schrodinger.application.jaguar.gui.tabs.input_tab module¶
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class
schrodinger.application.jaguar.gui.tabs.input_tab.
InputTabBase
(parent, input_selector=None)¶ Bases:
schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesStructuresMixin
,schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab
A tab for specifying settings for the structures currently selected in the project table. Note that this class is not intended to be directly instantiated. Instead, the InputTab or InputTabPka classes should be used.
Variables: - MODEL_CLASS (
schrodinger.application.jaguar.gui.input_tab_widgets. SelectedEntriesModel
) – The class to use for the table model - PROXY_CLASS (
schrodinger.application.jaguar.gui.input_tab_widgets. SelectedEntriesProxyModel
) – The class to use for the table proxy model - VIEW_CLASS (
schrodinger.application.jaguar.gui.input_tab_widgets. SelectedEntriesView
) – The class to use for the table view - strucSourceChanged (
QtCore.pyqtSignal
) – A signal emitted when the structure source changes from included to selected or vice versa.
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strucSourceChanged
¶
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NAME
= 'Input'¶
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MODEL_CLASS
¶ alias of
schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel
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PROXY_CLASS
¶ alias of
schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel
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VIEW_CLASS
¶ alias of
schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView
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setup
()¶ Perform tab specific initialization. This function should be defined in subclasses if initialization is needed.
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projectUpdated
()¶ When the project is updated, update the selected entries table
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workspaceChanged
(what_changed)¶ Update the table whenever the workspace changes in case the user changed the charge of a molecule.
Parameters: what_changed (str) – A flag indicating what changed in the workspace
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loadSettings
(jag_input)¶ Restore tab settings from mmjag keywords. This function should be defined in subclasses.
Parameters: jag_input ( schrodinger.application.jaguar.input.JaguarInput
) – The Jaguar settings to base the tab settings on
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validate
()¶ 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 causegetMmJagKeywords
to raise a JaguarSettingError. Any tab setting that allows mmjag keywords to be successfully generated but will result in a job failure should cause avalidate
fail. This function should be defined in subclasses if validation is needed.Returns: If the validation passes, None is returned. If the validation fails, a string that describes the error is returned. Return type: str or NoneType
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getStructures
()¶ Get all structures loaded into the tab and their associated Jaguar settings
Returns: A list of tuples. Each tuple represents a single structure and contains: - A
schrodinger.structure.Structure
object containing the structure itself - A dictionary of keywords specific to the structure
Return type: list - A
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getNumStructures
()¶
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getStructureTitleForJobname
()¶ Get the structure title to be used in the job name. If the tab includes multiple structures, then
MULTIPLE_STRUC_JOB_TITLE
should be returned. If no structures have been specified yet, then None should be returned.Returns: The structure title Return type: str or NoneType
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reset
()¶ Reset any structure specific settings in the table. (The non-struture specific settings will be reset via loadSettings())
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useFromComboChanged
()¶ Respond to the user changing the structure source (from included to selected or vice versa).
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usingSelected
()¶ Return True if the tab is set to use selected entries. False if the tab is set to use included entries.
- MODEL_CLASS (
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class
schrodinger.application.jaguar.gui.tabs.input_tab.
InputTab
(parent, input_selector=None)¶ Bases:
schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesBasisMixin
,schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase
An input tab that allows the user to specify basis sets.
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HELP_TOPIC
= 'JAGUAR_INPUT_TAB'¶
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UI_MODULES
= (<module 'schrodinger.application.jaguar.gui.ui.input_top_ui' from '/scr/buildbot/savedbuilds/2018-3/NB/build-149/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/input_top_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.input_std_bottom_ui' from '/scr/buildbot/savedbuilds/2018-3/NB/build-149/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/input_std_bottom_ui.py'>)¶
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setup
()¶ Perform tab specific initialization. This function should be defined in subclasses if initialization is needed.
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getMmJagKeywords
()¶ Get the symmetry-related mmjag keywords. All other keywords are per- structure
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getDefaultKeywords
()¶ The mmjag default basis set is “”, which would cause a warning, so we set the default basis.
Returns: A keyword dictionary with the default basis set Return type: dict
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loadSettings
(jag_input)¶ Restore tab settings from mmjag keywords. This function should be defined in subclasses.
