schrodinger.application.msv.gui.msv_gui module

class schrodinger.application.msv.gui.msv_gui.MSVPanel(**kwargs)

Bases: schrodinger.ui.qt.appframework2.af2.App

addTab(title=None, make_active=True)

Add a query tab with the specified title

Parameters:title (basestring) – The tab title

canRedoChanged(can_redo)

Update widget states to reflect availability of redo

canUndoChanged(can_undo)

Update widget states to reflect availability of undo

currentWidget()

Return the widget belonging to the currently active tab, or None if all tabs are closed

Return type:schrodinger.application.msv.gui.msv_widget.AbstractMsvWidget or None Returns:The current msv widget or None

current_widget

duplicateTab(index)

Duplicate the tab at the given index

Parameters:index (int) – The index of the tab to rename Returns:The duplicated tab. Return type:msv_widget.AbstractMsvWidget

getSequences()

Opens the widget’s Get Sequences dialog.

If the current tab is the workspace, the tab will be duplicated and the sequences will be added to the copy. If the current tab is a query tab, the sequences will be added to it.

importSequences()

Import sequences and structures from a user-specified file and add them to the alignment. If the user attempts to add structureless sequences to the workspace alignment, then we duplicate the tab and add the sequences to the duplicate.

layOut()

onBlastAddSequencesRequested(sequences)

Add sequences from BLAST to the current tab’s alignment (or a copy of the current tab if the current tab is the workspace tab).

Parameters:sequences (list[protein.ProteinSequence]) – List of sequences to incorporate

onClearFindClicked()

Callback for clear fetch/find button

onFetchFindRequested()

Dispatch fetch/find input to either fetch from PDB or Entrez by ID or find pattern in sequences.

onFindItemChanged(index)

Callback for “Select pattern” combo box

Parameters:index (int) – Index of selected item in combo box

onMovePatternClicked(forward=True)

Callback for prev_pattern and next_pattern buttons.

Parameters:forward (bool) – whether to move pattern view forward

onSequenceAlignmentRequested(seq_aln_mode)

Requests the appropriate sequence alignment from Quick Align

Parameters:seq_aln_mode (Enum) – type of alignment requested

onStructureAlignmentRequested(struct_aln_mode)

Requests the appropriate structure alignment from Quick Align

Parameters:struct_aln_mode (Enum) – type of alignment requested

redo()

Redo the last undone operation

removeSelectedSeqs()

Delete the selected sequences.

requestFetch(ids)

Fetch ID(s) from PDB or Entrez.

Parameters:ids (str) – Database ID or IDs (comma-separated)

requestFind(pattern)

Find pattern in sequences and select the matches.

Parameters:pattern (str) – PROSITE pattern (see protein.sequence.find_generalized_pattern for documentation).

reset()

Reset the panel. This will remove all query tabs (but not the workspace tab, if present) and add a new, empty query tab.

setOptionsModel()

Updated shared UI elements so they reflect the settings of the current MSV widget using the current widget’s option model.

setPanelOptions()

setReferenceSeq()

Set the currently selected sequence as the reference sequence

setRemoteServerAsk()

When the menu item for the Ask Remote Server option is clicked, this should update the preferences for whether the Do Not Show Again dialog is shown for remote searches.

setup()

show()

We call raise here so that the panel comes to the front on all platforms when running in standalone mode.

showDebugGui()

toggleHistory()

Toggle the history widget’s visibility

undo()

updateAllStatusLabels()

Get the status from the current widget and update status labels accordingly.

updateNumSelectedSeqsLabel(num_selected)

Update the label to the current number of selected sequences.

Parameters:num_selected (int) – Number of selected sequences.

updateNumSeqsLabel(num_seqs)

Update the label to the current alignment length.

Parameters:num_seqs (int) – Number of sequences in the alignment.

updateVizLabel(num_shown, num_hidden)

Update the label to the current number of sequences in the Workspace that are shown and hidden.

Parameters:

• num_shown (int) – Number of sequences in the Workspace that are visible.
• num_hidden (int) – Number of sequences in the Workspace that are hidden.

schrodinger.application.msv.gui.msv_gui.do_nothing(*args, **kwargs)

This function is used for no-effect callbacks on the current widget when there is no currentWidget defined.