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energy_based_clustering and silentfile option

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energy_based_clustering and silentfile option
#1

I want to use energy_based_clustering to cluster structures from a silentfile. I run `source/bin/energy_based_clustering.linuxgccrelease @cluster_flag`.

Here cluster_flag is:

-in:file:silent ../global_output/decoys_P_renumbered_0001_traj.out
-in:file:fullatom
-cluster:energy_based_clustering:limit_structures_per_cluster 0
-cluster:energy_based_clustering:cluster_radius 2.0
-cluster:energy_based_clustering:cluster_by bb_cartesian
-cluster:energy_based_clustering:alternative_score_file input_score.txt
-cluster:energy_based_clustering:silent_output

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input_score.txt is the score file I prepared:

$ head input_score.txt

P_renumbered_0001_003_00000001 -5825.852
P_renumbered_0001_002_00000001 1107.339
P_renumbered_0001_001_00000001 8082.621
P_renumbered_0001_003_00000002 -5853.732
P_renumbered_0001_001_00000002 8072.546
P_renumbered_0001_002_00000002 1101.128
P_renumbered_0001_003_00000003 -5841.483

...

-----------------------------------------------------------------------------

When I run the clustering, I receive error message:

[FILE]: src/protocols/energy_based_clustering/EnergyBasedClusteringProtocol.cc
[LINE]: 1670
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to assign loaded score to pose 'P_renumbered_0001_001_00000001_../global_output/decoys_P_renumbered_0001_traj.out'. Please check your score file.

-----------------------------------------------------------------------------

I would like to get help on how to solve this error. Thanks

 

 

 
 
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Wed, 2024-06-05 16:28
weiw26

First off, the separate score file is only needed if you want to sort based on something other than the total energies (e.g. by interface energy). If you're just using the full complext total score, you should be able to omit the scorefile altogether, and rely on Rosetta computing the total score.

But if you still want to use the separate score file, the core issue you're running into is that the descriptor string in the score file is not just the tag of the structure in the silent file. Things are set up such that you can run the application across multiple silent files. As such, the label in the score file is a combination of the pose tag and the input filename.

I'll admit that's a little unwieldy if you have a relative path to the file like you do here, but things were put together assuming you'll be reading the silent file(s) in the same directory you're running things in.

Thu, 2024-06-06 08:11
rmoretti