Parameters: jag_input ( schrodinger.application.jaguar.input.JaguarInput
) – The Jaguar settings to base the tab settings on
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getBasis
(mixed_name='Mixed')¶ Get the currently selected basis. If more than one basis set is specified,
mixed_name
will be returned. If the tab does not allow for specifying multiple basis sets, then this argument may be ignored.Parameters: mixed_name (str) – The name to return if more than one basis set is specified Returns: The currently selected basis Return type: str
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validate
()¶ 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 causegetMmJagKeywords
to raise a JaguarSettingError. Any tab setting that allows mmjag keywords to be successfully generated but will result in a job failure should cause avalidate
fail. This function should be defined in subclasses if validation is needed.Returns: If the validation passes, None is returned. If the validation fails, a string that describes the error is returned. Return type: str or NoneType
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getCommonBasis
()¶ If all structures use the same basis set, return the basis set name. Otherwise, return None.
Returns: The basis set name or None Return type: str or NoneType
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chargedStrucsPresent
()¶ Determine if the user has specified any molecular charges
Returns: True if the user has specified a molecular charge for any molecule. False otherwise. Return type: bool
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getBasisForEid
(eid, per_atom_name)¶ Get the basis set for the specified entry id. If there are per-atom basis sets specified for the structure, the
per_atom_name
will be returned.Parameters: - eid (str) – The entry id
- per_atom_name (str) – The name to return if per-atom basis sets are specified
Returns: The basis set name, or
per_atom_name
if per-atom basis sets are specifiedReturn type: Basis
or str
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class
schrodinger.application.jaguar.gui.tabs.input_tab.
InputTabPka
(parent, input_selector=None)¶ Bases:
schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase
An input tab that allows the user to specify pKa atoms.
Variables: set_pka_marker ( PyQt5.QtCore.pyqtSignal
) –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
)
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HELP_TOPIC
= 'JAGUAR_INPUT_TAB'¶
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UI_MODULES
= (<module 'schrodinger.application.jaguar.gui.ui.input_pka_top_ui' from '/scr/buildbot/savedbuilds/2018-3/NB/build-149/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/input_pka_top_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.input_pka_bottom_ui' from '/scr/buildbot/savedbuilds/2018-3/NB/build-149/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/input_pka_bottom_ui.py'>)¶
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MODEL_CLASS
¶ alias of
schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka
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VIEW_CLASS
¶ alias of
schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesViewPka
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set_pka_marker
¶
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SMARTS
= 'SMARTS'¶
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SMARTS_TOOLTIP
= ''¶
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AUTO
= 'Automatic search'¶
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AUTO_TOOLTIP
= 'Application will attempt to locate all pKa atoms in all structures.\nStructures must be in the appropriate protonation form.\nNote that this search is not perfect and may miss some atoms or include others erroneously.'¶
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setup
()¶ Perform tab specific initialization. This function should be defined in subclasses if initialization is needed.
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onFindCheckToggled
(state)¶ If checked, disable editing of pka atom and enable combobox for choosing of pick mode. Update model to reflect new pick mode. Show smarts selector if new picking mode is SMARTS.
Parameters: state (bool) – If checkbox is checked or not
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onPickModeComboChanged
()¶ Update model to reflect new pick mode. Show smarts selector if new picking mode is SMARTS.
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showSmartsSelector
()¶ Show the smarts selector next to the define label.
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onPickModeChanged
()¶ Update the model to reflect the new pick mode. If its SMARTS show and hide the define label and connect signals.
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showDefineButton
()¶ Show the define label
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hideDefineButton
()¶ Hide the define label
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getPickingMode
()¶ Determine the current picking mode the tab is in
Returns: picking mode Return type: input_tab_widgets_pka.PickingModes
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runSmartsSearch
()¶ Run SMARTS searches on the entries in the entry table if the pick mode is SMARTS
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getMmJagKeywords
()¶ Return all keywords that should be put into the mmjag handle. This function should be defined in subclasses.
Returns: All keywords that should be put into the mmjag handle Return type: dict Raises: schrodinger.application.jaguar.gui.utils.JaguarSettingError – If any settings are invalid.
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isZwitterionChecked
()¶
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isConformationalSearchesChecked
()¶
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validate
()¶ 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 causegetMmJagKeywords
to raise a JaguarSettingError. Any tab setting that allows mmjag keywords to be successfully generated but will result in a job failure should cause avalidate
fail. This function should be defined in subclasses if validation is needed.Returns: If the validation passes, None is returned. If the validation fails, a string that describes the error is returned. Return type: str or NoneType
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loadSettings
(jag_input)¶ Restore tab settings from mmjag keywords. This function should be defined in subclasses.
