schrodinger.application.jaguar.gui.tabs.input_tab module

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.

HELP_TOPIC = 'JAGUAR_INPUT_TAB'
UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.input_top_ui' from '/scr/buildbot/savedbuilds/2017-4/NB/build-152/internal/lib/python2.7/site-packages/schrodinger/application/jaguar/gui/ui/input_top_ui.pyc'>, <module 'schrodinger.application.jaguar.gui.ui.input_std_bottom_ui' from '/scr/buildbot/savedbuilds/2017-4/NB/build-152/internal/lib/python2.7/site-packages/schrodinger/application/jaguar/gui/ui/input_std_bottom_ui.pyc'>)
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
getBasis(mixed_name='Mixed')
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 specified
Return type:

Basis or str
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
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
loadSettings(jag_input)
setup()
validate()
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
  • SYMM_ITEMS (tuple) – The data to display in the symmetry combo box
  • strucSourceChanged (QtCore.pyqtSignal) – A signal emitted when the structure source changes from included to selected or vice versa.
MODEL_CLASS

alias of InputEntriesModel

NAME = 'Input'
PROXY_CLASS

alias of InputEntriesProxyModel

SYMM_ITEMS = ('Use if present', 'Off', 'Abelian')
VIEW_CLASS

alias of InputEntriesView

getMmJagKeywords()

Get the symmetry-related mmjag keywords. All other keywords are per- structure

getNumStructures()
getStructureTitleForJobname()
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:
Return type:list
loadSettings(jag_input)
projectUpdated()

When the project is updated, update the selected entries table

reset()

Reset any structure specific settings in the table. (The non-struture specific settings will be reset via loadSettings())

setup()
strucSourceChanged
useFromComboChanged()

Respond to the user changing the structure source (from included to selected or vice versa).

usingSelected()

Return True if the tab is set to use selected entries. False if the tab is set to use included entries.

validate()
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
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.

HELP_TOPIC = 'JAGUAR_INPUT_TAB'
MODEL_CLASS

alias of InputEntriesModelHB

SYMM_ITEMS = None
UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.input_top_ui' from '/scr/buildbot/savedbuilds/2017-4/NB/build-152/internal/lib/python2.7/site-packages/schrodinger/application/jaguar/gui/ui/input_top_ui.pyc'>, <module 'schrodinger.application.jaguar.gui.ui.input_hb_bottom_ui' from '/scr/buildbot/savedbuilds/2017-4/NB/build-152/internal/lib/python2.7/site-packages/schrodinger/application/jaguar/gui/ui/input_hb_bottom_ui.pyc'>)
VIEW_CLASS

alias of InputEntriesView

getMmJagKeywords()

There are no jaguar handle keywords that this tab sets, but we need this function to override the one in the base class.

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
isFastMode()

This function return True if ‘Fast Mode’ check box is checked.

Returns:True if ‘Fast Mode’ check box is toggled.
Return type:bool
loadSettings(jag_input)
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.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:
HELP_TOPIC = 'JAGUAR_INPUT_TAB'
MODEL_CLASS

alias of InputEntriesModelPka

UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.input_top_ui' from '/scr/buildbot/savedbuilds/2017-4/NB/build-152/internal/lib/python2.7/site-packages/schrodinger/application/jaguar/gui/ui/input_top_ui.pyc'>, <module 'schrodinger.application.jaguar.gui.ui.input_pka_bottom_ui' from '/scr/buildbot/savedbuilds/2017-4/NB/build-152/internal/lib/python2.7/site-packages/schrodinger/application/jaguar/gui/ui/input_pka_bottom_ui.pyc'>)
VIEW_CLASS

alias of InputEntriesViewPka

getMmJagKeywords()
isConformationalSearchesChecked()
isZwitterionChecked()
loadSettings(jag_input)
set_pka_marker
setup()
validate()
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)
DEFAULT_SUB_TAB_VISIBILITY = False
SUB_TAB_NAME = '%s (%i)'
UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.input_top_ui' from '/scr/buildbot/savedbuilds/2017-4/NB/build-152/internal/lib/python2.7/site-packages/schrodinger/application/jaguar/gui/ui/input_top_ui.pyc'>, <module 'schrodinger.application.jaguar.gui.ui.input_std_bottom_ui' from '/scr/buildbot/savedbuilds/2017-4/NB/build-152/internal/lib/python2.7/site-packages/schrodinger/application/jaguar/gui/ui/input_std_bottom_ui.pyc'>)
activate()

Activate the appropriate sub-tab (if any) when this tab is activated

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
addJaguarMarker
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.
deactivate()

Deactivate the active sub-tab (if any)

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
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
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
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
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
loadPerAtomSettings(jag_input, eid, title)
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
projectUpdated()

Whenever the project is updated, update the structure titles and the structures shown in the sub tabs.

removeJaguarMarker
reset()
saveSettings(jag_input, eid)
setMarkerHighlighting
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.
setup()
subTabChanged
subTabsVisible()

Are the sub-tabs currently visible?

Returns:True if the sub-tabs are visible. False otherwise.
Return type:bool
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”.
useFromComboChanged()

Update the sub-tabs when the user changes the structure source (from included to selected or vice versa).

validate()