Package schrodinger :: Package application :: Package jaguar :: Package gui :: Package tabs :: Module optimization_tab :: Class OptimizationTab

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Class OptimizationTab

       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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                 base_tab.BaseTab --+
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                                   OptimizationTab

This is Jaguar Optimization tab.

Nested Classes

[hide private]

Inherited from PyQt4.QtGui.QWidget: RenderFlag, RenderFlags

Inherited from PyQt4.QtGui.QPaintDevice: PaintDeviceMetric

Instance Methods

[hide private]

setup(self)
Setup for optimization tab

_resetDefaults(self)
This function resets coordinates table and sets coordinate picking to its default state.

dict

getMmJagKeywords(self)
This function returns dictionary of mmjag keywords for this tab.

dict

getConvergenceKeywords(self)
Get keywords from convergence criteria widgets.

loadSettings(self, jag_input)
Restore scan coordinates settings from Jaguar handle.

loadConvergenceKeywords(self, jag_input)
Load the convergence criteria settings.

loadConstraintCoordinates(self, jag_input)
Load constraint coordinates from Jaguar handle.

saveSettings(self, jag_input)
Save constraint coordinate settings in jaguar handle.

deleteCurrentRow(self)
This function is called to delete row which is currently selected from the coordinates table.

deleteAllRows(self)
This function is called to delete all rows from the coordinates table.

addCoordinate(self, st, atoms, coordinate_type, target_value=None)
Add new coordinate row.

coordinateTypeChanged(self, index)
This function is called when coordinate type is changed.

convergenceTypeChanged(self, index)
This function is called when convergence type is changed.

updateMarkers(self)
This function should make calls to show coordinate markers in Maestro workspace.

pickCompleted(self, atoms)
This slot is called when required number of atoms for the current coordinate type has been picked.

Inherited from base_tab.BaseTab: __init__, error, getDefaultKeywords, reset, validate, warning

Inherited from base_tab.BaseTab (private): _populateUi

Inherited from PyQt4.QtGui.QWidget: acceptDrops, accessibleDescription, accessibleName, actionEvent, actions, activateWindow, addAction, addActions, adjustSize, autoFillBackground, backgroundRole, baseSize, changeEvent, childAt, childrenRect, childrenRegion, clearFocus, clearMask, close, closeEvent, 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, hideEvent, inputContext, inputMethodEvent, inputMethodHints, inputMethodQuery, insertAction, insertActions, isActiveWindow, isAncestorOf, isEnabled, isEnabledTo, isEnabledToTLW, isFullScreen, isHidden, isLeftToRight, isMaximized, isMinimized, isModal, isRightToLeft, isTopLevel, isVisible, isVisibleTo, isWindow, isWindowModified, keyPressEvent, 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, show, showEvent, 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, parent, 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 object: __delattr__, __format__, __getattribute__, __hash__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables

[hide private]

str NAME = 'Optimization'
The name of the tab

tuple UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.o...
A tuple of ui modules defining the tab widgets.

str HELP_TOPIC = 'JAGUAR_TOPIC_OPTIMIZATION_FOLDER'
The help topic for the tab

CONVERGENCE_CRITERIA = OrderedDict([('Default', 2), ('Loose', ...

INITIAL_HESSIAN = OrderedDict([('Schlegel guess', 0), ('Fische...

COORDINATE_OPTS = OrderedDict([('Redundant internal', 1), ('Ca...

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 base_tab.BaseTab: input_selector, task_name, ui

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

setup(self)

Setup for optimization tab

Overrides: base_tab.BaseTab.setup

_resetDefaults(self)

This function resets coordinates table and sets coordinate picking to its default state. Note that this function is not called reset() since it does not need to be called from the panel class.

getMmJagKeywords(self)

This function returns dictionary of mmjag keywords for this tab. Since this tab does not set any keywords it returns an empty dictionary.

Returns: dict

mmjag keywords dictionary

Raises:

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

Overrides: base_tab.BaseTab.getMmJagKeywords

getConvergenceKeywords(self)

Get keywords from convergence criteria widgets.

Returns: dict: A dictionary of keywords

loadSettings(self, jag_input)

Restore scan coordinates settings from Jaguar handle.

Parameters:

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

Overrides: base_tab.BaseTab.loadSettings

loadConvergenceKeywords(self, jag_input)

Load the convergence criteria settings.

Parameters:

jag_input (schrodinger.application.jaguar.input.JaguarInput) - The Jaguar settings to load.

loadConstraintCoordinates(self, jag_input)

Load constraint coordinates from Jaguar handle.

Parameters:

jag_input (schrodinger.application.jaguar.input.JaguarInput) - The Jaguar handle where tab settings are saved.

saveSettings(self, jag_input)

Save constraint coordinate settings in jaguar handle.

Parameters:

jag_input (schrodinger.application.jaguar.input.JaguarInput) - The Jaguar handle where tab settings are saved.

Overrides: base_tab.BaseTab.saveSettings

addCoordinate(self, st, atoms, coordinate_type, target_value=None)

Add new coordinate row.

Parameters:

st (schrodinger.structure.Structure) - structure
atoms (list) - atom indices
coordinate_type (str) - coordinate type
target_value (float) - target coordinate value

coordinateTypeChanged(self, index)

This function is called when coordinate type is changed. It sets the correct index for the pick stacked widget.

Parameters:

index (int) - type combo box index

convergenceTypeChanged(self, index)

This function is called when convergence type is changed. If 'Custom' is selected extra options frame is shown. Otherwise, it is hidden.

Parameters:

index (int) - convergence type combo box index

updateMarkers(self)

This function should make calls to show coordinate markers in Maestro workspace. FIXME: currently there is no API to do this, so this function does nothing right now.

pickCompleted(self, atoms)

This slot is called when required number of atoms for the current coordinate type has been picked.

Parameters:

atoms (list) - list of atom indices

Class Variable Details

[hide private]

UI_MODULES

A tuple of ui modules defining the tab widgets. These ui modules should be listed top to bottom. Optionally, a tuple of (tab class, attribute name) may be listed instead of a ui file to include a subtab.

Type:: tuple

Value:

(<module 'schrodinger.application.jaguar.gui.ui.optimization_tab_ui' f
rom '/nfs/builds/objects/OB/2014-1/Linux-x86_64/build08/mmshare-v2.5/l
ib/Linux-x86_64/lib/python2.7/site-packages/schrodinger/application/ja
guar/gui/ui/optimization_tab_ui.pyc'>)

CONVERGENCE_CRITERIA

Value:

OrderedDict([('Default', 2), ('Loose', 3), ('Tight', 5), ('Custom', 6)
])

INITIAL_HESSIAN

Value:

OrderedDict([('Schlegel guess', 0), ('Fischer-Almlof guess', -1), ('Un
it Hessian', 1), ('Quantum-mechanical', 4)])

COORDINATE_OPTS

Value:

OrderedDict([('Redundant internal', 1), ('Cartesian', 0), ('Z-matrix',
 2)])