NAME
Chemistry::Clusterer - Cluster spatial variants of macromolecular
structures
VERSION
version 0.100870
SYNOPSIS
use Chemistry::Clusterer;
my $clusterer = Chemistry::Clusterer->new(
structures => \@structures,
grouping_method => { number => 10 },
);
say $clusterer->error;
say $clusterer->cluster_count;
foreach my $cluster ( @{ $clusterer->clusters } ) {
say $cluster->size;
say $cluster->centroid->coords;
}
DESCRIPTION
This module provides a means for clustering or grouping a collection of
structural/spacial variants of a macromolecular structure according to
their RMSD values. This helps reduce the complexity of the collection by
grouping together similar representations into clusters, which can be
then analyzed as a single entity.
The CPU intensive parts are done with the C Clustering library, by means
of the Algorithm::Cluster module.
ATTRIBUTES
structures
An array reference of Chemistry::Clusterer::Structure entities. You can
also provide an array reference of opened filehandles of each of the
structures, or a string with the contents of the PDB file of each
structure.
Required.
grouping_method
The criteria with which to choose the desired number of clusters.
Default is "distance => 5".
options are:
distance
grouping_method => { distance => $d }
The final number of clusters will be chosen so that the average distance
between the centroids of the members of a single cluster is less or
equal to $d Angstroms. In other words, it's the average radius of the
sphere that contains all centroids of each cluster.
number
grouping_method => { number => $n }
Simply select the exact number of clusters you want.
coordinates_from
Defines what subset of atoms to use for the clustering.
It's a Chemistry::Clusterer::CoordExtractor object that extracts the
coordinates of the desired atoms from each of the structures.
By default it uses coordinates from alpha carbons, using
Chemistry::Clusterer::CoordExtractor::AtomType.
If you wanted to also use the coordinates of, say, the rest of carbon
atoms, you'd say:
coordinates_from => { atom_type => ['CA', 'C'] };
The key of the hash reference selects which coordinate extractor to use,
in this case "AtomType". The value is an array reference with the atom
types to extract their coordinates from.
Other extractor classes to use are
Chemistry::Clusterer::CoordExtractor::Chain, which selects all atoms of
a given chain, and Chemistry::Clusterer::CoordExtractor::All, which
simply uses all atoms.
For instance:
coordinates_from => { chain => ['A', 'B'] };
coordinates_from => 'all'; # same as { all => [ undef ] };
clusters
An array reference of Chemistry::Clusterer::Cluster entities, each
representing a single cluster. It is lazily computed upon request.
METHODS
structure_count
Returns the total number of structures used for clustering.
cluster_count
The total number of clusters
error
The total clustering error
AUTHOR
Bruno Vecchi <vecchi.b gmail.com>
COPYRIGHT AND LICENSE
This software is copyright (c) 2010 by Bruno Vecchi.
This is free software; you can redistribute it and/or modify it under
the same terms as the Perl 5 programming language system itself.