CODEWITHSUNDEEP
python-3.xrdkitopenbabel
ista120
ista120

Reputation: 111

How can I generate a molecular image from the molecular structure provided in MBL molfile format?

from rdkit import Chem
from rdkit.Chem import AllChem, Draw
import matplotlib.pyplot as plt  

molfile_string = """
1 0 0 0 0 0             999 V2000
0.0000  0.0000  0.0000 O  0  -1  0  0
1.0000  0.8144  0.0000 H  0  1  0  0
0.0000 -0.8144  0.0000 H  0  1  0  0
M END
"""
mol = Chem.MolFromMolBlock(molfile_string)

gives me below error:

[18:47:21] Cannot convert '1.0' to unsigned int on line 4

I want to know what's wrong in the format and what should be the correct format so that I can view the image with following lines:

AllChem.Compute2DCoords(mol)
image = Draw.MolToImage(mol, size=(300, 300), kekulize=False)
plt.imshow(image, interpolation='nearest')
plt.axis('off')  # Turn off axis labels
plt.show()

Upvotes: 2

Views: 161

Answers (1)

rapelpy
rapelpy

Reputation: 1869

Your are missing some parts of the molfile.

The MDL Molfileformat starts with three lines (first and third can be blank) followed by a counts line, an atom and a bond block.

See: Wikipedia

from rdkit import Chem

molfile_string = """                                                  # first line
     RDKit          2D                                                # second line
                                                                      # third line
  3  2  0  0  0  0  0  0  0  0999 V2000                               # counts line: 3 atoms 2 bonds
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0 # atom block
    1.2990    0.7500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2990    0.7500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0                                                          # bond block
  1  3  1  0
M  END
"""
mol = Chem.MolFromMolBlock(molfile_string, removeHs=False)
mol

enter image description here

Upvotes: 1

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