--output-cluster-poses option

ccsb-scripps / AutoDock-GPU

AutoDock for GPUs and other accelerators

https://ccsb.scripps.edu/autodock

GNU General Public License v2.0

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--output-cluster-poses option #259

Open fedeserral opened 3 months ago

fedeserral commented 3 months ago

Hi! I have a question. I used to use the '--output-cluster-poses' parameter, but recently, after downloading adgpu again, I realized that the program doesn't have this parameter.

Is that possible? Is there any other parameter that replaced this one?

Thanks!

diogomart commented 3 months ago

I don't recognize that option name. Might it be --only-cluster-leads in meeko's mk_export.py? https://github.com/forlilab/Meeko/blob/3748b68edc4b7a0ecee90009499052bfca0d8ce1/scripts/mk_export.py#L45

rwxayheee commented 3 months ago

Hi @fedeserral Seems like --output-cluster-poses is included in commit 3893dd2; the description is: --output-cluster-poses | Output up to a certain number of poses per cluster | 0 (all)\n But it's likely not in any of the releases (since this commit is newer?). If this is what you're looking for, maybe try compiling the program and see if this option is recognized :>

fedeserral commented 3 months ago

Is there any option that allows obtaining one pose per cluster?

Thanks!

rwxayheee commented 3 months ago

hi @fedeserral Not 100% sure about the details but according to the description in https://github.com/ccsb-scripps/AutoDock-GPU/blob/f5cf6ffdd0c5b3f113d5cc424fabee51df04da7e/host/src/getparameters.cpp#L1780-L1783 --output-cluster-poses 1 might be able to output 1 pose per cluster. Let us know if it works as expected

atillack commented 3 months ago

@fedeserral I added --output-cluster-poses in PR #208 which is newer than the last release. We will create a new release soon as there's a ton more new things ;-)

For now, I would recommend to use the current develop version. --output-cluster-poses has three possible options:

all: output all poses per cluster (the default behavior)
auto: use the contact analysis (which needs the receptor pdbqt listed in the grid file to be present to work) and output poses in a cluster which have R (reactive) or H (hydrogen-bond) interactions (reactive uses special atom types and modified pair-parameters as described in https://pubs.acs.org/doi/abs/10.1021/acs.jcim.3c00832)
number >0: output up to this many poses per cluster

fedeserral commented 3 months ago

Hello! Thank you for all the responses, I'm going to review all the comments you made. I'll take them into account.

Thank you very much!