schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab module

class schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab(parent, input_selector=None)

Bases: schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab

” The Molecules tab used in the Reactions panel.

Note

This tab does not implement loadSettings() or reset(). However, resetting the Reactions tab will remove all structures, which will result in this tab being cleared. Also note that this tab does not load default mmjag settings into its MoleculeSubTab components. Instead, we assume that the initial settings for MoleculeSubTab conform to mmjag defaults, which they do, assuming that the mmjag defaults for symmetry, charge, and spin multiplicity don’t change.

NAME = 'Molecules'
HELP_TOPIC = 'JAGUAR_TOPIC_MOLECULE_FOLDER'
UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.reaction_molecules_tab_ui' from '/scr/buildbot/savedbuilds/2023-2/NB/build-121/internal/lib/python3.8/site-packages/schrodinger/application/jaguar/gui/ui/reaction_molecules_tab_ui.py'>,)
setup()

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

newParticipant(txt)

Adds a participant to the combo box, and adds a molecule widget to the stacked widget.

Parameters

txt (str) – The txt to show along with the participant in combo

removeParticipant(txt)

Removes participant from combo box and removes its molecule widget

Parameters

txt (str) – Text for molecule matching combo text

showMoleculeWidgetForParticipant(txt)

Show a molecule widget in the stackedWidget for a participant

Parameters

txt (str) – Text for molecule matching combo text

changeMoleculeForParticipant(txt, struct)

Show a molecule widget in the stackedWidget for a participant

Parameters

  • txt (str) – Text for molecule matching combo text

  • struct (structure.Structure) – The new structure for the participant

getParticipants()

Return structures and keywords for all participants

Returns

A tuple of:

  • A list of all reactants

  • A list of all products

Each participant is represented as a tuple of:

Return type

tuple

validate()

Make sure that all participants have a valid basis selected

Returns

None if all participants are valid. An error string otherwise.

Return type

NoneType or str

DrawChildren = 2
DrawWindowBackground = 1
IgnoreMask = 4
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
class RenderFlag(value)

Bases: enum.Flag

An enumeration.

DrawWindowBackground = 1
DrawChildren = 2
IgnoreMask = 4
__init__(parent, input_selector=None)

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

Parameters
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])
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)
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
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
getDefaultKeywords()

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

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.

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(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)
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
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]

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)
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
reset()

Reset the tab to its original state. Note that this function is only necessary for settings that are not stored in the mmjag handle. For mmjag settings, reset will be carried out using loadSettings with a default schrodinger.application.jaguar.input.JaguarInput object. This function should only be defined in subclasses if there are any settings that cannot be reset via loadSettings.

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
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)
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)
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)
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(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
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)
updatesEnabled(self) → bool
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