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class nglview.ASEStructure(ase_atoms, ext='pdb', params={})

Bases: nglview.base_adaptor.Structure

get_structure_string()

class nglview.ASETrajectory(ase_traj)

Bases: nglview.base_adaptor.Trajectory, nglview.base_adaptor.Structure

asetraj adaptor.

>>> import nglview as nv
>>> from ase.io.trajectory import Trajectory
>>> traj = Trajectory(nv.datafiles.ASE_Traj)
>>> t = nv.ASETrajectory(traj)
>>> w = nv.NGLWidget(t)
>>> w.add_spacefill()
>>> w

get_coordinates(index)

get_structure_string()

property n_frames

class nglview.BiopythonStructure(entity, ext='pdb', params={})

Bases: nglview.base_adaptor.Structure

get_structure_string()

class nglview.FileStructure(path)

Bases: nglview.base_adaptor.Structure

get_structure_string()

class nglview.HTMDTrajectory(mol)

Bases: nglview.base_adaptor.Trajectory

HTMD adaptor.

Takes a Molecule object.

>>> import nglview as nv
>>> from htmd import Molecule
>>> mol = Molecule(nv.datafiles.PDB)
>>> t = nv.HTMDTrajectory(mol)
>>> w = nv.NGLWidget(t)
>>> w

get_coordinates(index)

get_structure_string()

property n_frames

class nglview.IODataStructure(obj)

Bases: nglview.base_adaptor.Structure

get_structure_string()

Require ase package

class nglview.IOTBXStructure(obj, ext='pdb', params={})

Bases: nglview.base_adaptor.Structure

get_structure_string()

class nglview.MDAnalysisTrajectory(atomgroup)

Bases: nglview.base_adaptor.Trajectory, nglview.base_adaptor.Structure

MDAnalysis adaptor.

Can take either a Universe or AtomGroup.

>>> import nglview as nv
>>> import MDAnalysis as mda
>>> u = mda.Universe(nv.datafiles.GRO, nv.datafiles.XTC)
>>> prot = u.select_atoms('protein')
>>> t = nv.MDAnalysisTrajectory(prot)
>>> w = nv.NGLWidget(t)
>>> w

get_coordinates(index)

get_structure_string()

property n_frames

class nglview.MDTrajTrajectory(trajectory)

Bases: nglview.base_adaptor.Trajectory, nglview.base_adaptor.Structure

mdtraj adaptor.

>>> import nglview as nv
>>> import mdtraj as md
>>> traj = md.load(nv.datafiles.XTC, nv.datafiles.GRO)
>>> t = MDTrajTrajectory(traj)
>>> w = nv.NGLWidget(t)
>>> w

get_coordinates(index)

get_structure_string()

property n_frames

class nglview.NGLWidget(*args, **kwargs)

Bases: ipywidgets.widgets.domwidget.DOMWidget

add_component(filename, **kwargs)

add component from file/trajectory/struture

filename : str or Trajectory or Structure or their derived class or url **kwargs : additional arguments, optional

>>> import nglview
>>> view = nglview.NGLWidget()
>>> view 
... filename = 'somefile.ccp4'
... view.add_component(filename)

If you want to load binary file such as density data, mmtf format, it is faster to load file from current or subfolder.

add_pdbid(pdbid, **kwargs)

add new Structure view by fetching pdb id from rcsb

>>> import nglview
>>> view = nglview.NGLWidget()
>>> c = view.add_pdbid('1tsu')
>>> # which is equal to 
>>> # view.add_component('rcsb://1tsu.pdb')

add_representation(repr_type, selection='all', **kwargs)

Add structure representation (cartoon, licorice, …) for given atom selection.

repr_typestr

type of representation. Please see http://nglviewer.org/ngl/ for further info.

