schrodinger.ui.qt.ligand_list module¶

Present a list of all ligands that have been included in the Workspace or selected in the project, and allow the user to select their desired ligand or ligands.

LigandListWidget is the standard widget for including this list in a panel.

class schrodinger.ui.qt.ligand_list.LigSource(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶

Bases: enum.Enum

included = 1¶

selected = 2¶

class schrodinger.ui.qt.ligand_list.Ligand(found_lig, proj_row)¶

Bases: object

An object representing one ligand in the list. Contains a reference to the analyze.Ligand object.

__init__(found_lig, proj_row)¶

Parameters

found_lig (schrodinger.structutils.analyze.Ligand) – The ligand object found using schrodinger. structutils.analyze.AslLigandSearcher
proj_row (schrodinger.project.ProjectRow) – The Project Table row

property struc¶

getName(only_one_entry)¶

Get the name to use for this ligand in the ligand list. If the ligand is the entire entry, the structure title will be used. Otherwise, the entry title followed by the residue name and number will be used (or a multiple residue names and numbers for ligands that span multiple residues).

Parameters: only_one_entry (bool) – Whether only one entry is included in the workspace (all ligands in the list came from it). In this case, the entry title will be excluded from the row name. Note that this setting will be ignored when the ligand is the entire entry.
Returns: The properly formatted name
Return type: str

class schrodinger.ui.qt.ligand_list.LigandListView(parent=None)¶

Bases: schrodinger.ui.qt.appframework2.markers.MarkerMixin, PyQt6.QtWidgets.QListView

A list view for ligands. Note that multiple ligand selection can be enabled via ligand_list_view.setSelectionMode(QtWidgets.QListView.ExtendedSelection).

Variables: ligandSelectionChanged (QtCore.pyqtSignal) – A signal emitted when the selected ligands have changed.

ligandSelectionChanged¶

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

__init__(parent=None)¶

setAutoInclude(auto_include)¶

Specify whether ligands should be included in the Workspace when they are selected in the list. Only relevant when selecting ligands that are selected the Project Table.

Parameters: auto_include (bool) – True if ligands should be included. False otherwise.

setAutoFit(auto_fit)¶

Specify whether ligands should be zoomed in on in the Workspace when they are selected in the list. Requires auto-include.

Parameters: auto_fit (bool) – True if ligands should be zoomed in on. False otherwise.

setMarkSelectedLigands(use_markers)¶

Specify whether ligands that are selected in the ligand list should be marked in the workspace. See setMarkerColor to control the marker color.

Parameters: use_markers (bool) – True if workspace markers should be used. False otherwise.

setMarkerColor(color)¶

Specify the color of the workspace markers used to mark selected ligands. Only has an effect if setMarkSelectedLigands has been set to True.

Parameters: color (tuple) – A tuple of RGB float values for the marker color.

selectedLigands()¶: Return a list of Ligand objects for the selected rows.

selectLigandsFromAtoms(atoms)¶

Select all ligands containing the specified atom(s).

Parameters: atoms (list or schrodinger.structure._StructureAtom) – A list of atoms (schrodinger.structure._StructureAtom) or a single schrodinger.structure._StructureAtom. This atom must be from a Workspace or Project Table structure.
Raises: ValueError – If atoms doesn’t specify any ligands. ValueError will also be raised if atoms specified more than one ligand and the view is in SingleSelection selection mode.

selectLigandsFromWorkspaceAtomNums(atom_nums)¶

Select all ligands containing the specified atom(s).

Parameters: atoms (list or int) – A list of Workspace atom numbers (ints) or a single Workspace atom number.
Raises: ValueError – If atom_nums doesn’t specify any ligands. ValueError will also be raised if atom_nums specified more than one ligand and the view is in SingleSelection selection mode.

selectionChanged(self, selected: QItemSelection, deselected: QItemSelection)¶

selectIfNoSelection()¶: When called this function will select the first ligand in the list if no other ligand in the list is currently selected.

setModel(self, model: Optional[QAbstractItemModel])¶

class schrodinger.ui.qt.ligand_list.LigandListWidget(parent=None)¶

Bases: schrodinger.ui.qt.appframework2.maestro_callback.MaestroCallbackWidgetMixin, schrodinger.ui.qt.ligand_list.LigandListView

A list view for ligands that contains its own model. The model will be automatically updated whenever the project changes. As with LigandListView, multiple ligand selection can be enabled via ligand_list_widget.setSelectionMode(QtWidgets.QListView.ExtendedSelection).

__init__(parent=None)¶

setLigandSource(source)¶

Specify whether ligands should be taken from selected or included Project Table entries.

Parameters: source (LigSource) – The desired ligand source.

ligandSource()¶

Return whether ligands are currently being taken from selected or included Project Table entries.

Returns: The current ligand source.
Return type: LigSource

projectChanged()¶

projectClose()¶

class schrodinger.ui.qt.ligand_list.LigandListModel(parent=None, source=LigSource.included)¶

Bases: schrodinger.ui.qt.table_helper.RowBasedListModel

__init__(parent=None, source=LigSource.included)¶

Parameters

parent (QtWidgets.QWidget or NoneType) – The Qt parent widget.
source (LigSource) – The desired ligand source.

setLigandSource(source)¶

Specify whether ligands should be taken from selected or included Project Table entries.

Parameters: source (LigSource) – The desired ligand source.

ligandSource()¶

Return whether ligands are currently being taken from selected or included Project Table entries.

Returns: The current ligand source.
Return type: LigSource

updateLigandList()¶: Update the contents of the model. This method should be called whenever project inclusion or selection changes.

atomToLigNumMapping()¶: Return a dictionary of {(entry id, atom number): ligand row number} for all atoms in all ligands in the table.