schrodinger.application.bioluminate.pml_menus module¶

The module that creates the actions and menus for the Pymol-like interface of BioLuminate.

schrodinger.application.bioluminate.pml_menus.toggle_table = None¶: The parent Toggle Table widget

schrodinger.application.bioluminate.pml_menus.set_wait_cursor()¶: Set the cursor to a wait cursor if the toggle_table widget is defined

schrodinger.application.bioluminate.pml_menus.restore_cursor()¶: Restore the cursor to its nomral state if the toggle_table widget is defined

schrodinger.application.bioluminate.pml_menus.start_progress(maximum)¶

Show and restart the progress bar on the Toggle Table if the TT is defined

Parameters: maximum (int) – The maximum value of the progress bar

schrodinger.application.bioluminate.pml_menus.update_progress(inc=1, total=None)¶

Show the current progress on the progress bar on the Toggle Table if the TT is defined

Parameters

inc (int) – The amount to increment the progress bar value
total (int) – The absolute value to set the progress bar to

schrodinger.application.bioluminate.pml_menus.end_progress()¶: Finish the progress bar and hide it

schrodinger.application.bioluminate.pml_menus.show_result(msg)¶

class schrodinger.application.bioluminate.pml_menus.ResultsWindow(msg='')¶

Bases: PyQt6.QtWidgets.QFrame

__init__(msg='')¶

showMessage(msg)¶

closePanel()¶

schrodinger.application.bioluminate.pml_menus.maestro_command(command)¶: A wrapper that handles exceptions from Maestro commands

class schrodinger.application.bioluminate.pml_menus.MWidgetAction(widget, menu, asl=None, owner=None, tooltip=None)¶

Bases: PyQt6.QtWidgets.QWidgetAction

A QAction that performs a Maestro command

__init__(widget, menu, asl=None, owner=None, tooltip=None)¶

Create a MWidgetAction object

Parameters

widget (QWidget) – the widget to be displayed as the menu item
menu (QWidget) – the QWidget that owns this action, if a QMenu, the title property may be used when determining the command function when the action is triggered.
asl (str) – the asl this action will apply to. If not supplied, the asl is taken as the menu asl
owner (ToggleTableObject) – the object this Action will operate on
tooltip (str) – the string that will appear as a tooltip for this action

command()¶: Must be defined in subclasses

class schrodinger.application.bioluminate.pml_menus.MAction(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: PyQt6.QtGui.QAction

A QAction that performs a Maestro command

__init__(name, menu, asl=None, owner=None, tooltip=None)¶

Create a MAction object

Parameters

name (str) – the string that will appear in the menu for this action
menu (QWidget or None) – the QWidget that owns this action, if a QMenu, the title property may be used when determining the command function when the action is triggered.
asl (str) – the asl this action will apply to. If not supplied, the asl is taken as the menu asl
owner (ToggleTableObject) – the object this Action will operate on
tooltip (str) – the string that will appear as a tooltip for this action

command()¶: Must be defined in subclasses

class schrodinger.application.bioluminate.pml_menus.PMLMenu(parent, asl=None, owner=None)¶

Bases: PyQt6.QtWidgets.QMenu

The base menu class we subclass from

__init__(parent, asl=None, owner=None)¶

Create a PMLMenu object

Parameters

parent (QWidget) – the owner of this menu
asl (str) – the asl this action will apply to
owner (ToggleTableObject) – the object this Menu will operate on

class schrodinger.application.bioluminate.pml_menus.PMLContextMenu(parent, asl=None, owner=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The base menu class we subclass from for context menus

post()¶: Pop up this menu at the current cursor position

schrodinger.application.bioluminate.pml_menus.get_matching_ws_atoms(asl, extract=False)¶

Get the atoms in the workspace structure that match the given asl

Parameters

asl (str) – the asl this action will apply to
extract (bool) – True if a structure containing the matching atoms should be extracted and returned, False if not

Return type

tuple

Returns

workspace structure (schrodinger.Structure), list of matching atom indicies, matching structure (or None)

schrodinger.application.bioluminate.pml_menus.get_matching_ws_entries(owner, asl)¶

Get the entries in the workspace structure are affected by the given asl

Parameters

owner (ToggleTableObject) – the object this command will operate on
asl (str) – the asl this action will apply to

Return type

list or None

Returns

Each item of the list is a workspace entry (Structure) that is affected by asl. In case of error - normally caused by multiple Scratch entries - None is returned. An empty list is returned if ASL does not affect any workspace entries.

schrodinger.application.bioluminate.pml_menus.get_visible_ws_atoms()¶

Return list of the the Visible workspace atoms

Return type: list
Returns: list of atom indexes of visible workspace atoms

schrodinger.application.bioluminate.pml_menus.get_visible_ws_asl()¶

Return an ASL that represents the Visible workspace atoms

Return type: str
Returns: an ASL expression that represents the Visible workspace objects, or None if no atoms are visible

schrodinger.application.bioluminate.pml_menus.join_asls(asl1, asl2, joiner='AND')¶

Joins 2 asls with the given joiner (default is AND)

Parameters

asl1 (str) – the first asl
asl2 (str) – the second asl
joiner (str) – the linking logic (AND, AND NOT, OR…)

Return type

str

Returns

the two asls joined by the joiner

schrodinger.application.bioluminate.pml_menus.mod_asl(modifier, asl)¶

Puts a modifier in front of asl - which it protects in ()’s to make sure the modifier applies to the whole asl

Parameters

modifier (str) – the modifier to prepend to the asl (NOT, FILLRES, FILLMOL)
asl (str) – the asl

Return type

str

Returns

the modified asl with the modifier prepended to it

schrodinger.application.bioluminate.pml_menus.get_surfaces(entry)¶

Get the surfaces associated with entry_id entry

Parameters: entry (str) – The entry_id of the entry of interest
Return type: iterable
Returns: iterable object containing surfaces associated with this entry

schrodinger.application.bioluminate.pml_menus.find_all_table_entry_objects(owner)¶

Get the structures in the workspace referred to by a given toggle table entry

Parameters: owner (ToggleTableObject) – the object to retrieve entries from
Return type: list
Returns: a list of all ToggleTableEntries referred to by owner

schrodinger.application.bioluminate.pml_menus.display_atoms_as(asl, atoms, bonds=None, owner=None)¶

Display atoms and bonds with the given style, and turn off ribbons and surfaces

Parameters

asl (str) – the asl this action will apply to
atoms (str) – atom display style
bonds (str) – bond display style
owner (ToggleTableObject) – the object this command will operate on - used to see if the atoms should be made visible or not

schrodinger.application.bioluminate.pml_menus.display_atoms(asl, atoms, bonds=None, owner=None)¶

Display atoms and bonds with the given style, leaving ribbons as is

Parameters

asl (str) – the asl this action will apply to
atoms (str) – atom display style
bonds (str) – bond display style
owner (ToggleTableObject) – the object this command will operate on - used to see if the atoms should be made visible or not

schrodinger.application.bioluminate.pml_menus.display_ribbons(asl, style, hideatoms=False, scheme='calphaatom', owner=None)¶

Show ribbons

Parameters

asl (str) – the asl this action will apply to
style (str) – the ribbon style
hideatoms (bool) – True if atoms (i.e. the non-ribbon representation) should be hidden, False if not
scheme (str) – the ribbon scheme
owner (ToggleTableObject) – the object this command will operate on - used to see if the atoms should be made visible or not

class schrodinger.application.bioluminate.pml_menus.RockData(interval, amount, span)¶

Bases: object

Stores information about the current workspace rocking state

__init__(interval, amount, span)¶

Create a RockData object

Parameters

interval (int) – in units of ~1/20 second, the frequency at which the rocking movement should be made
amount (int) – The number of degrees the workspace should be rotated each rocking movement
span (int) – The amount to rotate in one direction (past 0) before reversing

schrodinger.application.bioluminate.pml_menus.rock_workspace(interval=1, amount=1, span=25)¶

Rotate the workspace back and forth smoothly by small degree increments over a span of degrees range. If called when rocking is currently occuring, will stop the rocking.

Parameters

interval (int) – in units of ~1/20 second, the frequency at which the rocking movement should be made
amount (int) – The number of degrees the workspace should be rotated each rocking movement
span (int) – The amount to rotate in one direction (past 0) before reversing

schrodinger.application.bioluminate.pml_menus.stop_rocking()¶: Stop any rocking currently happening

schrodinger.application.bioluminate.pml_menus.display_image(image_file)¶

Tries to display the image file in the default image viewer

Parameters: image_file (str) – The path to the image to be displayed

schrodinger.application.bioluminate.pml_menus.ensure_proper_extension(filename, extensions)¶

Ensure that filename ends with the proper extension

Parameters

filename (str) – the filename to check
extensions (str or list) – a list of valid extensions or a single extension. Extensions should include the ‘.’

