schrodinger.application.jaguar.gui.tabs.optimization_tab module¶
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class
schrodinger.application.jaguar.gui.tabs.optimization_tab.
OptimizationTab
(parent, input_selector=None)¶ Bases:
schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab
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NAME
= 'Optimization'¶
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UI_MODULES
= (<module 'schrodinger.application.jaguar.gui.ui.optimization_tab_ui' from '/scr/buildbot/savedbuilds/2018-3/NB/build-149/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/optimization_tab_ui.py'>,)¶
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HELP_TOPIC
= 'JAGUAR_TOPIC_OPTIMIZATION_FOLDER'¶
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CONVERGENCE_CRITERIA
= {'Custom': 6, 'Default': 2, 'Loose': 3, 'Tight': 5}¶
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INITIAL_HESSIAN
= {'Fischer-Almlof guess': -1, 'Quantum-mechanical': 4, 'Schlegel guess': 0, 'Unit Hessian': 1}¶
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COORDINATE_OPTS
= {'Cartesian': 0, 'Redundant internal': 1, 'Z-matrix': 2}¶
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ALL_CONSTRAINTS_BUTTON
= {0: (True, 'Add Selected Atoms'), 1: (True, 'Add Selected Atoms'), 2: (True, 'Add Selected Atoms'), 3: (True, 'Add Selected Atoms'), 4: (True, 'Add All Atom Pairs'), 5: (True, 'Add All Bond Angles'), 6: (True, 'Add All Torsions')}¶
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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
()¶ This function returns dictionary of mmjag keywords for this tab. Since this tab does not set any keywords it returns an empty dictionary.
Returns: mmjag keywords dictionary Return type: dict
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getConvergenceKeywords
()¶ Get keywords from convergence criteria widgets.
Returns: A dictionary of keywords Return type: dict
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loadSettings
(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
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loadConvergenceKeywords
(jag_input)¶ Load the convergence criteria settings.
Parameters: jag_input ( schrodinger.application.jaguar.input.JaguarInput
) – The Jaguar settings to load.
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loadConstraintCoordinates
(jag_input)¶ Load constraint coordinates from Jaguar handle.
Parameters: jag_input ( schrodinger.application.jaguar.input.JaguarInput
) – The Jaguar handle where tab settings are saved.
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saveSettings
(jag_input, eid=None)¶ Save constraint coordinate settings in jaguar handle.
See parent class for argument documentation
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deleteCurrentRow
()¶ This function is called to delete row which is currently selected from the coordinates table.
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deleteAllRows
()¶ This function is called to delete all rows from the coordinates table.
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addCoordinate
(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
- st (
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convergenceTypeChanged
(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
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pickCompleted
(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
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updateAllConstraintsPB
()¶ This function is called when coordinate type is changed to update text and visibility of the button that adds all constraints.
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addConsButtonPressed
()¶ 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.
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getAllAtomPairs
(st)¶ This function returns a list of all possible atom pairs in a given structure.
Parameters: st ( schrodinger.structure.Structure
) – structureReturns: list that contains pairs of atom indices Return type: list
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getAllAngles
(st)¶ This function returns list that contains lists of atoms for each bond angle in a given structure.
Parameters: st ( schrodinger.structure.Structure
) – structureReturns: list that contains lists of atom indices for each bond angle Return type: list
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getAllTorsions
(st)¶ This function returns list that contains lists of atoms for each torsion angle in a given structure.
Parameters: st ( schrodinger.structure.Structure
) – structureReturns: list that contains lists of atom indices for each torsion Return type: list
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class
schrodinger.application.jaguar.gui.tabs.optimization_tab.
ConstraintCoordinateColumns
¶ Bases:
object
Constants for table columns.
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NAMES
= ('Atom Indices', 'Coordinate', 'Type', 'Target Value')¶
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NUM_COLS
= 4¶
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INDICES
= 0¶
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COORD_NAME
= 1¶
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COORD_TYPE
= 2¶
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TARGET_VAL
= 3¶
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class
schrodinger.application.jaguar.gui.tabs.optimization_tab.
ConstraintCoordinateData
(st, atoms, coordinate_type, target_value=None)¶ Bases:
schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateData
This class stores all data for a single constraint coordinate.
