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rdk / p2rank

P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.

Home Page:https://rdk.github.io/p2rank/

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Feature implementation not found: conserv

skodapetr opened this issue · comments

commented

There are several conservation features named:

  • conserv_cloud
  • conserv
  • conservationcloud
  • conservationcloudscaled
  • conservation

However, not all of then works, for conserv I got:

java.lang.IllegalStateException: Feature implementation not found: conserv

I do not see a difference between the features - is there a description somewhere?
As far as I know, there is also no recommendation of which feature should be used.

commented

Where are they named?

List of currently available conservation based features is:

  • conservation, conservationcloud, conservationcloudscaled
  • conserv_sas, conserv_atomic, conserv_cloud

You can see that in cz.siret.prank.features.api.FeatureRegistry. First triplet are original features by Lukas and are described in his Bc. thesis (https://is.cuni.cz/webapps/zzp/detail/189243/41539668). Second triplet is new cleaner implementation by me that serve also as an example of using Residue/SAS/Atomic features framework and converters.

There is no recommendation which to use. Comprehensive experiments have not been performed, although I think you might find some comparison and discussion in Lukas's Bc. thesis. It is not hard to compare their contribution on your development dataset, either by calculating feature importances or comparing them one-by-one. My expectation would be that the difference between them is not substantial. They all start with the same information but map it onto SAS points in slightly different ways. Personally I would use second triplet in combination with tuning conserv_cloud_radius parameter.

commented

@skodapetr, is the explanation sufficient?

commented

The aim of the question was to found out why there is a class
https://github.com/rdk/p2rank/blob/develop/src/main/groovy/cz/siret/prank/features/implementation/conservation/ConservRF.groovy
with conservatio name conserv that when used throws java.lang.IllegalStateException: Feature implementation not found: conserv.

I would expect to be able to get the information you mention in your respojnse from a comment in the code or documentation. As now I know, but other person may not ... but at least there is chance that they may find this issue.