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RDKit

2D、3D结构之间的转换，操作详情见 RDKit_Doc；ToDo：复习化学后更新此页面。
懒人代码： RDKit.ipynb

结构文件

  • 1D(Smiles .smi)
  • 2D(MDL mol .mol)
  • 3D(sdf mol2)

获得1D/2D结构

MolFromXX

此外：SmilesMolSupplier(smi), SDMolSupplier(sdf)

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


m = Chem.MolFromSmarts('Cc1ccccc1')              ## 2D
_m = Chem.MolFromSmiles('C[C@H](O)c1ccccc1')     ## 2D
_m = Chem.MolFromPDBFile('pdb/1oky.pdb')         ## 3D
_m = Chem.MolFromFASTA('>aa\nTCGATCGATCGATCGA\n',flavor=7)   ## 2D & MMFFOptimize Fail
_m = Chem.MolFromSequence('KKVKKVKKV',flavor=1)              ## 2D & MMFFOptimize Fail



m = Chem.AddHs(m)                            ## 补全H        
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

MolFromSequence/MolFromFASTA 

        - flavor: (optional)
            - 0 Protein, L amino acids (default)
            - 1 Protein, D amino acids
            - 2 RNA, no cap
            - 3 RNA, 5' cap
            - 4 RNA, 3' cap
            - 5 RNA, both caps
            - 6 DNA, no cap
            - 7 DNA, 5' cap
            - 8 DNA, 3' cap
            - 9 DNA, both caps

1 2

MolToXX

与MolFromXX反一反

Chem.MolToSmiles(m)
Chem.MolToSmarts(m)
Chem.MolToFASTA(m)
Chem.MolToSequence(m)


Chem.Draw.MolToImage(m)

Edit

部分操作: 

m = Chem.Kekulize(m)                 ## 清除芳香环信息，但输出smile后再返回会恢复该信息

tt = Chem.MolFromSmiles('OC')
ss = Chem.MolFromSmarts('[$(NC(=O))]')
m = Chem.MolFromSmiles('CC(=O)N')
m = AllChem.ReplaceSubstructs(m,ss,tt)


m = Chem.MolFromSmiles('BrCCc1cncnc1C(=O)O')
core = Chem.MolFromSmiles('c1cncnc1')
m = Chem.ReplaceSidechains(m,core)   ## m = Chem.ReplaceCore(m,core)



m = Chem.MolFromSmiles('CC(=O)C=CC=C')
mw = Chem.RWMol(m)
mw.ReplaceAtom(4,Chem.Atom(7))
mw.AddAtom(Chem.Atom(6))
mw.AddBond(6,7,Chem.BondType.SINGLE)
mw.RemoveAtom(0)

参考

RDKit: http://www.rdkit.org/docs/GettingStartedInPython.html
RDKit: https://zhuanlan.zhihu.com/p/82497166