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.

Copyright (c) Schrodinger, LLC. All rights reserved.

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

Bases: PyQt5.QtCore.QAbstractTableModel

Class for storing the table information.

rowCount(parent=<PyQt5.QtCore.QModelIndex object>)

Returns number of rows

Parameters:parent (QtCore.QModelIndex) – unused
Return type:int
Returns:Number of rows
columnCount(parent=<PyQt5.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=0)

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: PyQt5.QtWidgets.QFrame

A QtWidgets.QFrame that contains a Protein Report

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
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’