NGLView

jupyter notebook 中展示3D分子结构（交互式）。懒人代码： NGLView.ipynb

load mol

import nglview
from rdkit import Chem
from rdkit.Chem import AllChem

m = Chem.MolFromFASTA('>aa\nTCGA\n',flavor=7)

AllChem.EmbedMolecule(m, randomSeed=3)       ## 通过距离几何算法计算3D坐标
AllChem.MMFFOptimizeMolecule(m)              ## 力场优化

_ = AllChem.EmbedMultipleConfs(m, useExpTorsionAnglePrefs=True, useBasicKnowledge=True)
view = nglview.show_rdkit(m)
view

load pdb

import nglview

view = nglview.show_file('http://www.rcsb.org/pdb/files/1oky.pdb')  ## or local
view = nglview.show_pdbid('1oky')

view                   ## can rotate/zoom

参考

nglview: http://nglviewer.org/nglview/latest/api.html