return type

int

event(self, e: QEvent) → bool

eventFilter(self, a0: QObject, a1: QEvent) → bool

find(a0: PyQt6.sip.voidptr) → QWidget

findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

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

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

findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

focusInEvent(self, a0: QFocusEvent)

focusNextChild(self) → bool

focusNextPrevChild(self, next: bool) → bool

focusOutEvent(self, a0: 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

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

grabGesture(self, type: Qt.GestureType, flags: Qt.GestureFlag = Qt.GestureFlags())

grabKeyboard(self)

grabMouse(self)

grabMouse(self, a0: Union[QCursor, Qt.CursorShape]) → None

grabShortcut(self, key: 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, a0: int) → int

heightMM(self) → int

hide(self)

hideEvent(event)

Emit a signal every time this pop up is hidden.

inherits(self, classname: str) → bool

initPainter(self, painter: QPainter)

initStyleOption(self, option: QStyleOptionFrame)

inputMethodEvent(self, a0: QInputMethodEvent)

inputMethodHints(self) → Qt.InputMethodHint

inputMethodQuery(self, a0: Qt.InputMethodQuery) → Any

insertAction(self, before: QAction, action: QAction)

insertActions(self, before: QAction, actions: Iterable[QAction])

installEventFilter(self, a0: QObject)

installPopUpEventFilter(event_filter)

Install the provided event filter on all widgets within this pop up that can receive focus.

Note

This function only installs the event filter on immediate children of this widget. As a result, keyboard events on grandchildren (or later descendant) widgets will not be handled properly. If this causes issues, the implementation will have to be modified.

Parameters

event_filter (_BasisSelectorPopUpEventFilter) – The event filter to install

isActiveWindow(self) → bool

isAncestorOf(self, child: QWidget) → bool

isEnabled(self) → bool

isEnabledTo(self, a0: 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, signal: QMetaMethod) → bool

isVisible(self) → bool

isVisibleTo(self, a0: QWidget) → bool

isWidgetType(self) → bool

isWindow(self) → bool

isWindowModified(self) → bool

isWindowType(self) → bool

keyPressEvent(self, a0: QKeyEvent)

keyReleaseEvent(self, a0: QKeyEvent)

keyboardGrabber() → QWidget

killTimer(self, id: int)

layout(self) → QLayout

layoutDirection(self) → Qt.LayoutDirection

leaveEvent(self, a0: QEvent)

lineEditUpdated(text)

Update this pop up in response to the user changing the line edit text. Note that, by default, this widget will not be able to send signals during execution of this method. This prevents an infinite loop of PopUp.lineEditUpdated and LineEditWithPopUp.popUpUpdated. To modify this behavior, subclass LineEditWithPopUp and reimplement LineEditWithPopUp.popUpUpdated.

Parameters

text (str) – The current text of the line edit

lineWidth(self) → int

locale(self) → QLocale

logicalDpiX(self) → int

logicalDpiY(self) → int

lower(self)

mapFrom(self, a0: QWidget, a1: QPoint) → QPoint

mapFrom(self, a0: QWidget, a1: QPointF) → QPointF

mapFromGlobal(self, a0: QPoint) → QPoint

mapFromGlobal(self, a0: QPointF) → QPointF

mapFromParent(self, a0: QPoint) → QPoint

mapFromParent(self, a0: QPointF) → QPointF

mapTo(self, a0: QWidget, a1: QPoint) → QPoint

mapTo(self, a0: QWidget, a1: QPointF) → QPointF

mapToGlobal(self, a0: QPoint) → QPoint

mapToGlobal(self, a0: QPointF) → QPointF

mapToParent(self, a0: QPoint) → QPoint

mapToParent(self, a0: QPointF) → QPointF

mask(self) → QRegion

maximumHeight(self) → int

maximumSize(self) → QSize

maximumWidth(self) → int

metaObject(self) → QMetaObject

metric(self, a0: QPaintDevice.PaintDeviceMetric) → int

midLineWidth(self) → int

minimumHeight(self) → int

minimumSize(self) → QSize

minimumSizeHint(self) → QSize

minimumWidth(self) → int

mouseDoubleClickEvent(self, a0: QMouseEvent)

mouseGrabber() → QWidget

mouseMoveEvent(self, a0: QMouseEvent)

mousePressEvent(self, a0: QMouseEvent)

mouseReleaseEvent(self, a0: QMouseEvent)

move(self, a0: QPoint)

move(self, ax: int, ay: int) → None

moveEvent(self, a0: QMoveEvent)

moveToThread(self, thread: QThread)

nativeEvent(self, eventType: QByteArray, message: PyQt6.sip.voidptr) → Tuple[bool, PyQt6.sip.voidptr]

nativeParentWidget(self) → QWidget

nextInFocusChain(self) → QWidget

normalGeometry(self) → QRect

objectName(self) → str

objectNameChanged

objectNameChanged(self, objectName: str) [signal]

overrideWindowFlags(self, type: Qt.WindowType)

overrideWindowState(self, state: Qt.WindowState)

paintEngine(self) → QPaintEngine

paintEvent(self, a0: QPaintEvent)

paintingActive(self) → bool

palette(self) → QPalette

parent(self) → QObject

parentWidget(self) → QWidget

physicalDpiX(self) → int

physicalDpiY(self) → int

popUpResized

pos(self) → QPoint

previousInFocusChain(self) → QWidget

property(self, name: 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, signal: PYQT_SIGNAL) → int

rect(self) → QRect

releaseKeyboard(self)

releaseMouse(self)

releaseShortcut(self, id: int)

removeAction(self, action: QAction)

removeEventFilter(self, a0: QObject)

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

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

repaint(self)

repaint(self, x: int, y: int, w: int, h: int) → None

repaint(self, a0: QRect) → None

repaint(self, a0: QRegion) → None

resize(self, a0: QSize)

resize(self, w: int, h: int) → None

resizeEvent(self, a0: QResizeEvent)

restoreGeometry(self, geometry: QByteArray) → bool

saveGeometry(self) → QByteArray

screen(self) → QScreen

scroll(self, dx: int, dy: int)

scroll(self, dx: int, dy: int, a2: QRect) → None

sender(self) → QObject

senderSignalIndex(self) → int

setAcceptDrops(self, on: bool)

setAccessibleDescription(self, description: str)

setAccessibleName(self, name: str)

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

setAutoFillBackground(self, enabled: bool)

setBackgroundRole(self, a0: QPalette.ColorRole)

setBaseSize(self, basew: int, baseh: int)

setBaseSize(self, s: QSize) → None

setContentsMargins(self, left: int, top: int, right: int, bottom: int)

setContentsMargins(self, margins: QMargins) → None

setContextMenuPolicy(self, policy: Qt.ContextMenuPolicy)

setCursor(self, a0: Union[QCursor, Qt.CursorShape])

setDisabled(self, a0: bool)

setEnabled(self, a0: bool)

setFixedHeight(self, h: int)

setFixedSize(self, a0: QSize)

setFixedSize(self, w: int, h: int) → None

setFixedWidth(self, w: int)

setFocus(self)

setFocus(self, reason: Qt.FocusReason) → None

setFocusPolicy(self, policy: Qt.FocusPolicy)

setFocusProxy(self, a0: QWidget)

setFont(self, a0: QFont)

setForegroundRole(self, a0: QPalette.ColorRole)

setFrameRect(self, a0: QRect)

setFrameShadow(self, a0: QFrame.Shadow)

setFrameShape(self, a0: QFrame.Shape)

setFrameStyle(self, a0: int)

setGeometry(self, a0: QRect)

setGeometry(self, ax: int, ay: int, aw: int, ah: int) → None

setGraphicsEffect(self, effect: QGraphicsEffect)

setHidden(self, hidden: bool)

setInputMethodHints(self, hints: Qt.InputMethodHint)

setLayout(self, a0: QLayout)

setLayoutDirection(self, direction: Qt.LayoutDirection)

setLineWidth(self, a0: int)

setLocale(self, locale: QLocale)

setMask(self, a0: QBitmap)

setMask(self, a0: QRegion) → None

setMaximumHeight(self, maxh: int)

setMaximumSize(self, maxw: int, maxh: int)

setMaximumSize(self, s: QSize) → None

setMaximumWidth(self, maxw: int)

setMidLineWidth(self, a0: int)

setMinimumHeight(self, minh: int)

setMinimumSize(self, minw: int, minh: int)

setMinimumSize(self, s: QSize) → None

setMinimumWidth(self, minw: int)

setMouseTracking(self, enable: bool)

setObjectName(self, name: str)

setPalette(self, a0: QPalette)

setParent(self, parent: QWidget)

setParent(self, parent: QWidget, f: Qt.WindowType) → None

setProperty(self, name: str, value: Any) → bool

setScreen(self, a0: QScreen)

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

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

setSizeIncrement(self, w: int, h: int)

setSizeIncrement(self, s: QSize) → None

setSizePolicy(self, a0: QSizePolicy)

setSizePolicy(self, hor: QSizePolicy.Policy, ver: QSizePolicy.Policy) → None

setStatusTip(self, a0: str)

setStyle(self, a0: QStyle)

setStyleSheet(self, styleSheet: str)

setTabOrder(a0: QWidget, a1: QWidget)

setTabletTracking(self, enable: bool)

setToolTip(self, a0: str)

setToolTipDuration(self, msec: int)

setUpdatesEnabled(self, enable: bool)

setVisible(self, visible: bool)

setWhatsThis(self, a0: str)

setWindowFilePath(self, filePath: str)

setWindowFlag(self, a0: Qt.WindowType, on: bool = True)

setWindowFlags(self, type: Qt.WindowType)

setWindowIcon(self, icon: QIcon)

setWindowIconText(self, a0: str)

setWindowModality(self, windowModality: Qt.WindowModality)

setWindowModified(self, a0: bool)

setWindowOpacity(self, level: float)

setWindowRole(self, a0: str)

setWindowState(self, state: Qt.WindowState)

setWindowTitle(self, a0: str)

sharedPainter(self) → QPainter

show(self)

showEvent(event)

Emit a signal every time this pop up is shown.

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, a0: QWidget)

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

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

statusTip(self) → str

style(self) → QStyle

styleSheet(self) → str

subWidgetHasFocus()

Return True if any widget within the pop up has focus. False otherwise.

Note

Note that combo boxes have various list view and frame children that can receive focus (and which of these widgets can receive focus varies by OS). As a result, we check the full ancestry of the focus widget here rather than just checking it’s parent. Also note that we can’t use Qt’s isAncestorOf() function to check ancestry, since combo box drop downs are considered to be their own window and isAncestorOf() requires ancestors to be part of the same window.

tabletEvent(self, a0: QTabletEvent)

testAttribute(self, attribute: Qt.WidgetAttribute) → bool

thread(self) → QThread

timerEvent(self, a0: QTimerEvent)

toolTip(self) → str

toolTipDuration(self) → int

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str

underMouse(self) → bool

ungrabGesture(self, type: Qt.GestureType)

unsetCursor(self)

unsetLayoutDirection(self)

unsetLocale(self)

update(self)

update(self, a0: QRect) → None

update(self, a0: QRegion) → None

update(self, ax: int, ay: int, aw: int, ah: int) → None

updateGeometry(self)

updateMicroFocus(self, query: Qt.InputMethodQuery = Qt.ImQueryAll)

updatesEnabled(self) → bool

visibilityChanged

visibleRegion(self) → QRegion

whatsThis(self) → str

wheelEvent(self, a0: QWheelEvent)

width(self) → int

widthMM(self) → int

winId(self) → PyQt6.sip.voidptr

window(self) → QWidget

windowFilePath(self) → str

windowFlags(self) → Qt.WindowType

windowHandle(self) → QWindow

windowIcon(self) → QIcon

windowIconChanged

windowIconChanged(self, icon: QIcon) [signal]

windowIconText(self) → str

windowIconTextChanged

windowIconTextChanged(self, iconText: str) [signal]

windowModality(self) → Qt.WindowModality

windowOpacity(self) → float

windowRole(self) → str

windowState(self) → Qt.WindowState

windowTitle(self) → str

windowTitleChanged

windowTitleChanged(self, title: str) [signal]

windowType(self) → Qt.WindowType

x(self) → int

y(self) → int

class schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin

Bases: object

NAME = 'Transition State'

HELP_TOPIC = 'JAGUAR_TOPIC_TRANSITION_STATE_FOLDER'

SA_LOWEST_HESSIAN = 'Lowest Hessian eigenvector'

SA_LOWEST_NON_TORSIONAL = 'Lowest non-torsional mode'

SA_LOWEST_BOND_STRETCH = 'Lowest bond-stretch mode'

SA_RP_PATH = 'Reactant-product path'

SA_USER = 'User-selected eigenvector'

SA_ACTIVE = 'Active coordinate eigenvector'

SEARCH_ALONG_VALUES = {'Active coordinate eigenvector': -6, 'Lowest Hessian eigenvector': 0, 'Lowest bond-stretch mode': -2, 'Lowest non-torsional mode': -1, 'Reactant-product path': -5, 'User-selected eigenvector': 'User-selected eigenvector'}

STANDARD_SEARCH_ALONG = ('Lowest Hessian eigenvector', 'Lowest non-torsional mode', 'Lowest bond-stretch mode', 'User-selected eigenvector')

ADDITIONAL_SEARCH_ALONGS = ()

SEARCH_STANDARD = 0

setup()

onHessianRefinementToggled(checked)

repopulateSearchAlongCombo(search_method)

Replace the contents of the search along combo boxes based on the current search method

searchAlongChanged()

Respond to the user changing the search along method by updating the status of the eigenvector input widgets

getMmJagKeywords()

loadSettings(jag_input)

class schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab(parent, input_selector=None)

Bases: schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin, schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab, schrodinger.ui.qt.appframework2.markers.MarkerMixin

Transition State tab.

Variables

searchMethodChanged (PyQt5.QtCore.pyqtSignal) – a signal emitted when the search method changes

UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.multi_structures_ui' from '/scr/buildbot/savedbuilds/2024-1/NB/build-133/internal/lib/python3.8/site-packages/schrodinger/application/jaguar/gui/ui/multi_structures_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.transition_state_bottom_ui' from '/scr/buildbot/savedbuilds/2024-1/NB/build-133/internal/lib/python3.8/site-packages/schrodinger/application/jaguar/gui/ui/transition_state_bottom_ui.py'>, (<class 'schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector'>, 'molecule_sub_tab'), <module 'schrodinger.application.jaguar.gui.tabs.per_atom_basis_pop_up.per_atom_basis_ui' from '/scr/buildbot/savedbuilds/2024-1/NB/build-133/internal/lib/python3.8/site-packages/schrodinger/application/jaguar/gui/tabs/per_atom_basis_pop_up/per_atom_basis_ui.py'>)

LST_SEARCH_ALONG = ('Lowest Hessian eigenvector', 'Lowest non-torsional mode', 'Lowest bond-stretch mode', 'Reactant-product path', 'User-selected eigenvector')

QST_SEARCH_ALONG = ('Reactant-product path',)

ADDITIONAL_SEARCH_ALONGS = (('Lowest Hessian eigenvector', 'Lowest non-torsional mode', 'Lowest bond-stretch mode', 'Reactant-product path', 'User-selected eigenvector'), ('Reactant-product path',))

SEARCH_LST = 1

SEARCH_QST = 2

searchMethodChanged

setup()

Perform tab specific initialization. This function should be defined in subclasses if initialization is needed.

resetPAB()

Reset per-atom basis pop-up

reset()

Clear the stored structures

onLoadClicked()

Load the entries into the structure combos

projectUpdated()

Update the entries in the structure combos on project updates.

loadEntriesIntoStrucCombos()

Load and select the structures in structure combos according to the given entry ids

strucComboSelectionChanged(struc_type: int)

Update the selections on the structure combos to avoid duplicate selection.

Parameters

struc_type – Type of the structure combo whose selection is changed

onSearchMethodChanged()

Respond to the user changing the search method by updating the structure selectors and the search along combo box

getStructures()

Get all of the structures that are loaded into the tab. When LST is selected, the structure types don’t map to the Z-matrices in the standard way, so we have to override the parent function.

Returns

A list of: - the structure to be loaded into ZMAT1 (or None) - the structure to be loaded into ZMAT2 (or None) - the structure to be loaded into ZMAT3 (or None)

Return type

list

getMmJagKeywords()

Return all keywords that should be put into the mmjag handle. This function should be defined in subclasses.

Returns

All keywords that should be put into the mmjag handle

Return type

dict

Raises

schrodinger.application.jaguar.gui.utils.JaguarSettingError – If any settings are invalid.

setStructures(entry_ids, jag_input=None)

Override the parent function so we can properly handle LST jobs (which use zmat 1 and 2 for reactant and product instead of transition state and reactant)

isLst(jag_input)

Does the Jaguar input specify an LST job? This answer isn’t guaranteed to be correct, since there’s no way to distinguish a fully- or partially-specified LST job from a partially-specified QST job if the default initial LST guess is used. If the input is ambiguous and LST or QST is already selected, then we try to keep the setting as is.

Parameters

jag_input (schrodinger.application.jaguar.input.JaguarInput) – A JaguarInput object containing the job settings

Returns

True if the specified job is likely to be LST. False otherwise.

Return type

bool

saveSettings(jag_input, eid)

Save tab settings in jaguar handle. It is only used for settings which are not defined using keywords (typically per-atom settings). This function should be defined in subclasses for any tabs that contain per- atom settings.

