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:
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
- 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
- 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’