Package schrodinger :: Package application :: Package jaguar :: Package gui :: Package tabs :: Module optimization_tab :: Class OptimizationTab

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Class OptimizationTab

PyQt4.QtGui.QWidget --+        
                      |        
       base_tab.BaseTab --+    
                          |    
  coordinates.CoordinateTab --+
                              |
                             OptimizationTab

Instance Methods

[hide private]

setup(self)
Perform tab specific initialization.

dict

getMmJagKeywords(self)
This function returns dictionary of mmjag keywords for this tab.

dict

getConvergenceKeywords(self)
Get keywords from convergence criteria widgets.

loadSettings(self, jag_input)
Restore scan coordinates settings from Jaguar handle.

loadConvergenceKeywords(self, jag_input)
Load the convergence criteria settings.

loadConstraintCoordinates(self, jag_input)
Load constraint coordinates from Jaguar handle.

saveSettings(self, jag_input, eid=None)
Save constraint coordinate settings in jaguar handle.

deleteCurrentRow(self)
This function is called to delete row which is currently selected from the coordinates table.

deleteAllRows(self)
This function is called to delete all rows from the coordinates table.

addCoordinate(self, st, atoms, coordinate_type, target_value=None)
Add new coordinate row.

convergenceTypeChanged(self, index)
This function is called when convergence type is changed.

pickCompleted(self, atoms)
This slot is called when required number of atoms for the current coordinate type has been picked.

updateAllConstraintsPB(self)
This function is called when coordinate type is changed to update text and visibility of the button that adds all constraints.

addConsButtonPressed(self)
This function is called when 'add all constraints/add selected atoms' button is clicked.

list

getAllAtomPairs(self, st)
This function returns a list of all possible atom pairs in a given structure.

list

getAllAngles(self, st)
This function returns list that contains lists of atoms for each bond angle in a given structure.

list

getAllTorsions(self, st)
This function returns list that contains lists of atoms for each torsion angle in a given structure.

Inherited from coordinates.CoordinateTab: setAcceptableContraintEids, stopPicking

Inherited from coordinates.CoordinateTab (private): _checkSelection, _determineIfConstraintsAddable, _emitCoordinateAdded, _emitCoordinateDeleted, _getAtomsForRow, _highlightSelectedMarkers, _resetDefaults

Inherited from base_tab.BaseTab: __init__, activate, deactivate, error, getDefaultKeywords, loadPerAtomSettings, reset, validate, warning

Inherited from base_tab.BaseTab (private): _populateUi

Class Variables

[hide private]

str NAME = "Optimization"
The name of the tab

tuple UI_MODULES = ui.optimization_tab_ui,
A tuple of ui modules defining the tab widgets.

str HELP_TOPIC = "JAGUAR_TOPIC_OPTIMIZATION_FOLDER"
The help topic for the tab

CONVERGENCE_CRITERIA = OrderedDict((("Default", mm.MMJAG_IACCG...

INITIAL_HESSIAN = OrderedDict((("Schlegel guess", mm.MMJAG_INH...

COORDINATE_OPTS = OrderedDict((("Redundant internal", mm.MMJAG...

ALL_CONSTRAINTS_BUTTON = {mm.MMJAG_COORD_CART_X:(True, "Add Se...

Inherited from coordinates.CoordinateTab: allCoordinatesDeleted, coordinateAdded, coordinateDeleted, coordinateDeselected, coordinateSelected, refreshMarkers

Instance Variables

[hide private]

Inherited from base_tab.BaseTab: input_selector, task_name, ui

Method Details

[hide private]

setup(self)

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

Overrides: base_tab.BaseTab.setup: (inherited documentation)

getMmJagKeywords(self)

This function returns dictionary of mmjag keywords for this tab. Since this tab does not set any keywords it returns an empty dictionary.

Returns: dict

mmjag keywords dictionary

Raises:

schrodinger.application.jaguar.gui.utils.JaguarSettingError - If any settings are invalid.

Overrides: base_tab.BaseTab.getMmJagKeywords

getConvergenceKeywords(self)

Get keywords from convergence criteria widgets.

