Hi I am using moleculeRecognize function to upload structures from images and I am attempting to convert the structures in .mol files. However every time I convert to .mol files the hydrogen atoms in the structures are not being accounted for. I was wondering if anyone has any way to overcome this.
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3$\begingroup$ Could you please include a sample image and the exact code you use? Paste the code in your question as text. $\endgroup$– MarcoBCommented Feb 9, 2022 at 21:31
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1 Answer
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Try this. Start with a suitable image. For example,
img = Image@MoleculePlot@Import@First@
FileNames["aspirin.mol", $InstallationDirectory, 6];
Show[img, ImageSize -> Small]
Now, apply MoleculeRecognize to the image and export the results as a .mol file with the IncludeHydrogens option, like this
Export["tmp.mol", MoleculeRecognize[img],
"MOL", IncludeHydrogens -> True];
Import[%, "Text"]
There is more to the .mol file than is shown above. Notice the 7 hydrogens at the end of the atom list.