Variables: - st (
schrodinger.structure.Structure
) – ct structure for which coordinates are defined - atom_indices (list) – indices of atoms, which define this coordinate
- coordinate_name (str) – name of this coordinate based on atom indices
- coordinate_type (int) – coordinate type
- target_value (float) – target value of this coordinate
- st (
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class
schrodinger.application.jaguar.gui.tabs.optimization_tab.
ConstraintCoordinatesDelegate
¶ Bases:
PyQt5.QtWidgets.QItemDelegate
This delegate is used to validate values entered in ‘target value’ column.
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COLUMN
= <schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinateColumns object>¶
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createEditor
(parent, option, index)¶ This function returns an editor widget (QLineEdit) for ‘target value’ column.
Parameters: - parent (
QtWidgets.QWidget
) – parent widget - option (
QtWidgets.QStyleOptionViewItem
) – not used, but kept for compatibility - index (
QtCore.QModelIndex
) – model index
Returns: QLineEdit editor widget
Return type: QtWidgets.QLineEdit
- parent (
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setEditorData
(editor, index)¶ This function read data from model, converts it to text and sets it in the editor widget.
Parameters: - editor (
QtWidgets.QLineEdit
) – editor widget - index (
QtCore.QModelIndex
) – model index
- editor (
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setModelData
(editor, model, index)¶ This function reads text from QLineEdit and writes it to the model
Parameters: - editor (
QtWidgets.QLineEdit
) – editor widget - model (
QtCore.QAbstractItemModel
) – data model - index (
QtCore.QModelIndex
) – model index
- editor (
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class
schrodinger.application.jaguar.gui.tabs.optimization_tab.
ConstraintCoordinatesProxyModel
(parent)¶ Bases:
PyQt5.QtCore.QSortFilterProxyModel
A proxy model that allows to hide columns.
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COLUMN
= <schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinateColumns object>¶
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filterAcceptsColumn
(column, index)¶ Modified from the parent class to define columns that should be visible.
Parameters: - column (int) – the column index
- index (
QModelIndex
) – Unused, but kept for PyQt compatibility
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class
schrodinger.application.jaguar.gui.tabs.optimization_tab.
ConstraintCoordinatesModel
(parent=None)¶ Bases:
schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel
A model to store scan tab coordinates data.
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COLUMN
= <schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinateColumns object>¶
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addCoordinate
(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
- st (
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appendFromModel
(model)¶ Append the rows in the given model to this model
Type: ConstraintCoordinatesModel
Param: The model to append rows from
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flags
(index)¶ Returns flags for the specified cell. Whether it is editable or not.
Parameters: index ( PyQt5.QtCore.QModelIndex
) – The index to retrieve flags for.
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data
(index, role=0)¶ Retrieve the requested data
Parameters: - index (
PyQt5.QtCore.QModelIndex
) – The index to retrieve data for - role (int) – The role to retrieve data for
Returns: The requested data
- index (
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setData
(index, value, role=2)¶ Modify coordinate values.
Parameters: - index (
QtCore.QModelIndex
) – the index of table cell - value (str) – new value
- role (int) – The role to set data for.
- index (
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class
schrodinger.application.jaguar.gui.tabs.optimization_tab.
ActiveOptimizationTab
(parent, input_selector=None)¶ Bases:
schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab
Tab used in place of optimization tab in Transition State Search panel
Variables: activeConstraintsToggled ( PyQt5.QtCore.pyqtSignal
) – A signal emitted when the active constraints check box is toggled-
activeConstraintsToggled
¶
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setup
()¶ Setup UI elements
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saveSettings
(jag_input, eid=None)¶ Save per-atom settings to Jaguar input.
Parameters: - jag_input (
schrodinger.application.jaguar.input.JaguarInput
) – A JaguarInput object to save settings to - eid (str or None) – the eid to save settings for, always None because Transition State Search panel uses a MultiStructureTab
- jag_input (
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loadConstraintCoordinates
(jag_input)¶ Load constraint coordinates from Jaguar handle.
Parameters: jag_input ( schrodinger.application.jaguar.input.JaguarInput
) – The Jaguar handle where tab settings are saved.
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enableActiveChkIfConstraintsAdded
()¶ Enable the active constraints check box if there are constraints added to the list or disable it if there are not.
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addCoordinate
(st, atoms, coordinate_type, target_value=None)¶ Add a coordinate and enable active checkbox if successfully added
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deleteAllRows
()¶ Delete all constraint rows and disable active checkbox
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deleteCurrentRow
()¶ Delete current row and disable active checkbox if no more rows remain
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