StructureViewer¶

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

Bases: object

Represents a viewer for biological molecules.

It contains NGL viewer inside. It may display .pdb or .mol formats. See full documentation here http://nglviewer.org

The following example shows how to load a PDB file from a local directory:

It has been created by the following code:

from visualife.widget import StructureViewer

panel3d_A = StructureViewer("show_3d_A",backgroundColor="white", width=200, height=200, menu_buttons={})
panel3d_A.add_model("1", "../_static/2q9f.pdb")
panel3d_B = StructureViewer("show_3d_B",backgroundColor="white", width=200, height=200, menu_buttons={})
panel3d_B.add_model("1", "2gb1")
pdb_txt = "ATOM    408  N   LYS A  28      -2.867   6.554  -3.724  1.00  0.17           N"
pdb_txt += "\n" + "ATOM    409  CA  LYS A  28      -2.011   7.699  -3.277  1.00  0.21           C"
pdb_txt += "\n" + "ATOM    410  C   LYS A  28      -1.865   7.707  -1.749  1.00  0.19           C"
pdb_txt += "\n" + "ATOM    411  O   LYS A  28      -0.810   8.013  -1.230  1.00  0.23           O"
panel3d_C = StructureViewer("show_3d_C",backgroundColor="white", width=200, height=200, menu_buttons={})
panel3d_C.add_model("1", pdb_txt)
panel3d_C.as_sticks()

Methods Summary

`add_model`(model_id, URL, **kwargs)	Adds a new structure to this viewer.
`add_style`(model_id, style[, …])	Modify a style used to display a structure
`add_to_menu`(button_name, callback)	Adds a button to the menu, binds a callback to the button_name
`as_cartoon`([evt])	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
`center`([evt])	Centers the scene
`clear`([evt])	Clears the scene
`color_ss`(model_id)	Color given model by secondary structure
`hide_model`(model_id)	Hides a requested structure (i.e.
`remove_model`(model_id)	Removes a model from this widget and from the NGL viewer
`remove_style`(model_id[, rep])	Remove a style used to structure
`replace_bfactors`(model_id, bf_values)	Replaces B-factor values with given values
`show_distance`(model_id, atom_pairs_list)	Show distance between pair of atom in a given model
`show_model`(model_id)	Makes visible a requested structure (i.e.
`zoom_heteroatom`(evt)	Zooms to the heteroatoms group
`zoom_to`(model_id, selection)	Zooms to the active selection

Methods Documentation

add_model(model_id, URL, **kwargs)¶

Adds a new structure to this viewer.

Parameters:

model_id – string ID used to identify that molecule
URL –
string | File | Blob either a URL or an object containing the file data:
- a four character string is assumed to be a PDB code of a protein to be downloaded from the PDB website
- a string that contains multiple lines is assumed to be a PDB-formatted text
- other strings are recognized as local file names
- blob and file objects are handled by NGL instance directly
kwargs – see below

Returns:

Promise object of StructureComponent or a SurfaceComponent

add_style(model_id, style, representation_parameters={})¶

Modify a style used to display a structure

Parameters:	model_id – `string` ID of a model to apply the style style – `string` name of the representation to be set, e.g. `"cartoon"` or `"licorice"` representation_parameters – dictionary used to create a `NGL.StructureRepresentationType` object
Returns:	None

add_to_menu(button_name, callback)¶

Adds a button to the menu, binds a callback to the button_name

Parameters:	button_name – `string` name for button callback – function or `string` to bind on click

as_cartoon(evt=None)¶

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

as_lines(evt=None)¶

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=None)¶

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=None)¶

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

center(evt=None)¶: Centers the scene

clear(evt=None)¶: Clears the scene

color_ss(model_id)¶

Color given model by secondary structure

Parameters:	model_id – `string` with model id

hide_model(model_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:	model_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(model_id)¶

Removes a model from this widget and from the NGL viewer

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

remove_style(model_id, rep=None)¶

Remove a style used to structure

Parameters:	model_id – `string` ID of a model to apply the style rep – `NGL.StructureRepresentationType` object
Returns:	None

replace_bfactors(model_id, bf_values)¶

Replaces B-factor values with given values

Every atom of an i-th residue gets bf_values[i] :param model_id: string id that define a model to be affected :param bf_values: list list of values to be used

show_distance(model_id, atom_pairs_list)¶

Show distance between pair of atom in a given model

Parameters:	model_id – id of model to mark the distances atom_pairs_list – `list` of tuples of atom pairs eg. [(13,31),(5,43)]

show_model(model_id)¶

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

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)

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(model_id, selection)¶

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