Package schrodinger :: Package application :: Package jaguar :: Package gui :: Module base_panel :: Class BaseJaguarPanel

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Class BaseJaguarPanel

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ui.qt.appframework2.maestro_callback.AbstractMaestroCallbackMixin --+            
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            ui.qt.appframework2.maestro_callback.MaestroCallbackMixin --+        
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                                                           object --+   |        
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                              ui.qt.appframework2.markers.MarkerMixin --+        
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                                                       object --+       |        
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                       ui.qt.appframework2.settings.SettingsMixin --+   |        
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                      ui.qt.appframework2.settings.SettingsPanelMixin --+        
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                                       object --+                       |        
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                                sip.simplewrapper --+                   |        
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                                          sip.wrapper --+               |        
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                                     PyQt4.QtCore.QObject --+           |        
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                                           object --+       |           |        
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                                    sip.simplewrapper --+   |           |        
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                                 PyQt4.QtGui.QPaintDevice --+           |        
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                                          PyQt4.QtGui.QWidget --+       |        
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                            ui.qt.appframework2.baseapp.BasePanel --+   |        
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                                                       object --+   |   |        
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                   ui.qt.appframework2.validation.ValidationMixin --+   |        
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                           ui.qt.appframework2.baseapp.ValidatedPanel --+        
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                                              ui.qt.appframework2.af2.App --+    
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                                               ui.qt.appframework2.af2.JobApp --+
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                                                                               BaseJaguarPanel

Known Subclasses:

A base class for all Jaguar GUIs. Subclasses should define TABS and TASK_NAME.

Nested Classes

[hide private]

Inherited from PyQt4.QtGui.QWidget: RenderFlag, RenderFlags

Inherited from PyQt4.QtGui.QPaintDevice: PaintDeviceMetric

Instance Methods

[hide private]

getTabParentAndLayout(self)
Get the parent widget for all tabs and layout to place the tabs into.

setPanelOptions(self)
Define instance variables that specify the creation of the panel.

setup(self)
Instantiate the tab widget and tabs.

schrodinger.application.jaguar.input.JaguarInput

_createDefaultJagInput(self)
Create a JaguarInput object containing default keywords taken from all tabs

getTab(self, tab_class)
Get the tab of the specified class

_help(self)
Display help for the current tab

schrodinger.job.jobcontrol.Job

launchJaguarJob(self, jag_input)
Launch the specified job.

createCmd(self)
Create the command line for job launching.

list

jobnameArg(self)
Build the command line arguments for passing the job name.

getNumStructures(self)
Get the number of structures that this panel is currently representing

bool or NoneType

reset(self)
Reset the panel after prompting the user for confirmation

_loadSettings(self, jag_input, eid=None, title=None)
Load the specified settings into the tabs and store them in self._jag_input.

_loadSettingsWithErrors(self, jag_input, eid=None, title=None)
Load the specified settings.

bool

_resetWarning(self)
Display a dialog to confirm that the user really wants to reset the panel

getConfigDialog(self)
Get the job configuration dialog

runTabValidation(self)
Run validation for each tab.

str

generateStatus(self)
Create the status bar message.

str or NoneType

generateJaguarStatus(self)
Create a Jaguar-specific status bar message.

_updateMmJag(self)
Update the mmjag object that will be used to build the input file

dict

getMmJagKeywords(self)
Get Jaguar keywords that are specific to this panel and not set in any of the tabs.

_runPreflight(self)
Run the mmjag preflight check, which checks settings for consistency.

_getAllJagSettings(self)
Get the Jaguar keywords from all tabs and store them in the JaguarInput handle.

_getPerAtomSettings(self, eid)
Load all per-atom settings into self._jag_input

_clearPerAtomSettings(self)
Remove all per-atom settings from the mmjag handle

_clearFreezeProperties(self, struc)
Delete all Maestro "freeze" atom properties, as these freezes didn't come from the panel but will be enforced as constraints by the Jaguar backend.

_cleanStructureForJagInput(self, struct)
Clean up a structure for use in Jaguar input, making sure it has proper atom names and removing any stale properties

_addStructureToMmJag(self)
Add the structure specified in the input selector frame to the mmjag handle.