selectionstr or 1D array (atom indices) or any iterator that returns integer, default ‘all’

atom selection

**kwargs: additional arguments for representation

>>> import nglview as nv
>>> import pytraj 
>>> t = pytraj.datafiles.load_tz2()
>>> w = nv.show_pytraj(t)
>>> w.add_representation('cartoon', selection='protein', color='blue')
>>> w.add_representation('licorice', selection=[3, 8, 9, 11], color='red')
>>> w 

User can also use shortcut

>>> selection = 'protein'
>>> w.add_cartoon(selection) # w.add_representation('cartoon', selection)

add_structure(structure, **kwargs)

add structure to view

structure : nglview.Structure object

>>> view.add_trajectory(traj0) 
... view.add_trajectory(traj1)
... # then add Structure
... view.add_structure(s)

nglview.NGLWidget.add_component

add_trajectory(trajectory, **kwargs)

add new trajectory to view

trajectory: nglview.Trajectory or its derived class or

a supported object, eg pytraj.Trajectory-like, mdtraj.Trajectory, MDAnalysis objects, etc

nglview.NGLWidget.add_component

>>> import nglview as nv, pytraj as pt
>>> traj = pt.load(nv.datafiles.TRR, nv.datafiles.PDB)
>>> view = nv.show_pytraj(traj)
>>> # show view first
>>> view 
>>> # add new Trajectory
>>> traj2 = pt.datafiles.load_tz2()
>>> c = view.add_trajectory(traj2)

background

A trait for unicode strings.

property camera

center(selection='*', duration=0, component=0, **kwargs)

center view for given atom selection

view.center_view(selection=’1-4’)

center_view(**kwargs)

clear(*args, **kwargs)

shortcut of clear_representations

clear_representations(component=0)

clear all representations for given component

componentint, default 0 (first model)

You need to keep track how many components you added.

color_by(color_scheme, component=0)

update color for all representations of given component

Unstable feature

color_scheme : str component : int, default 0

component index

>>> import nglview
>>> view = nglview.demo()
>>> # component 0
>>> view.color_by('atomindex')

>>> # component 1
>>> view.color_by('atomindex', component=1)

display(gui=False, style='ngl')

guibool

If True: turn on GUI

stylestr, {‘ngl’, ‘ipywidgets}, default ‘ngl’

GUI style (with gui=True)

download_image(filename='screenshot.png', factor=4, antialias=True, trim=False, transparent=False)

render and download scene at current frame

filename : str, default ‘screenshot.png’ factor : int, default 4

quality of the image, higher is better

antialias : bool, default True trim : bool, default False transparent : bool, default False

frame

An int trait.

gui_style

An enum of strings where the case should be ignored.

handle_resize()

hide(indices)

set invisibility for given component/struture/trajectory (by their indices)

loaded

A boolean (True, False) trait.

max_frame

An int trait.

n_components

An int trait.

on_loaded

property parameters

picked

An instance of a Python dict.

remove_component(c)

remove component by its uuid. If isinstance(c, ComponentViewer), c won’t be associated with self

c : Union[int, ComponentViewer]

>>> c0 = view.add_trajectory(traj0) 
... c1 = view.add_trajectory(traj1)
... c2 = view.add_struture(structure)
... # remove last component
... view.remove_component(c2)
... assert c2._view is None

render_image(frame=None, factor=4, antialias=True, trim=False, transparent=False)

render and get image as ipywidgets.widget_image.Image

frameint or None, default None

if None, use current frame if specified, use this number.

factorint, default 4

quality of the image, higher is better

antialias : bool, default True trim : bool, default False transparent : bool, default False

# tell NGL to render send image data to notebook. view.render_image()

# make sure to call get_image method view.get_image()

You need to call render_image and get_image in different notebook’s Cells

property representations

set_coordinates(arr_dict, movie_making=False, render_params=None)

