schrodinger.application.msv.gui.dialogs module

class schrodinger.application.msv.gui.dialogs.PatternEditDialog(parent)

Bases: PyQt5.QtWidgets.QDialog

This class implements a simple pattern editor dialog.

Variables:
  • patternListChanged (QtCore.pyqtSignal(list)) – signal emitted when the pattern list changes
  • cancelClicked (QtCore.pyqtSignal) – signal emitted when cancel is clicked
DEFAULT_FIND_PATTERNS = [('Deamidation Site', 'x-[NQ]-[GASHMYD]', '2', (255, 0, 0)), ('Glycosylation Site', 'N-{P}-[ST]-{P}', '1', (255, 0, 255)), ('Proteolysis Site', 'x-D-x', '2', (0, 0, 255)), ('Oxidation Site', '[HMCWY]', '1', (255, 255, 0))]
H_HEADER_LABELS = ['Pattern Name', 'Definition', 'Hotspot', 'Color']
addPatternRow(row, name, pattern, hotspot, color)

Add a single row to the pattern table.

Parameters:
  • row (int) – Row position to insert new.
  • name (str) – Name of pattern.
  • pattern (str) – PROSITE pattern (see protein.sequence.find_generalized_pattern for documentation)
  • hotspot (str) – Pattern hotspot
  • color (3-tuple of int) – Pattern color (RGB)
cancelClicked
display()

Brings up the dialog and waits for the user to close it.

emitPatternList()
highlightError(row, column)

Highlight a table item to indicate an error.

Parameters:
  • row (int) – Row index
  • column (int) – Column index
onAddNewClicked()

Add new callback

onCancelClicked()

Cancel button callback

onCellDoubleClicked(row, column)

User double clicked a cell.

Parameters:
  • row (int) – Row index
  • column (int) – Column index
onDeleteClicked()

Delete button callback

onOkClicked()

OK button callback

patternListChanged
setPatterns(pattern_list=None)

Set the patterns to the provided list of patterns.

Parameters:pattern_list (list of (str, str, str, tuple(int, int, int))) – List of pattern items, each of which is name, pattern, hotspot, and RGB color. If no pattern list is supplied, self.msv_patterns will be used instead.
updatePatternList()

Update the internal list of patterns with the patterns from the pattern table.

schrodinger.application.msv.gui.dialogs.clustal_progress_dialog(*args, **kwds)

A context manager for displaying a progress dialog for a clustal job.

Parameters:
  • job (clustal.ClustalJob) – The clustal job to display progress for.
  • text (str) – The text to display with the dialog.
  • parent (QtWidgets.QtWidget or None) – The parent of the dialog
  • total (int or float or None) – The total progress to use with the dialog. If None, default to job.maximum_progress.
schrodinger.application.msv.gui.dialogs.wait_dialog(*args, **kwds)

A context manager for displaying an uninterruptible “Please wait” dialog.

Parameters:
  • text (str) – The text to display with the dialog.
  • parent (QtWidgets.QtWidget or None) – The parent of the dialog