schrodinger.application.bioluminate.protein_report_widget module¶

Analyzes the quality of the structure in the workspace in terms of bond length, bond angles, dihedral values, peptide geometry, and other quantities.

class schrodinger.application.bioluminate.protein_report_widget.DataModel(master)¶

Bases: PyQt6.QtCore.QAbstractTableModel

Class for storing the table information.

__init__(master)¶: Create a DataModel instance

rowCount(parent=<PyQt6.QtCore.QModelIndex object>)¶

Returns number of rows

Parameters: parent (QtCore.QModelIndex) – unused
Return type: int
Returns: Number of rows

columnCount(parent=<PyQt6.QtCore.QModelIndex object>)¶

Returns number of columns

Parameters: parent (QtCore.QModelIndex) – unused
Return type: int
Returns: Number of rows

setData(data_list, headers)¶

Sets the internal data list to the specified list. NOTE: Will use the actual list passed to it (without making a copy)

Parameters

data_list (list) – the list of data for the model. Uses the actual list, not a copy
headers (list of str) – The column headers

data(index, role=ItemDataRole.DisplayRole)¶

Given a cell index, returns the data that should be displayed in that cell. Used by the view.

Parameters

index (QtCore.QModelIndex) – index of the cell to return data for
role (Qt.ItemDataRole) – The data role to return

Returns

the requested data for the requested index

headerData(section, orientation, role)¶

Returns the string that should be displayed in the specified header cell. Used by the View.

Parameters

section (int) – the row or column index requested
orientation (Qt.Orientation (Qt.Horizontal or Qt.Vertical)) – Whether this is for the horizontal or vertical header
role (Qt.ItemDataRole) – The data role to return - Qt.DisplayRole to return the text of the header.

Returns

the requested data for the requested header item

sort(Ncol, order)¶

Sort table by given column number. The first column will be sorted based on the first chain:residue number rather than a simple alphabetical sort. Note that this method changes the actual model._data property.

Parameters

Ncol (int) – The column index to sort
order (Qt.SortOrder (Qt.AscendingOrder or Qt.DescendingOrder)) – The order in which to sort the column

class schrodinger.application.bioluminate.protein_report_widget.ReportFrame(parent_layout=None, update_button=True, app_parent=None, load_proteins=True)¶

Bases: PyQt6.QtWidgets.QFrame

A QtWidgets.QFrame that contains a Protein Report

__init__(parent_layout=None, update_button=True, app_parent=None, load_proteins=True)¶

Create a ReportFrame object

Parameters

parent_layout (QLayout or None) – If given the ReportFrame will add itself to this layout
update_button (bool) – True if the report should have an update button, False if not.
app_parent (Deprecated; no longer used.) – Deprecated; no longer used.
load_proteins (bool) – If True, the panel will attempt to load proteins when created. If False (default), not attempt is made - the widgets are merely created.

getSelectedDataTitles(model)¶

Returns a list of selected data titles (the value in the first column)

Parameters: model (DataModel) – The model the data comes from
Return type: list
Returns: list of data titles (the value in the first column) for each selected row

selectionChangedCallback(selected=None, deselected=None)¶

Called when table selection is changed

Parameters

selected (QItemSelection) – Unused callback-required parameters
deselected (QItemSelection) – Unused callback-required parameters

getDataModelClass()¶

Returns the proper data model class to use, allows easy subclassing of the Model in report subclasses

Return type: DataModel
Returns: The CLASS used for the table data model in the report. Does not return a class instance, only the class itself.

getStructure(entry_id=None)¶

Return the structure to report on.

Parameters: entry_id (str or None) – Entry ID of the structure to use, or None (default) if the workspace structure is to be used. If entry_id is given, the structure is taken from the project table row for that entry_id (which may be different from the current workspace structure). If entry_id is None, the workspace structure is used, but crystal structure properties are taken from the included project table row
Return type: schrodinger.structure.Structure
Returns: The structure requested

updateTables(entry_id=None)¶

Calculate new data for the requested structure and load the data into the table.

Parameters: entry_id (str or None) – Entry ID of the structure to use, or None (default) if the workspace structure is to be used. If entry_id is given, the structure is taken from the project table row for that entry_id (which may be different from the current workspace structure). If entry_id is None, the workspace structure is used, but crystal structure properties are taken from the included project table row

clear()¶: Clear the widget. Used by PrepWizard.

setSets(all_titles, all_tooltips)¶

Populate the sets menu with the given items. Also takes in a list of tooltips, for each item.

Parameters

all_titles (list(str)) – List of item texts to add.
all_tooltips – List of tool tips for each item.

Type

all_tooltips: list(str)

exportTables(filename, tables_to_write)¶

Export the specified tables to the <filename> file.

Parameters

filename (str) – the path to the output file
tables_to_write (str) – the name of the set of data to write out

setChanged(selected_title)¶

Callback for when a new set of data is requested. Changes the data displayed in the table. This also changes the underlying model the table uses.

Parameters: selected_title (str) – The name of the set of data requested

exportCurrentTable()¶: Export only the current table.

exportAllTables()¶: Export all tables.

openHelp()¶: Display the help topic

closePanel()¶: Hide the panel

workspaceChanged(changed)¶

Keep track of when something changes in the workspace that would invalidate the current data.

Parameters: changed (str) – What changed in the workspace

close()¶: Close the frame, and clean up anything that needs to happen upon closing

schrodinger.application.bioluminate.protein_report_widget.panel()¶: Open (or re-open) the panel

schrodinger.application.bioluminate.protein_report_widget.quit()¶: To force quit the GUI in Maestro, call ‘app.quit’