Trees       Indices       Help   
2016-4 Schrodinger Python API
Package schrodinger :: Package application :: Package jaguar :: Package gui :: Package tabs :: Module transition_state_tab :: Class TransitionStateTab
[hide private]
[frames] | no frames]

Class TransitionStateTab

                           object --+    
                                    |    
                 TransitionStateMixin --+
                                        |
       object --+                       |
                |                       |
sip.simplewrapper --+                   |
                    |                   |
          sip.wrapper --+               |
                        |               |
     PyQt4.QtCore.QObject --+           |
                            |           |
           object --+       |           |
                    |       |           |
    sip.simplewrapper --+   |           |
                        |   |           |
 PyQt4.QtGui.QPaintDevice --+           |
                            |           |
          PyQt4.QtGui.QWidget --+       |
                                |       |
      base_tab.ProvidesBasisMixin --+   |
                                    |   |
       object --+                   |   |
                |                   |   |
sip.simplewrapper --+               |   |
                    |               |   |
          sip.wrapper --+           |   |
                        |           |   |
     PyQt4.QtCore.QObject --+       |   |
                            |       |   |
           object --+       |       |   |
                    |       |       |   |
    sip.simplewrapper --+   |       |   |
                        |   |       |   |
 PyQt4.QtGui.QPaintDevice --+       |   |
                            |       |   |
          PyQt4.QtGui.QWidget --+   |   |
                                |   |   |
 base_tab.ProvidesStructuresMixin --+   |
                                    |   |
       object --+                   |   |
                |                   |   |
sip.simplewrapper --+               |   |
                    |               |   |
          sip.wrapper --+           |   |
                        |           |   |
     PyQt4.QtCore.QObject --+       |   |
                            |       |   |
           object --+       |       |   |
                    |       |       |   |
    sip.simplewrapper --+   |       |   |
                        |   |       |   |
 PyQt4.QtGui.QPaintDevice --+       |   |
                            |       |   |
          PyQt4.QtGui.QWidget --+   |   |
                                |   |   |
                 base_tab.BaseTab --+   |
                                    |   |
multi_structure_tab.MultiStructureTab --+
                                        |
                                       TransitionStateTab
Nested Classes [hide private]

Inherited from base_tab.ProvidesStructuresMixin: __metaclass__

Inherited from PyQt4.QtGui.QWidget: RenderFlag, RenderFlags

Inherited from PyQt4.QtGui.QPaintDevice: PaintDeviceMetric

Instance Methods [hide private]
 
setup(self)
Perform tab specific initialization.
 
searchMethodChanged(self)
Respond to the user changing the search method by updating the structure selectors and the search along combo box
list
getStructures(self)
Get all of the structures that are loaded into the tab.
dict
getMmJagKeywords(self)
Return all keywords that should be put into the mmjag handle.
dict
_getSearchMethodKeyword(self)
Get the keyword for the search method
 
_loadSearchMethod(self, jag_input)
Load the search method settings
 
setStructures(self, entry_ids, jag_input=None)
Override the parent function so we can properly handle LST jobs (which use zmat 1 and 2 for reactant and product instead of transition state and reactant)
bool
isLst(self, jag_input)
Does the Jaguar input specify an LST job? This answer isn't guaranteed to be correct, since there's no way to distinguish a fully- or partially-specified LST job from a partially-specified QST job if the default initial LST guess is used.
 
structureChanged(...)

Inherited from TransitionStateMixin: loadSettings, repopulateSearchAlongCombo, searchAlongChanged

Inherited from TransitionStateMixin (private): _getSearchAlongAndHessianKeywords, _loadHessianRefinement, _loadSearchAlong

Inherited from multi_structure_tab.MultiStructureTab: chooseEntry, getBasis, getDefaultKeywords, getEids, getRepresentativeStructure, getStructureTitleForJobname, projectUpdated, reset, setStructureSelectorsEnabled, structureCbToggled, validate

Inherited from multi_structure_tab.MultiStructureTab (private): _compareAtomicNumbersAndAtomNames, _compareStrucs, _getAtomicNumbersAndAtomNames, _getRow, _getStruc, _updateMoleculeSubTabStruc, _updateStrucListings, _updateStructureWarningLabel