Return type

str or None

Returns

either - filename if filename has a valid extension - filename + ext if filename has no extension, ext is the value of, or the first item in extensions, - None if filename has an extension not given by extensions

class schrodinger.application.bioluminate.pml_menus.LigandActionMixin¶

Bases: object

Class that contains a method to restrict the asl to Ligands only

makeLigandASL()¶

Returns an ASL that is restricted to only the ligands

Return type: str
Returns: an ASL based off of self.asl that is restricted to ligands

class schrodinger.application.bioluminate.pml_menus.ShowLines(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Show atoms as sticks only

class schrodinger.application.bioluminate.pml_menus.ShowLigandLines(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.ShowLines, schrodinger.application.bioluminate.pml_menus.LigandActionMixin

command()¶: Show atoms as sticks only

class schrodinger.application.bioluminate.pml_menus.ShowTubes(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Show atoms as tubes only

class schrodinger.application.bioluminate.pml_menus.ShowLigandTubes(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.ShowTubes, schrodinger.application.bioluminate.pml_menus.LigandActionMixin

command()¶: Show atoms as sticks only

class schrodinger.application.bioluminate.pml_menus.ShowBAndS(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Show atoms as Ball and Stick only

class schrodinger.application.bioluminate.pml_menus.ShowNonBonded(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

showAtoms(style='none')¶: Show non-bonded atoms

command()¶: Show non-bonded atoms

class schrodinger.application.bioluminate.pml_menus.ShowNonBondedSpheres(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.ShowNonBonded

command()¶: Show non-bonded atoms as spheres

class schrodinger.application.bioluminate.pml_menus.ShowSpheres(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Show atoms as CPK spheres only

class schrodinger.application.bioluminate.pml_menus.ShowLigandSpheres(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.ShowSpheres, schrodinger.application.bioluminate.pml_menus.LigandActionMixin

command()¶: Show atoms as sticks only

class schrodinger.application.bioluminate.pml_menus.ShowCartoonOrRibbon(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

RIBBON_SCHEME = None¶

command()¶: Show atoms as cartoon-style ribbons only

class schrodinger.application.bioluminate.pml_menus.ShowCartoon(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.ShowCartoonOrRibbon

RIBBON_SCHEME = 'cartoon'¶

class schrodinger.application.bioluminate.pml_menus.ShowRibbon(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.ShowCartoonOrRibbon

RIBBON_SCHEME = 'calphatube'¶

class schrodinger.application.bioluminate.pml_menus.ShowLabel(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Show the atom labels

schrodinger.application.bioluminate.pml_menus.create_surface(entry, asl, name, transparency=0, quality=0, style='solid', viewasl=None, viewdistance='3', scheme='"Atom Color"', owner=None)¶

Create a surface

Parameters

entry (str) – The entry id to create the surface for
asl (str) – The ASL defining the atoms to create the surface for
name (str) – The name given to the created surface
style (str or None) – One of the following values - ‘solid’ (default) - ‘mesh’ - ‘dots’
quality (int) – The quality of the displayed surface. - 1 is medium quality (default) - 2 is high quality
transparancy (int) – transparancy % of the surface. Default is 0 (solid), max is 100.
viewasl (str) – The ASL that defines the portion of the surface to view - default is to view the entire surface
viewdistance (str) – A string representation of a number that defines how close the suface needs to be to the set of viewasl atoms to be shown. Default is 3 Angstroms.
scheme (str) – The coloring scheme for the surface (default is Atom Color)
owner (ToggleTableEntry) – The object this command will operate on. This is used to decide if the surface will be shown or not. Default is to show the surface

class schrodinger.application.bioluminate.pml_menus.SurfaceRender(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

Base class for actions that render a surface

renderSurface(style='solid')¶

class schrodinger.application.bioluminate.pml_menus.ShowSurface(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.SurfaceRender

command()¶: Show a surface displaying the electrostatic potential

class schrodinger.application.bioluminate.pml_menus.ShowMesh(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.SurfaceRender

command()¶: Show a mesh VDW surface

schrodinger.application.bioluminate.pml_menus.create_show_menu(menu, owner)¶

Parameters

menu (QMenu) – the QMenu that owns this action
owner (ToggleTableObject) – the object this Menu will operate on

schrodinger.application.bioluminate.pml_menus.create_show_substructure_menu(menu, owner)¶

Parameters

menu (QMenu) – the QMenu that owns this action
owner (ToggleTableObject) – the object this Menu will operate on

schrodinger.application.bioluminate.pml_menus.create_show_organic_menu(menu, owner)¶

Parameters

menu (QMenu) – the QMenu that owns this action
owner (ToggleTableObject) – the object this Menu will operate on

class schrodinger.application.bioluminate.pml_menus.ShowSubstructureMenu(parent, owner, name, asl)¶

Bases: PyQt6.QtWidgets.QMenu

The Show->substructure submenus

__init__(parent, owner, name, asl)¶

Create a ShowSubstructureMenu submenu object

Parameters

parent (QWidget) – the owner of this menu
owner (ToggleTableObject) – the object this Menu will operate on
name (str) – the name of this submenu
asl (str) – the asl that restricts what substructure to show

class schrodinger.application.bioluminate.pml_menus.ShowOrganicMenu(parent, owner)¶

Bases: PyQt6.QtWidgets.QMenu

The Show->Organic submenus

__init__(parent, owner)¶

Create a ShowOrganicMenu submenu object

Parameters

parent (QWidget) – the owner of this menu
owner (ToggleTableObject) – the object this Menu will operate on

class schrodinger.application.bioluminate.pml_menus.AsMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The Show->As submenu

__init__(*args, **kwargs)¶

Create a As submenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.ShowMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The Show menu

__init__(*args, **kwargs)¶

Create a show menu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.Zoom(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Fit the object into the workspace

class schrodinger.application.bioluminate.pml_menus.Orient(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Orient the object to fit nicely in the workspace

class schrodinger.application.bioluminate.pml_menus.Center(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Center the object into the workspace

class schrodinger.application.bioluminate.pml_menus.Origin(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Set the origin of the Workspace rotation to be the center of these atoms

class schrodinger.application.bioluminate.pml_menus.Clean(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Minimize the entry. Since this command only works on the entire workspace or selected atoms, we select the atoms involved and then minimize. Since we don’t know when the minimization ends, we can’t deselect the atoms. So we’ll consider the selection of the clean’d moiety a feature.

class schrodinger.application.bioluminate.pml_menus.Rename(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Rename the object

class schrodinger.application.bioluminate.pml_menus.DeleteWS(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Delete the object

class schrodinger.application.bioluminate.pml_menus.DeleteProject(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Delete the object

class schrodinger.application.bioluminate.pml_menus.Duplicate(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Duplicate the object

class schrodinger.application.bioluminate.pml_menus.MakeProjectEntry(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

Copies the atoms into a new project entry and includes it in the workspace

__init__(*args, **kwargs)¶

Create a MakeProjectEntry object

Parameters: extract (bool) – True if the atoms specified by the owner should be extracted (deleted) from the owner, False (default) if the atoms should be copied from the owner.

command()¶: Copies the atoms into a new project entry and includes it in the workspace

class schrodinger.application.bioluminate.pml_menus.Ray(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

Use PyMOL to make a ray-traced image

command(show=True, orient=False)¶

Make a ray-trace

Parameters

show (bool) – True (default) if image should be displayed after created, False if not
orient (bool) – True if structure should be re-oriented by PyMOL, False (default) if not

schrodinger.application.bioluminate.pml_menus.find_all_entries(owner=None, asl=None)¶

Find all the entries specified by the given owner or asl

Parameters

owner (ToggleTableObject) – The ToggleTableObject this function applies to, if None and asl is None,(the default), then all included entry id’s are returned
asl (str) – The asl to find entries for

Return type

list

Returns

list of entry ID’s the asl spans

schrodinger.application.bioluminate.pml_menus.find_center_of_atoms(struct)¶

Finds the x,y,z coordinates of the center of the atoms

Parameters: struct (schrodinger.Structure object) – structure containing the atoms
Return type: list
Returns: [x, y, z] specifying the center of the atoms

class schrodinger.application.bioluminate.pml_menus.Extend(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

Expand the selection to the atoms within X bonds of the ASL for this object

__init__(*args, **kwargs)¶

Create an Extend object

Parameters

bonds (int) – The number of bonds to extend the selection
residue (bool) – True if the selection should be done by residue, False if by atom (False is default)

See parent class for additional documentation

command()¶: Expand the selection to the atoms around the ASL for this object

class schrodinger.application.bioluminate.pml_menus.InvertCompleteSelection(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

Invert or complete the selection within an object

__init__(*args, **kwargs)¶

Create a InvertCompleteSelection object

Parameters: mytype (str) – Either ‘invert’ or ‘complete’ to control the selection behavior

