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bioexcel / biobb_vs

Biobb_vs is the Biobb module collection to perform virtual screening studies.
https://mmb.irbbarcelona.org/biobb/
Apache License 2.0
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Addition of "exhaustiveness" option for vina run #7

Closed PabloNA97 closed 8 months ago

PabloNA97 commented 8 months ago

The default value of exhaustiveness when running Autodock Vina is 8.

At least in some cases, using a lower value of exhaustiveness may lead to similarly good results while reducing substantially the computational effort. Thus it would be very interesting to have this parameter available at the Biobb level so it can be lowered when doing high-thoughput virtual screenings.

This option can be implemented similarly to the --cpu option that is already available.

You may search for --exhaustiveness in the Autodock Vina manual.

Thank you! :)

gbayarri commented 8 months ago

Hi @PabloNA97 which range can have this property? 0-10, 1-100?

Thanks!

PabloNA97 commented 8 months ago

From what I understand in the following manual, exhaustiveness controls the number of runs of the search algorithm: "...the number of runs is set by the exhaustiveness parameter..."

So I guess the answer would be 1 or greater than 1.

gbayarri commented 8 months ago

Hi @PabloNA97, I've implemented it and it will be added to the new release.

https://github.com/bioexcel/biobb_vs/blob/master/biobb_vs/vina/autodock_vina_run.py#L131

Best.

PabloNA97 commented 8 months ago

Thank you very much! :)