I'm trying to use nglview to visualize some pymatgen structures in a jupyter lab notebook.
Simply using import nglview returns the following error:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[51], line 1
----> 1 import nglview
2 view = nglview.show_pdbid("3pqr") # load "3pqr" from RCSB PDB and display viewer widget
3 view
File ~/anaconda3/envs/py38tensorflow/lib/python3.8/site-packages/nglview/__init__.py:4
1 import warnings
3 # for doc
----> 4 from . import adaptor, datafiles, show, widget
5 from ._version import get_versions
6 from .adaptor import *
File ~/anaconda3/envs/py38tensorflow/lib/python3.8/site-packages/nglview/show.py:13
3 from . import datafiles
4 from .adaptor import (ASEStructure, ASETrajectory, BiopythonStructure,
5 FileStructure, HTMDTrajectory, IODataStructure,
6 IOTBXStructure, MDAnalysisTrajectory, MDTrajTrajectory,
(...)
11 RdkitStructure,
12 TextStructure)
---> 13 from .widget import NGLWidget
15 __all__ = [
16 'demo',
17 'show_pdbid',
(...)
40 'show_biopython',
41 ]
44 def show_pdbid(pdbid, **kwargs):
File ~/anaconda3/envs/py38tensorflow/lib/python3.8/site-packages/nglview/widget.py:19
15 from traitlets import (Bool, CaselessStrEnum, Dict, Instance, Int, Integer,
16 List, Unicode, observe, validate)
17 import traitlets
---> 19 from . import color, interpolate
20 from .adaptor import Structure, Trajectory
21 from .component import ComponentViewer
File ~/anaconda3/envs/py38tensorflow/lib/python3.8/site-packages/nglview/color.py:114
110 else:
111 raise ValueError(f"{obj} must be either list of list or string")
--> 114 ColormakerRegistry = _ColormakerRegistry()
File ~/anaconda3/envs/py38tensorflow/lib/python3.8/site-packages/nglview/base.py:10, in _singleton.<locals>.getinstance()
8 def getinstance():
9 if cls not in instances:
---> 10 instances[cls] = cls()
11 return instances[cls]
File ~/anaconda3/envs/py38tensorflow/lib/python3.8/site-packages/nglview/color.py:47, in _ColormakerRegistry.__init__(self, *args, **kwargs)
45 try:
46 get_ipython() # only display in notebook
---> 47 self._ipython_display_()
48 except NameError:
49 pass
File ~/anaconda3/envs/py38tensorflow/lib/python3.8/site-packages/nglview/color.py:54, in _ColormakerRegistry._ipython_display_(self, **kwargs)
52 if self._ready:
53 return
---> 54 super()._ipython_display_(**kwargs)
AttributeError: 'super' object has no attribute '_ipython_display_'
Moreover, I tried installing nglview-js-widgets and got the following but I already have nodejs installed:
Extension Installation Error
An error occurred installing
nglview-js-widgets.Error message:
Please install Node.js and npm before continuing installation. You may be able to install Node.js from your package manager, from conda, or directly from the Node.js website (https://nodejs.org).