See parent class for additional documentation

class schrodinger.application.bioluminate.pml_menus.SelectWithinEntry(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.InvertCompleteSelection

command()¶: Invert the selection of the chains holding the atoms int the ASL for this object

class schrodinger.application.bioluminate.pml_menus.SelectWithinChain(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.InvertCompleteSelection

command()¶: Invert the selection of the chains holding the atoms int the ASL for this object

class schrodinger.application.bioluminate.pml_menus.SelectWithinResidue(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.InvertCompleteSelection

command()¶: Invert the selection of the residues holding the atoms int the ASL for this object

class schrodinger.application.bioluminate.pml_menus.SelectWithinMolecule(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.InvertCompleteSelection

command()¶: Invert the selection of the residues holding the atoms int the ASL for this object

class schrodinger.application.bioluminate.pml_menus.SelectWithinAny(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.InvertCompleteSelection

command()¶: Invert the selection of the residues holding the atoms int the ASL for this object

class schrodinger.application.bioluminate.pml_menus.SelectWithinCalpha(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.InvertCompleteSelection

command()¶: Invert the selection of the residues holding the atoms int the ASL for this object

class schrodinger.application.bioluminate.pml_menus.Expand(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

Expand the selection to the atoms around the ASL for this object

__init__(*args, **kwargs)¶

Create an Expand object

Parameters

distance (float) – The distance around the object to expand the selection
residue (bool) – True if the selection should be done by residue, False if by atom (False is default)

See parent class for additional documentation

command()¶: Expand the selection to the atoms around the ASL for this object

class schrodinger.application.bioluminate.pml_menus.Around(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.Expand

command()¶: Change the selection to the atoms around the ASL for this object. The atoms in this object’s ASL will not be selected.

class schrodinger.application.bioluminate.pml_menus.EntrySubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

A submenu that lists all enabled Entry objects

__init__(*args, **kwargs)¶

Create an Around or Expand SubMenu object

Parameters: action (QAction) – The action this menu should call when one of its items are selected.

See parent class for argument documentation

updateItems()¶: Update the items in the menu just before showing

class schrodinger.application.bioluminate.pml_menus.SelectionSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

A submenu that lists all enabled Entry objects

__init__(*args, **kwargs)¶

Create an Around or Expand SubMenu object

Parameters: action (QAction) – The action this menu should call when one of its items are selected.

See parent class for argument documentation

updateItems()¶: Update the items in the menu just before showing

class schrodinger.application.bioluminate.pml_menus.RestrictSelection(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

Restrict the selection to a specific object

__init__(*args, **kwargs)¶

Create a RestrictSelection object

Parameters: obj (ToggleTableObject) – The ToggleTableObject the selection should be restricted to.

See parent class for additional documentation

command()¶: Expand the selection to the atoms around the ASL for this object

class schrodinger.application.bioluminate.pml_menus.RestrictToVisible(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Restrict a selection to the visible atoms

class schrodinger.application.bioluminate.pml_menus.RestrictToPolymer(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Restrict a selection to the backbone

class schrodinger.application.bioluminate.pml_menus.RestrictToOrganic(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction, schrodinger.application.bioluminate.pml_menus.LigandActionMixin

command()¶: Restrict a selection to just ligand atoms

class schrodinger.application.bioluminate.pml_menus.RestrictToSolvent(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Restrict a selection to the solvent atoms

class schrodinger.application.bioluminate.pml_menus.RestrictToInorganic(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Restrict a selection to the inorganic atoms

class schrodinger.application.bioluminate.pml_menus.RestrictSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The modify-restrict submenu of the action menu

__init__(*args, **kwargs)¶

Create a Restrict SubMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.IncludeInSelection(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.RestrictSelection

Include a specific object in the selection

command()¶: Include self.obj in the selection

class schrodinger.application.bioluminate.pml_menus.IncludeVisibleInSelection(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Include visible atoms in the selection

class schrodinger.application.bioluminate.pml_menus.ExcludeFromSelection(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.RestrictSelection

command()¶: Exclude a specific object from the selection

class schrodinger.application.bioluminate.pml_menus.ExcludeVisibleFromSelection(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Exclude a specific object from the selection

class schrodinger.application.bioluminate.pml_menus.ExcludePolymerFromSelection(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Restrict a selection to the visible atoms

class schrodinger.application.bioluminate.pml_menus.ExcludeOrganicFromSelection(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction, schrodinger.application.bioluminate.pml_menus.LigandActionMixin

command()¶: Restrict a selection to just ligand atoms

class schrodinger.application.bioluminate.pml_menus.ExcludeSolventFromSelection(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Exclude solvent atoms from the selection

class schrodinger.application.bioluminate.pml_menus.ExcludeInorganicFromSelection(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Exclude inorganic atoms from the selection

class schrodinger.application.bioluminate.pml_menus.IncludeSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The modify-include submenu of the action menu

__init__(*args, **kwargs)¶

Create a Include SubMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.ExcludeSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The modify-exclude submenu of the action menu

__init__(*args, **kwargs)¶

Create a Exclude SubMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.AroundExpandSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The modify-around submenu of the action menu

__init__(*args, **kwargs)¶

Create an Around or Expand SubMenu object

Parameters: title (str) – Title of the menu (‘Around’ or ‘Expand’ - the name triggers what type of selection is done

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.ExtendSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The modify-extend submenu of the action menu

__init__(*args, **kwargs)¶

Create an Extend SubMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.InvertSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The modify-invert submenu of the action menu

__init__(*args, **kwargs)¶

Create an Invert SubMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.CompleteSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The modify-complete submenu of the action menu

__init__(*args, **kwargs)¶

Create a Complete SubMenu object

See parent class for argument documentation

schrodinger.application.bioluminate.pml_menus.create_modify_menu(menu)¶: Creates a Modify menu for selections

class schrodinger.application.bioluminate.pml_menus.ModifySubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The modify submenu of the action menu

__init__(*args, **kwargs)¶

Create a ModifySubMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.PresetAction(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction, schrodinger.application.bioluminate.pml_menus.LigandActionMixin

Base class for Preset Actions

reset(undoblock_description, steps=5)¶

Reset any current display settings

Parameters

steps (int) – Progess bar steps for this action
undoblock_description (string) – Undo block description

finish()¶

class schrodinger.application.bioluminate.pml_menus.SimplePreset(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PresetAction

__init__(*args, **kwargs)¶

Create a SimplePreset object

See parent class for argument documentation

Parameters: show_solvent (bool) – True if this action should show solvent molecules, False if not

command()¶: Simple preset Show everything as ribbons, colored by chain Disulphides: Show CA, CB & S as lines Ligands + 2 bonds as tubes Color by default atom color if lines or sticks are shown Display Ligands, solvent & ions as lines

class schrodinger.application.bioluminate.pml_menus.BAndSPreset(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.PresetAction

command()¶: Show atoms as ball and sticks

class schrodinger.application.bioluminate.pml_menus.BFactorPreset(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.PresetAction

command()¶: Draw ribbons as tubes, colored by atom B-Factor

class schrodinger.application.bioluminate.pml_menus.TechnicalPreset(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.PresetAction

command()¶: Show the CATrace ribbons Color chains as chainbows Show ligands as tubes Show all other atoms as lines Reset atoms to default colors Show all polar contacts

class schrodinger.application.bioluminate.pml_menus.LigandPreset(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PresetAction

__init__(*args, **kwargs)¶

Create a LigandPreset Action object

Parameters

ribbon_type (str) – The ribbon type to display. Default is calphatube.
surface_style (str or None) – One of the following values - None if no surface (default) - ‘solid’ - ‘mesh’ - ‘dots’
surface_quality (int) – The quality of the displayed surface. - 1 is medium quality (default) - 2 is high quality
surface_transparancy (int) – transparancy % of the surface. Default is 0 (solid), max is 100.

See parent class for addition keyword documentation

command()¶: Color chains as chainbows Reset ligand atoms and non-carbons to default colors Show the protein as ribbons Show residues within 5 A of ligand as lines Show ligand as sticks Show solvent within 5 A of Ligand as sticks (near solvent) Show polar contacts between (host & near solvent) and (ligand & near solvent) Show any nonbonded atoms within 5 A of Ligand Zoom in on any ligands

class schrodinger.application.bioluminate.pml_menus.PrettyPubPreset(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PresetAction

Show the object as nice-looking cartoon ribbons

__init__(*args, **kwargs)¶

Create a PrettyPubPreset object

Parameters

solvent (bool) – True if solvent should be shown (Default), False if the solvent should not be shown
publish (bool) – True if set for publication (helicies will be dual-colors, grey in back), False (default) if Pretty mode (helicies will be same-colored on both sides).

