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schrojunzhang / KarmaDock

https://www.nature.com/articles/s43588-023-00511-5
Apache License 2.0
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screening results poses #22

Closed CLG68 closed 6 months ago

CLG68 commented 6 months ago

Hi,

When I run the ex using pkd1, I get 3 poses per ligand.. ex:

BDB2695_pred_uncorrected.sdf BDB2695_pred_ff_corrected.sdf BDB2695_pred_align_corrected.sdf

Which one should be kept as the final pose? If there is only one of the 3 to consider, is there an argument that will prevent the other 2 to be saved? It would be more practical if only one pose would be saved, in the context of multi-million files are screened. A script could always get rid of the other 2. However, this would be done once the screen is completed so the size of the folder would already be huge.

Thanks for your help, Christian

CLG68 commented 6 months ago

I did not pay enough attention to the command line... I guess I just have to remove: --out_uncoorected --out_corrected

What is the advantage of keeping those files, are they useful for some applications?

I think the argument should be corrected from --out_uncoorected to --out_uncorrected