NAME

Chemistry::File::PDB

SYNOPSIS

use Chemistry::File::PDB 'pdb_read';

my $macro_mol = pdb_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 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_mol().

The PDB reader returns a Chemistry::MacroMol object, by default, but the user is free to give any object to the pdb_read subroutine, as long as it implements the same interface as Chemistry::Mol.

FUNCTIONS

$my_mol = pdb_read($fname, option => value...)

Returns a Chemistry::MacroMol object (by default) from the specified PDB file. The only option so far is mol => $my_mol, which would use a previously created object instead of creating a new MacroMol object. The object should be a Chemistry::Mol object or a derived class.

is_pdb($fname)

Returns true if the specified file is a PDB file. The test is not incredibly smart; it assumes that a file is a PDB if the name ends with .pdb or if it has any line beginning with "ATOM ".

SEE ALSO

Chemistry::MacroMol, Chemistry::Mol

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>