Package schrodinger :: Package application :: Package jaguar :: Package gui :: Package tabs :: Module input_tab :: Class InputTabPka

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Class InputTabPka

       object --+                        
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sip.simplewrapper --+                    
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     PyQt4.QtCore.QObject --+            
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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.ProvidesStructuresMixin --+    
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       object --+                   |    
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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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                         InputTabBase --+
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                                       InputTabPka

An input tab that allows the user to specify pKa atoms.

Nested Classes

[hide private]

schrodinger.application.jaguar.gui.input_tab_widgets. SelectedEntriesModel MODEL_CLASS
The class to use for the table model

schrodinger.application.jaguar.gui.input_tab_widgets. SelectedEntriesView VIEW_CLASS
The class to use for the table view

Inherited from InputTabBase: PROXY_CLASS, __metaclass__

Inherited from PyQt4.QtGui.QWidget: RenderFlag, RenderFlags

Inherited from PyQt4.QtGui.QPaintDevice: PaintDeviceMetric

Instance Methods

[hide private]

setup(self)
Perform tab specific initialization.

dict

getMmJagKeywords(self)
Get the symmetry-related mmjag keywords.

dict

_getKeywordsForStruc(self, cur_struc)
Get mmjag keywords for the specified structure

isZwitterionChecked(self)

isConformationalSearchesChecked(self)

str or NoneType

validate(self)
Make sure that the tab settings will allow a job to be run successfully.

loadSettings(self, jag_input)
Restore tab settings from mmjag keywords.

_loadPkaAtom(self, jag_input)
Load the pKa atom from the mmjag keywords.

strucSourceChanged(...)
A signal emitted when the structure source changes from included to selected or vice versa.

structureChanged(...)

Inherited from InputTabBase: getNumStructures, getStructureTitleForJobname, getStructures, projectUpdated, reset, useFromComboChanged, usingSelected, workspaceChanged

Inherited from InputTabBase (private): _checkSingleStructure, _loadChargeAndSpinMult, _loadSymmetry

Inherited from base_tab.BaseTab: __init__, activate, deactivate, error, getDefaultKeywords, loadPerAtomSettings, saveSettings, 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 HELP_TOPIC = 'JAGUAR_INPUT_TAB'
The help topic for the tab

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

Inherited from InputTabBase: NAME, SYMM_ITEMS

Inherited from base_tab.ProvidesStructuresMixin: MULTIPLE_STRUC_JOB_TITLE

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]

set_pka_marker(...)
A signal emitted when a new pKa atom should be marked in the workspace.

Inherited from base_tab.BaseTab: input_selector, task_name, ui

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

setup(self)

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

Overrides: base_tab.BaseTab.setup: (inherited documentation)

getMmJagKeywords(self)

Get the symmetry-related mmjag keywords. All other keywords are per- structure

Returns: dict

All keywords that should be put into the mmjag handle

Raises:

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

Overrides: base_tab.BaseTab.getMmJagKeywords

(inherited documentation)

_getKeywordsForStruc(self, cur_struc)

Get mmjag keywords for the specified structure

Parameters:

cur_struc - Data about the current structure

Returns: dict

A dictionary of Jaguar keywords

Overrides: InputTabBase._getKeywordsForStruc

(inherited documentation)

validate(self)

Make sure that the tab settings will allow a job to be run successfully. Note that this validation should not be redundant with that performed in getMmJagKeywords. Any tab setting that prevents valid mmjag keywords from being generated should cause getMmJagKeywords to raise a JaguarSettingError. Any tab setting that allows mmjag keywords to be successfully generated but will result in a job failure should cause a validate fail. This function should be defined in subclasses if validation is needed.

Returns: str or NoneType: If the validation passes, None is returned. If the validation fails, a string that describes the error is returned.
Overrides: base_tab.BaseTab.validate: (inherited documentation)

loadSettings(self, jag_input)

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

Parameters:

jag_input - The Jaguar settings to base the tab settings on

Overrides: base_tab.BaseTab.loadSettings

(inherited documentation)

_loadPkaAtom(self, jag_input)

Load the pKa atom from the mmjag keywords. Note that the setting will be ignored if it is set to the default (i.e. no pKa atom name). If the setting is non-default, then a warning will be issued unless there is exactly one structure loaded into the table.

Parameters:

jag_input (schrodinger.application.jaguar.input.JaguarInput) - A JaguarInput object containing the settings to load

strucSourceChanged(...)

A signal emitted when the structure source changes from included to selected or vice versa.

Overrides: InputTabBase.strucSourceChanged

structureChanged(...)

Overrides: base_tab.ProvidesStructuresMixin.structureChanged

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.input_top_ui' from '/n
fs/builds/objects/NB/2016-2/Linux-x86_64/build-131/mmshare-v3.4/lib/Li
nux-x86_64/lib/python2.7/site-packages/schrodinger/application/jaguar/
gui/ui/input_top_ui.pyc'>,
 <module 'schrodinger.application.jaguar.gui.ui.input_pka_bottom_ui' f
rom '/nfs/builds/objects/NB/2016-2/Linux-x86_64/build-131/mmshare-v3.4
/lib/Linux-x86_64/lib/python2.7/site-packages/schrodinger/application/
jaguar/gui/ui/input_pka_bottom_ui.pyc'>)

Instance Variable Details

[hide private]

set_pka_marker(...)

A signal emitted when a new pKa atom should be marked in the workspace. Emitted with two arguments:

The entry id of the structure to be marked (str)
The atom to be marked (schrodinger.structure._StructureAtom)