Include filtering by PLIF in get_sdf_from_easydock

[DrrDom]

This may be a convenient option to retrieve structures from a database based on filtering by PLIF or PLIF similarity. Currently this would require to get molecule ids with easydock_plif first and afterwards passing them to get_sdf_from_easydock.

[Feriolet]

Hi! I would like to ask if this is still in WIP. I tried to use the documentation from the PLIF analysis, but they does not seem to work. The code I am referring to is highlighted below:

3. Calculate similarity for docked molecules:

easydock_plif -i output.db -p protein.pdb -o similarity.txt \
    --ref_plif ala31.a.hydrophobic asp86.a.cationic -c 4

4. Extract top scoring by PLIF similarity:

get_sdf_from_easydock -i output.db -o output.sdf \
    --fields plif_similarity \
    --add_sql 'plif_similarity > 0.8'

seems that the easydock_plif saves the similarity in the output.txt under the plif_sim column, and they are not updated in the output.db as I expected.

[DrrDom]

Thank you for reporting!

This is a non-implemented feature which sneaked to the docs. I updated the documentation to provide a correct example.
Molecules should be selected externally from a text output file and passed to get_sdf_from_easydock script. This is less convenient, therefore, we will implement this feature in future versions.

By design, similarity will not be stored in DB, because the user may use different contacts to calculate PLIF similarity for the same database. We store only found contacts. Therefore, it is expected that similarity will be calculated on-the-fly when get_sdf_from_easydock is invoked with a specific argument.