GLViewerWidget¶

class visualife.widget.GLViewerWidget(div_id, **kwargs)¶

Bases: object

Represents a viewer for biological molecules.

It contains 3DMol viewer inside. It may display .pdb or .mol formats. See full documentation here https://3dmol.csb.pitt.edu/index.html

Methods Summary

`active_selection`(selection_dict)	Defines an active selection.
`add_atom`(a, cor[, model])	Adds an atom to a viewer
`add_model`(name, pdb_text[, if_show])	Adds a new structure to this viewer.
`add_on_clear`(callback)	Add a callback function to be called when this viewer is cleared, e.g.
`add_style`(selection, style)	Modify a style used to display a fragment of a model :param selection: dictionary used to create a `3DMol.AtomSelectionSpec` object :param style: dictionary used to create a `3DMol.AtomStyleSpec` object :return: None
`add_to_menu`(button_name, callback)
`as_cartoon`(evt, **kwargs)	Displays a molecule or its fragment as cartoon
`as_lines`(evt)	Displays a molecule or its fragment as lines
`as_spheres`(evt)	Displays a molecule or its fragment as spheres
`as_sticks`(evt)	Displays a molecule or its fragment as sticks
`atomcallback`(atom, viewer, b, a)	Function to run on atom click
`center`(evt)	Zooms out so the whole structure is visible :param evt: event object; its not used by this method must must appear in the method definition so it can be used as a callback for an HTML event :return:
`check_clicked_atoms`(ev)	Returns a list of atoms that are clicked
`clear`()	Clears this panel and removes all structures from memory
`clear_all`(evt)
`finalize`()	Force the viewer to refresh
`hide_structure`(structure_id)	Hides a requested structure (i.e.
`remove_model`(structure_id)	Removes a model from this widget and from the 3Dmol viewer
`save_as_png`(evt)
`show_ligand_contacts`(ligand_code, …)	Show contacts between ligand and receptor
`show_structure`(structure_id)	Makes visible a requested structure (i.e.
`update_viewer`(decoys)	Shows decoys from a given list
`zoom_heteroatom`(evt)	Zooms to the heteroatoms group
`zoom_to`(evt)	Zooms to the active selection

Methods Documentation

active_selection(selection_dict)¶

Defines an active selection.

The selected residues will be subjected to as_sticks(), as_lines(), as_spheres(), as_cartoon() and zoom_to() methods. By default the whole molecule is selected.

Parameters:	selection_dict – selection as JSON-like dictionary; must a valid argument

for 3DMol.AtomSelectionSpec object. A few examples are given below:

{chain:'B'} : selects chain B
resi:["91-95","42-50"] : selects two ranges of residues
{resn:'PMP', byres:true,expand:5} : selects residue PMP and then extends the selection to any residue whose

atom is within 5A
{chain:'B', invert: True} : selects everything but chain B

Returns:	None

add_atom(a, cor, model=0)¶: Adds an atom to a viewer

add_model(name, pdb_text, if_show=True)¶

Adds a new structure to this viewer.

Parameters:	name – `string` ID used to identify that molecule pdb_text – `string` biomalecule structure as PDB data (text) if_show – `bool` if True, the structure will be immediately visible in the viewer
Returns:	`$3Dmol.GLModel` object

add_on_clear(callback)¶

Add a callback function to be called when this viewer is cleared, e.g. by calling clear() method

Parameters:	callback – a function to be called
Returns:	None

add_style(selection, style)¶: Modify a style used to display a fragment of a model :param selection: dictionary used to create a 3DMol.AtomSelectionSpec object :param style: dictionary used to create a 3DMol.AtomStyleSpec object :return: None

add_to_menu(button_name, callback)¶

as_cartoon(evt, **kwargs)¶

Displays a molecule or its fragment as cartoon

The method will be applied to residues (chains, atoms) that have been recently selected by active_selection() method. By default the whole structure is selected

Parameters:	evt – event object; its not used by this method must must appear in the method definition so it can be used as a callback for an HTML event kwargs – see below
Returns:	None

as_lines(evt)¶

Displays a molecule or its fragment as lines

The method will be applied to residues (chains, atoms) that have been recently selected by active_selection() method. By default the whole structure is selected

Parameters:	evt – event object; its not used by this method must must appear in the method definition so it can be used as a callback for an HTML event kwargs – see below
Returns:	None

as_spheres(evt)¶

Displays a molecule or its fragment as spheres

The method will be applied to residues (chains, atoms) that have been recently selected by active_selection() method. By default the whole structure is selected

Parameters:	evt – event object; its not used by this method must must appear in the method definition so it can be used as a callback for an HTML event kwargs – see below
Returns:	None

as_sticks(evt)¶

Displays a molecule or its fragment as sticks

The method will be applied to residues (chains, atoms) that have been recently selected by active_selection() method. By default the whole structure is selected

Parameters:	evt – event object; its not used by this method must must appear in the method definition so it can be used as a callback for an HTML event kwargs – see below
Returns:	None

atomcallback(atom, viewer, b, a)¶: Function to run on atom click

center(evt)¶

Zooms out so the whole structure is visible :param evt: event object; its not used by this method must must appear

in the method definition so it can be used as a callback for an HTML event

Returns:

check_clicked_atoms(ev)¶

Returns a list of atoms that are clicked

Returns a list of clicked atoms serial number

clear()¶

Clears this panel and removes all structures from memory

This call also triggers all on_clear callbacks functions

clear_all(evt)¶

finalize()¶: Force the viewer to refresh

hide_structure(structure_id)¶

Hides a requested structure (i.e. a model).

This method does not remove the structure, it just make it invisible. You can always show the structure again by calling show() method. The structure must have been already added to this Widget

Parameters:	structure_id – `string` ID of a model to show
Returns:	True if shown successfully, false if this called failed (e.g. when the requested structure has not been registered in this Widget)

remove_model(structure_id)¶

Removes a model from this widget and from the 3Dmol viewer

Parameters:	structure_id – `string` ID of a model to be removed
Returns:	True if the structure was actually removed

save_as_png(evt)¶

show_ligand_contacts(ligand_code, ligand_atom, rcptr_resi, rcptr_atoms)¶: Show contacts between ligand and receptor

show_structure(structure_id)¶

Makes visible a requested structure (i.e. a model).

The structure must have been already added to this Widget :param structure_id: string ID of a model to show :return: True if shown successfully, false if this called failed

(e.g. when the requested structure has not been registered in this Widget)

update_viewer(decoys)¶: Shows decoys from a given list

zoom_heteroatom(evt)¶

Zooms to the heteroatoms group

Parameters:	evt – event object; its not used by this method must must appear in the method definition so it can be used as a callback for an HTML event kwargs – see below
Returns:	None

zoom_to(evt)¶

Zooms to the active selection

The method will zoom and center the view on residues (chains, atoms) that have been recently selected by active_selection() method. By default the whole structure is selected

Parameters:	evt – event object; its not used by this method must must appear in the method definition so it can be used as a callback for an HTML event kwargs – see below
Returns:	None