Inherited from base_tab.ProvidesBasisMixin: basis_changed

Inherited from base_tab.BaseTab: __init__, activate, deactivate, error, 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]
tuple UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.t...
A tuple of ui modules defining the tab widgets.
  LST_SEARCH_ALONG = ('Lowest Hessian eigenvector', 'Lowest non-...
  QST_SEARCH_ALONG = ('Reactant-product path')
  ALL_SEARCH_ALONG = (('Lowest Hessian eigenvector', 'Lowest non...
  SEARCH_LST = 1
  SEARCH_QST = 2

Inherited from TransitionStateMixin: HELP_TOPIC, NAME, SA_LOWEST_BOND_STRETCH, SA_LOWEST_HESSIAN, SA_LOWEST_NON_TORSIONAL, SA_RP_PATH, SA_USER, SEARCH_ALONG_VALUES, SEARCH_STANDARD, STANDARD_SEARCH_ALONG

Inherited from multi_structure_tab.MultiStructureTab: ALL_STRUCS, ATOMS, ATOM_LABELS, ENTRY_TYPE_NAMES, PRODUCT, REACTANT, STRUC_DIFF_WARNING, TRANSITION_STATE

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]

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)

getStructures(self)

 

Get all of the structures that are loaded into the tab. When LST is selected, the structure types don't map to the Z-matrices in the standard way, so we have to override the parent function.

Returns: list
A list of:
  • the structure to be loaded into ZMAT1 (or None)
  • the structure to be loaded into ZMAT2 (or None)
  • the structure to be loaded into ZMAT3 (or None)
Overrides: multi_structure_tab.MultiStructureTab.getStructures

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)

_getSearchMethodKeyword(self)

 

Get the keyword for the search method

Returns: dict
A keyword dictionary

_loadSearchMethod(self, jag_input)

 

Load the search method settings

Parameters:
Overrides: TransitionStateMixin._loadSearchMethod

setStructures(self, entry_ids, jag_input=None)

 

Override the parent function so we can properly handle LST jobs (which use zmat 1 and 2 for reactant and product instead of transition state and reactant)

Parameters:
  • entry_ids - A list of
    • the transition state structure entry ID
    • the reactant structure entry ID
    • the product structure entry ID

    Note that this value must be a list, not a tuple.

  • jag_input - A JaguarInput object containing the job settings. Note that this argument is only used for the Transition State tab version of this function in order to determine if the search method is LST, as this will affect how the structures are loaded.
Overrides: multi_structure_tab.MultiStructureTab.setStructures

isLst(self, jag_input)

 

Does the Jaguar input specify an LST job? This answer isn't guaranteed to be correct, since there's no way to distinguish a fully- or partially-specified LST job from a partially-specified QST job if the default initial LST guess is used. If the input is ambiguous and LST or QST is already selected, then we try to keep the setting as is.

Parameters:
Returns: bool
True if the specified job is likely to be LST. False otherwise.

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.transition_state_top_u\
i' from '/scr/buildbot/savedbuilds/NB/2016-4/build-126/mmshare-v3.6/li\
b/Linux-x86_64/lib/python2.7/site-packages/schrodinger/application/jag\
uar/gui/ui/transition_state_top_ui.pyc'>,
 <module 'schrodinger.application.jaguar.gui.ui.multi_structures_ui' f\
rom '/scr/buildbot/savedbuilds/NB/2016-4/build-126/mmshare-v3.6/lib/Li\
nux-x86_64/lib/python2.7/site-packages/schrodinger/application/jaguar/\
gui/ui/multi_structures_ui.pyc'>,
...

LST_SEARCH_ALONG

Value:
('Lowest Hessian eigenvector',
 'Lowest non-torsional mode',
 'Lowest bond-stretch mode',
 'Reactant-product path',
 'User-selected eigenvector')

ALL_SEARCH_ALONG

Value:
(('Lowest Hessian eigenvector',
  'Lowest non-torsional mode',
  'Lowest bond-stretch mode',
  'User-selected eigenvector'),
 ('Lowest Hessian eigenvector',
  'Lowest non-torsional mode',
  'Lowest bond-stretch mode',
  'Reactant-product path',
...

   Trees       Indices       Help   
2016-4 Schrodinger Python API
Generated by Epydoc 3.0.1 on Wed Oct 26 00:59:47 2016 http://epydoc.sourceforge.net