Package schrodinger :: Package application :: Package jaguar :: Package gui :: Package tabs :: Module molecule_tab :: Class MoleculeTabPka

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Class MoleculeTabPka

       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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                      MoleculeTabBase --+
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                                       MoleculeTabPka

The molecule tab used in the PKA panel

Nested Classes

[hide private]

Inherited from PyQt4.QtGui.QWidget: RenderFlag, RenderFlags

Inherited from PyQt4.QtGui.QPaintDevice: PaintDeviceMetric

Instance Methods

[hide private]

setup(self)
Perform tab specific initialization.

reset(self)
Reset the tab to its original state.

_updatePickWarningAndCheckBoxes(self)
If there are multiple structures selected or if the input selector is set to File, display a warning.

_getNumWorkspaceStructures(self)
Return the number of structures that are included in the workspace.

_pickAtomRbToggled(self)
When the user choose "Use this atom" or "Use pKa atoms from the project table", update the picking check boxes.

pickThisAtom(self, atom_num)
Respond to the atom picking at atom in the "Use this atom" section.

pickProjTableAtom(self, atom_num)
Respond to the atom picking at atom in the "Use pKa atoms from the project table" section.

str

_getAtomName(self, atom, struc)
Get the atom name for the specified atom after applying the jaguar naming scheme to the structure.

_getPkaAtom(self)
Return the currently selected pKa atom

dict

getMmJagKeywords(self)
Return all keywords that should be put into the mmjag handle.

str or NoneType

validate(self)
Make sure that a pka atom has been selected and is a valid atom for the currently selected structure

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

_createPkaProperties(self)
Create a pKa property in the project table for the structures that are currently selected in the input selector.

isZwitterionChecked(self)

isConformationalSearchesChecked(self)

Inherited from MoleculeTabBase: createChargeProperties

Inherited from MoleculeTabBase (private): _checkAndFixSpin, _createChargePropertiesForEsl, _createChargePropertiesSanityCheck, _fixSpinAndUpdateWarning, _getChargeFromGui, _getChargeFromProjTable, _getNumStructures, _getStructure, _getSymmetryKeywords, _loadCharge, _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]

MULTIPLE_STRUC_PICK_WARNING = 'Warning: Pick options cannot be...

FILE_PICK_WARNING = 'Warning: Pick options cannot be used when...

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

PKA_ATOM_PROP = 's_m_pKa_atom'

Inherited from MoleculeTabBase: CHARGE_SPIN_INCONSISTANT_WARNING, HELP_TOPIC, MULTIPLE_STRUC_WARNING, NAME

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)

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

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

reset(self)

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.

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

_updatePickWarningAndCheckBoxes(self)

If there are multiple structures selected or if the input selector is set to File, display a warning. Also update the enabled status of the picking check boxes.

_getNumWorkspaceStructures(self)

Return the number of structures that are included in the workspace. Note that scratch structures are ignored.

_pickAtomRbToggled(self)

When the user choose "Use this atom" or "Use pKa atoms from the project table", update the picking check boxes. Also create pKa properties in the project table if necessary.

pickThisAtom(self, atom_num)

Respond to the atom picking at atom in the "Use this atom" section.

Parameters:

atom_num (int) - The atom number that was just picked

pickProjTableAtom(self, atom_num)

Respond to the atom picking at atom in the "Use pKa atoms from the project table" section.

Parameters:

atom_num (int) - The atom number that was just picked

_getAtomName(self, atom, struc)

Get the atom name for the specified atom after applying the jaguar naming scheme to the structure.

Parameters:

atom (schrodinger.structure._StructureAtom) - The atom to get the name of
struc - The structure containing atom

Returns: str

The atom name

getMmJagKeywords(self)

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

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)

validate(self)

Make sure that a pka atom has been selected and is a valid atom for the currently selected structure

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

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)

_createPkaProperties(self)

Create a pKa property in the project table for the structures that are currently selected in the input selector. Note that this function has no effect if Files is selected.

Class Variable Details

[hide private]

MULTIPLE_STRUC_PICK_WARNING

Value:

'''Warning: Pick options cannot be used when
more than one entry is in the Workspace'''

FILE_PICK_WARNING

Value:

'''Warning: Pick options cannot be used when
using structures from files.'''

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.molecule_top_ui' from 
'/scr/buildbot/savedbuilds/NB/2016-4/build-126/mmshare-v3.6/lib/Linux-
x86_64/lib/python2.7/site-packages/schrodinger/application/jaguar/gui/
ui/molecule_top_ui.pyc'>,
 <module 'schrodinger.application.jaguar.gui.ui.molecule_pka_bottom_ui
' from '/scr/buildbot/savedbuilds/NB/2016-4/build-126/mmshare-v3.6/lib
/Linux-x86_64/lib/python2.7/site-packages/schrodinger/application/jagu
ar/gui/ui/molecule_pka_bottom_ui.pyc'>)