Used for update coordinates of a given trajectory >>> # arr: numpy array, ndim=2 >>> # update coordinates of 1st trajectory >>> view.set_coordinates({0: arr})# doctest: +SKIP

set_representations(representations, component=0)

representations : list of dict

show(**kwargs)

shortcut of show_only

show_only(indices='all', **kwargs)

set visibility for given components (by their indices)

indices : {‘all’, array-like}, component index, default ‘all’

update_representation(component=0, repr_index=0, **parameters)

componentint, default 0

component index

repr_indexint, default 0

representation index for given component

parameters : dict

class nglview.OpenbabelStructure(obj)

Bases: nglview.base_adaptor.Structure

get_structure_string()

class nglview.ParmEdTrajectory(trajectory)

Bases: nglview.base_adaptor.Trajectory, nglview.adaptor.ParmEdStructure

ParmEd adaptor.

get_coordinates(index)

property n_frames

class nglview.PdbIdStructure(pdbid)

Bases: nglview.base_adaptor.Structure

get_structure_string()

class nglview.ProdyStructure(obj)

Bases: nglview.base_adaptor.Structure

get_structure_string()

class nglview.ProdyTrajectory(obj)

Bases: nglview.base_adaptor.Trajectory, nglview.adaptor.ProdyStructure

get_coordinates(index)

property n_frames

class nglview.Psi4Structure(obj)

Bases: nglview.adaptor.QCElementalStructure

class nglview.PyTrajTrajectory(trajectory)

Bases: nglview.base_adaptor.Trajectory, nglview.base_adaptor.Structure

PyTraj adaptor.

>>> import nglview as nv
>>> import pytraj as pt
>>> traj = pt.load(nv.datafiles.TRR, nv.datafiles.PDB)
>>> t = nv.PyTrajTrajectory(traj)
>>> w = nv.NGLWidget(t)
>>> w

get_coordinates(index)

get_structure_string(index=0)

property n_frames

class nglview.QCElementalStructure(obj)

Bases: nglview.base_adaptor.Structure

get_structure_string()

class nglview.RdkitStructure(rdkit_mol, ext='pdb', conf_id=- 1)

Bases: nglview.base_adaptor.Structure

get_structure_string()

class nglview.RosettaStructure(pose, ext='pdb', params={})

Bases: nglview.base_adaptor.Structure

get_structure_string()

class nglview.SchrodingerStructure(structure, ext='pdb')

Bases: nglview.base_adaptor.Structure

Only read first structure

get_structure_string()

class nglview.SchrodingerTrajectory(structure, traj)

Bases: nglview.adaptor.SchrodingerStructure, nglview.base_adaptor.Trajectory

Require parmed package.

classmethod from_files(cms_fname, traj_fname)

get_coordinates(index)

get_structure_string()

Require parmed package.

property n_frames

class nglview.SimpletrajTrajectory(path, structure_path)

Bases: nglview.base_adaptor.Trajectory, nglview.base_adaptor.Structure

simpletraj adaptor.

>>> import nglview as nv
>>> t = nv.SimpletrajTrajectory(nv.datafiles.XTC, nv.datafiles.GRO)
>>> w = nv.NGLWidget(t)
>>> w

get_coordinates(index)

get_structure_string()

property n_frames

class nglview.TextStructure(text, ext='pdb', params={})

Bases: nglview.base_adaptor.Structure

get_structure_string()

nglview.demo(*args, **kwargs)

>>> import nglview as nv
>>> view = nv.demo()
>>> view 

class nglview.register_backend(package_name)

Bases: object

nglview.show_ase(ase_atoms, **kwargs)

>>> import nglview as nv
>>> from ase import Atom, Atoms
>>> dimer = Atoms([Atom('X', (0, 0, 0)),
...                Atom('X', (0, 0, 1))])
>>> dimer.set_positions([(1, 2, 3), (4, 5, 6.2)])
>>> w = nv.show_ase(dimer)
>>> w 

nglview.show_asetraj(ase_traj, **kwargs)

Show ase trajectory and structure file.

