openpharmacophore.Viewer

class openpharmacophore.Viewer[source]

Bases: object

Class to visualize molecular systems and pharmacophores.

Wrapper around nglview NGLWidget

Methods

`add_chem_feats`	Add chemical features to the viewer.
`add_components`	Add multiple components to the viewer, such as Proteins, Ligands and BindingSites.
`add_pharmacophore`	Add a pharmacophore to the viewer
`load_component`	Load a component to the viewer, such as a Protein, Ligand or BindingSite so, it can be visualized.
`set_protein_style`	Set the style of the protein.
`show`	Shows the visualization.
`to_nglview`	Get an NGLView widget representing the view.

Attributes

`has_chem_feats`	Returns true if the visualization contains chemical features.
`has_ligand`	Returns true if the visualization contains a ligand.
`has_pharmacophore`	Returns true if the visualization contains a pharmacophore.
`has_protein`	Returns true if the visualization contains a protein.
`n_components`

add_chem_feats(chem_feats)[source]

Add chemical features to the viewer.

add_components(components)[source]

Add multiple components to the viewer, such as Proteins, Ligands and BindingSites.

add_pharmacophore(pharmacophore)[source]

Add a pharmacophore to the viewer

property has_chem_feats: bool: Returns true if the visualization contains chemical features.

property has_ligand: bool: Returns true if the visualization contains a ligand.

property has_pharmacophore: bool: Returns true if the visualization contains a pharmacophore.

property has_protein: bool: Returns true if the visualization contains a protein.

load_component(component, struct)[source]

Load a component to the viewer, such as a Protein, Ligand or BindingSite so, it can be visualized.

Parameters:

set_protein_style(style)[source]

Set the style of the protein.

show(struct=0)[source]

Shows the visualization.

Parameters:: struct (int, optional) – Frame, structure or conformer index to show if there are any proteins, ligands or pharmacophores with multiple structures.
Return type:: nv.NGLWidget

to_nglview()[source]

Get an NGLView widget representing the view.