energy_based_clustering.cc File Reference

Cluster a set of structures using an energy-biased cluster centre selection algorithm. More...

#include <devel/init.hh>
#include <protocols/energy_based_clustering/EnergyBasedClusteringProtocol.hh>
#include <basic/Tracer.hh>
#include <utility/excn/Exceptions.hh>
#include <cstdio>

Functions
int	main (int argc, char *argv[])
	Minimial main() function for energy_based_clustering application. Most of the heavy lifting is done by the protocols::energy_based_clustering::EnergyBasedClusteringProtocol class. More...

Variables
static basic::Tracer	TR ("apps.public.clustering.energy_based_clustering")

Detailed Description

Cluster a set of structures using an energy-biased cluster centre selection algorithm.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

This file started off as the bettercluster.cc pilot app in src/apps/pilot/vmullig/.

This uses a "cookie-cutter" based approach.  The basic algorithm is as follows:
    1.  Score all input structures, and store minimal information needed for clustering for each structure in an unclustered pool.
    2.  Select the lowest-energy structure in the pool, and transfer it from the pool into a new cluster.  This is now the centre of the new
    cluster.  Calculate the RMSD of every structure remaining in the unclustered pool to the new cluster centre.  (If necessary, consider
    circular permutations as well).  Transfer any structure with an RMSD below the threshold from the unclustered pool to the new cluster.
    3.  Repeat step 2 with the structures remaining in the unclustered pool, generating new clusters until no structures remain.

This algorithm has the advantage of exactness and non-stochasticity without requiring a full RMSD matrix of all structures to all structures.
It works well for very large datasets.

Original description: A better clustering algorithm for generating conformational libraries for explicit multistate design.

History: –File created 6 May 2013 by Vikram K. Mulligan, Baker Laboratory. –Modified 3 Jun 2013 to make Cartesian-based clustering much faster. (No more rebuilding poses). –Modified 5 Jun 2013 to allow clustering of backbone-cyclized peptides. –Modified 28 Aug 2013 to allow N-offset cyclic permutations to be clustered. (e.g. Offsets are incremented by 2 residues, or by 3 residues, or whatever.) –Modified 4 Sept 2013 to allow clustering of peptides with beta-amino acid residues: –check for beta residues based on first structure loaded (they must be consistent – DONE). –align CM atoms, if present (DONE). –update information that is stored for cartesian or dihedral clustering (DONE). –update PCA file output –> list of backbone dihedrals must include theta (DONE, though other apps must also be updated to READ these properly). –Modified 9 Oct 2013 to allow clustering of homooligomers (with swapping of oligomer subunits during RMSD calculation). TODO: –store jumps for PCA analysis –calculate RMSD for all possible permutations of homooligomer subunits and keep lowest –Modified 21 May 2014 to allow silent file output. –Modified 22 May 2014: –Added support for constraints files. –Added support for a user-defined list of additional atoms to use in RMSD calculation. –Modified 18 June 2014: –Took out all references to the Alglib library, because of the asenine Rosettacommons rules about third-party libraries. –Added a PCA function to the numeric library, and linked this to that. –Modified 11 Aug 2014: –Added an option to ignore entire chains in the RMSD calculation. –Added an option to skip PCA analysis. –Modified 21 Sept 2015: –Added an option to dump out only the first N clusters. –Modified 30 Jan 2017: –Added an option to filter out structures that aren't symmetric. –Modified 18 July 2017: –Converted to a true public application, added tests, and cleaned up implementation. Temporarily disabled PCA analysis.

Function Documentation

int main	(	int	argc,
		char *	argv[]
	)

Minimial main() function for energy_based_clustering application. Most of the heavy lifting is done by the protocols::energy_based_clustering::EnergyBasedClusteringProtocol class.

References utility::io::oc::cerr, basic::options::OptionKeys::cluster::energy_based_clustering::energy_based_clustering, devel::init(), options, register_options(), utility::excn::Exception::show(), and TR.

Variable Documentation

basic::Tracer TR("apps.public.clustering.energy_based_clustering")

static

Referenced by main().