NAME

Chemistry::File::PDB

SYNOPSIS

use Chemistry::File::PDB;

my $macro_mol = Chemistry::MacroMo->read("myfile.pdb");

DESCRIPTION

This module reads PDB files. The PDB file format is commonly used to describe proteins, particularly those stored in the Protein Data Bank (http://www.rcsb.org/pdb/). The current version of this module only reads the ATOM and HETATM records, ignoring everything else.

This module automatically registers the 'pdb' format with Chemistry::Mol, so that PDB files may be identified and read by Chemistry::Mol->read(). For autodetection purpuses, it assumes that files ending in .pdb or having a line matching /^(ATOM |HETATM)/ are PDB files.

The PDB reader is designed for generating Chemistry::MacroMol objects, but it can also create Chemistry::Mol objects by throwing some information away.

Properties

When reading the file, this PDB reades stores some of the information in the following places:

$domain->type

The residue type, such as "ARG".

$domain->name

The type and sequence number, such as "ARG114". The system doesn't deal with chains yet.

$atom->name

The PDB atom name, such as "CA".

$atom->attr("pdb/residue_name")

The name of the residue, as discussed above.

VERSION

0.15

SEE ALSO

Chemistry::MacroMol, Chemistry::Mol, http://www.perlmol.org/.

The PDB format description at http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html

AUTHOR

Ivan Tubert-Brohman <itub@cpan.org>