NAME

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

VERSION

version 0.041

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, uses HackaMol::PeriodicTable to map 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. If you see one of these messages for a common atom, please submit an issue or pull request so the atom can be added!

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) 2017 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.