Parameters

• jag_input (schrodinger.application.jaguar.input.JaguarInput) – The Jaguar handle to store the tab settings in

• eid (str) – The entry id of the structure in jag_input

loadPerAtomSettings(jag_input, eid=None, title=None)

Restore per-atom tab settings from mmjag keywords. This function should be defined in subclasses for any tabs that contain per-atom settings.

Parameters

• jag_input (schrodinger.application.jaguar.input.JaguarInput) – The Jaguar settings to base the tab settings on

• eid (str) – The entry id of the structure in jag_input

• title (str) – The title of the structure in jag_input

addPABJaguarMarker(atoms: list[_StructureAtom], settings: dict)

Add a workspace marker corresponding to the selected atoms for per-atom basis setting. Marker is also added to all the atoms with same name across the loaded structures

Parameters

• atoms – List of atoms to add the marker for

• settings – The marker settings

removePABJaguarMarker(atoms: list[_StructureAtom])

Remove the workspace markers corresponding to the given atoms per-atom basis setting. Also remove markers corresponding to all the atoms with same name across the loaded structures

Parameters

atoms – List of atoms to remove the marker for

setPABJaguarMarkerHighlighting(atoms: list[_StructureAtom], highlight: bool)

Change the workspace marker highlighting for the specified atom marker.

Parameters

• atoms – A list of atoms to change the highlighting for

• highlight – Whether to highlight the specified marker

ALL_STRUCS = [0, 1, 2]

ATOMS = 'atoms'

ATOM_LABELS = 'atom labels'

DrawChildren = 2

DrawWindowBackground = 1

ENTRY_TYPE_NAMES = ('transition state', 'reactant', 'product')

HELP_TOPIC = 'JAGUAR_TOPIC_TRANSITION_STATE_FOLDER'

IgnoreMask = 4

MULTIPLE_STRUC_JOB_TITLE = 'batch'

NAME = 'Transition State'

NEW_STRUC_DIFF_WARNING = '%s and %s entries have different %s.'

PRODUCT = 2

class PaintDeviceMetric(value)

Bases: enum.Enum

An enumeration.

PdmWidth = 1

PdmHeight = 2

PdmWidthMM = 3

PdmHeightMM = 4

PdmNumColors = 5

PdmDepth = 6

PdmDpiX = 7

PdmDpiY = 8

PdmPhysicalDpiX = 9

PdmPhysicalDpiY = 10

PdmDevicePixelRatio = 11

PdmDevicePixelRatioScaled = 12

PdmDepth = 6

PdmDevicePixelRatio = 11

PdmDevicePixelRatioScaled = 12

PdmDpiX = 7

PdmDpiY = 8

PdmHeight = 2

PdmHeightMM = 4

PdmNumColors = 5

PdmPhysicalDpiX = 9

PdmPhysicalDpiY = 10

PdmWidth = 1

PdmWidthMM = 3

REACTANT = 1

class RenderFlag(value)

Bases: enum.Flag

An enumeration.

DrawWindowBackground = 1

DrawChildren = 2

IgnoreMask = 4

SA_ACTIVE = 'Active coordinate eigenvector'

SA_LOWEST_BOND_STRETCH = 'Lowest bond-stretch mode'

SA_LOWEST_HESSIAN = 'Lowest Hessian eigenvector'

SA_LOWEST_NON_TORSIONAL = 'Lowest non-torsional mode'

SA_RP_PATH = 'Reactant-product path'

SA_USER = 'User-selected eigenvector'

SEARCH_ALONG_VALUES = {'Active coordinate eigenvector': -6, 'Lowest Hessian eigenvector': 0, 'Lowest bond-stretch mode': -2, 'Lowest non-torsional mode': -1, 'Reactant-product path': -5, 'User-selected eigenvector': 'User-selected eigenvector'}

SEARCH_STANDARD = 0

STANDARD_SEARCH_ALONG = ('Lowest Hessian eigenvector', 'Lowest non-torsional mode', 'Lowest bond-stretch mode', 'User-selected eigenvector')

TRANSITION_STATE = 0

__init__(parent, input_selector=None)

Perform common tab initialization. All tab specific initialization should go in setup().

Parameters

• parent (PyQt5.QtWidgets.QWidget) – The Qt parent widget

• input_selector (schrodinger.ui.qt.input_selector.InputSelector) – The panel’s input selector widget, if available.

acceptDrops(self) → bool

accessibleDescription(self) → str

accessibleName(self) → str

actionEvent(self, a0: QActionEvent)

actions(self) → List[QAction]

activate()

This function will be called whenever the user selects this tab. Subclasses can override it if necessary to, e.g., activate picking.

activateWindow(self)

addAction(self, action: QAction)

addActions(self, actions: Iterable[QAction])

addJaguarMarker(atoms, color=None, icon=None, text='', alt_color=None, highlight=False)

Add a marker to the specified atom(s)

Parameters

• atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to mark. A list may contain between one and four atoms (inclusive).

• color (tuple, str, int, or schrodinger.structutils.color) – The color of the marker and icon. May be an RGB tuple, color name, color index, or schrodinger.structutils.color instance. If not given, white will be used.

• icon (int) – The icon to draw next to the marker. Should be one the self.MARKER_ICONS constants. If not given, no icon will be drawn.

• text (str) – The text to display next to the marker. If not given, no text will be displayed. Note that this argument will be ignored when marking a single atom.

• alt_color (tuple, str, int, or schrodinger.structutils.color) – The alternate marker color. This color is always used for text, and is used for the marker and icon when highlight is True. If not given, color will be used.

• highlight (bool) – Whether the marker should be highlighted. A highlighted marker is indicated with thicker lines and is colored using alt_color instead of color.

Returns

The newly created marker

Return type

schrodinger.maestro.markers._BaseMarker

Raises

ValueError – If a marker already exists for the specified atoms

Note

Either an icon or text may be displayed on a marker, but not both. If both are given, only the text will be shown.

addMarker(atoms, color=(1.0, 1.0, 1.0), group_name=None)

Generates a set of simple, dot-styled markers for a group of atoms.

Parameters

• atoms (list or schrodinger.structure._StructureAtom) – List of atoms to be marked

• color (tuple of 3 floats) – The amount of red, green and blue to use, each ranging from 0.0 to 1.0. Default is white (1., 1., 1.).

@group_name: Optional string to set as the name of this group of markers in Maestro. If not set, a unique identifier will be generated.

addMarkerFromAsl(asl, color=(1.0, 1.0, 1.0), group_name=None)

Generates a set of simple, dot-styled markers for group of Workspace atoms that match the given ASL. Same atoms continue to be marked even if the Workspace is later modified such that ASL matching changes.

Parameters

• asl – ASL for the atoms to mark.

• color (tuple of 3 floats) – The amount of red, green and blue to use, each ranging from 0.0 to 1.0. Default is white (1., 1., 1.).

@group_name: Optional string to set as the name of this group of markers in Maestro. If not set, a unique identifier will be generated.

Returns

Marker object

Return type

markers.Marker

adjustSize(self)

autoFillBackground(self) → bool

backgroundRole(self) → QPalette.ColorRole

baseSize(self) → QSize

basis_changed

blockSignals(self, b: bool) → bool

changeEvent(self, a0: QEvent)

childAt(self, p: QPoint) → QWidget

childAt(self, ax: int, ay: int) → QWidget

childEvent(self, a0: QChildEvent)

children(self) → List[QObject]

childrenRect(self) → QRect

childrenRegion(self) → QRegion

clearFocus(self)

clearMask(self)

close(self) → bool

closeEvent(self, a0: QCloseEvent)

colorCount(self) → int

connectNotify(self, signal: QMetaMethod)

contentsMargins(self) → QMargins

contentsRect(self) → QRect

contextMenuEvent(self, a0: QContextMenuEvent)

contextMenuPolicy(self) → Qt.ContextMenuPolicy

create(self, window: PyQt6.sip.voidptr = 0, initializeWindow: bool = True, destroyOldWindow: bool = True)

createWindowContainer(window: QWindow, parent: typing.Optional[QWidget] = None, flags: Qt.WindowType = Qt.WindowFlags()) → QWidget

cursor(self) → QCursor

customContextMenuRequested

customContextMenuRequested(self, pos: QPoint) [signal]

customEvent(self, a0: QEvent)

deactivate()

This function will be called whenever the user selects a different tab. Subclasses can override it if necessary to, e.g., deactivate picking.

deleteLater(self)

depth(self) → int

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

destroyed

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

devType(self) → int

devicePixelRatio(self) → float

devicePixelRatioF(self) → float

devicePixelRatioFScale() → float

disconnect(a0: QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, signal: QMetaMethod)

dragEnterEvent(self, a0: QDragEnterEvent)

dragLeaveEvent(self, a0: QDragLeaveEvent)

dragMoveEvent(self, a0: QDragMoveEvent)

dropEvent(self, a0: QDropEvent)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

effectiveWinId(self) → PyQt6.sip.voidptr

enableStructureCombos(should_enable: bool)

Enable all the structure combos and corresponding structure type column entry

Parameters

should_enable – Should the structure combos be enabled

ensurePolished(self)

enterEvent(self, event: QEnterEvent)

error(msg)

Display an error dialog with the specified message

Parameters

msg (str) – The message to include in the error dialog

event(self, a0: QEvent) → bool

eventFilter(self, a0: QObject, a1: QEvent) → bool

find(a0: PyQt6.sip.voidptr) → QWidget

findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

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

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

findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

focusInEvent(self, a0: QFocusEvent)

focusNextChild(self) → bool

focusNextPrevChild(self, next: bool) → bool

focusOutEvent(self, a0: 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

getAllJaguarMarkers()

Get all markers._BaseMarker currently loaded into the panel

Returns

An iterator of markers._BaseMarker

Return type

iterator

getAllMarkers()

Get all markers.Marker loaded into the panel

Returns

list(markers.Marker)

Return type

list

getBasis(ignored=None)

Get the currently selected basis. If more than one basis set is specified, mixed_name will be returned. If the tab does not allow for specifying multiple basis sets, then this argument may be ignored.

