HackaMol::PdbRole - PdbRole of lazy attributes for HackaMol atoms
version 0.00_01
use Atom;
my $atom = Atom->new(Z=>6);
print $atom->$_ foreach ( qw( record_name serial occ bfact resname chain altloc resid iatom pdbid segid ) );
PdbRole provides atom attributes for PDB parsing. All attributes are 'rw' and lazy, so they will not contaminate the namespace unless called upon. The functionality of the PdbRole may be extended in the future. See HackaMolX::PDB for more information about parsing pdbs. name from PhysVec provide the attr for namd in the pdb (cols 13-16). symbol -> pdb element and charge -> pdb charge
pdb cols 1-6: ATOM|HETATM. default = 'HETATM'
pdb cols 7-11: index. default = 0
pdb cols 55-60: occupancy. range 0 to 1. default = 1.0 (all there)
pdb cols 61-66: temperature factor. see Willis and Pryor. default = 20.0
pdb col 17. is AHIS and BHIS above. default = ' '
pdb cols 18-20: residue name. defaults to 'ALA'
pdb cols 22. protein chain. default = 'AA'
pdb cols 23-26. residue index. PDB calls is resSeq, but resid is more familiar (to me). default = 64
pdb cols 27. see code comments or http://www.wwpdb.org/documentation/format23/sect9.html
a place to store which PDB it came from
a CHARMMish parameter that may not belong here. default = 'TIP3'
this is a place for the actual index. Segid does not have to start from 0 (cut and paste as above, etc).
http://www.pdb.org
Demian Riccardi <demianriccardi@gmail.com>
This software is copyright (c) 2013 by Demian Riccardi.
This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.
To install HackaMol, copy and paste the appropriate command in to your terminal.
cpanm
cpanm HackaMol
CPAN shell
perl -MCPAN -e shell install HackaMol
For more information on module installation, please visit the detailed CPAN module installation guide.