Inherited from ui.qt.appframework2.af2.JobApp: __init__, cleanup, cleanupWriteCmd, closeEvent, cmdListToCmd, configDialogSettings, createBottomBar, createJobDir, getCmdListArgValue, getJobSpec, jobDir, jobname, jobnameData, jobnameDataChanged, lastJobCompleted, launchFromJobSpec, launchJobCmd, launchLauncher, launchScript, launcherToCmdList, layOut, makeLauncher, registerJob, runMaestro, sanitizeJobnameText, setConfigDialogSettings, setDefaults, setJobname, setupJobCmd, showSTUDialog, syncConfigDialog, updateJobname, updateStatusBar, writeJobCmd

Inherited from ui.qt.appframework2.af2.JobApp (private): _addCmdParam, _addJaguarOptions, _formJaguarCPUFlags, _getSHFilename, _getSTUZIPFilename, _getStandardJobnames, _makeLocaleIndependent, _periodicJobCheck, _populateEmptyJobname, _settings, _start, _startOrWrite, _write, _writeSTU

Inherited from ui.qt.appframework2.af2.App: addMainTaskRunner, createInputSelector, currentTaskRunner, getWorkspaceStructure, processSettings, processTaskMessage, resetAllRunners, setCurrentTask, setupTaskRunner, showEvent, showProgressBarForJob

Inherited from ui.qt.appframework2.af2.App (private): _applySettingsFromGroup, _close, _getSettingsForGroup, _prestart, _prewrite, _read, _reset, _statusShrunk, _updateProgressBar

Inherited from ui.qt.appframework2.maestro_callback.AbstractMaestroCallbackMixin: buildCallbackDicts, ignoreMaestroCallbacks

Inherited from ui.qt.appframework2.maestro_callback.AbstractMaestroCallbackMixin (private): _addCallbacks, _closeEvent, _delayedCallbacks, _removeCallbacks, _showEvent

Inherited from ui.qt.appframework2.markers.MarkerMixin: addJaguarMarker, addMarker, addMarkerFromAsl, getAllJaguarMarkers, getAllMarkers, getJaguarMarker, hideAllJaguarMarkers, hideAllMarkers, hideEvent, removeAllJaguarMarkers, removeAllJaguarMarkersForEntry, removeAllMarkers, removeJaguarMarker, removeJaguarMarkerForAtoms, removeMarker, show, showAllJaguarMarkers, showAllMarkers

Inherited from ui.qt.appframework2.markers.MarkerMixin (private): _calcEntryAtomTotal, _canonicalizeAtomOrder, _clearInvalidatedJaguarMarkers, _createAtomAsl, _createJaguarMarker, _createMarker, _eidsFromHashable, _genMarkerHash, _hideAll, _setMarkerHash, _showAll, _updateMarkers

Inherited from ui.qt.appframework2.settings.SettingsPanelMixin: definePanelSettings, getPanelState, loadPanelState, setPanelState, writePanelState

Inherited from ui.qt.appframework2.settings.SettingsPanelMixin (private): _configurePanelSettings

Inherited from ui.qt.appframework2.settings.SettingsMixin: __getitem__, __setitem__, applyAliasedSettings, applySettings, getAliasedSettings, getAliasedValue, getObjValue, getPersistenceKey, getSettings, loadPersistentOptions, savePersistentOptions, setAlias, setAliasedValue, setAliases, setObjValue, setPersistent

Inherited from ui.qt.appframework2.baseapp.ValidatedPanel: reportValidation

Inherited from ui.qt.appframework2.baseapp.BasePanel: __str__, error, info, keyPressEvent, parent, question, restoreCursor, run, runCanvas, runMode, runStandalone, runSubpanel, setWaitCursor, startUp, warning

Inherited from ui.qt.appframework2.baseapp.BasePanel (private): _dockPrefChanged, _layOutDockWidget

