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2016-4 Schrodinger Python API
Package schrodinger :: Package application :: Package jaguar :: Package gui :: Package tabs :: Module solvation_tab :: Class SolvationTab
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Class SolvationTab

       object --+                        
                |                        
sip.simplewrapper --+                    
                    |                    
          sip.wrapper --+                
                        |                
     PyQt4.QtCore.QObject --+            
                            |            
           object --+       |            
                    |       |            
    sip.simplewrapper --+   |            
                        |   |            
 PyQt4.QtGui.QPaintDevice --+            
                            |            
          PyQt4.QtGui.QWidget --+        
                                |        
                 base_tab.BaseTab --+    
                                    |    
                           SolventTab --+
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                                       SolvationTab
Known Subclasses:

The Solvation tab, which includes solvent model and gas-phase reference energy

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.
 
solventModelChanged(self)
Called when a new item is selected in the solvent model type menu.
 
gasPhaseReferenceChanged(self)
Called when a new radio button is clicked in the gas phase section.
dict
getMmJagKeywords(self)
Return all keywords that should be put into the mmjag handle.
dict
_getSolventModelKeyword(self)
Get the solvent model keyword
dict
_getOtherSolventKeywords(self)
Get the dielectric and probe radius keywords if the solvent type is set to "other".
dict
_getGasPhaseKeywords(self)
Get the gas phase reference energy keywords
 
loadSettings(self, jag_input)
Restore tab settings from mmjag keywords.
 
_checkSolventSettings(self, jag_input)
Make sure that the solvent settings are consistent.
 
_loadSolventModelAndTypeSettings(self, jag_input)
Load the solvent model and solvent type settings.
 
_loadOtherSolventSettings(self, jag_input)
Load the solvent settings for an "other" solvent
 
_loadGasPhaseSettings(self, jag_input)
Load the gas phase reference energy settings

Inherited from SolventTab: calculateProbeRadius, solventTypeChanged

Inherited from SolventTab (private): _getSolventTypeKeyword

Inherited from base_tab.BaseTab: __init__, activate, deactivate, error, getDefaultKeywords, loadPerAtomSettings, reset, saveSettings, 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 = 'Solvation'
The name of the tab
tuple UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.s...
A tuple of ui modules defining the tab widgets.
  SHOW_DIELECTRIC = True
hash(x)
  SOLVENTS = [Solvent(name='Water', keyvalue='water', dielectric...
  SOLVENT_MODELS = OrderedDict([('None', 0), ('PBF', 2), ('SM6',...

Inherited from SolventTab: HELP_TOPIC

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)

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

_getSolventModelKeyword(self)

 

Get the solvent model keyword

Returns: dict
A dictionary of keywords

_getOtherSolventKeywords(self)

 

Get the dielectric and probe radius keywords if the solvent type is set to "other".

Returns: dict
If the solvent type is set to "Other", a dictionary of dielectric and probe radius keywords. Otherwise, an empty dictionary.

Note: The molecular weight and density options are used to compute the probe radius

_getGasPhaseKeywords(self)

 

Get the gas phase reference energy keywords

Returns: dict
A dictionary of keywords

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)

_checkSolventSettings(self, jag_input)

 

Make sure that the solvent settings are consistent. Issue warnings for any inconsistencies.

Parameters:

_loadSolventModelAndTypeSettings(self, jag_input)

 

Load the solvent model and solvent type settings. If solvent model is not PBF, then a solvent type of water is used regardless of the jag_input setting.

Parameters:

_loadOtherSolventSettings(self, jag_input)

 

Load the solvent settings for an "other" solvent

Parameters:

Note: If we load probe radius, we have to clear the molecular weight and density values, since they no longer match the probe radius and will overwrite it the next time calculateProbeRadius() is called. As a result, we only load the probe radius if it's different than what's already in the panel so that we don't unnecessarily clear the molecular weight and density values.

_loadGasPhaseSettings(self, jag_input)

 

Load the gas phase reference energy settings

Parameters:

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.solvation_solvent_mode\
l_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/solvation_solvent_model_ui.pyc'>,
 <module 'schrodinger.application.jaguar.gui.ui.solvent_tab_ui' from '\
/scr/buildbot/savedbuilds/NB/2016-4/build-126/mmshare-v3.6/lib/Linux-x\
86_64/lib/python2.7/site-packages/schrodinger/application/jaguar/gui/u\
i/solvent_tab_ui.pyc'>,
...

SOLVENTS

Value:
[Solvent(name='Water', keyvalue='water', dielectric=80.37, radius=1.4,\
 weight=18.02, density=0.99823),
 Solvent(name='Acetonitrile', keyvalue='acetonitrile', dielectric=37.5\
, radius=2.19, weight=41.05, density=0.777),
 Solvent(name='Benzene', keyvalue='benzene', dielectric=2.284, radius=\
2.6, weight=78.12, density=0.87865),
 Solvent(name='Carbon tetrachloride', keyvalue='carbon_tet', dielectri\
c=2.238, radius=2.67, weight=153.82, density=1.594),
...

SOLVENT_MODELS

Value:
OrderedDict([('None', 0), ('PBF', 2), ('SM6', 5), ('SM8', 6)])

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2016-4 Schrodinger Python API
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