Parameters: jag_input ( schrodinger.application.jaguar.input.JaguarInput
) – The Jaguar settings to base the tab settings on
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setPickMethodToManual
()¶
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setPickMethodToAuto
()¶
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class
schrodinger.application.jaguar.gui.tabs.input_tab.
InputTabHB
(parent, input_selector=None)¶ Bases:
schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase
An input tab that is used with Hydrogen Bond task.
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HELP_TOPIC
= 'JAGUAR_INPUT_TAB'¶
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UI_MODULES
= (<module 'schrodinger.application.jaguar.gui.ui.input_top_ui' from '/scr/buildbot/savedbuilds/2018-3/NB/build-149/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/input_top_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.input_hb_bottom_ui' from '/scr/buildbot/savedbuilds/2018-3/NB/build-149/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/input_hb_bottom_ui.py'>)¶
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MODEL_CLASS
¶ alias of
schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesModelHB
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VIEW_CLASS
¶ alias of
schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView
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getMmJagKeywords
()¶ There are no jaguar handle keywords that this tab sets, but we need this function to override the one in the base class.
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loadSettings
(jag_input)¶ Restore tab settings from mmjag keywords. This function should be defined in subclasses.
Parameters: jag_input ( schrodinger.application.jaguar.input.JaguarInput
) – The Jaguar settings to base the tab settings on
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isFastMode
()¶ This function return True if ‘Fast Mode’ check box is checked.
Returns: True if ‘Fast Mode’ check box is toggled. Return type: bool
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getOptimizationCmd
()¶ This function returns command argument corresponding to the checked optimization option. If ‘Optimize all structure’ option is selected this function returns None.
Returns: optimization command argument Return type: string or None
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reset
()¶ This function resets optimization and ‘fast mode’ settings to default state. This function needs to be called every time when input file is loaded.
-
-
class
schrodinger.application.jaguar.gui.tabs.input_tab.
InputTabWithSubTabs
(parent, input_selector=None)¶ Bases:
schrodinger.application.jaguar.gui.tabs.input_tab.InputTab
An Input tab with sub-tabs on the bottom. Sub-tabs can be set using
addSubTabs
, which is normally accessed by setting the INPUT_SUB_TABS panel class variable.Variables: - DEFAULT_SUB_TAB_VISIBILITY (bool) – Whether the sub-tabs should be visible by
default. Sub-tab visibility can be toggled at any time using
setSubTabsVisible
, which is connected to the “Atom-Level Settings” button. - subTabChanged (
PyQt5.QtCore.pyqtSignal
) – A signal emitted when the active sub-tab has been changed, or when the sub-tab visibility has been toggled. - addJaguarMarker (
PyQt5.QtCore.pyqtSignal
) –A signal emitted when a workspace marker should be added. Emitted with:
- The list of atoms to add the marker for (list)
- The marker settings (dict)
- The name of the sub-tab that the marker is for (str)
- removeJaguarMarker (
PyQt5.QtCore.pyqtSignal
) –A signal emitted when a workspace marker should be removed. Emitted with:
- The list of atoms to remove the marker for (list)
- The name of the sub-tab that the marker is for (str)
- setMarkerHighlighting (
PyQt5.QtCore.pyqtSignal
) –A signal emitted when the highlighting of a workspace marker should be changed. Emitted with:
- The list of atoms to change the highlighting for (list)
- Whether the marker should be highlighted (True) or unhighlighted (False) (bool)
- The name of the sub-tab that the marker is for (str)
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UI_MODULES
= (<module 'schrodinger.application.jaguar.gui.ui.input_top_ui' from '/scr/buildbot/savedbuilds/2018-3/NB/build-149/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/input_top_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.input_std_bottom_ui' from '/scr/buildbot/savedbuilds/2018-3/NB/build-149/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/input_std_bottom_ui.py'>)¶
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DEFAULT_SUB_TAB_VISIBILITY
= False¶
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SUB_TAB_NAME
= '%s (%i)'¶
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subTabChanged
¶
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addJaguarMarker
¶
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removeJaguarMarker
¶
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setMarkerHighlighting
¶
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addSubTabs
(sub_tab_classes)¶ Add a sub tab for each of the specified classes. Note that this function should be called only once per instance.