See parent class for additional keyword documentation

command()¶: Show the object as nice-looking cartoon ribbons

class schrodinger.application.bioluminate.pml_menus.DefaultPreset(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.PresetAction

command()¶: Show the object as lines with default colors

class schrodinger.application.bioluminate.pml_menus.InterfaceMixin¶

Bases: object

Determine the Protein-Protein interface atoms

getInterfaceASL(match_ws_entries=True)¶

Return an ASL for residues at Protein-Protein interfaces. An interface is defined as atoms in a chain of > 300 atoms that are within 4.5 A of atoms in another chain of > 300 atoms.

Parameters: match_ws_entries (bool) – default parameter used to determine if matching workspace entries should be used or if the entries to be checked are from maestro.
Return type: str
Returns: An ASL defining the atoms at a protein interface

class schrodinger.application.bioluminate.pml_menus.InterfacePreset(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.PresetAction, schrodinger.application.bioluminate.pml_menus.InterfaceMixin

command()¶: Color the Calpha carbons in each chain differently Show the atoms at chain interfaces as ball and stick. Non-interface atoms are shown as cartoon.

class schrodinger.application.bioluminate.pml_menus.RegionInfo(name, red, green, blue, entry_id, asl=None, chains=None)¶

Bases: object

__init__(name, red, green, blue, entry_id, asl=None, chains=None)¶

addResidue(residue)¶

Add a residue to this region

Parameters: residue (schrodinger.structure._Residue) – The residue object to add

formASL()¶

Form the ASL that specifies these atoms

Return type: str
Returns: The string that specifies these atoms

colorAtoms()¶: Color all the atoms in this region

class schrodinger.application.bioluminate.pml_menus.AntibodyPreset(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PresetAction

__init__(*args, **kwargs)¶

Create a MAction object

Parameters

name (str) – the string that will appear in the menu for this action
menu (QWidget or None) – the QWidget that owns this action, if a QMenu, the title property may be used when determining the command function when the action is triggered.
asl (str) – the asl this action will apply to. If not supplied, the asl is taken as the menu asl
owner (ToggleTableObject) – the object this Action will operate on
tooltip (str) – the string that will appear as a tooltip for this action

createTextSequence(chain)¶

Create a text sequence (string of 1-letter residue codes) from a chain

Parameters: chain (schrodinger.structure._Chain) – The chain to turn into a text sequence
Return type: str
Returns: A string of 1-letter residue codes that describes Chain

command()¶: Must be defined in subclasses

findAntibodyRegions(scheme_name)¶

Identify regions in an antibody structure Show everything as cartoon ribbons Heavy chains in Cyan

Parameters: scheme_name (str) – The name of the antibody numbering scheme

class schrodinger.application.bioluminate.pml_menus.AntibodyPresetChothia(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.AntibodyPreset

Applies the Chothia antibody numbering scheme

__init__(*args, **kwargs)¶

Create a MAction object

Parameters

name (str) – the string that will appear in the menu for this action
menu (QWidget or None) – the QWidget that owns this action, if a QMenu, the title property may be used when determining the command function when the action is triggered.
asl (str) – the asl this action will apply to. If not supplied, the asl is taken as the menu asl
owner (ToggleTableObject) – the object this Action will operate on
tooltip (str) – the string that will appear as a tooltip for this action

class schrodinger.application.bioluminate.pml_menus.AntibodyPresetEnhancedChothia(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.AntibodyPreset

Applies the Enhanced Chothia antibody numbering scheme

__init__(*args, **kwargs)¶

Create a MAction object

Parameters

name (str) – the string that will appear in the menu for this action
menu (QWidget or None) – the QWidget that owns this action, if a QMenu, the title property may be used when determining the command function when the action is triggered.
asl (str) – the asl this action will apply to. If not supplied, the asl is taken as the menu asl
owner (ToggleTableObject) – the object this Action will operate on
tooltip (str) – the string that will appear as a tooltip for this action

class schrodinger.application.bioluminate.pml_menus.AntibodyPresetKabat(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.AntibodyPreset

Applies the Kabat antibody numbering scheme

__init__(*args, **kwargs)¶

Create a MAction object

Parameters

name (str) – the string that will appear in the menu for this action
menu (QWidget or None) – the QWidget that owns this action, if a QMenu, the title property may be used when determining the command function when the action is triggered.
asl (str) – the asl this action will apply to. If not supplied, the asl is taken as the menu asl
owner (ToggleTableObject) – the object this Action will operate on
tooltip (str) – the string that will appear as a tooltip for this action

class schrodinger.application.bioluminate.pml_menus.AntibodyPresetIMGT(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.AntibodyPreset

Applies the IMGT antibody numbering scheme

__init__(*args, **kwargs)¶

Create a MAction object

Parameters

name (str) – the string that will appear in the menu for this action
menu (QWidget or None) – the QWidget that owns this action, if a QMenu, the title property may be used when determining the command function when the action is triggered.
asl (str) – the asl this action will apply to. If not supplied, the asl is taken as the menu asl
owner (ToggleTableObject) – the object this Action will operate on
tooltip (str) – the string that will appear as a tooltip for this action

class schrodinger.application.bioluminate.pml_menus.AntibodyPresetAHo(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.AntibodyPreset

Applies the AHo antibody numbering scheme

__init__(*args, **kwargs)¶

Create a MAction object

Parameters

name (str) – the string that will appear in the menu for this action
menu (QWidget or None) – the QWidget that owns this action, if a QMenu, the title property may be used when determining the command function when the action is triggered.
asl (str) – the asl this action will apply to. If not supplied, the asl is taken as the menu asl
owner (ToggleTableObject) – the object this Action will operate on
tooltip (str) – the string that will appear as a tooltip for this action

class schrodinger.application.bioluminate.pml_menus.AntibodyPresetSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The Antibody presets submenu

__init__(*args, **kwargs)¶

Create a LigandSitesSubMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.LigandSitesSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The Action-Preset-Ligand Sites submenu

__init__(*args, **kwargs)¶

Create a LigandSitesSubMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.PresetSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The Preset submenu

__init__(*args, **kwargs)¶

Create a PresetSubMenu object

See parent class for argument documentation

schrodinger.application.bioluminate.pml_menus.find_polar_contacts(asl1, asl2=None)¶

Finds all polar contacts (hydrogen bonds) between asl1 and asl2.

Parameters

asl1 (str) – ASL defining one set of atoms to find H-bonds between. If asl2 is defined, then H-bonds are found between the two sets, but not within. If asl2 is not defined, then H-bonds are found within asl1.
asl2 (str) – ASL defining one set of atoms to find H-bonds between. If asl2 is defined, then H-bonds are found between asl1 and asl2, but not within. If asl2 is not defined, then H-bonds are found within asl1.

class schrodinger.application.bioluminate.pml_menus.PolarContactsObject(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Find Hydrogen bonds within the object

class schrodinger.application.bioluminate.pml_menus.PolarContactsWithSidechains(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Find Hydrogen bonds that involve a SIDECHAIN atom

class schrodinger.application.bioluminate.pml_menus.PolarContactsWithSolvent(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Find Hydrogen bonds that involve a solvent

class schrodinger.application.bioluminate.pml_menus.PolarContactsWithoutSolvent(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Find Hydrogen bonds that don’t involve a solvent

class schrodinger.application.bioluminate.pml_menus.PolarContactsWithoutMainchain(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Find Hydrogen bonds that don’t include the mainchain

class schrodinger.application.bioluminate.pml_menus.PolarContactsWithoutIntraMainchain(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Find Hydrogen bonds that aren’t both mainchain atoms

class schrodinger.application.bioluminate.pml_menus.PolarContactsOnlySidechain(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Find Hydrogen bonds that only involve sidechain atoms

class schrodinger.application.bioluminate.pml_menus.PolarContactsOnlyMainchain(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Find Hydrogen bonds that only involve mainchain atoms

class schrodinger.application.bioluminate.pml_menus.PolarContactsToEntry(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Find Hydrogen bonds to other atoms in the entry not defined by self.asl

class schrodinger.application.bioluminate.pml_menus.PolarContactsToEntryWithoutSolvent(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Find Hydrogen bonds to other atoms in the entry not defined by self.asl

class schrodinger.application.bioluminate.pml_menus.PolarContactsToAnyAtoms(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Find Hydrogen bonds to other atoms in the entry not defined by self.asl

class schrodinger.application.bioluminate.pml_menus.PolarContactsToAnyNonSolvent(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Find Hydrogen bonds to other atoms in the entry not defined by self.asl

class schrodinger.application.bioluminate.pml_menus.FindPCSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The Find Polar Contacts submenu

__init__(*args, **kwargs)¶

Create a FindPCSubMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.RemovePC(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Undisplay polar contacts

class schrodinger.application.bioluminate.pml_menus.PolarContactsSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The Polar Contacts submenu

