Re: [rDock-list-def] extract score from rescoring without writing a sd file

[Sergio R. C. <sru...@gm...>]

Dear Jose Manuel,

Sorry for the delay.
I am afraid there is not any trivial solution to what you are asking.
rDock needs an output file to write the results on-the-fly.
A workaround that I would suggest you is to run "sdreport -t OUTPUTFILE.sd
> OUTPUTFILE_scores.txt" just after each job is finished to save all the
different scores and then remove "OUTPUTFILE.sd".
The function of the -t argument for rbdock is to control how many runs for
each ligand are performed and which of the docking poses generated are
written depending on the score, but it is not related to the creation or
not of the output file independently from the scoring.
Best,

Sergio


2015-12-18 17:26 GMT+01:00 Jose Manuel Gally <
jos...@un...>:

> Hi,
>
> I rescore poses using rbdock with the score.prm protocol as routine on a
> single molecule within a script.
>
> I would like to avoid writing output files and just extract the SCORE
> and SCORE.INTER properties directly from the STDOUT.
> However, when I remove the -o argument, I cannot access the scores at
> all and something like -o /dev/stdout returns an error since the
> programme still wants to write a file.
>
> Is there a way to achieve this without modifying the source code (I
> don't know much about C++...!)?
> If not, could you kindly tell me what I should change in the rbdock.cxx
> to make it work?
>
> I also tried to use the -T argument but could not find the scores among
> the displayed info. Did I miss something?
>
> Thank you for your help!
>
> Cheers,
> Jose Manuel
>
> Supplementary information:
> OS: Centos 6x
> tested system: 1g9v from Selfdocking dataset found at
> http://www.ysbl.york.ac.uk/rDock/test_data/Selfdock_Test.tar.gz
> tested commands:
> rbdock -i 1g9v_output.sd -r 1g9v.prm -p score.prm -n 1 -T 3 -o
> 1g9v_output_score > 1g9v_output_score.log
> rbdock -i 1g9v_output.sd -r 1g9v.prm -p score.prm -n 1 -T 3 >
> 1g9v_output_score_noOutput.log
> I can send the log files directly if requested.
>
>
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