Parameters

mixed_name (str) – The name to return if more than one basis set is specified

Returns

The currently selected basis

Return type

str

getDefaultKeywords()

Get the default keywords for this tab. Note that defaults that exist in mmjag should not be explicitly set here.

getEids()

Get the entry ids loaded into the tab

Returns

A tuple of - A list of entry ids loaded into the tab - Whether the structures have matching atoms and atom names (bool)

Return type

tuple

getJaguarMarker(atoms)

Retrieve a marker for the specified atom(s)

Parameters

atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to retrieve the marker for. A list may contain between one and four atoms (inclusive).

Returns

The requested marker

Return type

schrodinger.maestro.markers._BaseMarker

Raises

ValueError – If no marker exists for the specified atoms

Note

As indicated by the return type, this function only returns schrodinger.maestro.markers._BaseMarker derived markers. Multi atom schrodinger.maestro.markers.Marker type markers are not accessible in this way.

getRepresentativeStructure()

Retrieve one structure that can be used for basis selector calculations.

Returns

A single representative structure, or None if no structures are loaded.

Return type

schrodinger.structure.Structure or NoneType

getStructureTitleForJobname()

Get the structure title to be used in the job name. If the tab includes multiple structures, then MULTIPLE_STRUC_JOB_TITLE should be returned. If no structures have been specified yet, then None should be returned.

Returns

The structure title

Return type

str or NoneType

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

grabGesture(self, type: Qt.GestureType, flags: Qt.GestureFlag = Qt.GestureFlags())

grabKeyboard(self)

grabMouse(self)

grabMouse(self, a0: Union[QCursor, Qt.CursorShape]) → None

grabShortcut(self, key: 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, a0: int) → int

heightMM(self) → int

hide(self)

hideAllJaguarMarkers()

Hide all schrodinger.maestro.markers._BaseMarker markers for this panel

hideAllMarkers()

Hide all schrodinger.maestro.markers.Marker markers for this panel.

hideEvent(self, a0: QHideEvent)

inherits(self, classname: str) → bool

initPainter(self, painter: QPainter)

inputMethodEvent(self, a0: QInputMethodEvent)

inputMethodHints(self) → Qt.InputMethodHint

inputMethodQuery(self, a0: Qt.InputMethodQuery) → Any

insertAction(self, before: QAction, action: QAction)

insertActions(self, before: QAction, actions: Iterable[QAction])

installEventFilter(self, a0: QObject)

isActiveWindow(self) → bool

isAncestorOf(self, child: QWidget) → bool

isEnabled(self) → bool

isEnabledTo(self, a0: 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, signal: QMetaMethod) → bool

isVisible(self) → bool

isVisibleTo(self, a0: QWidget) → bool

isWidgetType(self) → bool

isWindow(self) → bool

isWindowModified(self) → bool

isWindowType(self) → bool

keyPressEvent(self, a0: QKeyEvent)

keyReleaseEvent(self, a0: QKeyEvent)

keyboardGrabber() → QWidget

killTimer(self, id: int)

layout(self) → QLayout

layoutDirection(self) → Qt.LayoutDirection

leaveEvent(self, a0: QEvent)

loadSettings(jag_input)

Restore tab settings from mmjag keywords. This function should be defined in subclasses.

Parameters

jag_input (schrodinger.application.jaguar.input.JaguarInput) – The Jaguar settings to base the tab settings on

locale(self) → QLocale

logicalDpiX(self) → int

logicalDpiY(self) → int

lower(self)

mapFrom(self, a0: QWidget, a1: QPoint) → QPoint

mapFrom(self, a0: QWidget, a1: QPointF) → QPointF

mapFromGlobal(self, a0: QPoint) → QPoint

mapFromGlobal(self, a0: QPointF) → QPointF

mapFromParent(self, a0: QPoint) → QPoint

mapFromParent(self, a0: QPointF) → QPointF

mapTo(self, a0: QWidget, a1: QPoint) → QPoint

mapTo(self, a0: QWidget, a1: QPointF) → QPointF

mapToGlobal(self, a0: QPoint) → QPoint

mapToGlobal(self, a0: QPointF) → QPointF

mapToParent(self, a0: QPoint) → QPoint

mapToParent(self, a0: QPointF) → QPointF

mask(self) → QRegion

maximumHeight(self) → int

maximumSize(self) → QSize

maximumWidth(self) → int

metaObject(self) → QMetaObject

metric(self, a0: QPaintDevice.PaintDeviceMetric) → int

minimumHeight(self) → int

minimumSize(self) → QSize

minimumSizeHint(self) → QSize

minimumWidth(self) → int

mouseDoubleClickEvent(self, a0: QMouseEvent)

mouseGrabber() → QWidget

mouseMoveEvent(self, a0: QMouseEvent)

mousePressEvent(self, a0: QMouseEvent)

mouseReleaseEvent(self, a0: QMouseEvent)

move(self, a0: QPoint)

move(self, ax: int, ay: int) → None

moveEvent(self, a0: QMoveEvent)

moveToThread(self, thread: QThread)

nativeEvent(self, eventType: QByteArray, message: PyQt6.sip.voidptr) → Tuple[bool, PyQt6.sip.voidptr]

nativeParentWidget(self) → QWidget

nextInFocusChain(self) → QWidget

normalGeometry(self) → QRect

objectName(self) → str

objectNameChanged

objectNameChanged(self, objectName: str) [signal]

onHessianRefinementToggled(checked)

onStrucListingsUpdated()

Update the structure warning label and molecule sub tab structure

overrideWindowFlags(self, type: Qt.WindowType)

overrideWindowState(self, state: Qt.WindowState)

paintEngine(self) → QPaintEngine

paintEvent(self, a0: 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, name: 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, signal: PYQT_SIGNAL) → int

rect(self) → QRect

releaseKeyboard(self)

releaseMouse(self)

releaseShortcut(self, id: int)

removeAction(self, action: QAction)

removeAllJaguarMarkers()

Remove all markers schrodinger.maestro.markers._BaseMarker markers from this panel

removeAllJaguarMarkersForEntry(eid)

Remove all markers for the specified entry id from this panel

Parameters

eid (str) – The entry id to remove markers for

removeAllMarkers()

Remove all schrodinger.maestro.markers.Marker markers from this panel.

removeEventFilter(self, a0: QObject)

removeJaguarMarker(marker)

Removes the specified marker

Parameters

marker (schrodinger.maestro.markers._BaseMarker) – The marker to remove

Raises

ValueError – If there is no marker on the specified atoms

removeJaguarMarkerForAtoms(atoms)

Removes the marker for specified atom(s)

Parameters

atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to retrieve the marker for. A list may contain between one and four atoms (inclusive).

Raises

ValueError – If no marker exists for the specified atoms

removeMarker(marker)

Remove the schrodinger.maestro.markers.Marker

Parameters

marker (schrodinger.maestro.markers.Marker) – Marker to remove

Raises

ValueError – If marker is the wrong type or is not associated with the panel.