__init__(*args, **kwargs)¶

Create a PolarContactsSubMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.GenerateSelection(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

Select the atoms, then generate a selection object from them

__init__(*args, **kwargs)¶

Create a GenerateSelection object

See parent class for argument documentation

Parameters: mytype (str) – The string to append to the name of new objects created by this action

makeSelection(asl)¶

Select the atoms, then generate a selection object from them

Parameters: asl (str) – The ASL defining the atoms to select

command()¶: Select the atoms, then generate a selection object from them

class schrodinger.application.bioluminate.pml_menus.GenerateInterfaceSelection(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.GenerateSelection, schrodinger.application.bioluminate.pml_menus.InterfaceMixin

command()¶: Select atoms at Protein-Protein interfaces

class schrodinger.application.bioluminate.pml_menus.GenerateLigandSelection(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.GenerateSelection, schrodinger.application.bioluminate.pml_menus.LigandActionMixin

command()¶: Select the ligand atoms, then generate a selection object from them

class schrodinger.application.bioluminate.pml_menus.GenerateSurfResSelection(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.GenerateSelection

command()¶: Find all the residues on the surface and select them

class schrodinger.application.bioluminate.pml_menus.GenSelectionSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The Action Generate Selection submenu

__init__(*args, **kwargs)¶

Create a GenSelectionSubMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.GenerateSymmetryMates(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

Generate all the symmetry mates and show those within X angstroms

__init__(*args, **kwargs)¶

Create a GenerateSymmetryMates object

See parent class for argument documentation

Parameters: dist (int or 'all') – The maximum distance from the object to show the mates’ atoms. If ‘all’, the entire symmetry mates will be shown.

command()¶: Generate all the symmetry mates and show those within X angstroms

class schrodinger.application.bioluminate.pml_menus.HideSymmetryMates(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Don’t show crystal mates in the workspace

class schrodinger.application.bioluminate.pml_menus.GenSymMatesSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The Action Generate Symmetry Mates submenu

__init__(*args, **kwargs)¶

Create a GenSymMatesSubMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.GenerateSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The Action Generate submenu

__init__(*args, **kwargs)¶

Create a GenerateSubMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.AddHydrogens(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Add hydrogen atoms

class schrodinger.application.bioluminate.pml_menus.RemoveHydrogens(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Remove hydrogen atoms

class schrodinger.application.bioluminate.pml_menus.RemoveWaters(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Remove hydrogen atoms

class schrodinger.application.bioluminate.pml_menus.DeleteAtoms(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Remove hydrogen atoms

class schrodinger.application.bioluminate.pml_menus.HydrogenSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The Action Hydrogen submenu

__init__(*args, **kwargs)¶

Create a HydrogenSubMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.CountAtoms(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Count the atoms

class schrodinger.application.bioluminate.pml_menus.SumFormalCharge(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Compute the sum of the atomic formal charges

class schrodinger.application.bioluminate.pml_menus.SumPartialCharge(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Count the sum of the atomic partial charges

class schrodinger.application.bioluminate.pml_menus.ComputeSurfaceArea(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

__init__(*args, **kwargs)¶

Create a ComputeSurfaceArea object

Parameters

radius (float) – The solvent radius to use in computing the surface area. Use 0.0 to get a molecular surface area.
stype (str) – The string type of this surface area, such as SASA, MSA, etc.

See MAction for additional parameter documentation

command()¶: Compute the solvent accessible surface area for the object in the context of all visible atoms (EV:119704)

class schrodinger.application.bioluminate.pml_menus.SurfaceAreaSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The Action Surface Area submenu

__init__(*args, **kwargs)¶

Create a SurfaceAreaSubMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.ComputeSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The Action Compute submenu

__init__(*args, **kwargs)¶

Create a ComputeSubMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.DeleteSelections(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Delete all selection objects and deselect all atoms

schrodinger.application.bioluminate.pml_menus.create_action_menu(menu, owner)¶

Parameters

menu (QMenu) – the QMenu that owns this action
owner (ToggleTableObject) – the object this Menu will operate on

class schrodinger.application.bioluminate.pml_menus.ActionMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The Action menu

__init__(*args, **kwargs)¶

Create a ActionMenu object

See parent class for argument documentation

schrodinger.application.bioluminate.pml_menus.hide_atoms(asl=None, owner=None)¶

Hide the atoms given by asl

Parameters

asl (str) – the asl this action will apply to. Must be given if owner is None
owner (ToggleTableObject) – the object this action will apply to. Must be given if asl is None

schrodinger.application.bioluminate.pml_menus.hide_ribbons(asl=None, owner=None)¶

Hide ribbons

Parameters

asl (str) – the asl this action will apply to. If None, then owner must be given, and all atoms specified by owner will be hidden.
owner (ToggleTableObject) – The object to hide ribbons in. If given and the entry is currently invisible, the ribbons will be appropriately updated. If not given, no invisible atoms will be hidden

schrodinger.application.bioluminate.pml_menus.hide_surface(entry_id=None, owner=None, asl=None)¶

Hide a surface

Parameters

entry_id (str) – the entry_id this action will apply to
owner (ToggleTableObject) – The object to hide surfaces from. Used to determine if an entry is invisible. If not given, no invisible atoms will be hidden
asl (str) – The ASL describing atoms to hide the surface of. If this ASL is given and does not contain any protein atoms, then the no surfaces will be hidden. Otherwise, all surfaces of the specified entry will be hidden.

schrodinger.application.bioluminate.pml_menus.hide_labels(asl=None, owner=None)¶

Hide the labels

Parameters

asl (str) – The ASL defining the atoms whose labels will be hidden. If not given, the asl from owner will be used
owner (ToggleTableObject) – If asl is None, the object containing the labels to be hidden

schrodinger.application.bioluminate.pml_menus.hide_everything(asl=None, entry_id=None, owner=None)¶

Hide atoms, ribbons and surfaces

Parameters

asl (str) – the asl this action will apply to
entry_id (str) – the entry_id this action will apply to

Note

At least one argument must be provided.

class schrodinger.application.bioluminate.pml_menus.HideEverything(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Hide the atom display

class schrodinger.application.bioluminate.pml_menus.HideAtoms(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Hide the atom display

class schrodinger.application.bioluminate.pml_menus.HideNonBonded(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Hide the atom display

class schrodinger.application.bioluminate.pml_menus.HideRibbons(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Hide the atom display

class schrodinger.application.bioluminate.pml_menus.HideSurface(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Hide the atom display

class schrodinger.application.bioluminate.pml_menus.HideLabel(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Hide the atom labels

class schrodinger.application.bioluminate.pml_menus.HideMainChain(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Hide the atom display

class schrodinger.application.bioluminate.pml_menus.HideSideChain(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Hide the atom display

class schrodinger.application.bioluminate.pml_menus.HideWaters(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Hide the atom display

class schrodinger.application.bioluminate.pml_menus.HideHydrogens(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Hide the atom display

class schrodinger.application.bioluminate.pml_menus.HideAllOthers(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Hide the atom display

class schrodinger.application.bioluminate.pml_menus.HidePolarHydrogens(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Hide the atom display

class schrodinger.application.bioluminate.pml_menus.HideHydrogenSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The Hide Hydrogen submenu

__init__(*args, **kwargs)¶

Create a HideHydrogenSubMenu object

See parent class for argument documentation

schrodinger.application.bioluminate.pml_menus.create_hide_menu(menu, owner)¶

Create the Hide menu

Parameters

menu (QMenu) – the QMenu that owns this action
owner (ToggleTableObject) – the object this Menu will operate on

class schrodinger.application.bioluminate.pml_menus.HideMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The Hide menu

__init__(*args, **kwargs)¶

Create a HideMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.LabelAtom(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

A QAction that performs labels atoms with the given label

__init__(*args, **kwargs)¶

Create a MAction object

See parent class for argument documentation

Parameters: label (str) – the label to use, values should be taken from the Maestro labelatom command documentation

command()¶: Clears all the atom labels and then labels the atoms in self.asl with any label defined by self.label

class schrodinger.application.bioluminate.pml_menus.LabelAtomByProp(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

