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', 'Step Size')¶

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¶

STEP_SIZE = 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/2024-4/NB/build-117/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.

addCoordinate(st, atoms, coordinate_type, start_value=None, final_value=None, step_size=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
step_size (float) – step size

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/2024-4/NB/build-117/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/2024-4/NB/build-117/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, step_size=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
step_size (float) – step size

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_STEP_SIZE = 0.1¶

COORDINATE_ANGLE_OFFSET = 20.0¶

COORDINATE_ANGLE_STEP_SIZE = 5.0¶

__init__(st, atoms, coordinate_type, start_value=None, final_value=None, step_size=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
step_size (float) – step size
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, step_size=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
step_size (float) – step size
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.