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

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

repaint(self)

repaint(self, x: int, y: int, w: int, h: int) → None

repaint(self, a0: QRect) → None

repaint(self, a0: QRegion) → None

repopulateSearchAlongCombo(search_method)

Replace the contents of the search along combo boxes based on the current search method

resize(self, a0: QSize)

resize(self, w: int, h: int) → None

resizeEvent(self, a0: QResizeEvent)

restoreGeometry(self, geometry: QByteArray) → bool

saveGeometry(self) → QByteArray

screen(self) → QScreen

scroll(self, dx: int, dy: int)

scroll(self, dx: int, dy: int, a2: QRect) → None

searchAlongChanged()

Respond to the user changing the search along method by updating the status of the eigenvector input widgets

sender(self) → QObject

senderSignalIndex(self) → int

setAcceptDrops(self, on: bool)

setAccessibleDescription(self, description: str)

setAccessibleName(self, name: str)

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

setAutoFillBackground(self, enabled: bool)

setBackgroundRole(self, a0: QPalette.ColorRole)

setBaseSize(self, basew: int, baseh: int)

setBaseSize(self, s: QSize) → None

setContentsMargins(self, left: int, top: int, right: int, bottom: int)

setContentsMargins(self, margins: QMargins) → None

setContextMenuPolicy(self, policy: Qt.ContextMenuPolicy)

setCursor(self, a0: Union[QCursor, Qt.CursorShape])

setDisabled(self, a0: bool)

setEnabled(self, a0: bool)

setFixedHeight(self, h: int)

setFixedSize(self, a0: QSize)

setFixedSize(self, w: int, h: int) → None

setFixedWidth(self, w: int)

setFocus(self)

setFocus(self, reason: Qt.FocusReason) → None

setFocusPolicy(self, policy: Qt.FocusPolicy)

setFocusProxy(self, a0: QWidget)

setFont(self, a0: QFont)

setForegroundRole(self, a0: QPalette.ColorRole)

setGeometry(self, a0: QRect)

setGeometry(self, ax: int, ay: int, aw: int, ah: int) → None

setGraphicsEffect(self, effect: QGraphicsEffect)

setHidden(self, hidden: bool)

setInputLoaded(input_loaded: bool)

setInputMethodHints(self, hints: Qt.InputMethodHint)

setLayout(self, a0: QLayout)

setLayoutDirection(self, direction: Qt.LayoutDirection)

setLocale(self, locale: QLocale)

setMask(self, a0: QBitmap)

setMask(self, a0: QRegion) → None

setMaximumHeight(self, maxh: int)

setMaximumSize(self, maxw: int, maxh: int)

setMaximumSize(self, s: QSize) → None

setMaximumWidth(self, maxw: int)

setMinimumHeight(self, minh: int)

setMinimumSize(self, minw: int, minh: int)

setMinimumSize(self, s: QSize) → None

setMinimumWidth(self, minw: int)

setMouseTracking(self, enable: bool)

setObjectName(self, name: str)

setPalette(self, a0: QPalette)

setParent(self, parent: QWidget)

setParent(self, parent: QWidget, f: Qt.WindowType) → None

setProperty(self, name: str, value: Any) → bool

setScreen(self, a0: QScreen)

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

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

setSizeIncrement(self, w: int, h: int)

setSizeIncrement(self, s: QSize) → None

setSizePolicy(self, a0: QSizePolicy)

setSizePolicy(self, hor: QSizePolicy.Policy, ver: QSizePolicy.Policy) → None

setStatusTip(self, a0: str)

setStructureSelectorsEnabled(*enabled_list)

Enable or disable the three structure selection rows

setStyle(self, a0: QStyle)

setStyleSheet(self, styleSheet: str)

setTabOrder(a0: QWidget, a1: QWidget)

setTabletTracking(self, enable: bool)

setToolTip(self, a0: str)

setToolTipDuration(self, msec: int)

setUpdatesEnabled(self, enable: bool)

setVisible(self, visible: bool)

setWhatsThis(self, a0: str)

setWindowFilePath(self, filePath: str)

setWindowFlag(self, a0: Qt.WindowType, on: bool = True)

setWindowFlags(self, type: Qt.WindowType)

setWindowIcon(self, icon: QIcon)

setWindowIconText(self, a0: str)

setWindowModality(self, windowModality: Qt.WindowModality)

setWindowModified(self, a0: bool)

setWindowOpacity(self, level: float)

setWindowRole(self, a0: str)

setWindowState(self, state: Qt.WindowState)

setWindowTitle(self, a0: str)

setupInWorkspaceColumn()

Set up the In Workspace column.

sharedPainter(self) → QPainter

show(self)

showAllJaguarMarkers()

Show all schrodinger.maestro.markers._BaseMarker markers for which all marked atoms are in the workspace. Hide all other markers.

showAllMarkers()

Set all schrodinger.maestro.markers.Marker markers to be shown if the relevant atoms are in the workspace. These markers are hidden automatically by Maestro when atoms are excluded.

showEvent(self, a0: 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, a0: QWidget)

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

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

statusTip(self) → str

structureCbToggled(struc_type)

Respond to the specified structure inclusion checkbox being toggled by including or excluding the relevant structure from the workspace.

structureChanged

style(self) → QStyle

styleSheet(self) → str

tabletEvent(self, a0: QTabletEvent)

testAttribute(self, attribute: Qt.WidgetAttribute) → bool

thread(self) → QThread

timerEvent(self, a0: QTimerEvent)

toolTip(self) → str

toolTipDuration(self) → int

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str

underMouse(self) → bool

ungrabGesture(self, type: Qt.GestureType)

unsetCursor(self)

unsetLayoutDirection(self)

unsetLocale(self)

update(self)

update(self, a0: QRect) → None

update(self, a0: QRegion) → None

update(self, ax: int, ay: int, aw: int, ah: int) → None

updateGeometry(self)

updateMicroFocus(self, query: Qt.InputMethodQuery = Qt.ImQueryAll)

updateStrucCbsState()

Update the state of all structure checkboxes

updatesEnabled(self) → bool

validate()

Make sure that all of the appropriate structures are loaded and that they all have the same atoms.

validateStrucCombos() → str

Make sure that the structures are loaded in each of the required structure combos

visibleRegion(self) → QRegion

warning(msg)

Display a warning dialog with the specified message

Parameters

msg (str) – The message to include in the warning dialog

whatsThis(self) → str

wheelEvent(self, a0: QWheelEvent)

width(self) → int

widthMM(self) → int

winId(self) → PyQt6.sip.voidptr

window(self) → QWidget

windowFilePath(self) → str

windowFlags(self) → Qt.WindowType

windowHandle(self) → QWindow

windowIcon(self) → QIcon

windowIconChanged

windowIconChanged(self, icon: QIcon) [signal]

windowIconText(self) → str

windowIconTextChanged

windowIconTextChanged(self, iconText: str) [signal]

windowModality(self) → Qt.WindowModality

windowOpacity(self) → float

windowRole(self) → str

windowState(self) → Qt.WindowState

windowTitle(self) → str

windowTitleChanged

windowTitleChanged(self, title: str) [signal]

windowType(self) → Qt.WindowType

x(self) → int

y(self) → int

class schrodinger.application.jaguar.gui.tabs.transition_state_tab.ActiveTransitionStateTab(parent, input_selector=None)

Bases: schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab

Tab used in place of transition state tab in Transition State Search panel

STANDARD_SEARCH_ALONG = ('Lowest Hessian eigenvector', 'Lowest non-torsional mode', 'Lowest bond-stretch mode', 'User-selected eigenvector', 'Active coordinate eigenvector')

setup()

Setup UI elements

onSearchMethodChanged()

Respond to the user changing the search method by updating the structure selectors and the search along combo box

getActiveCoordItem()

Return the combobox item corresponding to “Active coordinate eigenvector” (itrvec=-6) or None if combobox does not have this item.

Returns

The model item corresponding to the Active Coordinates option in the search-along combo box

Return type

QtGui.QStandardItem or None

onActiveConstraintsChkChanged(state)

Enable or disable relevant UI elements when constraints are set as active on the optimization tab.

Parameters

state (bool) – Checked or not checked

onHessianRefinementToggled(checked)

Enable active coordinates radio button if active constraints

Parameters

checked (bool) – checked or not checked

repopulateSearchAlongCombo(search_method)

Replace the contents of the search along combo boxes based on the current search method

loadSettings(jag_input)

Restore settings from Jaguar input handle.

Parameters

jag_input (schrodinger.application.jaguar.input.JaguarInput) – The Jaguar settings to base the tab settings on

ADDITIONAL_SEARCH_ALONGS = (('Lowest Hessian eigenvector', 'Lowest non-torsional mode', 'Lowest bond-stretch mode', 'Reactant-product path', 'User-selected eigenvector'), ('Reactant-product path',))

ALL_STRUCS = [0, 1, 2]

ATOMS = 'atoms'

ATOM_LABELS = 'atom labels'

DrawChildren = 2

DrawWindowBackground = 1

ENTRY_TYPE_NAMES = ('transition state', 'reactant', 'product')

HELP_TOPIC = 'JAGUAR_TOPIC_TRANSITION_STATE_FOLDER'

IgnoreMask = 4

LST_SEARCH_ALONG = ('Lowest Hessian eigenvector', 'Lowest non-torsional mode', 'Lowest bond-stretch mode', 'Reactant-product path', 'User-selected eigenvector')

MULTIPLE_STRUC_JOB_TITLE = 'batch'

NAME = 'Transition State'

NEW_STRUC_DIFF_WARNING = '%s and %s entries have different %s.'

