schrodinger.application.bioluminate.ssv.toolbars module

Toolbars for the SimplifiedSequenceViewer

class schrodinger.application.bioluminate.ssv.toolbars.ImportToolBar(parent, title=None, action_order=None, text=True)

Bases: PyQt6.QtWidgets.QToolBar

Get the toolbar that has the import dialogs. This toolbar has a single action, that when clicked opens a menu of different import options.

__init__(parent, title=None, action_order=None, text=True)
Parameters

  • title (str) – The title of the toolbar. Used in right-click menu in a main window’s toolbar area.

  • action_order – Order of the actions displayed in the popup menu

See

schrodinger.application.bioluminate.actions.config.IMPORT_STRUCTURES

openMenu()

Opens the import pull-down menu

class schrodinger.application.bioluminate.ssv.toolbars.FindToolBar(parent, title=None)

Bases: PyQt6.QtWidgets.QToolBar

Create an instance of the “Find Pattern” toolbar from the MSV.

__init__(parent, title=None)

Construct toolbar. Here the parent should be an instance of a schrodinger.ui.sequencealignment.sequence_viewer.SequenceViewer. If it is not the parent will need a findPattern method.

findTextChanged(string)

Called whenever text in “Find pattern” widget has changed.

Parameters

string (str) – pattern string

class schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar(parent)

Bases: PyQt6.QtWidgets.QToolBar

A toolbar associated with the viewer that will handle display options. These actions will be available through the toolbar:

  • Display the first protein in the sequence viewer

  • Display all proteins in the sequence viewer, superimposed

  • Toggle waters between visible/hidden

  • Toggle counterions between visible/hidden

  • Toggle ligands between visible/hidden

  • Display consensus waters

  • Display consensus counterions

  • Display consensus ligands

ASL_WATER = '(water AND (NOT atom.ele H))'
ASL_IONS = 'ions'
ASL_LIGAND = '(((m.atoms 5-130)) and not ((ions) or (res.pt ACE ACT ACY BCT BME BOG CAC CIT CO3 DMS EDO EGL EPE FES FMT FS3 FS4 GOL HEC HED HEM IOD IPA MES MO6 MPD MYR NAG NCO NH2 NH3 NO3 PG4 PO4 POP SEO SO4 SPD SPM SUC SUL TRS )))'
__init__(parent)

The parent needs to be an instance of the SimplifiedSequenceViewer.

initActionStates()
Called when a set of structures are imported. This will:

  • Include all structures in the WS

  • Hide waters

  • Hide ions

  • Show all ligands

property water_action

Get the toggle_water action for the corresponding toolbar button

Return type

action

property ion_action

Get the toggle_counterions action for the corresponding toolbar button

Return type

action

property ligand_action

Get the toggle_ligands action for the corresponding toolbar button

Return type

action

getReferenceEntryId()

Gets the PT entry ID for the reference structure.

Returns

Reference entry id

Return type

int

viewFirstProtein()

Displays only the reference st in the workspace

viewAllProteins()

Includes all structures in the sequence viewer in the Workspace

toggleWaters()

Slot to show/hide all waters

consensusWaters()

Slot to show all consensus waters

toggleCounterions()

Slot to show/hide all ions

consensusCounterions()

Slot to show all consensus ions

toggleLigands()

Slot to show/hide all ligands

consensusLigands()

Slot to show all consensus ligands

class schrodinger.application.bioluminate.ssv.toolbars.AntibodyNumberingToolBar(parent, title='Antibody numbering scheme')

Bases: PyQt6.QtWidgets.QToolBar

Get the toolbar that has the combobox with the antibody numering schemes. This toolbar has a single action. When the combobox’s index is changed the numbering scheme chosen is applied to the SimplifiedSequenceViewer

SCHEMES = [('Chothia', 'Chothia'), ('EnhancedChothia', 'Enhanced Chothia'), ('Kabat', 'Kabat'), ('IMGT', 'IMGT'), ('AHo', 'AHo')]

Antibody numbering schemes to choose from. Each item in the list is a tuple of: (<backend name>, <display name>).

__init__(parent, title='Antibody numbering scheme')
Parameters

title (str) – The title of the toolbar. Used in right-click menu in a main window’s toolbar area.

currentScheme(idx=None)

Returns the backend name of the scheme matching the specified index or the current index on the combobox, if no index is supplied.

Parameters

idx (int) – The index of the scheme

Return type

str

Returns

The name of the requested backend scheme

showScheme(scheme=None)

Shows the specified scheme in the viewer, or, if no scheme is specified, shows the scheme currently selected in the combobox.

Parameters

scheme (str) – The scheme to show

hideScheme()

Removes the antibody scheme from the viewer altogether

indexChanged(idx)

Slot called when the combobox’s index is changed. This will change the SimplifiedSequenceViewer antibody numbering scheme.