Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
PDB(3)		      User Contributed Perl Documentation		PDB(3)

NAME
       Chemistry::File::PDB - Protein Data Bank	file format reader/writer

SYNOPSIS
	   use Chemistry::File::PDB;

	   # read a PDB	file
	   my $macro_mol = Chemistry::MacroMol->read("myfile.pdb");

	   # write a PDB file
	   $macro_mol->write("out.pdb");

	   # read all models in	a multi-model file
	   my @mols = Chemistry::MacroMol->read("models.pdb");

	   # read one model at a time
	   my $file = Chemistry::MacroMol->file("models.pdb");
	   $file->open;
	   while (my $mol = $file->read_mol($file->fh))	{
	       # do something with $mol
	   }

DESCRIPTION
       This module reads and writes 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 following record types, ignoring everything else:

	   ATOM
	   HETATM
	   ENDMDL
	   END

       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 and writer is designed for dealing with
       Chemistry::MacroMol objects, but	it can also create and use
       Chemistry::Mol objects by throwing some information away.

   Properties
       When reading and	writing	files, this module stores or gets 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".

       $domain->attr("pdb/sequence_number")
	   The residue sequence	number as given	in the PDB file.

       $domain->attr("pdb/chain_id")
	   The chain to	which this residue belongs (one	character).

       $domain->attr("pdb/insertion_code")
	   The residue insertion code (see the PDB specification for details).

       $atom->name
	   The PDB atom	name, such as "CA".

       $atom->attr("pdb/residue_name")
	   The name of the residue, as discussed above.

       $atom->attr("pdb/serial_number")
	   The serial number for the atom, as given in the PDB file.

       If some of this information is not available when writing a PDB file,
       this module tries to make it up (by counting the	atoms or residues, for
       example).  The default residue name for writing is UNK (unknown). Atom
       names are just the atomic symbols.

   Multi-model files
       If a PDB	file has multiple models (separated by END or ENDMDL records),
       each call to read_mol will return one model.

   Output features
       On writing Chemistry::Mol objects, which	don't have macromolecule
       information and usually don't have atom names, the atom names are made
       up by concatenating the atomic symbol with a unique ID (up to 1296
       atoms are possible). The	ID can be disabled by setting the option
       'noid':

	   $mol->write("out.pdb", noid => 1);

       The molecule's name is written as a HEADER record; A REMARK record is
       added listing the version of Chemistry::File::PDB that was used.

VERSION
       0.23

SEE ALSO
       Chemistry::MacroMol, Chemistry::Mol, Chemistry::File,
       <http://www.perlmol.org/>.

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

       There is	another	PDB reader in Perl, as part of the BioPerl project:
       Bio::Structure::IO::pdb.

AUTHOR
       Ivan Tubert-Brohman <itub@cpan.org>

COPYRIGHT
       Copyright (c) 2009 Ivan Tubert-Brohman. All rights reserved. This
       program is free software; you can redistribute it and/or	modify it
       under the same terms as Perl itself.

perl v5.32.0			  2009-05-10				PDB(3)

NAME | SYNOPSIS | DESCRIPTION | VERSION | SEE ALSO | AUTHOR | COPYRIGHT

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Chemistry::File::PDB&sektion=3&manpath=FreeBSD+12.2-RELEASE+and+Ports>

home | help