PRODUCT = 2

class PaintDeviceMetric(value)

Bases: enum.Enum

An enumeration.

PdmWidth = 1

PdmHeight = 2

PdmWidthMM = 3

PdmHeightMM = 4

PdmNumColors = 5

PdmDepth = 6

PdmDpiX = 7

PdmDpiY = 8

PdmPhysicalDpiX = 9

PdmPhysicalDpiY = 10

PdmDevicePixelRatio = 11

PdmDevicePixelRatioScaled = 12

PdmDepth = 6

PdmDevicePixelRatio = 11

PdmDevicePixelRatioScaled = 12

PdmDpiX = 7

PdmDpiY = 8

PdmHeight = 2

PdmHeightMM = 4

PdmNumColors = 5

PdmPhysicalDpiX = 9

PdmPhysicalDpiY = 10

PdmWidth = 1

PdmWidthMM = 3

QST_SEARCH_ALONG = ('Reactant-product path',)

REACTANT = 1

class RenderFlag(value)

Bases: enum.Flag

An enumeration.

DrawWindowBackground = 1

DrawChildren = 2

IgnoreMask = 4

SA_ACTIVE = 'Active coordinate eigenvector'

SA_LOWEST_BOND_STRETCH = 'Lowest bond-stretch mode'

SA_LOWEST_HESSIAN = 'Lowest Hessian eigenvector'

SA_LOWEST_NON_TORSIONAL = 'Lowest non-torsional mode'

SA_RP_PATH = 'Reactant-product path'

SA_USER = 'User-selected eigenvector'

SEARCH_ALONG_VALUES = {'Active coordinate eigenvector': -6, 'Lowest Hessian eigenvector': 0, 'Lowest bond-stretch mode': -2, 'Lowest non-torsional mode': -1, 'Reactant-product path': -5, 'User-selected eigenvector': 'User-selected eigenvector'}

SEARCH_LST = 1

SEARCH_QST = 2

SEARCH_STANDARD = 0

TRANSITION_STATE = 0

UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.multi_structures_ui' from '/scr/buildbot/savedbuilds/2024-1/NB/build-133/internal/lib/python3.8/site-packages/schrodinger/application/jaguar/gui/ui/multi_structures_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.transition_state_bottom_ui' from '/scr/buildbot/savedbuilds/2024-1/NB/build-133/internal/lib/python3.8/site-packages/schrodinger/application/jaguar/gui/ui/transition_state_bottom_ui.py'>, (<class 'schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector'>, 'molecule_sub_tab'), <module 'schrodinger.application.jaguar.gui.tabs.per_atom_basis_pop_up.per_atom_basis_ui' from '/scr/buildbot/savedbuilds/2024-1/NB/build-133/internal/lib/python3.8/site-packages/schrodinger/application/jaguar/gui/tabs/per_atom_basis_pop_up/per_atom_basis_ui.py'>)

__init__(parent, input_selector=None)

Perform common tab initialization. All tab specific initialization should go in setup().

Parameters

• parent (PyQt5.QtWidgets.QWidget) – The Qt parent widget

• input_selector (schrodinger.ui.qt.input_selector.InputSelector) – The panel’s input selector widget, if available.

acceptDrops(self) → bool

accessibleDescription(self) → str

accessibleName(self) → str

actionEvent(self, a0: QActionEvent)

actions(self) → List[QAction]

activate()

This function will be called whenever the user selects this tab. Subclasses can override it if necessary to, e.g., activate picking.

activateWindow(self)

addAction(self, action: QAction)

addActions(self, actions: Iterable[QAction])

addJaguarMarker(atoms, color=None, icon=None, text='', alt_color=None, highlight=False)

Add a marker to the specified atom(s)

Parameters

• atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to mark. A list may contain between one and four atoms (inclusive).

• color (tuple, str, int, or schrodinger.structutils.color) – The color of the marker and icon. May be an RGB tuple, color name, color index, or schrodinger.structutils.color instance. If not given, white will be used.

• icon (int) – The icon to draw next to the marker. Should be one the self.MARKER_ICONS constants. If not given, no icon will be drawn.

• text (str) – The text to display next to the marker. If not given, no text will be displayed. Note that this argument will be ignored when marking a single atom.

• alt_color (tuple, str, int, or schrodinger.structutils.color) – The alternate marker color. This color is always used for text, and is used for the marker and icon when highlight is True. If not given, color will be used.

• highlight (bool) – Whether the marker should be highlighted. A highlighted marker is indicated with thicker lines and is colored using alt_color instead of color.

Returns

The newly created marker

Return type

schrodinger.maestro.markers._BaseMarker

Raises

ValueError – If a marker already exists for the specified atoms

Note

Either an icon or text may be displayed on a marker, but not both. If both are given, only the text will be shown.

addMarker(atoms, color=(1.0, 1.0, 1.0), group_name=None)

Generates a set of simple, dot-styled markers for a group of atoms.

Parameters

• atoms (list or schrodinger.structure._StructureAtom) – List of atoms to be marked

• color (tuple of 3 floats) – The amount of red, green and blue to use, each ranging from 0.0 to 1.0. Default is white (1., 1., 1.).

@group_name: Optional string to set as the name of this group of markers in Maestro. If not set, a unique identifier will be generated.

addMarkerFromAsl(asl, color=(1.0, 1.0, 1.0), group_name=None)

Generates a set of simple, dot-styled markers for group of Workspace atoms that match the given ASL. Same atoms continue to be marked even if the Workspace is later modified such that ASL matching changes.

Parameters

• asl – ASL for the atoms to mark.

• color (tuple of 3 floats) – The amount of red, green and blue to use, each ranging from 0.0 to 1.0. Default is white (1., 1., 1.).

@group_name: Optional string to set as the name of this group of markers in Maestro. If not set, a unique identifier will be generated.

Returns

Marker object

Return type

markers.Marker

addPABJaguarMarker(atoms: list[_StructureAtom], settings: dict)

Add a workspace marker corresponding to the selected atoms for per-atom basis setting. Marker is also added to all the atoms with same name across the loaded structures

Parameters

• atoms – List of atoms to add the marker for

• settings – The marker settings

adjustSize(self)

autoFillBackground(self) → bool

backgroundRole(self) → QPalette.ColorRole

baseSize(self) → QSize

basis_changed

blockSignals(self, b: bool) → bool

changeEvent(self, a0: QEvent)

childAt(self, p: QPoint) → QWidget

childAt(self, ax: int, ay: int) → QWidget

childEvent(self, a0: QChildEvent)

children(self) → List[QObject]

childrenRect(self) → QRect

childrenRegion(self) → QRegion

clearFocus(self)

clearMask(self)

close(self) → bool

closeEvent(self, a0: QCloseEvent)

colorCount(self) → int

connectNotify(self, signal: QMetaMethod)

contentsMargins(self) → QMargins

contentsRect(self) → QRect

contextMenuEvent(self, a0: QContextMenuEvent)

contextMenuPolicy(self) → Qt.ContextMenuPolicy

create(self, window: PyQt6.sip.voidptr = 0, initializeWindow: bool = True, destroyOldWindow: bool = True)

createWindowContainer(window: QWindow, parent: typing.Optional[QWidget] = None, flags: Qt.WindowType = Qt.WindowFlags()) → QWidget

cursor(self) → QCursor

customContextMenuRequested

customContextMenuRequested(self, pos: QPoint) [signal]

customEvent(self, a0: QEvent)

deactivate()

This function will be called whenever the user selects a different tab. Subclasses can override it if necessary to, e.g., deactivate picking.

deleteLater(self)

depth(self) → int

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

destroyed

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

devType(self) → int

devicePixelRatio(self) → float

devicePixelRatioF(self) → float

devicePixelRatioFScale() → float

disconnect(a0: QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, signal: QMetaMethod)

dragEnterEvent(self, a0: QDragEnterEvent)

dragLeaveEvent(self, a0: QDragLeaveEvent)

dragMoveEvent(self, a0: QDragMoveEvent)

dropEvent(self, a0: QDropEvent)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

effectiveWinId(self) → PyQt6.sip.voidptr

enableStructureCombos(should_enable: bool)

Enable all the structure combos and corresponding structure type column entry

Parameters

should_enable – Should the structure combos be enabled

ensurePolished(self)

enterEvent(self, event: QEnterEvent)

error(msg)

Display an error dialog with the specified message

Parameters

msg (str) – The message to include in the error dialog

event(self, a0: QEvent) → bool

eventFilter(self, a0: QObject, a1: QEvent) → bool

find(a0: PyQt6.sip.voidptr) → QWidget

findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

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

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

findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

focusInEvent(self, a0: QFocusEvent)

focusNextChild(self) → bool

focusNextPrevChild(self, next: bool) → bool

focusOutEvent(self, a0: 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

getAllJaguarMarkers()

Get all markers._BaseMarker currently loaded into the panel

Returns

An iterator of markers._BaseMarker

Return type

iterator

getAllMarkers()

Get all markers.Marker loaded into the panel

Returns

list(markers.Marker)

Return type

list

getBasis(ignored=None)

Get the currently selected basis. If more than one basis set is specified, mixed_name will be returned. If the tab does not allow for specifying multiple basis sets, then this argument may be ignored.