Returns: dict: A dictionary of keywords

loadSettings(self, jag_input)

Restore scan coordinates settings from Jaguar handle.

Parameters:

jag_input (schrodinger.application.jaguar.input.JaguarInput) - The Jaguar settings to base the tab settings on

Overrides: base_tab.BaseTab.loadSettings

loadConvergenceKeywords(self, jag_input)

Load the convergence criteria settings.

Parameters:

jag_input (schrodinger.application.jaguar.input.JaguarInput) - The Jaguar settings to load.

loadConstraintCoordinates(self, jag_input)

Load constraint coordinates from Jaguar handle.

Parameters:

jag_input (schrodinger.application.jaguar.input.JaguarInput) - The Jaguar handle where tab settings are saved.

saveSettings(self, jag_input, eid=None)

Save constraint coordinate settings in jaguar handle.

See parent class for argument documentation

Parameters:

jag_input - The Jaguar handle to store the tab settings in
eid - The entry id of the structure in jag_input

Overrides: base_tab.BaseTab.saveSettings

addCoordinate(self, st, atoms, coordinate_type, target_value=None)

Add new coordinate row.

Parameters:

st (schrodinger.structure.Structure) - structure
atoms (list) - atom indices
coordinate_type (int) - coordinate type
target_value (float) - target coordinate value

convergenceTypeChanged(self, index)

This function is called when convergence type is changed. If 'Custom' is selected extra options frame is shown. Otherwise, it is hidden.

Parameters:

index (int) - convergence type combo box index

pickCompleted(self, atoms)

This slot is called when required number of atoms for the current coordinate type has been picked.

Parameters:

atoms (list) - list of atom indices

addConsButtonPressed(self)

This function is called when 'add all constraints/add selected atoms' button is clicked. It determines current coordinate type and calls appropriate function to add all/selected constraints.

getAllAtomPairs(self, st)

This function returns a list of all possible atom pairs in a given structure.

Parameters:

st (schrodinger.structure.Structure) - structure

Returns: list

list that contains pairs of atom indices

getAllAngles(self, st)

This function returns list that contains lists of atoms for each bond angle in a given structure.

Parameters:

st (schrodinger.structure.Structure) - structure

Returns: list

list that contains lists of atom indices for each bond angle

getAllTorsions(self, st)

This function returns list that contains lists of atoms for each torsion angle in a given structure.

Parameters:

st (schrodinger.structure.Structure) - structure

Returns: list

list that contains lists of atom indices for each torsion

Class Variable Details

[hide private]

CONVERGENCE_CRITERIA

Value:

OrderedDict((("Default", mm.MMJAG_IACCG_ACCURATE), ("Loose", mm.MMJAG_
IACCG_QUICK), ("Tight", mm.MMJAG_IACCG_TIGHT), ("Custom", mm.MMJAG_IAC
CG_CUSTOM)))

INITIAL_HESSIAN

Value:

OrderedDict((("Schlegel guess", mm.MMJAG_INHESS_SCHLEGEL), ("Fischer-A
lmlof guess", mm.MMJAG_INHESS_FISCHER), ("Unit Hessian", mm.MMJAG_INHE
SS_UNIT), ("Quantum-mechanical", mm.MMJAG_INHESS_QM)))

COORDINATE_OPTS

Value:

OrderedDict((("Redundant internal", mm.MMJAG_INTOPT_RED), ("Cartesian"
, mm.MMJAG_INTOPT_CART), ("Z-matrix", mm.MMJAG_INTOPT_ZMAT)))

ALL_CONSTRAINTS_BUTTON

Value:

{mm.MMJAG_COORD_CART_X:(True, "Add Selected Atoms"), mm.MMJAG_COORD_CA
RT_Y:(True, "Add Selected Atoms"), mm.MMJAG_COORD_CART_Z:(True, "Add S
elected Atoms"), mm.MMJAG_COORD_CART_XYZ:(True, "Add Selected Atoms"),
 mm.MMJAG_COORD_DISTANCE:(True, "Add All Atom Pairs"), mm.MMJAG_COORD_
ANGLE:(True, "Add All Bond Angles"), mm.MMJAG_COORD_TORSION:(True, "Ad
d All Torsions")}