Labels all atoms by a custom atom property

getProperty(atomobj)¶

Get the atom property for this action

Parameters: atomobj (schrodinger.structure._StructureAtom object) – The atom object to retrieve the property from
Return type: str
Returns: The atom property converted to a string appropriate for display

command()¶: Clears all the atom labels and then labels the atoms in self.asl with any label defined by self.label

class schrodinger.application.bioluminate.pml_menus.LabelAtomByVDW(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.LabelAtomByProp

getProperty(atomobj)¶

Get the atom property for this action

Parameters: atomobj (schrodinger.structure._StructureAtom object) – The atom object to retrieve the property from
Return type: str
Returns: The atom property converted to a string appropriate for display

class schrodinger.application.bioluminate.pml_menus.LabelAtomByOccupancy(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.LabelAtomByProp

getProperty(atomobj)¶

Get the atom property for this action

Parameters: atomobj (schrodinger.structure._StructureAtom object) – The atom object to retrieve the property from
Return type: str
Returns: The atom property converted to a string appropriate for display

class schrodinger.application.bioluminate.pml_menus.LabelAtomByNumType(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.LabelAtomByProp

getProperty(atomobj)¶

Get the atom property for this action

Parameters: atomobj (schrodinger.structure._StructureAtom object) – The atom object to retrieve the property from
Return type: str
Returns: The atom property converted to a string appropriate for display

class schrodinger.application.bioluminate.pml_menus.LabelAtomByStereo(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Clears all the atom labels and then labels the atoms in self.asl with any label defined by self.label

class schrodinger.application.bioluminate.pml_menus.LabelAtomByEntryIndex(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.LabelAtomByProp

getProperty(atomobj)¶

Get the atom property for this action

Parameters: atomobj (schrodinger.structure._StructureAtom object) – The atom object to retrieve the property from
Return type: str
Returns: The atom property converted to a string appropriate for display

class schrodinger.application.bioluminate.pml_menus.LabelAtomByMolIndex(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.LabelAtomByProp

getProperty(atomobj)¶

Get the atom property for this action

Parameters: atomobj (schrodinger.structure._StructureAtom object) – The atom object to retrieve the property from
Return type: str
Returns: The atom property converted to a string appropriate for display

class schrodinger.application.bioluminate.pml_menus.LabelResidues(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Label the alpha carbon in each residue with the residue name

class schrodinger.application.bioluminate.pml_menus.LabelChains(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Label the first and last alpha carbon in each chain with the chain name

class schrodinger.application.bioluminate.pml_menus.LabelOtherSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The Label Other Properties submenu

__init__(*args, **kwargs)¶

Create a LabelOtherSubMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.LabelAtomIdentSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The Label Atom Identifiers submenu

__init__(*args, **kwargs)¶

Create a LabelAtomIdentSubMenu object

See parent class for argument documentation

schrodinger.application.bioluminate.pml_menus.create_label_menu(menu, owner)¶: Put all the menu items in the Label menu

class schrodinger.application.bioluminate.pml_menus.LabelMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The Label menu

__init__(*args, **kwargs)¶

Create a LabelMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.ColorChooserPanel(colors)¶

Bases: PyQt6.QtWidgets.QDialog

A window that lets the user choose a Maestro color. The window simply consists of a table with cells colored by each known Maestro color. The user chooses the color by clicking on the cell.

Easiest use is to access this via the get_color() function, which creates the panel, displays it and returns the chosen color Maestro name and RGBA values.

__init__(colors)¶

Create a ColorChoosePanel instance

Parameters: colors (dict) – a dictionary with the Maestro colors in it whose keys are a RGB tuple and values are Maestro color name

picked(row, column)¶

Sets the self.picked_color attribute to the (color name, RGBA) tuple selected by the user. RGBA is a tuple of 4 integers giving the red, green, blue and alpha values of the color.

This then closes the window.

schrodinger.application.bioluminate.pml_menus.get_color()¶

Get a user-specified color from the list of known Maestro colors

Return type: tuple
Returns: (Maestro color name, (R, G, B, Alpha)) or (None, None) if the user cancels the window.

schrodinger.application.bioluminate.pml_menus.color_atoms(color_name, asl)¶

Colors the specified atoms with the given color

Parameters

color_name (str) – a Maestro-recognized color name, found in mmshare/data/colors.res
asl (str) – The ASL specifying the atoms to color

schrodinger.application.bioluminate.pml_menus.color_atoms_rgb(red, green, blue, asl)¶

Colors the specified atoms with the given RGB colors

Parameters

red (int) – integer between 0 and 255
green (int) – integer between 0 and 255
blue (int) – integer between 0 and 255
asl (str) – The ASL specifying the atoms to color

schrodinger.application.bioluminate.pml_menus.make_color_asl_for_element(asl, element)¶

Form an ASL that restricts the given ASL to those atoms of a specific element

Parameters

asl (str) – The general asl to make element specific
element (str) – an atomic symbol to restrict the ASL to

Return type

str

Param

asl restricted to atoms of element

class schrodinger.application.bioluminate.pml_menus.ColorRibbonMixin¶

Bases: object

fixRibbons()¶

class schrodinger.application.bioluminate.pml_menus.CustomColor(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction, schrodinger.application.bioluminate.pml_menus.ColorRibbonMixin

__init__(*args, **kwargs)¶

Subclass of MAction that Accepts the additional keyword arguments:

Parameters: color_name (str) – The Maestro color name to be used rather than asking the user to pick a color

schrodinger.application.bioluminate.pml_menus.color_by_element(base_asl, hydrogen='white', carbon='green', nitrogen='user27', oxygen='red', sulfur='orange')¶

Color H, C, N, O and S by colors

Parameters

base_asl (str) – asl defining the group of atoms to color
hydrogen (str) – the Maestro color string defining the color for H atoms
carbon (str) – the Maestro color string defining the color for C atoms
nitrogen (str) – the Maestro color string defining the color for N atoms
oxygen (str) – the Maestro color string defining the color for O atoms
sulfur (str) – the Maestro color string defining the color for S atoms

schrodinger.application.bioluminate.pml_menus.save_new_color(color_name, rgba, mytype)¶

The user has selected a new (or re-selected an existing custom set) - add it to the list of custom sets (or move it to the end) so it ends up at the top of the menu

Parameters

color_name (str) – the Maestro color name of the color to save
rgba (4-tuple or None) – tuple of (red, blue, green, alpha) if this is a new color, or None if this is already an existing color
mytype (str) – the type of color this is (HYDROGEN_COLOR, CARBON_COLOR, OBJECT_COLOR)

class schrodinger.application.bioluminate.pml_menus.ColorHydrogens(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.CustomColor

command()¶

Allow the user to pick a color and then color hydrogens by that color and CNOS by set colors

Save this new color to place in the recent choices list

class schrodinger.application.bioluminate.pml_menus.ColorCarbons(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.CustomColor

command()¶

Allow the user to pick a color and then color carbons by that color and HNOS by set colors

Save this new color to place in the recent choices list

class schrodinger.application.bioluminate.pml_menus.ColorHNOS(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Reset H, N, O, and S to their default colors, but leave C alone

class schrodinger.application.bioluminate.pml_menus.ColorObject(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.CustomColor

command()¶

Allow the user to pick a color and then color a set of atoms by that color

Save this new color to place in the recent choices list

class schrodinger.application.bioluminate.pml_menus.ColorRecentCarbons(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.CustomRecentColor

command()¶: Color atoms by a set of colors from the recent choices list, and rework the list to put this color at the top since it is the most recent choice

class schrodinger.application.bioluminate.pml_menus.ColorRecentHydrogens(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.CustomRecentColor

command()¶: Color atoms by a set of colors from the recent choices list, and rework the list to put this color at the top since it is the most recent choice

class schrodinger.application.bioluminate.pml_menus.ColorRecentObjects(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.CustomRecentColor

command()¶: Color atoms by a set of colors from the recent choices list, and rework the list to put this color at the top since it is the most recent choice

schrodinger.application.bioluminate.pml_menus.get_asl_chain_name(cname)¶

Maestro doesn’t like blank chain names in ASL without quotes so add the quotes if necessary

Parameters: cname (str) – the chain name
Return type: str
Returns: cname if cname is not blank, otherwise a double-quoted space

schrodinger.application.bioluminate.pml_menus.atom_b_factor(atom, zeros=True)¶

Returns the atom B-factor

Parameters

atom (schrodinger._Atom) – atom object to return the B-factor for
zeros (bool) – True if atoms with No B-factor should return 0.0, False if it should return None

Return type

float or None

Returns

the B-factor of the given atom

class schrodinger.application.bioluminate.pml_menus.ColorChains(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction, schrodinger.application.bioluminate.pml_menus.ColorRibbonMixin

colorChains(sub_asl=None)¶

Colors each chain in the struct a different color

command()¶: Colors each chain a different color

class schrodinger.application.bioluminate.pml_menus.ColorChainsByCarbon(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.ColorChains

command()¶: Colors the carbons in each chain a different color

class schrodinger.application.bioluminate.pml_menus.ColorChainsByCalpha(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.ColorChains

command()¶: Colors the alpha carbons in each chain a different color

class schrodinger.application.bioluminate.pml_menus.ColorAtomsBySpectrum(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction, schrodinger.application.bioluminate.pml_menus.ColorRibbonMixin

makeSpectrum(sub_asl=None)¶

Color a structure like a rainbow! Each group of atoms within a chain gets a different color. Groups are created to (roughly) equal number of atoms in each group. Color changes can be restricted to just atoms defined additionally by sub_asl.

command()¶: Color all the atoms like a rainbow

class schrodinger.application.bioluminate.pml_menus.ColorCarbonsBySpectrum(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.ColorAtomsBySpectrum

command()¶: Color all the atoms like a rainbow

class schrodinger.application.bioluminate.pml_menus.ColorCalphasBySpectrum(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.ColorAtomsBySpectrum

command()¶: Color all the atoms like a rainbow

schrodinger.application.bioluminate.pml_menus.bin_b_factors(struct, atoms, groups)¶

Divide atoms up into bins based on their B-factor (temperature factor). The groups are determined to span equal ranges of b-factor (some groups may therefore contain no atoms).

