rdkit 力场优化UFFOptimizeMolecule、MMFFOptimizeMolecule

rdkit 力场优化UFFOptimizeMolecule、MMFFOptimizeMolecule

参考：https://zhuanlan.zhihu.com/p/82588052
https://projects.volkamerlab.org/teachopencadd/talktorials/T010_binding_site_comparison.html

EmbedMolecule模块将二维分子图转化为三维分子坐标

原始没优化前分子

from rdkit import Chem
from rdkit.Chem import Draw, AllChem

smiles = Chem.MolFromSmiles("CN1CCN(Cc2ccc(cc2)C(=O)Nc2ccc(C)c(Nc3nccc(n3)-c3cccnc3)c2)CC1")
smiles
1
2
3
4
5

molecule = Chem.AddHs(smiles)  ##加氢
molecule
1
2

##保存3D分子生成 sdf


SDFfile1 = Chem.SDWriter('UFFOptimizeMolecule.sdf') 
SDFfile1.write(molecule)

SDFfile1.close()
1
2
3
4
5
6
7