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: 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_set, 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_set (prosane.data_set) – Instance of the “data_set” object that contains all the data for the model.
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

rowBeyondThreshold(row)¶

class schrodinger.application.bioluminate.protein_report_widget.ProxyModel(parent)¶

Bases: QSortFilterProxyModel

Proxy model that allows filtering rows by threshold.

__init__(parent)¶

setFilterEnabled(enable_filter)¶

filterAcceptsRow(self, source_row: int, source_parent: QModelIndex) → bool¶

residue_formatter(item)¶

Column 0 labels have various formats, but all of them start with Chain:ResName ResNum. A simple sort sorts on ResName before ResNum, but that isn’t very useful. This sorts on Chain:ResNum

Return type:: str
Returns:: key to sort item by

lessThan(left, right)¶

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: 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’