Parameters

atoms (list) – list of atom indexes to bin
groups (int) – The number of bins to create

Return type

list

Returns

List of binned atom indexes - each item of the list is a list containing the atom indexes for that bin. Item 0 are the lowest B-Factors.

class schrodinger.application.bioluminate.pml_menus.ColorAtomsByBFactor(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction, schrodinger.application.bioluminate.pml_menus.ColorRibbonMixin

makeSpectrum(sub_asl=None)¶

Color a structure like a rainbow! Each atom is colored based on its B-factor (temperature factor) - the range of colors is set based on the B-factors of the group being plotted. The minimum b-factor gets blue and the maximum gets deep red. The groups are determined to span equal ranges of b-factor (some groups may therefore contain no atoms. Color changes can be restricted to just atoms defined additionally by sub_asl.

command()¶: Color all the atoms like a rainbow based on their b-factors

class schrodinger.application.bioluminate.pml_menus.ColorCalphasByBFactor(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.ColorAtomsByBFactor

command()¶: Color all the alpha carbon atoms like a rainbow based on their b-factors

schrodinger.application.bioluminate.pml_menus.color_chainbow_groups(asl, ribbons=None)¶

Color all the atoms (and sometimes the ribbons) as chainbows

Parameters

asl (str) – the asl this action will apply to
ribbons (str) – The type of ribbons to create with these colorings. The default is not to create ribbons.

Color each chain like a rainbow! Each group of atoms within a chain gets different colors. Groups are created to (roughly) equal number of atoms in each group, and all the atoms in a residue are given the same color (if the residue != UNK).

class schrodinger.application.bioluminate.pml_menus.ColorChainbows(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction, schrodinger.application.bioluminate.pml_menus.ColorRibbonMixin

__init__(*args, **kwargs)¶

Create a MAction object

Parameters

name (str) – the string that will appear in the menu for this action
menu (QWidget or None) – the QWidget that owns this action, if a QMenu, the title property may be used when determining the command function when the action is triggered.
asl (str) – the asl this action will apply to. If not supplied, the asl is taken as the menu asl
owner (ToggleTableObject) – the object this Action will operate on
tooltip (str) – the string that will appear as a tooltip for this action

command()¶: Color each chain like a rainbow! Each group of atoms within a chain gets different colors. Groups are created to (roughly) equal number of atoms in each group, and all the atoms in a residue are given the same color (if the residue != UNK).

class schrodinger.application.bioluminate.pml_menus.ColorLabel(text, menu, bg_normal='black', bg_mouseover='grey')¶

Bases: PyQt6.QtWidgets.QLabel

A label that shows off the color each element will be colored if this menu item is chosen.

The label changes its background color when the mouse is over it

__init__(text, menu, bg_normal='black', bg_mouseover='grey')¶

Create a ColorLabel instance

Parameters

text (str) – The text this label will display - should be rich text with background-color:bg_normal within it in order to change colors when the mouse is over the label.
menu (str) – The menu this label will be placed in
bg_normal (str) – the normal background color of the label
bg_mouseover (str) – the background color of the label when the mouse is over it

enterEvent(event)¶

Flip the background color when the mouse enters the label

Parameters: event (unused) – unused

leaveEvent(event)¶

Restore the background color when the mouse leaves the label

Parameters: event (unused) – unused

mousePressEvent(event)¶

Trigger this labels action when it is clicked on and close the menu

Parameters: event (unused) – unused

class schrodinger.application.bioluminate.pml_menus.RecentColorSubMenu(parent_menu, title)¶

Bases: PyQt6.QtWidgets.QMenu

A submenu that shows the most recently chosen colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.

__init__(parent_menu, title)¶

updateItems()¶

Update the menu list with the most recent colors chosen

Must be overwritten in the subclass to build the menu each time it shows

class schrodinger.application.bioluminate.pml_menus.RecentCarbonColorSubMenu(parent_menu, title)¶

Bases: schrodinger.application.bioluminate.pml_menus.RecentColorSubMenu

A submenu that shows the most recently chosen carbon colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.

updateItems()¶: Update the menu list with the most recent colors chosen

class schrodinger.application.bioluminate.pml_menus.RecentHydrogenColorSubMenu(parent_menu, title)¶

Bases: schrodinger.application.bioluminate.pml_menus.RecentColorSubMenu

A submenu that shows the most recently chosen hydrogen colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.

updateItems()¶: Update the menu list with the most recent colors chosen

class schrodinger.application.bioluminate.pml_menus.RecentObjectColorSubMenu(parent_menu, title)¶

Bases: schrodinger.application.bioluminate.pml_menus.RecentColorSubMenu

A submenu that shows the most recently chosen object colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.

updateItems()¶: Update the menu list with the most recent colors chosen

schrodinger.application.bioluminate.pml_menus.create_colorbyele_menu(menu, owner, c_menu, h_menu)¶

Parameters

menu (QMenu) – the QMenu that owns this action
owner (ToggleTableObject) – the object this Menu will operate on
c_menu (QMenu) – Submenu for recent custom carbon colors
h_menu (QMenu) – Submenu for recent custom hydrogen colors

class schrodinger.application.bioluminate.pml_menus.ColorByElementSubMenu(parent, asl=None, owner=None)¶

Bases: PyQt6.QtWidgets.QMenu

The Color by Element submenu

__init__(parent, asl=None, owner=None)¶

Create a ColorByElementSubMenu object

Parameters

asl (str) – the asl this action will apply to
owner (ToggleTableObject) – the object this Menu will operate on

class schrodinger.application.bioluminate.pml_menus.ColorChainSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The ColorChainSubMenu menu

__init__(*args, **kwargs)¶

Create a ColorChainSubMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.ColorSpectrumSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The ColorSpectrumSubMenu menu

__init__(*args, **kwargs)¶

Create a ColorSpectrumSubMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.CustomRecentColor(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.MWidgetAction

__init__(*args, **kwargs)¶

Subclass of MWidgetAction that Accepts the additional keyword arguments:

Parameters: color_name (str) – The Maestro color name to be used rather than asking the user to pick a color

class schrodinger.application.bioluminate.pml_menus.ColorBySubstructure(menu, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.MWidgetAction, schrodinger.application.bioluminate.pml_menus.ColorRibbonMixin

__init__(menu, **kwargs)¶

Create a MWidgetAction object

Parameters

widget (QWidget) – the widget to be displayed as the menu item
menu (QWidget) – the QWidget that owns this action, if a QMenu, the title property may be used when determining the command function when the action is triggered.
asl (str) – the asl this action will apply to. If not supplied, the asl is taken as the menu asl
owner (ToggleTableObject) – the object this Action will operate on
tooltip (str) – the string that will appear as a tooltip for this action

command()¶: Color the helix, sheet and loop objects in the structure

class schrodinger.application.bioluminate.pml_menus.ColorSubstructureSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The ColorSubstructureSubMenu menu

__init__(*args, **kwargs)¶

Create a ColorMenuSubstructureSubMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.AutoCycleColor(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction, schrodinger.application.bioluminate.pml_menus.ColorRibbonMixin

colorAtoms(asl)¶

Color all atoms specified by asl by the next color in the cycle for this owner

Parameters: asl (str) – the asl this action will apply to

command()¶: Color all atoms by the next color in the cycle for this owner

class schrodinger.application.bioluminate.pml_menus.AutoCycleCarbonColor(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.AutoCycleColor

command()¶: Color all carbons by the next color in the cycle for this owner

class schrodinger.application.bioluminate.pml_menus.AutoColorObjects(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction, schrodinger.application.bioluminate.pml_menus.ColorRibbonMixin

colorAtoms(asl)¶

Color each entry (or each partial entry if a selection) with a different color

Parameters: asl (str) – the asl this action will apply to

command()¶: Color all carbons by the next color in the cycle for this owner

class schrodinger.application.bioluminate.pml_menus.AutoColorCarbons(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.AutoColorObjects

command()¶: Color all carbons by the next color in the cycle for this owner

class schrodinger.application.bioluminate.pml_menus.AutoColorSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The Color menu

