schrodinger.application.jaguar.gui.tabs.solvation_tab module¶
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schrodinger.application.jaguar.gui.tabs.solvation_tab.
different
(value1, value2)¶ Return True if the given float values are different from each other (tiny differences are not considered).
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class
schrodinger.application.jaguar.gui.tabs.solvation_tab.
SolventTab
(parent, input_selector=None)¶ Bases:
schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab
The Solvent tab that contains only solvent model widgets. This is common part of Solvation tab for multiple panels.
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NAME
= 'Solvent'¶
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HELP_TOPIC
= 'JAGUAR_TOPIC_SOLVATION_FOLDER'¶
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UI_MODULES
= (<module 'schrodinger.application.jaguar.gui.ui.solvent_tab_ui' from '/scr/buildbot/savedbuilds/2018-2/NB/build-169/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/solvent_tab_ui.py'>,)¶
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SOLVENTS
= [Solvent(name='Water', keyvalue='water', dielectric=80.37, radius=1.4, weight=18.02, density=0.99823), Solvent(name='DMSO', keyvalue='dmso', dielectric=36.7, radius=2.41, weight=78.13, density=1.1014)]¶
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SHOW_DIELECTRIC
= False¶
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setup
()¶ Perform tab specific initialization. This function should be defined in subclasses if initialization is needed.
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solventTypeChanged
()¶ Called when a new item is selected from the solvent menu.
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calculateProbeRadius
()¶ Calculate the solvent probe radius from the density and molecular weight.
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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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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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class
schrodinger.application.jaguar.gui.tabs.solvation_tab.
SolventPkaTab
(parent, input_selector=None)¶ Bases:
schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventTab
The Solvent tab for the Pka panel.
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UI_MODULES
= (<module 'schrodinger.application.jaguar.gui.ui.solvent_tab_ui' from '/scr/buildbot/savedbuilds/2018-2/NB/build-169/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/solvent_tab_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.solvation_pka_ui' from '/scr/buildbot/savedbuilds/2018-2/NB/build-169/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/solvation_pka_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
()¶ 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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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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class
schrodinger.application.jaguar.gui.tabs.solvation_tab.
SolvationTab
(parent, input_selector=None)¶ Bases:
schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventTab
The Solvation tab, which includes solvent model and gas-phase reference energy
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NAME
= 'Solvation'¶
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UI_MODULES
= (<module 'schrodinger.application.jaguar.gui.ui.solvation_solvent_model_ui' from '/scr/buildbot/savedbuilds/2018-2/NB/build-169/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/solvation_solvent_model_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.solvent_tab_ui' from '/scr/buildbot/savedbuilds/2018-2/NB/build-169/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/solvent_tab_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.solvation_gas_phase_ui' from '/scr/buildbot/savedbuilds/2018-2/NB/build-169/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/solvation_gas_phase_ui.py'>)¶
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SHOW_DIELECTRIC
= True¶
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SOLVENTS
= [Solvent(name='Water', keyvalue='water', dielectric=80.37, radius=1.4, weight=18.02, density=0.99823), Solvent(name='Acetonitrile', keyvalue='acetonitrile', dielectric=37.5, radius=2.19, weight=41.05, density=0.777), Solvent(name='Benzene', keyvalue='benzene', dielectric=2.284, radius=2.6, weight=78.12, density=0.87865), Solvent(name='Carbon tetrachloride', keyvalue='carbon_tet', dielectric=2.238, radius=2.67, weight=153.82, density=1.594), Solvent(name='Chlorobenzene', keyvalue='chlorobenzene', dielectric=5.708, radius=2.72, weight=112.56, density=1.1058), Solvent(name='Chloroform', keyvalue='chloroform', dielectric=4.806, radius=2.52, weight=119.38, density=1.4832), Solvent(name='Cyclohexane', keyvalue='cyclohexane', dielectric=2.023, radius=2.78, weight=84.16, density=0.77855), Solvent(name='1,2-dichloroethane', keyvalue='dichloroethane', dielectric=10.65, radius=2.51, weight=98.96, density=1.2351), Solvent(name='Dichloromethane', keyvalue='dichloromethane', dielectric=8.93, radius=2.33, weight=84.93, density=1.3266), Solvent(name='Dimethylformamide', keyvalue='dimethylformamide', dielectric=36.7, radius=2.49, weight=73.09, density=0.944), Solvent(name='DMSO', keyvalue='dmso', dielectric=36.7, radius=2.41, weight=78.13, density=1.1014), Solvent(name='Ethanol', keyvalue='ethanol', dielectric=24.85, radius=2.27, weight=46.07, density=0.785), Solvent(name='Methanol', keyvalue='methanol', dielectric=33.62, radius=2.0, weight=32.04, density=0.7914), Solvent(name='Nitrobenzene', keyvalue='nitrobenzene', dielectric=35.74, radius=2.73, weight=123.11, density=1.2037), Solvent(name='Tetrahydrofuran', keyvalue='tetrahydrofuran', dielectric=7.6, radius=2.52, weight=72.11, density=0.8892), Solvent(name='Other', keyvalue='other', dielectric=None, radius=None, weight=None, density=None)]¶
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NO_SOLVENT_MODEL
= 'None'¶
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SOLVENT_MODELS
= {'None': 0, 'PBF': 2, 'SM6': 5, 'SM8': 6}¶
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setup
()¶ Perform tab specific initialization. This function should be defined in subclasses if initialization is needed.
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solventModelChanged
()¶ Called when a new item is selected in the solvent model type menu.
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gasPhaseReferenceChanged
()¶ Called when a new radio button is clicked in the gas phase section.
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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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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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class
schrodinger.application.jaguar.gui.tabs.solvation_tab.
SolvationTabNoOptimized
(parent, input_selector=None)¶ Bases:
schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab
A solvation tab that doesn’t allow “Optimized gas-phase structure”.
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setup
()¶ Perform tab specific initialization. This function should be defined in subclasses if initialization is needed.
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