Accessing output of RDKIT Chem.FindAllSubgraphsOfLengthN(mol,n)

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英文:

Accessing output of RDKIT Chem.FindAllSubgraphsOfLengthN(mol,n)

问题

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英文:

I am attempting to use RDKIT Chem.FindAllSubgraphsOfLengthN(mol,n) function but am unable to callout the information from using this function. It runs, but I am unable to obtain the substructures.

Does anyone have suggestions on successfully calling out the information from the output of this function after it runs?

I am expecting an output, either in tuple or string form, that lists all substructures with Length N atoms. In my explicit case, I am looking for 4 atoms. Attached is code I have run with also listing the output errors.

  1. from rdkit import Chem
  2. from rdkit.Chem import Draw
  3. from rdkit.Chem.Draw import IPythonConsole
  4. from rdkit.Chem import AllChem
  5. AllChem.SetPreferCoordGen(True)
  6. from rdkit.Chem import rdmolops
  8. mol = Chem.MolFromSmiles('C=C(S)C(N)(O)C')
  9. mol
  1. structures = Chem.FindAllSubgraphsOfLengthN(mol,4)
  2. structures
  3. print(structures[1])

Output:
<rdkit.rdBase._vectint object at 0x0000024C16BBA2E0>

  1. structures[0]

Output:
<rdkit.rdBase._vectint at 0x24c16ba62e0>

答案1

得分: 1

你必须转换为list()。

而且，由于FindAllSubgraphsOfLengthN返回的是键而不是原子，所以你需要寻找三个键。

  1. from rdkit import Chem
  2. from rdkit.Chem import rdDepictor
  3. rdDepictor.SetPreferCoordGen(True)
  4. from rdkit.Chem.Draw import IPythonConsole
  5. IPythonConsole.drawOptions.addBondIndices = True
  7. mol = Chem.MolFromSmiles('C=C(S)C(N)(O)C')
  8. mol
  10. [![enter image description here][1]][1]
  12. threebonds = Chem.FindAllSubgraphsOfLengthN(mol, 3)
  14. for n in threebonds:
  15.     print(list(n))
  17. Output:
  19. [0, 2, 5]
  20. [0, 2, 4]
  21. [0, 2, 3]
  22. [0, 2, 1]
  23. [1, 2, 5]
  24. [1, 2, 4]
  25. [1, 2, 3]
  26. [2, 5, 4]
  27. [2, 5, 3]
  28. [2, 4, 3]
  29. [3, 5, 4]
  32. [1]: https://i.stack.imgur.com/qdXBf.png
  35. <details>
  36. <summary>英文:</summary>
  38. You have to convert to `list()`.
  40. And since `FindAllSubgraphsOfLengthN` returns bonds and not atoms, you have to look for three bonds.
  42.     from rdkit import Chem
  43.     from rdkit.Chem import rdDepictor
  44.     rdDepictor.SetPreferCoordGen(True)
  45.     from rdkit.Chem.Draw import IPythonConsole
  46.     IPythonConsole.drawOptions.addBondIndices = True
  47.     
  48.     mol = Chem.MolFromSmiles(&#39;C=C(S)C(N)(O)C&#39;)
  49.     mol
  51. [![enter image description here][1]][1]
  53.     threebonds = Chem.FindAllSubgraphsOfLengthN(mol, 3)
  54.     
  55.     for n in threebonds:
  56.         print(list(n))
  58. Output:
  60.     [0, 2, 5]
  61.     [0, 2, 4]
  62.     [0, 2, 3]
  63.     [0, 2, 1]
  64.     [1, 2, 5]
  65.     [1, 2, 4]
  66.     [1, 2, 3]
  67.     [2, 5, 4]
  68.     [2, 5, 3]
  69.     [2, 4, 3]
  70.     [3, 5, 4]
  73.   [1]: https://i.stack.imgur.com/qdXBf.png
  75. </details>
  79. # 答案2
  80. **得分**: 0
  82. 以下是代码部分的翻译：
  84. ```python
  85. 我的一个团队成员成功生成了一段代码，用于访问路径或子图信息。为了澄清，路径不具有分支，而子图则具有分支。
  87. from rdkit import Chem
  88. from rdkit.Chem import Draw
  89. from rdkit.Chem.Draw import IPythonConsole
  90. from rdkit.Chem import AllChem
  91. AllChem.SetPreferCoordGen(True)
  92. from rdkit.Chem import rdmolops
  93. import csv
  95. mol = Chem.MolFromSmiles('C=C(S)C(N)(O)C')
  96. mol
  98. # 在分子中查找长度为3的所有子图
  99. # 子图具有分支
  100. subgraphs = Chem.FindAllSubgraphsOfLengthN(mol, 3)
  102. # 路径没有分支
  103. # subgraphs = Chem.FindAllPathsOfLengthN(mol, 3)
  104. print(len(subgraphs))
  106. # 打印每个子图的连接SMILES
  107. for subgraph in subgraphs:
  108.     # 将子图作为新的分子对象获取
  109.     sub_mol = Chem.PathToSubmol(mol, subgraph)
  110.     # 生成子图的连接SMILES字符串
  111.     subgraph_smiles = Chem.MolToSmiles(sub_mol, kekuleSmiles=True)
  112.     print(subgraph_smiles)
  114. 输出
  115. 11
  116. C=CCC
  117. C=CCO
  118. C=CCN
  119. C=C(C)S
  120. CCCS
  121. OCCS
  122. NCCS
  123. CC(C)O
  124. CC(C)N
  125. CC(N)O
  126. CC(N)O
英文:

A team member of mine was able to generate a code as to access the paths or subgraphs information. To clarify, paths don't have branching where subgraphs do.

  1. from rdkit import Chem
  2. from rdkit.Chem import Draw
  3. from rdkit.Chem.Draw import IPythonConsole
  4. from rdkit.Chem import AllChem
  5. AllChem.SetPreferCoordGen(True)
  6. from rdkit.Chem import rdmolops
  7. import csv
  8. mol = Chem.MolFromSmiles(&#39;C=C(S)C(N)(O)C&#39;)
  9. mol
  10. # Find all subgraphs of length 3 in the molecule
  11. #Subgraphs have branching
  12. subgraphs = Chem.FindAllSubgraphsOfLengthN(mol, 3)
  13. #Paths is no branching
  14. #subgraphs = Chem.FindAllPathsOfLengthN(mol, 3)
  15. print(len(subgraphs))
  16. # Print out the connected SMILES for each subgraph
  17. for subgraph in subgraphs:
  18. # Get the subgraph as a new molecule object
  19. sub_mol = Chem.PathToSubmol(mol, subgraph)
  20. # Generate the connected SMILES string for the subgraph
  21. subgraph_smiles = Chem.MolToSmiles(sub_mol, kekuleSmiles=True)
  22. print(subgraph_smiles)
  23. Output
  24. 11
  25. C=CCC
  26. C=CCO
  27. C=CCN
  28. C=C(C)S
  29. CCCS
  30. OCCS
  31. NCCS
  32. CC(C)O
  33. CC(C)N
  34. CC(N)O
  35. CC(N)O

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  • 本文由 发表于 2023年4月20日 00:41:40
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  • cheminformatics
  • chemistry
  • python
  • rdkit
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