__init__(*args, **kwargs)¶

Create a ColorMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.ColorMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The Color menu

__init__(*args, **kwargs)¶

Create a ColorMenu object

See parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.ToggleState(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

A MAction that toggles the enabled/disabled state of an object

__init__(*args, **kwargs)¶

Create a ToggleState object

See parent class for argument documentation

Parameters

enable (bool) – True if this action should enable the owner object, False if it should disable it
visible_objects (bool) – True if this action acts on all visible objects, False if it acts on some other set

command()¶: Toggle the state of the the owner object.

class schrodinger.application.bioluminate.pml_menus.DeleteAll(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Delete All the Toggle Table objects

class schrodinger.application.bioluminate.pml_menus.Reinitialize(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Reinitialize the workspace - in Maestro this means closing the current project, so check to make sure that’s OK if there is a scratch project

class schrodinger.application.bioluminate.pml_menus.Quit(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Quit Maestro

class schrodinger.application.bioluminate.pml_menus.Select(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Select the atoms

class schrodinger.application.bioluminate.pml_menus.Disable(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Select the atoms

class schrodinger.application.bioluminate.pml_menus.CreateEntry(name, menu, asl=None, owner=None, tooltip=None)¶

Bases: schrodinger.application.bioluminate.pml_menus.MAction

command()¶: Create a new entry from the atoms

schrodinger.application.bioluminate.pml_menus.add_common_context_items(menu, select=True)¶

Adds items common to many context menus

Parameters

menu (PMLMenu) – the menu to add items to
select (bool) – True if Select is on the menu, False if not

class schrodinger.application.bioluminate.pml_menus.GeneralContextSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The submenu that contains all the main actions used for most context menus

__init__(*args, **kwargs)¶

Create a GeneralContextSubMenu item

See Parent class for argument documentation

Parameters: title (str) – The title for this submenu

class schrodinger.application.bioluminate.pml_menus.SubstructureContextSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.GeneralContextSubMenu

The GeneralContextSubMenu for a right-click that is on an atom

__init__(*args, **kwargs)¶

Create a SubstructureContextSubMenu item

See Parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.ObjectFreeContextSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.GeneralContextSubMenu

The GeneralContextSubMenu for a right-click that is not on an object

__init__(*args, **kwargs)¶

Create an ObjectFreeContextSubMenu item

See Parent class for argument documentation

class schrodinger.application.bioluminate.pml_menus.ToggleStateSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The submenu that allows the user to enable/disable individual objects

__init__(*args, **kwargs)¶

Create a ToggleStateSubMenu object

See parent class for argument documentation

Parameters

title (str) – The title of this menu
visible_objects (bool) – True if this menu acts on all visible objects, False if it acts on some other set

class schrodinger.application.bioluminate.pml_menus.SelectedAtomContextActionSubMenu(*args, **kwargs)¶

Bases: schrodinger.application.bioluminate.pml_menus.PMLMenu

The submenu that allows the user to enable/disable individual objects

__init__(*args, **kwargs)¶

Create a SelectedAtomContextActionSubMenu object

See parent class for argument documentation

Parameters

title (str) – The title of this menu
enable – True if this menu acts on all visible objects, False if it acts on some other set

schrodinger.application.bioluminate.pml_menus.color_dict = {(0, 0, 0): 'black', (0, 0, 38): 'user63', (0, 0, 128): 'user2', (0, 0, 255): 'user26', (0, 31, 191): 'userK', (0, 51, 204): 'user25', (0, 51, 255): 'user60', (0, 102, 153): 'user24', (0, 102, 255): 'user59', (0, 153, 102): 'user23', (0, 153, 255): 'user58', (0, 191, 127): 'userM', (0, 204, 51): 'user22', (0, 204, 255): 'user57', (0, 255, 51): 'user53', (0, 255, 102): 'user54', (0, 255, 153): 'user55', (0, 255, 204): 'user56', (0, 255, 255): 'user4', (7, 7, 255): 'blue1', (15, 0, 255): 'user27', (15, 15, 255): 'blue2', (23, 23, 255): 'blue3', (30, 0, 255): 'user28', (30, 30, 225): 'blue', (30, 225, 30): 'green', (31, 31, 255): 'blue4', (31, 255, 102): 'userL', (34, 139, 34): 'user3', (39, 39, 255): 'blue5', (44, 60, 60): 'user1', (45, 0, 255): 'user29', (47, 47, 255): 'blue6', (51, 255, 0): 'user21', (55, 55, 255): 'blue7', (60, 0, 255): 'user30', (63, 63, 255): 'blue8', (63, 191, 76): 'userI', (71, 71, 255): 'blue9', (75, 0, 255): 'user31', (79, 79, 255): 'blue10', (87, 87, 255): 'blue11', (90, 0, 255): 'user32', (95, 63, 255): 'userR', (95, 95, 255): 'blue12', (95, 255, 51): 'userV', (102, 255, 0): 'user20', (103, 103, 255): 'blue13', (107, 142, 35): 'olive', (111, 111, 255): 'blue14', (112, 219, 147): 'aquamarine', (119, 119, 255): 'blue15', (120, 0, 255): 'user61', (127, 127, 255): 'blue16', (127, 191, 25): 'userP', (135, 135, 255): 'blue17', (142, 35, 107): 'maroon', (143, 143, 255): 'blue18', (151, 151, 255): 'blue19', (153, 255, 0): 'user19', (159, 159, 255): 'blue20', (159, 210, 255): 'userW', (159, 255, 0): 'userA', (159, 255, 191): 'userF', (160, 82, 45): 'sienna', (160, 160, 160): 'gray', (165, 42, 42): 'brown', (167, 167, 255): 'blue21', (173, 234, 234): 'turquoise', (175, 175, 255): 'blue22', (180, 0, 255): 'user62', (183, 183, 255): 'blue23', (191, 0, 191): 'userQ', (191, 127, 25): 'userC', (191, 159, 255): 'userH', (191, 191, 255): 'blue24', (191, 255, 51): 'userG', (192, 192, 192): 'user7', (199, 199, 255): 'blue25', (204, 255, 0): 'user18', (205, 133, 63): 'peru', (207, 207, 255): 'blue26', (210, 127, 36): 'user6', (215, 215, 255): 'blue27', (216, 191, 216): 'thistle', (220, 20, 60): 'user5', (223, 63, 0): 'userD', (223, 223, 0): 'userS', (223, 223, 255): 'blue28', (224, 224, 224): 'user8', (225, 30, 30): 'red', (225, 30, 225): 'purple', (225, 127, 80): 'coral', (225, 193, 37): 'goldenrod', (225, 225, 30): 'yellow', (231, 231, 255): 'blue29', (234, 130, 50): 'orange', (234, 173, 234): 'plum', (239, 239, 255): 'blue30', (245, 222, 179): 'wheat', (247, 247, 255): 'blue31', (255, 0, 31): 'userE', (255, 0, 159): 'userN', (255, 7, 7): 'red1', (255, 15, 15): 'red2', (255, 23, 23): 'red3', (255, 30, 0): 'user9', (255, 31, 31): 'red4', (255, 39, 39): 'red5', (255, 47, 47): 'red6', (255, 55, 55): 'red7', (255, 60, 0): 'user10', (255, 63, 63): 'red8', (255, 71, 71): 'red9', (255, 79, 79): 'red10', (255, 87, 87): 'red11', (255, 90, 0): 'user11', (255, 95, 95): 'red12', (255, 103, 103): 'red13', (255, 111, 111): 'red14', (255, 119, 119): 'red15', (255, 120, 0): 'user12', (255, 127, 127): 'red16', (255, 135, 135): 'red17', (255, 143, 143): 'red18', (255, 150, 0): 'user13', (255, 151, 151): 'red19', (255, 152, 163): 'pink', (255, 159, 159): 'red20', (255, 167, 167): 'red21', (255, 175, 175): 'red22', (255, 180, 0): 'user14', (255, 183, 183): 'red23', (255, 191, 51): 'userT', (255, 191, 191): 'red24', (255, 199, 199): 'red25', (255, 207, 207): 'red26', (255, 210, 0): 'user15', (255, 215, 215): 'red27', (255, 223, 159): 'userY', (255, 223, 223): 'red28', (255, 231, 231): 'red29', (255, 239, 239): 'red30', (255, 240, 0): 'user16', (255, 247, 247): 'red31', (255, 255, 0): 'user17', (255, 255, 255): 'white'}¶: keys of colors are RGB tuple, values are color name

schrodinger.application.bioluminate.pml_menus.custom_color_dicts = {'carbon': {}, 'hydrogen': {}, 'object': {}}¶: Keys of custom_color_dicts the type of set this applies to (custom carbons, custom hydrogens, custom objects), values are dictionaries containing recent choices for that object