>>> import nglview as nv
>>> from ase.io.trajectory import Trajectory
>>> traj = Trajectory(nv.datafiles.ASE_Traj)
>>> view = nv.show_asetraj(traj)
>>> view.add_spacefill()
>>> view 

nglview.show_biopython(entity, **kwargs)

Show NGL widget with Biopython structural entity.

Takes a Structure, Model, Chain, Residue or Atom from Bio.PDB as its data input.

>>> import nglview as nv 
... from Bio.PDB import PDBParser
... parser = PDBParser()
... structure = parser.get_structure("protein", "protein.pdb")
... w = nv.show_biopython(structure[0]["A"])
... w

nglview.show_file(path, **kwargs)

Show any supported file format (e.g: .gro, .dx, …)

>>> import nglview as nv
... w = nv.show_file('my.dx')
... w 

nglview.show_htmd(mol, **kwargs)

Show NGL widget with HTMD Molecule.

Takes a Molecule object as its data input.

>>> import nglview as nv 
... from htmd import Molecule
... mol = Molecule(nv.datafiles.PDB)
... mol.filter('protein')
... w = nv.show_htmd(mol)
... w

nglview.show_iodata(obj, **kwargs)

Show iodata’s IOData (require ase package).

>>> import nglview as nv
>>> from iodata import IOData 
... obj = IOData.from_file('what.xyz')
... view = nv.show_iodata(obj)
... view

nglview.show_iotbx(mol, **kwargs)

>>> import iotbx.pdb
... x = iotbx.pdb.hierarchy.input('file.pdb')
... mol = x.construct_hierarchy()
... view = nglview.show_iotbx(hi)
... view 

nglview.show_mdanalysis(atomgroup, **kwargs)

Show NGL widget with MDAnalysis AtomGroup.

Can take either a Universe or AtomGroup as its data input.

>>> import nglview as nv 
... import MDAnalysis as mda
... u = mda.Universe(nv.datafiles.GRO, nv.datafiles.XTC)
... prot = u.select_atoms('protein')
... w = nv.show_mdanalysis(prot)
... w

nglview.show_mdtraj(mdtraj_trajectory, **kwargs)

Show mdtraj trajectory.

>>> import nglview as nv 
... import mdtraj as md
... t = md.load(nv.datafiles.XTC, top=nv.datafiles.GRO)
... w = nv.show_mdtraj(t)
... w

nglview.show_openbabel(obj, **kwargs)

Show openbabel’s Omol

>>> import nglview
>>> mol = openbabel.OBMol() 
... obConversion = openbabel.OBConversion() 
... obConversion.SetInFormat('xyz')
... obConversion.ReadFile(mol, 'what.xyz')
... nglview.show_openbabel(mol)

nglview.show_parmed(parmed_structure, **kwargs)

Show pytraj trajectory.

>>> import nglview as nv
>>> import parmed as pmd
>>> t = pmd.load_file(nv.datafiles.PDB)
>>> w = nv.show_parmed(t)
>>> w 

nglview.show_pdbid(pdbid, **kwargs)

Show PDB entry.

>>> import nglview as nv
>>> w = nv.show_pdbid("3pqr")
>>> w 

nglview.show_prody(obj, **kwargs)

>>> import nglview as nv 
... import prody
... structure = prody.parsePDB('what.pdb')
... ensemble = prody.parseDCD('what.dcd')
... ensemble.setAtoms(structure)
... nv.show_prody(ensemble)
... # nv.show_prody(structure)

nglview.show_psi4(obj, **kwargs)

Show Psi4’s Molecule.

>>> import nglview as nv
>>> import psi4 
... mol = psi4.geometry('xyz content here')
... view = nv.show_psi4(mol)
... view

nglview.show_pymatgen(struct, **kwargs)

Require ase package.

>>> import nglview as nv 
... import pymatgen as mg
... lattice = mg.Lattice.cubic(4.2)
... structure = mg.Structure(lattice, ["Cs", "Cl"],
                      [[0, 0, 0], [0.5, 0.5, 0.5]])
... view = nv.show_pymatgen(structure)
... view

nglview.show_pytraj(pytraj_trajectory, **kwargs)

Show pytraj trajectory.