Parameters

mixed_name (str) – The name to return if more than one basis set is specified

Returns

The currently selected basis

Return type

str

getDefaultKeywords()

Get the default keywords for this tab. Note that defaults that exist in mmjag should not be explicitly set here.

getEids()

Get the entry ids loaded into the tab

Returns

A tuple of - A list of entry ids loaded into the tab - Whether the structures have matching atoms and atom names (bool)

Return type

tuple

getJaguarMarker(atoms)

Retrieve a marker for the specified atom(s)

Parameters

atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to retrieve the marker for. A list may contain between one and four atoms (inclusive).

Returns

The requested marker

Return type

schrodinger.maestro.markers._BaseMarker

Raises

ValueError – If no marker exists for the specified atoms

Note

As indicated by the return type, this function only returns schrodinger.maestro.markers._BaseMarker derived markers. Multi atom schrodinger.maestro.markers.Marker type markers are not accessible in this way.

getMmJagKeywords()

Return all keywords that should be put into the mmjag handle. This function should be defined in subclasses.

Returns

All keywords that should be put into the mmjag handle

Return type

dict

Raises

schrodinger.application.jaguar.gui.utils.JaguarSettingError – If any settings are invalid.

getRepresentativeStructure()

Retrieve one structure that can be used for basis selector calculations.

Returns

A single representative structure, or None if no structures are loaded.

Return type

schrodinger.structure.Structure or NoneType

getStructureTitleForJobname()

Get the structure title to be used in the job name. If the tab includes multiple structures, then MULTIPLE_STRUC_JOB_TITLE should be returned. If no structures have been specified yet, then None should be returned.

Returns

The structure title

Return type

str or NoneType

getStructures()

Get all of the structures that are loaded into the tab. When LST is selected, the structure types don’t map to the Z-matrices in the standard way, so we have to override the parent function.

Returns

A list of: - the structure to be loaded into ZMAT1 (or None) - the structure to be loaded into ZMAT2 (or None) - the structure to be loaded into ZMAT3 (or None)

Return type

list

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

grabGesture(self, type: Qt.GestureType, flags: Qt.GestureFlag = Qt.GestureFlags())

grabKeyboard(self)

grabMouse(self)

grabMouse(self, a0: Union[QCursor, Qt.CursorShape]) → None

grabShortcut(self, key: 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, a0: int) → int

heightMM(self) → int

hide(self)

hideAllJaguarMarkers()

Hide all schrodinger.maestro.markers._BaseMarker markers for this panel

hideAllMarkers()

Hide all schrodinger.maestro.markers.Marker markers for this panel.

hideEvent(self, a0: QHideEvent)

inherits(self, classname: str) → bool

initPainter(self, painter: QPainter)

inputMethodEvent(self, a0: QInputMethodEvent)

inputMethodHints(self) → Qt.InputMethodHint

inputMethodQuery(self, a0: Qt.InputMethodQuery) → Any

insertAction(self, before: QAction, action: QAction)

insertActions(self, before: QAction, actions: Iterable[QAction])

installEventFilter(self, a0: QObject)

isActiveWindow(self) → bool

isAncestorOf(self, child: QWidget) → bool

isEnabled(self) → bool

isEnabledTo(self, a0: QWidget) → bool

isFullScreen(self) → bool

isHidden(self) → bool

isLeftToRight(self) → bool

isLst(jag_input)

Does the Jaguar input specify an LST job? This answer isn’t guaranteed to be correct, since there’s no way to distinguish a fully- or partially-specified LST job from a partially-specified QST job if the default initial LST guess is used. If the input is ambiguous and LST or QST is already selected, then we try to keep the setting as is.

Parameters

jag_input (schrodinger.application.jaguar.input.JaguarInput) – A JaguarInput object containing the job settings

Returns

True if the specified job is likely to be LST. False otherwise.

Return type

bool

isMaximized(self) → bool

isMinimized(self) → bool

isModal(self) → bool

isRightToLeft(self) → bool

isSignalConnected(self, signal: QMetaMethod) → bool

isVisible(self) → bool

isVisibleTo(self, a0: QWidget) → bool

isWidgetType(self) → bool

isWindow(self) → bool

isWindowModified(self) → bool

isWindowType(self) → bool

keyPressEvent(self, a0: QKeyEvent)

keyReleaseEvent(self, a0: QKeyEvent)

keyboardGrabber() → QWidget

killTimer(self, id: int)

layout(self) → QLayout

layoutDirection(self) → Qt.LayoutDirection

leaveEvent(self, a0: QEvent)

loadEntriesIntoStrucCombos()

Load and select the structures in structure combos according to the given entry ids

loadPerAtomSettings(jag_input, eid=None, title=None)

Restore per-atom tab settings from mmjag keywords. This function should be defined in subclasses for any tabs that contain per-atom settings.

Parameters

• jag_input (schrodinger.application.jaguar.input.JaguarInput) – The Jaguar settings to base the tab settings on

• eid (str) – The entry id of the structure in jag_input

• title (str) – The title of the structure in jag_input

locale(self) → QLocale

logicalDpiX(self) → int

logicalDpiY(self) → int

lower(self)

mapFrom(self, a0: QWidget, a1: QPoint) → QPoint

mapFrom(self, a0: QWidget, a1: QPointF) → QPointF

mapFromGlobal(self, a0: QPoint) → QPoint

mapFromGlobal(self, a0: QPointF) → QPointF

mapFromParent(self, a0: QPoint) → QPoint

mapFromParent(self, a0: QPointF) → QPointF

mapTo(self, a0: QWidget, a1: QPoint) → QPoint

mapTo(self, a0: QWidget, a1: QPointF) → QPointF

mapToGlobal(self, a0: QPoint) → QPoint

mapToGlobal(self, a0: QPointF) → QPointF

mapToParent(self, a0: QPoint) → QPoint

mapToParent(self, a0: QPointF) → QPointF

mask(self) → QRegion

maximumHeight(self) → int

maximumSize(self) → QSize

maximumWidth(self) → int

metaObject(self) → QMetaObject

metric(self, a0: QPaintDevice.PaintDeviceMetric) → int

minimumHeight(self) → int

minimumSize(self) → QSize

minimumSizeHint(self) → QSize

minimumWidth(self) → int

mouseDoubleClickEvent(self, a0: QMouseEvent)

mouseGrabber() → QWidget

mouseMoveEvent(self, a0: QMouseEvent)

mousePressEvent(self, a0: QMouseEvent)

mouseReleaseEvent(self, a0: QMouseEvent)

move(self, a0: QPoint)

move(self, ax: int, ay: int) → None

moveEvent(self, a0: QMoveEvent)

moveToThread(self, thread: QThread)

nativeEvent(self, eventType: QByteArray, message: PyQt6.sip.voidptr) → Tuple[bool, PyQt6.sip.voidptr]

nativeParentWidget(self) → QWidget

nextInFocusChain(self) → QWidget

normalGeometry(self) → QRect

objectName(self) → str

objectNameChanged

objectNameChanged(self, objectName: str) [signal]

onLoadClicked()

Load the entries into the structure combos

onStrucListingsUpdated()

Update the structure warning label and molecule sub tab structure

overrideWindowFlags(self, type: Qt.WindowType)

overrideWindowState(self, state: Qt.WindowState)

paintEngine(self) → QPaintEngine

paintEvent(self, a0: 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

projectUpdated()

Update the entries in the structure combos on project updates.

property(self, name: 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, signal: PYQT_SIGNAL) → int

rect(self) → QRect

releaseKeyboard(self)

releaseMouse(self)

releaseShortcut(self, id: int)

removeAction(self, action: QAction)

removeAllJaguarMarkers()

Remove all markers schrodinger.maestro.markers._BaseMarker markers from this panel

removeAllJaguarMarkersForEntry(eid)

Remove all markers for the specified entry id from this panel

Parameters

eid (str) – The entry id to remove markers for

removeAllMarkers()

Remove all schrodinger.maestro.markers.Marker markers from this panel.

removeEventFilter(self, a0: QObject)

removeJaguarMarker(marker)

Removes the specified marker

Parameters

marker (schrodinger.maestro.markers._BaseMarker) – The marker to remove

Raises

ValueError – If there is no marker on the specified atoms

removeJaguarMarkerForAtoms(atoms)

Removes the marker for specified atom(s)

Parameters

atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to retrieve the marker for. A list may contain between one and four atoms (inclusive).

