Metadata

Author: Andrew Watkins

Added to documentation: Feb 2018

Code and Demo

The central code for the rna_score application is in apps/public/rna/util/rna_score.cc

Application purpose

This code is intended to cluster silent files (ideally, those containing RNA) in a manner that's fairly robust to features that the original "SWA legacy clusterer" could not have anticipated but that are common today (for example, noncanonical/chemically modified nucleic acids).

Input Files

Required files

A silent file(s) containing RNA to cluster

Options

-cluster:radius                A radius in Angstroms separating cluster centers
-cluster:score_diff_cut        What score cutoff (from the minimum score)  of the silent file(s)
                               should be clustered? Defaults to clustering everything (well, within
                               1000000 units)
-cluster:auto_tune             As clustering proceeds, increase radius from 0.1 to 50.0A (default false)

Sample command line

rna_cluster –in:file:silent swm_rebuild_full_model.out –nstruct 100 –cluster:radius 2.0 –out:file:silent TOP_ENERGY_CLUSTERS/top_energy_clusters.rna_cluster.out -in:file:native t_loop_modified_fixed_NATIVE_1ehz.pdb

Documentation for rna_cluster