Inherited from PyQt4.QtGui.QWidget: acceptDrops, accessibleDescription, accessibleName, actionEvent, actions, activateWindow, addAction, addActions, adjustSize, autoFillBackground, backgroundRole, baseSize, changeEvent, childAt, childrenRect, childrenRegion, clearFocus, clearMask, close, contentsMargins, contentsRect, contextMenuEvent, contextMenuPolicy, create, cursor, customContextMenuRequested, destroy, devType, dragEnterEvent, dragLeaveEvent, dragMoveEvent, dropEvent, effectiveWinId, enabledChange, ensurePolished, enterEvent, event, find, focusInEvent, focusNextChild, focusNextPrevChild, focusOutEvent, focusPolicy, focusPreviousChild, focusProxy, focusWidget, font, fontChange, fontInfo, fontMetrics, foregroundRole, frameGeometry, frameSize, geometry, getContentsMargins, grabGesture, grabKeyboard, grabMouse, grabShortcut, graphicsEffect, graphicsProxyWidget, handle, hasFocus, hasMouseTracking, height, heightForWidth, hide, inputContext, inputMethodEvent, inputMethodHints, inputMethodQuery, insertAction, insertActions, isActiveWindow, isAncestorOf, isEnabled, isEnabledTo, isEnabledToTLW, isFullScreen, isHidden, isLeftToRight, isMaximized, isMinimized, isModal, isRightToLeft, isTopLevel, isVisible, isVisibleTo, isWindow, isWindowModified, keyReleaseEvent, keyboardGrabber, languageChange, layout, layoutDirection, leaveEvent, locale, lower, mapFrom, mapFromGlobal, mapFromParent, mapTo, mapToGlobal, mapToParent, mask, maximumHeight, maximumSize, maximumWidth, metric, minimumHeight, minimumSize, minimumSizeHint, minimumWidth, mouseDoubleClickEvent, mouseGrabber, mouseMoveEvent, mousePressEvent, mouseReleaseEvent, move, moveEvent, nativeParentWidget, nextInFocusChain, normalGeometry, overrideWindowFlags, overrideWindowState, paintEngine, paintEvent, palette, paletteChange, parentWidget, pos, previousInFocusChain, raise_, rect, releaseKeyboard, releaseMouse, releaseShortcut, removeAction, render, repaint, resetInputContext, resize, resizeEvent, restoreGeometry, saveGeometry, scroll, setAcceptDrops, setAccessibleDescription, setAccessibleName, setAttribute, setAutoFillBackground, setBackgroundRole, setBaseSize, setContentsMargins, setContextMenuPolicy, setCursor, setDisabled, setEnabled, setFixedHeight, setFixedSize, setFixedWidth, setFocus, setFocusPolicy, setFocusProxy, setFont, setForegroundRole, setGeometry, setGraphicsEffect, setHidden, setInputContext, setInputMethodHints, setLayout, setLayoutDirection, setLocale, setMask, setMaximumHeight, setMaximumSize, setMaximumWidth, setMinimumHeight, setMinimumSize, setMinimumWidth, setMouseTracking, setPalette, setParent, setShortcutAutoRepeat, setShortcutEnabled, setShown, setSizeIncrement, setSizePolicy, setStatusTip, setStyle, setStyleSheet, setTabOrder, setToolTip, setUpdatesEnabled, setVisible, setWhatsThis, setWindowFilePath, setWindowFlags, setWindowIcon, setWindowIconText, setWindowModality, setWindowModified, setWindowOpacity, setWindowRole, setWindowState, setWindowTitle, showFullScreen, showMaximized, showMinimized, showNormal, size, sizeHint, sizeIncrement, sizePolicy, stackUnder, statusTip, style, styleSheet, tabletEvent, testAttribute, toolTip, topLevelWidget, underMouse, ungrabGesture, unsetCursor, unsetLayoutDirection, unsetLocale, update, updateGeometry, updateMicroFocus, updatesEnabled, visibleRegion, whatsThis, wheelEvent, width, winId, window, windowActivationChange, windowFilePath, windowFlags, windowIcon, windowIconText, windowModality, windowOpacity, windowRole, windowState, windowTitle, windowType, x, x11Info, x11PictureHandle, y