Raises

ValueError – If no marker exists for the specified atoms

removeMarker(marker)

Remove the schrodinger.maestro.markers.Marker

Parameters

marker (schrodinger.maestro.markers.Marker) – Marker to remove

Raises

ValueError – If marker is the wrong type or is not associated with the panel.

removePABJaguarMarker(atoms: list[_StructureAtom])

Remove the workspace markers corresponding to the given atoms per-atom basis setting. Also remove markers corresponding to all the atoms with same name across the loaded structures

Parameters

atoms – List of atoms to remove the marker for

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

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

repaint(self)

repaint(self, x: int, y: int, w: int, h: int) → None

repaint(self, a0: QRect) → None

repaint(self, a0: QRegion) → None

reset()

Clear the stored structures

resetPAB()

Reset per-atom basis pop-up

resize(self, a0: QSize)

resize(self, w: int, h: int) → None

resizeEvent(self, a0: QResizeEvent)

restoreGeometry(self, geometry: QByteArray) → bool

saveGeometry(self) → QByteArray

saveSettings(jag_input, eid)

Save tab settings in jaguar handle. It is only used for settings which are not defined using keywords (typically per-atom settings). This function should be defined in subclasses for any tabs that contain per- atom settings.

Parameters

• jag_input (schrodinger.application.jaguar.input.JaguarInput) – The Jaguar handle to store the tab settings in

• eid (str) – The entry id of the structure in jag_input

screen(self) → QScreen

scroll(self, dx: int, dy: int)

scroll(self, dx: int, dy: int, a2: QRect) → None

searchAlongChanged()

Respond to the user changing the search along method by updating the status of the eigenvector input widgets

searchMethodChanged

sender(self) → QObject

senderSignalIndex(self) → int

setAcceptDrops(self, on: bool)

setAccessibleDescription(self, description: str)

setAccessibleName(self, name: str)

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

setAutoFillBackground(self, enabled: bool)

setBackgroundRole(self, a0: QPalette.ColorRole)

setBaseSize(self, basew: int, baseh: int)

setBaseSize(self, s: QSize) → None

setContentsMargins(self, left: int, top: int, right: int, bottom: int)

setContentsMargins(self, margins: QMargins) → None

setContextMenuPolicy(self, policy: Qt.ContextMenuPolicy)

setCursor(self, a0: Union[QCursor, Qt.CursorShape])

setDisabled(self, a0: bool)

setEnabled(self, a0: bool)

setFixedHeight(self, h: int)

setFixedSize(self, a0: QSize)

setFixedSize(self, w: int, h: int) → None

setFixedWidth(self, w: int)

setFocus(self)

setFocus(self, reason: Qt.FocusReason) → None

setFocusPolicy(self, policy: Qt.FocusPolicy)

setFocusProxy(self, a0: QWidget)

setFont(self, a0: QFont)

setForegroundRole(self, a0: QPalette.ColorRole)

setGeometry(self, a0: QRect)

setGeometry(self, ax: int, ay: int, aw: int, ah: int) → None

setGraphicsEffect(self, effect: QGraphicsEffect)

setHidden(self, hidden: bool)

setInputLoaded(input_loaded: bool)

setInputMethodHints(self, hints: Qt.InputMethodHint)

setLayout(self, a0: QLayout)

setLayoutDirection(self, direction: Qt.LayoutDirection)

setLocale(self, locale: QLocale)

setMask(self, a0: QBitmap)

setMask(self, a0: QRegion) → None

setMaximumHeight(self, maxh: int)

setMaximumSize(self, maxw: int, maxh: int)

setMaximumSize(self, s: QSize) → None

setMaximumWidth(self, maxw: int)

setMinimumHeight(self, minh: int)

setMinimumSize(self, minw: int, minh: int)

setMinimumSize(self, s: QSize) → None

setMinimumWidth(self, minw: int)

setMouseTracking(self, enable: bool)

setObjectName(self, name: str)

setPABJaguarMarkerHighlighting(atoms: list[_StructureAtom], highlight: bool)

Change the workspace marker highlighting for the specified atom marker.

Parameters

• atoms – A list of atoms to change the highlighting for

• highlight – Whether to highlight the specified marker

setPalette(self, a0: QPalette)

setParent(self, parent: QWidget)

setParent(self, parent: QWidget, f: Qt.WindowType) → None

setProperty(self, name: str, value: Any) → bool

setScreen(self, a0: QScreen)

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

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

setSizeIncrement(self, w: int, h: int)

setSizeIncrement(self, s: QSize) → None

setSizePolicy(self, a0: QSizePolicy)

setSizePolicy(self, hor: QSizePolicy.Policy, ver: QSizePolicy.Policy) → None

setStatusTip(self, a0: str)

setStructureSelectorsEnabled(*enabled_list)

Enable or disable the three structure selection rows

setStructures(entry_ids, jag_input=None)

Override the parent function so we can properly handle LST jobs (which use zmat 1 and 2 for reactant and product instead of transition state and reactant)

setStyle(self, a0: QStyle)

setStyleSheet(self, styleSheet: str)

setTabOrder(a0: QWidget, a1: QWidget)

setTabletTracking(self, enable: bool)

setToolTip(self, a0: str)

setToolTipDuration(self, msec: int)

setUpdatesEnabled(self, enable: bool)

setVisible(self, visible: bool)

setWhatsThis(self, a0: str)

setWindowFilePath(self, filePath: str)

setWindowFlag(self, a0: Qt.WindowType, on: bool = True)

setWindowFlags(self, type: Qt.WindowType)

setWindowIcon(self, icon: QIcon)

setWindowIconText(self, a0: str)

setWindowModality(self, windowModality: Qt.WindowModality)

setWindowModified(self, a0: bool)

setWindowOpacity(self, level: float)

setWindowRole(self, a0: str)

setWindowState(self, state: Qt.WindowState)

setWindowTitle(self, a0: str)

setupInWorkspaceColumn()

Set up the In Workspace column.

sharedPainter(self) → QPainter

show(self)

showAllJaguarMarkers()

Show all schrodinger.maestro.markers._BaseMarker markers for which all marked atoms are in the workspace. Hide all other markers.

showAllMarkers()

Set all schrodinger.maestro.markers.Marker markers to be shown if the relevant atoms are in the workspace. These markers are hidden automatically by Maestro when atoms are excluded.

showEvent(self, a0: 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, a0: QWidget)

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

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

statusTip(self) → str

strucComboSelectionChanged(struc_type: int)

Update the selections on the structure combos to avoid duplicate selection.

Parameters

struc_type – Type of the structure combo whose selection is changed

structureCbToggled(struc_type)

Respond to the specified structure inclusion checkbox being toggled by including or excluding the relevant structure from the workspace.

structureChanged

style(self) → QStyle

styleSheet(self) → str

tabletEvent(self, a0: QTabletEvent)

testAttribute(self, attribute: Qt.WidgetAttribute) → bool

thread(self) → QThread

timerEvent(self, a0: QTimerEvent)

toolTip(self) → str

toolTipDuration(self) → int

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str

underMouse(self) → bool

ungrabGesture(self, type: Qt.GestureType)

unsetCursor(self)

unsetLayoutDirection(self)

unsetLocale(self)

update(self)

update(self, a0: QRect) → None

update(self, a0: QRegion) → None

update(self, ax: int, ay: int, aw: int, ah: int) → None

updateGeometry(self)

updateMicroFocus(self, query: Qt.InputMethodQuery = Qt.ImQueryAll)

updateStrucCbsState()

Update the state of all structure checkboxes

updatesEnabled(self) → bool

validate()

Make sure that all of the appropriate structures are loaded and that they all have the same atoms.

validateStrucCombos() → str

Make sure that the structures are loaded in each of the required structure combos

visibleRegion(self) → QRegion

warning(msg)

Display a warning dialog with the specified message

Parameters

msg (str) – The message to include in the warning dialog

whatsThis(self) → str

wheelEvent(self, a0: QWheelEvent)

width(self) → int

widthMM(self) → int

winId(self) → PyQt6.sip.voidptr

window(self) → QWidget

windowFilePath(self) → str

windowFlags(self) → Qt.WindowType

windowHandle(self) → QWindow

windowIcon(self) → QIcon

windowIconChanged

windowIconChanged(self, icon: QIcon) [signal]

windowIconText(self) → str

windowIconTextChanged

windowIconTextChanged(self, iconText: str) [signal]

windowModality(self) → Qt.WindowModality

windowOpacity(self) → float

windowRole(self) → str

windowState(self) → Qt.WindowState

windowTitle(self) → str

windowTitleChanged

windowTitleChanged(self, title: str) [signal]

windowType(self) → Qt.WindowType

x(self) → int

y(self) → int