问题

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from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import AllChem
AllChem.SetPreferCoordGen(True)
from rdkit.Chem import rdmolops

mol = Chem.MolFromSmiles('C=C(S)C(N)(O)C')
mol

structures = Chem.FindAllSubgraphsOfLengthN(mol,4)
structures
print(structures[1])

structures[0]

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。

from rdkit import Chem
from rdkit.Chem import rdDepictor
rdDepictor.SetPreferCoordGen(True)
from rdkit.Chem.Draw import IPythonConsole
IPythonConsole.drawOptions.addBondIndices = True

mol = Chem.MolFromSmiles('C=C(S)C(N)(O)C')
mol

[![enter image description here][1]][1]

threebonds = Chem.FindAllSubgraphsOfLengthN(mol, 3)

for n in threebonds:
    print(list(n))

Output:

[0, 2, 5]
[0, 2, 4]
[0, 2, 3]
[0, 2, 1]
[1, 2, 5]
[1, 2, 4]
[1, 2, 3]
[2, 5, 4]
[2, 5, 3]
[2, 4, 3]
[3, 5, 4]


[1]: https://i.stack.imgur.com/qdXBf.png


<details>
<summary>英文:</summary>

You have to convert to `list()`.

And since `FindAllSubgraphsOfLengthN` returns bonds and not atoms, you have to look for three bonds.

    from rdkit import Chem
    from rdkit.Chem import rdDepictor
    rdDepictor.SetPreferCoordGen(True)
    from rdkit.Chem.Draw import IPythonConsole
    IPythonConsole.drawOptions.addBondIndices = True
    
    mol = Chem.MolFromSmiles(&#39;C=C(S)C(N)(O)C&#39;)
    mol

[![enter image description here][1]][1]

    threebonds = Chem.FindAllSubgraphsOfLengthN(mol, 3)
    
    for n in threebonds:
        print(list(n))

Output:

    [0, 2, 5]
    [0, 2, 4]
    [0, 2, 3]
    [0, 2, 1]
    [1, 2, 5]
    [1, 2, 4]
    [1, 2, 3]
    [2, 5, 4]
    [2, 5, 3]
    [2, 4, 3]
    [3, 5, 4]


  [1]: https://i.stack.imgur.com/qdXBf.png

</details>



# 答案2
**得分**: 0

以下是代码部分的翻译：

```python
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。

from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import AllChem
AllChem.SetPreferCoordGen(True)
from rdkit.Chem import rdmolops
import csv

mol = Chem.MolFromSmiles('C=C(S)C(N)(O)C')
mol

# 在分子中查找长度为3的所有子图
# 子图具有分支
subgraphs = Chem.FindAllSubgraphsOfLengthN(mol, 3)

# 路径没有分支
# subgraphs = Chem.FindAllPathsOfLengthN(mol, 3)
print(len(subgraphs))

# 打印每个子图的连接SMILES
for subgraph in subgraphs:
    # 将子图作为新的分子对象获取
    sub_mol = Chem.PathToSubmol(mol, subgraph)
    # 生成子图的连接SMILES字符串
    subgraph_smiles = Chem.MolToSmiles(sub_mol, kekuleSmiles=True)
    print(subgraph_smiles)

输出
11
C=CCC
C=CCO
C=CCN
C=C(C)S
CCCS
OCCS
NCCS
CC(C)O
CC(C)N
CC(N)O
CC(N)O

from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import AllChem
AllChem.SetPreferCoordGen(True)
from rdkit.Chem import rdmolops
import csv
mol = Chem.MolFromSmiles('C=C(S)C(N)(O)C')
mol
# Find all subgraphs of length 3 in the molecule
#Subgraphs have branching
subgraphs = Chem.FindAllSubgraphsOfLengthN(mol, 3)
#Paths is no branching
#subgraphs = Chem.FindAllPathsOfLengthN(mol, 3)
print(len(subgraphs))
# Print out the connected SMILES for each subgraph
for subgraph in subgraphs:
# Get the subgraph as a new molecule object
sub_mol = Chem.PathToSubmol(mol, subgraph)
# Generate the connected SMILES string for the subgraph
subgraph_smiles = Chem.MolToSmiles(sub_mol, kekuleSmiles=True)
print(subgraph_smiles)
Output
11
C=CCC
C=CCO
C=CCN
C=C(C)S
CCCS
OCCS
NCCS
CC(C)O
CC(C)N
CC(N)O
CC(N)O