schrodinger.application.jaguar.gui.tabs.molecule_tab module¶
- class schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase(parent, input_selector=None)¶
Bases:
schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab
The base class for all molecule tabs. This class defines functionality for the top half of the tab, which is constant between subclasses.
- NAME = 'Molecule'¶
- HELP_TOPIC = 'JAGUAR_TOPIC_MOLECULE_FOLDER'¶
- MULTIPLE_STRUC_WARNING = 'Warning: Charge and spin multiplicity\ncannot be changed when more than one\nentry is selected.'¶
- CHARGE_SPIN_INCONSISTANT_WARNING = 'Warning: Charge and spin multiplicity are inconsistent.'¶
- setup()¶
Perform tab specific initialization. This function should be defined in subclasses if initialization is needed.
- createChargeProperties()¶
Create charge and spin properties in the project table in response to the user clicking on the Create Properties button.
- 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.
- loadSettings(keywords)¶
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
- class schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab(parent, input_selector=None)¶
Bases:
schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesBasisMixin
,schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase
The standard molecule tab
- UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.molecule_top_ui' from '/scr/buildbot/savedbuilds/2024-3/NB/build-133/internal/lib/python3.11/site-packages/schrodinger/application/jaguar/gui/ui/molecule_top_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.molecule_std_bottom_ui' from '/scr/buildbot/savedbuilds/2024-3/NB/build-133/internal/lib/python3.11/site-packages/schrodinger/application/jaguar/gui/ui/molecule_std_bottom_ui.py'>)¶
- setup()¶
Perform tab specific initialization. This function should be defined in subclasses if initialization is needed.
- 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
- getBasis(ignored=None)¶
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
- 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.
- 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
- loadSettings(keywords)¶
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
- class schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka(parent, input_selector=None)¶
Bases:
schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase
The molecule tab used in the PKA panel
- MULTIPLE_STRUC_PICK_WARNING = 'Warning: Pick options cannot be used when\nmore than one entry is in the Workspace'¶
- FILE_PICK_WARNING = 'Warning: Pick options cannot be used when\nusing structures from files.'¶
- UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.molecule_top_ui' from '/scr/buildbot/savedbuilds/2024-3/NB/build-133/internal/lib/python3.11/site-packages/schrodinger/application/jaguar/gui/ui/molecule_top_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.molecule_pka_bottom_ui' from '/scr/buildbot/savedbuilds/2024-3/NB/build-133/internal/lib/python3.11/site-packages/schrodinger/application/jaguar/gui/ui/molecule_pka_bottom_ui.py'>)¶
- PKA_ATOM_PROP = 's_m_pKa_atom'¶
- setup()¶
Perform tab specific initialization. This function should be defined in subclasses if initialization is needed.
- reset()¶
Reset the tab to its original state. Note that this function is only necessary for settings that are not stored in the mmjag handle. For mmjag settings, reset will be carried out using
loadSettings
with a defaultschrodinger.application.jaguar.input.JaguarInput
object. This function should only be defined in subclasses if there are any settings that cannot be reset vialoadSettings
.
- pickThisAtom(atom_num)¶
Respond to the atom picking at atom in the “Use this atom” section.
- Parameters
atom_num (int) – The atom number that was just picked
- pickProjTableAtom(atom_num)¶
Respond to the atom picking at atom in the “Use pKa atoms from the project table” section.
- Parameters
atom_num (int) – The atom number that was just picked
- 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.
- validate()¶
Make sure that a pka atom has been selected and is a valid atom for the currently selected structure
- 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
- isZwitterionChecked()¶
- isConformationalSearchesChecked()¶
- class schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector(parent, input_selector=None)¶
Bases:
schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab
A Molecule tab that does not use the input selector
- setup()¶
Perform tab specific initialization. This function should be defined in subclasses if initialization is needed.
- setStructure(struc)¶
Change the structure that this tab is representing
- Parameters
struc (
schrodinger.structure.Structure
) – The structure
- structureUpdated()¶
React to a change in the structure described by self._struc. i.e. The
schrodinger.structure.Structure
object passed tosetStructure
has not changed, but the structure described by that object has.
- getStructure()¶
Get the structure that this panel is currently representing
- createChargeProperties()¶
Create charge and spin properties in the project table in response to the user clicking on the Create Properties button.