Inherited from PyQt4.QtCore.QObject: __getattr__, blockSignals, childEvent, children, connect, connectNotify, customEvent, deleteLater, destroyed, disconnect, disconnectNotify, dumpObjectInfo, dumpObjectTree, dynamicPropertyNames, emit, eventFilter, findChild, findChildren, inherits, installEventFilter, isWidgetType, killTimer, metaObject, moveToThread, objectName, property, pyqtConfigure, receivers, removeEventFilter, sender, senderSignalIndex, setObjectName, setProperty, signalsBlocked, startTimer, thread, timerEvent, tr, trUtf8

Inherited from PyQt4.QtGui.QPaintDevice: colorCount, depth, heightMM, logicalDpiX, logicalDpiY, numColors, paintingActive, physicalDpiX, physicalDpiY, widthMM

Inherited from sip.simplewrapper: __new__

Inherited from ui.qt.appframework2.validation.ValidationMixin: runValidation, validationEnabled

Inherited from ui.qt.appframework2.validation.ValidationMixin (private): _validate, _validateAdded, _validateChildren, _validateOwn

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Class Methods

[hide private]

Inherited from ui.qt.appframework2.af2.App: panel

Class Variables

[hide private]

str TASK_NAME = ''
The name of the panel

str SHORT_NAME = ''
A shortened version of TASK_NAME.

list TABS = []
The list of tabs that a panel should contain.

list INPUT_SUB_TABS = []
The list of sub-tabs for the Input tab.

Inherited from ui.qt.appframework2.af2.JobApp: NO_PROGRESS_BAR, PROGRESS_BAR_NO_TEXT, PROGRESS_BAR_WITH_TEXT

Inherited from ui.qt.appframework2.af2.App (private): _singleton

Inherited from PyQt4.QtGui.QWidget: DrawChildren, DrawWindowBackground, IgnoreMask

Inherited from PyQt4.QtCore.QObject: staticMetaObject

Inherited from PyQt4.QtGui.QPaintDevice: PdmDepth, PdmDpiX, PdmDpiY, PdmHeight, PdmHeightMM, PdmNumColors, PdmPhysicalDpiX, PdmPhysicalDpiY, PdmWidth, PdmWidthMM

Instance Variables

[hide private]

Inherited from ui.qt.appframework2.markers.MarkerMixin: MARKER_ICONS

Inherited from ui.qt.appframework2.markers.MarkerMixin (private): _marked_eid_lengths, _markers, _multi_atom_markers

Properties

[hide private]

Inherited from ui.qt.appframework2.baseapp.BasePanel: title

Inherited from object: __class__

Method Details

[hide private]

setPanelOptions(self)

Define instance variables that specify the creation of the panel.

Overrides: ui.qt.appframework2.baseapp.BasePanel.setPanelOptions

setup(self)

Instantiate the tab widget and tabs. Sub-tabs will also be added to the Input tab if necessary.

Overrides: ui.qt.appframework2.baseapp.BasePanel.setup

_createDefaultJagInput(self)

Create a JaguarInput object containing default keywords taken from all tabs

Returns: schrodinger.application.jaguar.input.JaguarInput: A JaguarInput object containing default keywords

Note: An "empty" JaguarInput object contains all mmjag defaults, so most tabs will not return any default keywords. Mmjag defaults do not specify a theory level or a DFT functional, however, and the panel expects defaults for these.

getTab(self, tab_class)

Get the tab of the specified class

Parameters:

tab_class (type) - The class of the tab to retrieve

_help(self)

Display help for the current tab

Overrides: ui.qt.appframework2.af2.App._help

launchJaguarJob(self, jag_input)

Launch the specified job.

Parameters:

jag_input (schrodinger.application.jaguar.input.JaguarInput) - A JaguarInput object to run

Returns: schrodinger.job.jobcontrol.Job

A job object for the launched job

createCmd(self)

Create the command line for job launching. Note that the input file name will be added in launchJaguarJob.

Note: This function is intended to be overridden in BaseJaguarPanel subclassses that use different command lines. This code should not be moved into launchJaguarJob.

jobnameArg(self)

Build the command line arguments for passing the job name.