>>> import nglview as nv
>>> import pytraj as pt
>>> t = pt.load(nv.datafiles.TRR, nv.datafiles.PDB)
>>> w = nv.show_pytraj(t)
>>> w 

nglview.show_qcelemental(obj, **kwargs)

Show QCElemental’s Molecule.

>>> import nglview as nv
>>> import qcelemental as qcel 
... mol = qcel.models.Molecule.from_data("He 0 0 0")
... view = nv.show_qcelemental(mol)
... view

nglview.show_rdkit(rdkit_mol, **kwargs)

Show rdkit’s Mol.

rdkit_mol : rdkit.Chem.rdchem.Mol kwargs : additional keyword argument If kwargs contains the “conf_id” key, this will be passed to the RDKit Chem.MolToXXXBlock function as the confId parameter. If the “conf_id” key is not provided, -1 will be used as confId. If kwargs contains the “fmt” key, this will be used to decide whether rdkit_mol should be visualized as a PDB block (fmt == “pdb”) or as a SDF block (fmt == “sdf”). If the “fmt” key is not provided, a simple heuristic is used: if the first atom contains PDB residue information, rdkit_mol is visualized as a PDB block, otherwise as a SDF block.

>>> import nglview as nv
>>> from rdkit import Chem 
... from rdkit.Chem import AllChem
... m = Chem.AddHs(Chem.MolFromSmiles('COc1ccc2[C@H](O)[C@@H](COc2c1)N3CCC(O)(CC3)c4ccc(F)cc4'))
... _ = AllChem.EmbedMultipleConfs(m, useExpTorsionAnglePrefs=True, useBasicKnowledge=True)
... view = nv.show_rdkit(m)
... view 

>>> # add component m2
>>> # create file-like object
>>> from nglview.show import StringIO
>>> m2 = Chem.AddHs(Chem.MolFromSmiles('N[C@H](C)C(=O)O')) 
... fh = StringIO(Chem.MolToPDBBlock(m2))
... view.add_component(fh, ext='pdb')

>>> # load as trajectory, need to have ParmEd
>>> view = nv.show_rdkit(m, parmed=True) 

nglview.show_rosetta(pose, **kwargs)

>>> from pyrosetta import pose_from_sequence, init
... init()
... pose = pose_from_sequence('AAAAAA')
... view = nglview.show_rosetta(pose)
... view 

nglview.show_schrodinger(mol, traj=None, **kwargs)

Show NGL widget with Schrodinger’s Structure

EXPERIMENTAL

>>> import nglview as nv 
... from schrodinger.structure import StructureReader
... for s in StructureReader(fn):
...    break
... w = nv.show_schrodinger(s)
... w

nglview.show_simpletraj(traj, **kwargs)

Show simpletraj trajectory and structure file.

>>> import nglview as nv
>>> traj = nv.SimpletrajTrajectory(nv.datafiles.XTC, nv.datafiles.GRO)
>>> view = nv.show_simpletraj(traj)
>>> view 

nglview.show_structure_file(path, **kwargs)

Show structure file. Allowed are text-based structure file formats that are by supported by NGL, including pdb, gro, mol2, sdf.

>>> import nglview as nv
>>> w = nv.show_structure_file(nv.datafiles.GRO)
>>> w 

nglview.show_text(text, **kwargs)

for development

nglview.show_url(url, **kwargs)

nglview.write_html(fp, views, frame_range=None)

EXPERIMENTAL. Likely will be changed.

Make html file to display a list of views. For further options, please check ipywidgets.embed module.

fp : str or file handle views : a DOMWidget view or a list of views. frame_range : None or a tuple of int

>>> import nglview
>>> view = nglview.show_pdbid('1tsu')
>>> view 
>>> nglview.write_html('index.html', [view]) 
>>> nglview.write_html('index.html', [view], frame_range=(0, 5)) 

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