Package schrodinger :: Package application :: Package jaguar :: Package gui :: Package tabs :: Module transition_state_tab :: Class TransitionStateTab

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Class TransitionStateTab

          PyQt4.QtGui.QWidget --+        
                                |        
      base_tab.ProvidesBasisMixin --+    
                                    |    
          PyQt4.QtGui.QWidget --+   |    
                                |   |    
 base_tab.ProvidesStructuresMixin --+    
                                    |    
          PyQt4.QtGui.QWidget --+   |    
                                |   |    
                 base_tab.BaseTab --+    
                                    |    
multi_structure_tab.MultiStructureTab --+
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                                       TransitionStateTab

Nested Classes

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Inherited from base_tab.ProvidesStructuresMixin: __metaclass__

Instance Methods

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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

repopulateSearchAlongCombo(self, search_method)
Replace the contents of the search along combo boxes based on the current search method

searchAlongChanged(self)
Respond to the user changing the search along method by updating the status of the eigenvector input widgets

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

dict

_getSearchAlongAndHessianKeywords(self)
Get the keywords for the search along and Hessian settings

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

_loadSearchMethod(self, jag_input)
Load the search method settings

_loadSearchAlong(self, jag_input)
Load the search along settings

_loadHessianRefinement(self, jag_input)
Load the hessian refinement 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.

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.BaseTab: __init__, activate, deactivate, error, loadPerAtomSettings, saveSettings, warning

Inherited from base_tab.BaseTab (private): _populateUi

Class Variables

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str NAME = "Transition State"
The name of the tab

str HELP_TOPIC = "JAGUAR_TOPIC_TRANSITION_STATE_FOLDER"
The help topic for the tab

tuple UI_MODULES = ui.transition_state_top_ui, ui.multi_structures_u...
A tuple of ui modules defining the tab widgets.

SA_LOWEST_HESSIAN = "Lowest Hessian eigenvector"

SA_LOWEST_NON_TORSIONAL = "Lowest non-torsional mode"

SA_LOWEST_BOND_STRETCH = "Lowest bond-stretch mode"

SA_RP_PATH = "Reactant-product path"

SA_USER = "User-selected eigenvector"

SEARCH_ALONG_VALUES = {SA_LOWEST_HESSIAN: mm.MMJAG_ITRVEC_HESS...

STANDARD_SEARCH_ALONG = SA_LOWEST_HESSIAN, SA_LOWEST_NON_TORSI...

LST_SEARCH_ALONG = SA_LOWEST_HESSIAN, SA_LOWEST_NON_TORSIONAL,...

QST_SEARCH_ALONG = SA_RP_PATH,

ALL_SEARCH_ALONG = STANDARD_SEARCH_ALONG, LST_SEARCH_ALONG, QS...

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

Inherited from base_tab.ProvidesBasisMixin: basis_changed

Inherited from base_tab.ProvidesStructuresMixin: MULTIPLE_STRUC_JOB_TITLE

Instance Variables

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Inherited from base_tab.BaseTab: input_selector, task_name, ui

Method Details

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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:

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

Overrides: base_tab.BaseTab.getMmJagKeywords

(inherited documentation)

_getSearchMethodKeyword(self)

Get the keyword for the search method

Returns: dict: A keyword dictionary

_getSearchAlongAndHessianKeywords(self)

Get the keywords for the search along and Hessian settings

Returns: dict: A keyword dictionary

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)

_loadSearchMethod(self, jag_input)

Load the search method settings

Parameters:

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

_loadSearchAlong(self, jag_input)

Load the search along settings

Parameters:

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

_loadHessianRefinement(self, jag_input)

Load the hessian refinement settings

Parameters:

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

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:

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

Returns: bool

True if the specified job is likely to be LST. False otherwise.

Class Variable Details

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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:

ui.transition_state_top_ui, ui.multi_structures_ui, ui.transition_stat
e_bottom_ui, (MoleculeTabNoInputSelector, "molecule_sub_tab")

SEARCH_ALONG_VALUES

Value:

{SA_LOWEST_HESSIAN: mm.MMJAG_ITRVEC_HESSIAN, SA_LOWEST_NON_TORSIONAL: 
mm.MMJAG_ITRVEC_NONTOR, SA_LOWEST_BOND_STRETCH: mm.MMJAG_ITRVEC_STRETC
H, SA_RP_PATH: mm.MMJAG_ITRVEC_QST, SA_USER: SA_USER}

STANDARD_SEARCH_ALONG

Value:

SA_LOWEST_HESSIAN, SA_LOWEST_NON_TORSIONAL, SA_LOWEST_BOND_STRETCH, SA
_USER

LST_SEARCH_ALONG

Value:

SA_LOWEST_HESSIAN, SA_LOWEST_NON_TORSIONAL, SA_LOWEST_BOND_STRETCH, SA
_RP_PATH, SA_USER

ALL_SEARCH_ALONG

Value:

STANDARD_SEARCH_ALONG, LST_SEARCH_ALONG, QST_SEARCH_ALONG