Question

我正在尝试关注this，但它失败了

import MDAnalysis as mda
import nglview as nv
from nglview.datafiles import PDB, XTC

u = mda.Universe(PDB, XTC)

protein = u.select_atoms('protein')

当我尝试做的时候：

w = nv.show_mdanalysis(protein)
w

我明白了：

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-2-499e28f0ffd3> in <module>()
----> 1 w = nv.show_mdanalysis(protein)
      2 w

~/anaconda3/lib/python3.6/site-packages/nglview-0.4-py3.5.egg/nglview/__init__.py in show_mdanalysis(atomgroup, **kwargs)
    118     '''
    119     structure_trajectory = MDAnalysisTrajectory(atomgroup)
--> 120     return NGLWidget(structure_trajectory, **kwargs)
    121 
    122 

~/anaconda3/lib/python3.6/site-packages/nglview-0.4-py3.5.egg/nglview/__init__.py in __init__(self, structure, trajectory, representations, parameters, **kwargs)
    347         if parameters:
    348             self.parameters = parameters
--> 349         self.set_structure(structure)
    350         if trajectory:
    351             self.trajectory = trajectory

~/anaconda3/lib/python3.6/site-packages/nglview-0.4-py3.5.egg/nglview/__init__.py in set_structure(self, structure)
    372     def set_structure(self, structure):
    373         self.structure = {
--> 374             "data": structure.get_structure_string(),
    375             "ext": structure.ext,
    376             "params": structure.params

~/anaconda3/lib/python3.6/site-packages/nglview-0.4-py3.5.egg/nglview/__init__.py in get_structure_string(self)
    313                 "'MDAnalysisTrajectory' requires the 'MDAnalysis' package"
    314             )
--> 315         import cStringIO
    316         u = self.atomgroup.universe
    317         u.trajectory[0]

ModuleNotFoundError: No module named 'cStringIO'

Answer 1

我会尝试通过conda（和Anaconda distribution）获得干净的nglview安装：

尝试使用

卸载nglview

conda remove nglview

以防万一有一个旧版本。如果此conda删除失败，则说明该软件包可能是pip或easy_installed。尝试pip remove nglview。如果仍然不能解决问题，则必须查找已安装的nglview软件包，并使用rm手动将其删除，但是我不想在此处放置复制和粘贴说明，因为这需要仔细查看文件。

所有nglview痕迹均已删除后，请使用conda安装最新版本的nglview from the conda-forge channel：

conda install -c conda-forge nglview

如何在Jupyter笔记本中显示Protein Data Bank PDB？

1 个答案: