--output-cluster-poses option

[fedeserral]

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]

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]

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]

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

Thanks!

[rwxayheee]

hi @fedeserral
Not 100% sure about the details but according to the description in

AutoDock-GPU/host/src/getparameters.cpp

Lines 1780 to 1783 in f5cf6ff

	// Argument: output up to a certain number of poses per cluster
	// -1 ... auto based on contact analysis
	// 0 ... all poses per cluster are output (default)
	// >0 ... up to this many per cluster

--output-cluster-poses 1 might be able to output 1 pose per cluster. Let us know if it works as expected

[atillack]

@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]

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!