schrodinger.application.jaguar.gui.tabs.scan_tab module

class schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns

Bases: object

Constants for the full (i.e. hidden as well) table columns

NAMES = ('Atom Indices', 'Coordinate', 'Type', 'Steps', 'Fixed Value', 'Current Value', 'Starting Value', 'Final Value', 'Increment')
NUM_COLS = 9
INDICES = 0
COORD_NAME = 1
COORD_TYPE = 2
STEPS = 3
FIXED_VALUE = 4
CURRENT_VAL = 5
START_VAL = 6
FINAL_VAL = 7
INCREMENT = 8
class schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesProxyModel(parent)

Bases: PyQt6.QtCore.QSortFilterProxyModel

A proxy model that allows to hide columns.

COLUMN = <schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns object>
VISIBLE_COLUMNS = (1, 2, 3)
__init__(parent)
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

class schrodinger.application.jaguar.gui.tabs.scan_tab.RelaxedScanCoordinatesProxyModel(parent)

Bases: schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesProxyModel

A proxy model that allows to hide columns in Relaxed Coordinate Scan tab.

COLUMN = <schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns object>
VISIBLE_COLUMNS = (1, 2, 3, 4)
class schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab(parent, input_selector=None)

Bases: schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab

NAME = 'Scan'
HELP_TOPIC = 'JAGUAR_TOPIC_SCAN_FOLDER'
UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.scan_tab_ui' from '/scr/buildbot/savedbuilds/2024-3/NB/build-133/internal/lib/python3.11/site-packages/schrodinger/application/jaguar/gui/ui/scan_tab_ui.py'>,)
COLUMN = <schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns object>
PROXY_MODEL_CLASS

alias of schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesProxyModel

MAX_ROW_COUNT = 5
ALLOW_SCAN_CONSTRAINT = False
setup()

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

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

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

saveSettings(jag_input, eid=None)

Save scan coordinate settings in jaguar handle.

See parent class for argumnet documentation

updateMapperWidgets(selected, deselected)

This slot is called when selection in coordinates table is changed.

Parameters

  • selected (QtCore.QItemSelection) – selected indices

  • deselected (QtCore.QItemSelection) – deselected indices

enableSelectedCoordinates(enable)

This function is called to enable/disable widgets in ‘selected coordinate’ box. When enable argument is False we also clear text in all widgets.

Parameters

enable (bool) – True/False to enable/disable widgets

deleteCurrentRow()

This function is called to delete row which is currently selected from the coordinates table.

deleteAllRows()

This function is called to delete all rows from the coordinates table.

validateCoordinateScanRange()

Ensure that the start value is always less than the final value.

If the user has entered a new start value greater than the current final value, or a new final value less than the current start value, swap the current and start values in the UI and update the model.

addCoordinate(st, atoms, coordinate_type, start_value=None, final_value=None, increment=None, const_type=4)

Add new coordinate row.

Parameters

  • st (schrodinger.structure.Structure) – structure

  • atoms (list) – atom indices

  • coordinate_type (int) – coordinate type

  • start_value (float) – starting coordinate value

  • final_value (float) – final coordinate value

  • increment (float) – increment value

updateTotalStructures()

Calculate total number of structures to be calculated and update the label.

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

class schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTabNextGeom(parent, input_selector=None)

Bases: schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab

A scan tab that allows the user to configure how the determine the next initial geometry

COLUMN = <schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns object>
PROXY_MODEL_CLASS

alias of schrodinger.application.jaguar.gui.tabs.scan_tab.RelaxedScanCoordinatesProxyModel

UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.scan_tab_ui' from '/scr/buildbot/savedbuilds/2024-3/NB/build-133/internal/lib/python3.11/site-packages/schrodinger/application/jaguar/gui/ui/scan_tab_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.scan_tab_nextgeom_ui' from '/scr/buildbot/savedbuilds/2024-3/NB/build-133/internal/lib/python3.11/site-packages/schrodinger/application/jaguar/gui/ui/scan_tab_nextgeom_ui.py'>)
class NextGeomFrom(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: enum.Enum

