Comments (3)
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.
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@skodapetr, is the explanation sufficient?
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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.
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Related Issues (20)
- Does p2rank require git ? HOT 1
- Add README section about running dockerized version
- Any idea why there is a difference?
- Java options unrecognized by OpenJDK 15 HOT 1
- Make p2rank behave more like a standard unix program by default (wrt output location and working directory) HOT 2
- Add probability to output *_predictions.csv file HOT 1
- Add README section abut P2Rank framework
- Extend and reorganize documentation
- Bug in -conservation_dirs argument parsing HOT 2
- Output directory parameter `-o` is sometimes ignored. HOT 1
- Building on WSL failing HOT 2
- easy way to get features HOT 2
- Issue with loading mmCIF files created in PyMOL HOT 3
- Out of memory error HOT 1
- installation not clear? HOT 12
- dataset-joined pdb_residues file doesn`t match with fasta sequence
- File path in *.ds file HOT 3
- [SUGGESTION] Release Binary Should Log To STDERR instead of to install directory HOT 1
- Dataset contains invalid files HOT 2
- No SLF4J providers were found! HOT 5
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