NAME
Chemistry::ContactMap::Polyhedra - Calculate contacts with the Voroni
Polyhedra method
VERSION
version 0.100890
SYNOPSIS
my $cmap = Chemistry::ContactMap::Polyhedra->new( structures => [ $mol1, $mol2 ] );
foreach my $contact ( @{ $cmap->contacts } ) {
# get the intervening atoms
my ($atom1, $atom2) = $contact->atoms;
say $_->name, $_->number for ($atom1, $atom2);
say $contact->length(), $contact->attr('area'), $contact->type();
}
DESCRIPTION
This class implements the calculation of inter-atom and inter-residue
non-covalent contacts between macromolecules using the Voronoi Polyhedra
Method.
It consumes the Chemistry::ContactMap interface, interacts seamlessly
with PerlMol, and uses Bio::Tools::Run::QCons, a Perl wrapper over
Tsai's QCons program.
ATTRIBUTES
structures
Two Chemistry::MacroMol objects whose contact information you want to
calculate. Required.
add_bonds_to_structures
A boolean value that sets whether to add the atom-atom contacts found
between the macromolecules for each atom pair, as a Chemistry::Bond
object of order one. It is set as 0 by default.
contacts
An array reference of Chemistry::Bond objects that represent the
non-covalent (order 0) bonds between atom-atom pairs that are found to
be interacting.
The contact type (Van der Waals, Ionic, Hydrogen bond or Hydrophobic),
the total contact area and the bond length are saved in the object.
See Chemistry::Bond for details on how to use the bond class.
residue_contacts
An array reference with residue-residue contact information. This data
structure is identical to that returned by Bio::Tools::Run::QCons, see
the docs there to find out how to extract the relevant information from
it.
atom_contacts
An array reference with atom-atom contact information. Identical to that
returned by Bio::Tools::Run::QCons. See its doc for more information.
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.