NAME

HackaMol::Roles::ReadPdbRole - Read files with molecular information

VERSION

version 0.023

SYNOPSIS

my @atoms = HackaMol->new
                    ->read_pdb_atoms("some.pdb");

DESCRIPTION

The HackaMol::Roles::ReadPdbRole provides read_pdb_atoms reading protein database files.

METHODS

read_pdb_atoms

One argument: the filename Returns a list of HackaMol::Atom objects.

Additional information

According to the PDB specification, the element symbol should be present in columns 77-78. The element is often ommitted by programs, such as charmm, that can write pdbs because it makes the file larger, and the information is accessible somewhere else (protein structure file). Unfortunately, other programs require the information. HackaMol::MolReadRole, loads a hash (KNOWN_NAMES) from HackaMol::PeriodicTable that maps common names to the element (e.g. POT => 'K'). read_pdb_atoms will carp if the name is not in the hash, and then set the element to the first letter of the name.

SEE ALSO

• HackaMol

• HackaMol::Atom

• HackaMol::Roles::MolReadRole

• Protein Data Bank

AUTHOR

Demian Riccardi <demianriccardi@gmail.com>

COPYRIGHT AND LICENSE

This software is copyright (c) 2015 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.