Init = 1
Prev = 2
ALLOW_SCAN_CONSTRAINT = True
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 default schrodinger.application.jaguar.input.JaguarInput object. This function should only be defined in subclasses if there are any settings that cannot be reset via loadSettings.

nextGeom()

Return the setting for the next initial geometry

Returns

The next initial geometry settings

Return type

NextGeomFrom

class schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateData(st, atoms, coordinate_type, start_value=None, final_value=None, increment=None, fixed_value=False)

Bases: schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateData

This class stores all data for a single scan coordinate.

Variables

  • COORDINATE_FUNCS (dict) – dictionary that maps coordinate type to mmct function uses to calculate coordinate value.

  • 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

  • num_steps (int) – number of steps

  • current_value (float) – current value of this coordinate

  • start_value (float) – starting coordinate value

  • final_value (float) – final coordinate value

  • increment (float) – increment value

COORDINATE_FUNCS = {0: <built-in function mmct_atom_get_x>, 1: <built-in function mmct_atom_get_y>, 2: <built-in function mmct_atom_get_z>, 4: <built-in function mmct_atom_get_distance>, 5: <built-in function mmct_atom_get_bond_angle>, 6: <built-in function mmct_atom_get_dihedral_angle>}
COORDINATE_DISTANCE_OFFSET = 0.2
COORDINATE_DISTANCE_INCREMENT = 0.1
COORDINATE_ANGLE_OFFSET = 20.0
COORDINATE_ANGLE_INCREMENT = 5.0
__init__(st, atoms, coordinate_type, start_value=None, final_value=None, increment=None, fixed_value=False)

Initialize coordinates data given a structure, set of atom indices and coordinate type.

Parameters

  • st (schrodinger.structure.Structure) – structure

  • atoms (list) – atom indices

  • coordinate_type (int) – coordinate type

  • start_value (float) – starting coordinate value

  • final_value (float) – final coordinate value

  • increment (float) – increment value

  • fixed_value (bool) – ‘fixed value’ data

class schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesDelegate

Bases: PyQt6.QtWidgets.QItemDelegate

This delegate is used to define how float coordinate values are displayed in a line edit widget. This class is needed for mapping between table view and other widgets as defined via QDataWidgetMapper.

COLUMN = <schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns object>
setEditorData(editor, index)

This function is used to initialize editor with the relevant data.

Parameters

  • editor (QtWidgets.QWidget) – editor

  • index (QtCore.QModelIndex) – index of data in source model

setModelData(editor, model, index)

This function is responsible for transferring data from the editors back to the model. So, here we convert text string into float number.

Parameters

  • editor (QtWidgets.QWidget) – editor

  • model (QtCore.QAbstractItemModel) – data model

  • index (QtCore.QModelIndex) – index of data in source model

class schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesModel(parent=None)

Bases: schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel

A model to store scan tab coordinates data.

COLUMN = <schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns object>
addCoordinate(st, atoms, coordinate_type, start_value=None, final_value=None, increment=None, fixed_value=True)

Add new coordinate row.

Parameters

  • st (schrodinger.structure.Structure) – structure

  • atoms (list) – atom indices

  • coordinate_type (int) – coordinate type

  • start_value (float) – starting coordinate value

  • final_value (float) – final coordinate value

  • increment (float) – increment value

  • fixed_value (bool) – whether fixed value or dynamic constraint should be used

Returns

returns True if this is a new coordinate and False otherwise.

Return type

bool

data(index, role=ItemDataRole.DisplayRole)

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

setData(index, value, role=ItemDataRole.EditRole)

Modify coordinate values.

Parameters

  • index (QtCore.QModelIndex) – the index of table cell

  • value – new value

  • role (int) – The role to set data for.

flags(index)

See base class for documentation.