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

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.
strucSourceChanged
NAME = 'Input'
MODEL_CLASS

alias of schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel

PROXY_CLASS

alias of schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel

VIEW_CLASS

alias of schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView

setup()

Perform tab specific initialization. This function should be defined in subclasses if initialization is needed.

projectUpdated()

When the project is updated, update the selected entries table

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
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
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 cause getMmJagKeywords to raise a JaguarSettingError. Any tab setting that allows mmjag keywords to be successfully generated but will result in a job failure should cause a validate 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
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
getNumStructures()
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
reset()

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

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.

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/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'>)
setup()

Perform tab specific initialization. This function should be defined in subclasses if initialization is needed.

getMmJagKeywords()

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

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)

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
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
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 cause getMmJagKeywords to raise a JaguarSettingError. Any tab setting that allows mmjag keywords to be successfully generated but will result in a job failure should cause a validate 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
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
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
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

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'
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'>)
MODEL_CLASS

alias of schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka

VIEW_CLASS

alias of schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesViewPka

set_pka_marker
SMARTS = 'SMARTS'
SMARTS_TOOLTIP = ''
AUTO = 'Automatic search'
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.'
setup()

Perform tab specific initialization. This function should be defined in subclasses if initialization is needed.

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
onPickModeComboChanged()

Update model to reflect new pick mode. Show smarts selector if new picking mode is SMARTS.

showSmartsSelector()

Show the smarts selector next to the define label.

onPickModeChanged()

Update the model to reflect the new pick mode. If its SMARTS show and hide the define label and connect signals.

showDefineButton()

Show the define label

hideDefineButton()

Hide the define label

getPickingMode()

Determine the current picking mode the tab is in

Returns:picking mode
Return type:input_tab_widgets_pka.PickingModes
runSmartsSearch()

Run SMARTS searches on the entries in the entry table if the pick mode is SMARTS

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.
isZwitterionChecked()
isConformationalSearchesChecked()
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 cause getMmJagKeywords to raise a JaguarSettingError. Any tab setting that allows mmjag keywords to be successfully generated but will result in a job failure should cause a validate 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
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
setPickMethodToManual()
setPickMethodToAuto()
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'
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'>)
MODEL_CLASS

alias of schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesModelHB

VIEW_CLASS

alias of schrodinger.application.jaguar.gui.input_tab_widgets.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.

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
isFastMode()

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

Returns:True if ‘Fast Mode’ check box is toggled.
Return type:bool
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
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)
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'>)
DEFAULT_SUB_TAB_VISIBILITY = False
SUB_TAB_NAME = '%s (%i)'
subTabChanged
addJaguarMarker
removeJaguarMarker
setMarkerHighlighting
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.
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
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
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
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())

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
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 cause getMmJagKeywords to raise a JaguarSettingError. Any tab setting that allows mmjag keywords to be successfully generated but will result in a job failure should cause a validate 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:
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:
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
activate()

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

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
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
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
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).