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Open Babel descriptor export in text?

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Open Babel descriptor export in text?

Kimmy Laugh
Hi,

I am quite new to open babel. I have some SDF files of thousands of molecules and I would like to calculate some of their descriptors. I saw that in openbabel, there are several descriptors, but how can export them in text?

Thank you all!

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Re: Open Babel descriptor export in text?

Geoff Hutchison
> I am quite new to open babel. I have some SDF files of thousands of molecules and I would like to calculate some of their descriptors.

It depends on what you want. For example:
https://open-babel.readthedocs.io/en/latest/Command-line_tools/Rosetta.html

obabel benzodiazepine.sdf.gz -otxt --title "" --append atoms -d

> The txt format outputs only the title but we set that to nothing and then append the result. The atoms descriptor counts the number of atoms after the -d option has removed the hydrogens.

https://open-babel.readthedocs.io/en/latest/Command-line_tools/Rosetta.html#calculate-tpsa

obabel -:CN2C(=O)N(C)C(=O)C1=C2N=CN1C -osmi --append TPSA

Gives a SMILES and then the TPSA descriptor. You can use —append to add various descriptors.

Personally, I’d write up a short Python script, but it can be done with the command-line tools as well.

Hope that helps,
-Geoff
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