Parameters: sub_tab_classes (iterable) – An iterable of schrodinger.application.jaguar. gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab
sub-classes to be instantiated.
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getChargeConstraintSubTab
()¶ Get the subtab that holds the charge constraint settings
Return type: schrodinger.application.jaguar.gui.input_sub_tabs. ChargeConstraintsSubTab
Returns: The charge constraint subtab, or None if no such tab exists
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getBasisSetSubTab
()¶ Get the subtab that holds the by-atom basis set settings
Return type: schrodinger.application.jaguar.gui.input_sub_tabs. BasisSetSubTab
Returns: The by-atom basis set subtab, or None if no such tab exists
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getSubTab
(sub_tab_class)¶ Get the sub-tab of the specified class
Parameters: sub_tab_class (type) – The class of the sub-tab to retrieve
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setup
()¶ Perform tab specific initialization. This function should be defined in subclasses if initialization is needed.
-
projectUpdated
()¶ Whenever the project is updated, update the structure titles and the structures shown in the sub tabs.
-
reset
()¶ Reset any structure specific settings in the table. (The non-struture specific settings will be reset via loadSettings())
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setSubTabsVisible
(visible=None)¶ Set whether the sub-tabs are visible in response to the user clicking on the “Atom-Level Settings” button.
Parameters: visible (bool or NoneType) – Should the sub-tabs be made visible. If not specified, the visibility will be toggled.
-
subTabsVisible
()¶ Are the sub-tabs currently visible?
Returns: True if the sub-tabs are visible. False otherwise. Return type: bool
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validate
()¶ 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 causegetMmJagKeywords
to raise a JaguarSettingError. Any tab setting that allows mmjag keywords to be successfully generated but will result in a job failure should cause avalidate
fail. This function should be defined in subclasses if validation is needed.Returns: If the validation passes, None is returned. If the validation fails, a string that describes the error is returned. Return type: str or NoneType
-
saveSettings
(jag_input, eid)¶ Save tab settings in jaguar handle. It is only used for settings which are not defined using keywords (typically per-atom settings). This function should be defined in subclasses for any tabs that contain per- atom settings.
Parameters: - jag_input (
schrodinger.application.jaguar.input.JaguarInput
) – The Jaguar handle to store the tab settings in - eid (str) – The entry id of the structure in
jag_input
- jag_input (
-
loadPerAtomSettings
(jag_input, eid, title)¶ Restore per-atom tab settings from mmjag keywords. This function should be defined in subclasses for any tabs that contain per-atom settings.
Parameters: - jag_input (
schrodinger.application.jaguar.input.JaguarInput
) – The Jaguar settings to base the tab settings on - eid (str) – The entry id of the structure in
jag_input
- title (str) – The title of the structure in
jag_input
- jag_input (
-
activeSubTab
()¶ Get the active sub tab
Returns: The active sub-tab or None if the sub-tabs are not visible Return type: schrodinger.application.jaguar.gui.input_sub_tabs. base_sub_tab.BaseSubTab
or NoneType
-
activeSubTabName
()¶ Get the name of the active sub-tab
Returns: The name of the active sub-tab or None if the sub-tabs are not visible Return type: str or NoneType
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activate
()¶ Activate the appropriate sub-tab (if any) when this tab is activated
-
deactivate
()¶ Deactivate the active sub-tab (if any)
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displayedEntryIds
()¶ Return the entry IDs for all structures that are currently displayed in the input table
Returns: A set of entry ids Return type: set
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perAtomBasisSetsPresent
()¶ Have any per-atom basis sets been set?
Returns: True if there are per-atom basis sets for any currently selected structures. False otherwise. Return type: bool
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getCommonBasis
()¶ If all structures use the same basis set and there are no per-atom basis sets, return the basis set name. Otherwise, return None.
Returns: The basis set name or None Return type: str or NoneType
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theoryChanged
(theory_level)¶ If there is a Charge Constraints sub-tab, disable or enable it when the level of theory changes.
Parameters: theory_level (str) – The current level of theory. Should be one of “DFT”, “HF”, or “LMP2”.
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useFromComboChanged
()¶ Update the sub-tabs when the user changes the structure source (from included to selected or vice versa).
- DEFAULT_SUB_TAB_VISIBILITY (bool) – Whether the sub-tabs should be visible by
default. Sub-tab visibility can be toggled at any time using