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I have edited the molecule as I wanted. Now I have to export it. But mol blocks always look 2D. So my molecules become 2D. I want to get a 3D structure. Does anyone know the solution? (look at the image for the screenshot)

enter image description here

betelgeuse
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Aykut Elmas
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  • Please provide enough code so others can better understand or reproduce the problem. – MD. RAKIB HASAN Dec 21 '21 at 06:36
  • I found the solution. I added AllChem.EmbedMolecule(m4, useRandomCoords=True , randomSeed=0xf00d) random coords commmand and embed function returned 0. Problem was the molecule. It is so big. Thank you for your effort my friend – Aykut Elmas Jan 05 '22 at 14:45

1 Answers1

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No issues with the code as below (version 2021.03.3):

m_smiles = 'c1ccccc1'
mol = Chem.MolFromSmiles(m_smiles)
mol = Chem.AddHs(mol)

AllChem.EmbedMolecule(mol, randomSeed=0xf00d)
print(Chem.MolToMolBlock(mol))

...


     RDKit          3D

 12 12  0  0  0  0  0  0  0  0999 V2000
   -0.2995   -1.3510    0.0141 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3055   -0.4032    0.0428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0307    0.9497    0.0294 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3037    1.3426   -0.0142 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2985    0.3934   -0.0425 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0206   -0.9630   -0.0291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5031   -2.4015    0.0241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3381   -0.7237    0.0766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8299    1.6790    0.0523 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5056    2.4116   -0.0242 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3290    0.7220   -0.0763 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8494   -1.6559   -0.0530 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  1  1  0
  1  7  1  0
  2  8  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
  6 12  1  0
M  END

Some things to check:

Check if the embed function returns a non-zero exit status, it is possible that the function failed to embed your molecule

result = AllChem.EmbedMolecule(mol, randomSeed=0xf00d)
assert result != 0

Check if the conformer is marked as 3D

result = AllChem.EmbedMolecule(mol, randomSeed=0xf00d)
c = mol.GetConformer()
print(c.Is3D())
...
True

Print the coordinates of the conformer

result = AllChem.EmbedMolecule(mol, randomSeed=0xf00d)
c = mol.GetConformer()
print(c.GetPositions())
...
[[-0.29949394 -1.35098866  0.01410225]
 [-1.30551208 -0.40318505  0.04275071]
 [-1.03072469  0.949724    0.02942649]
 [ 0.30371624  1.34255959 -0.01420523]
 [ 1.29846541  0.39342702 -0.04249222]
 [ 1.02064112 -0.96295912 -0.02906111]
 [-0.50308026 -2.40153594  0.0241313 ]
 [-2.33811252 -0.72370675  0.07656442]
 [-1.82994742  1.67895926  0.0522682 ]
 [ 0.50563305  2.41164485 -0.02424598]
 [ 2.32904788  0.72199377 -0.07627234]
 [ 1.8493672  -1.65593298 -0.05296649]]
Oliver Scott
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  • Thank you for your answer my friend. My embed function returns -1 I think it is the problem. May the problem comes from my SMILES string? Because at the image above begining of the string is SMILES but then continues as SMARTS string. If this is not the problem, what it may be? – Aykut Elmas Dec 14 '21 at 11:59
  • Can you share the SMILES string? – Oliver Scott Dec 14 '21 at 12:07
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    I found the solution. I added AllChem.EmbedMolecule(m4, useRandomCoords=True , randomSeed=0xf00d) random coords commmand and embed function returned 0. Problem was the molecule. It is so big. Thank you for your effort my friend. – Aykut Elmas Dec 14 '21 at 14:23