electroshape is not printing the similarity score

[Scott Bembenek]

I'm using the command line version of ODDT to calculate the electroshape score as:

oddt_cli database.sdf --similarity electroshape --cutoff 0.8 --query query.sdf -O scored.sdf

And while it seems to work correctly, it does not print out the actual similarity score. 

please advise.

Scott

[Maciek Wójcikowski]

Hi Scott,

Unfortunately printing of the similarities was never a feature, since the CLI was intended to be used for large datasets. To get them you'd have to create a short script to print all of them in a loop. Here is a simplistic example on how it should look like https://oddt.readthedocs.io/en/latest/index.html?highlight=api#molecular-shape-comparison

results = []
query_shape = usr(query)
for mol in database: 
    mol_shape = usr(mol)
    similarity = usr_similarity(query_shape, mol_shape)
    if similarity > 0.7: 
        results.append(mol)
        print(similarity)

Let me know if that works for you.

Best,

Maciej

----

Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

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