Returns: list: A list of command line arguments

reset(self)

Reset the panel after prompting the user for confirmation

Returns: bool or NoneType

Returns False if the user does not want to reset. This will prevent AF2 from resetting the input selector.

Decorators:

@af2.appmethods.reset("Reset Panel")

_loadSettings(self, jag_input, eid=None, title=None)

Load the specified settings into the tabs and store them in self._jag_input. This function should not be called directly. Instead, _loadSettingsWithErrors(), _loadSettingsWithEditDialogWarnings(), or _loadSettingsWithReadWarnings() should be used so warnings are handled properly.

Parameters:

jag_input (schrodinger.application.jaguar.input.JaguarInput) - The Jaguar settings to load
eid (str) - The entry id of the structure in jag_input. Only necessary if jag_input contains per-atom settings.
title (str) - The title of the structure in jag_input. Only necessary if jag_input contains per-atom settings.

_loadSettingsWithErrors(self, jag_input, eid=None, title=None)

Load the specified settings. If a warning is raised, it will immediately be raised as an exception. This function should be used when reading in default settings, since all default settings should be properly handled by the panel.

See _loadSettings for argument documentation.

Raises:

JaguarSettingWarning - If a tab cannot properly handle a specified setting

_resetWarning(self)

Display a dialog to confirm that the user really wants to reset the panel

Returns: bool: True if the user wants to reset. False otherwise.

getConfigDialog(self)

Get the job configuration dialog

Overrides: ui.qt.appframework2.af2.JobApp.getConfigDialog

runTabValidation(self)

Run validation for each tab. If any tab raises an error, immediately switch to that tab and return the error.

Decorators:

@af2.validator()

generateStatus(self)

Create the status bar message. This function will prepend any Jaguar- specific status bar message before the standard job information. The Jaguar-specific status bar message can be generated by defining generateJaguarStatus().

Returns: str: The text to put into the status bar
Overrides: ui.qt.appframework2.af2.JobApp.generateStatus

generateJaguarStatus(self)

Create a Jaguar-specific status bar message. This function should be defined in any subclass that wishes to modify the status bar message.

Returns: str or NoneType: The Jaguar-specific status bar message, or None if no such message is desired.

_updateMmJag(self)

Update the mmjag object that will be used to build the input file

Raises:

JaguarSettingError - If any settings are invalid.

getMmJagKeywords(self)

Get Jaguar keywords that are specific to this panel and not set in any of the tabs.

Returns: dict: A dictionary of Jaguar keywords

_runPreflight(self)

Run the mmjag preflight check, which checks settings for consistency.

Raises:

JaguarSettingError - If any warnings were raised by the preflight check.

_getAllJagSettings(self)

Get the Jaguar keywords from all tabs and store them in the JaguarInput handle. Also get and store any task-specific keywords.

Raises:

JaguarSettingError - If any settings are invalid.

_getPerAtomSettings(self, eid)

Load all per-atom settings into self._jag_input

Parameters:

eid (str) - The entry id to load settings for

_clearFreezeProperties(self, struc)

Delete all Maestro "freeze" atom properties, as these freezes didn't come from the panel but will be enforced as constraints by the Jaguar backend. (See PANEL-3518.)

_cleanStructureForJagInput(self, struct)

Clean up a structure for use in Jaguar input, making sure it has proper atom names and removing any stale properties

Parameters:

struct (schrodinger.structure.Structure) - The structure to clean

_addStructureToMmJag(self)

Add the structure specified in the input selector frame to the mmjag handle.

Raises:

JaguarSettingError - If the input selector is set to Files and the file can't be read.

Class Variable Details

[hide private]

SHORT_NAME

A shortened version of TASK_NAME. Used in constructing job names.

Type:: str

Value:

''

TABS

The list of tabs that a panel should contain. Each tab must be a schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab subclass.

Type:: list

Value:

[]

INPUT_SUB_TABS

The list of sub-tabs for the Input tab. Only used if TABS contains a subclass of schrodinger.application.jaguar.gui.tabs. input_tab.InputTabWithSubTabs. Each sub-tab must be a schrodinger. application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab subclass.

Type:: list

Value:

[]