Raul Alcantara Aragon > Bio-PDB-Structure > Bio::PDB::Structure

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NAME ^

Bio::PDB::Structure - Perl module for parsing and manipulating Protein Databank (PDB) files

SYNOPSIS ^

  use Bio::PDB::Structure;
  
  $mol1= Bio::PDB::Structure::Molecule -> new;
  $mol2= Bio::PDB::Structure::Molecule -> new;
  $mol1 -> read("molecule.pdb",0);         #read the first model
  $mol2 -> read("molecule.pdb",1);         #read the second model
  $mol1b = $mol1 -> backbone;              #create a list with the backbone of mol1
  $mol2b = $mol2 -> backbone;              #create a list with the backbone of mol2
  @transform = $mol2b ->superpose($mol1b); #compute alignment of mol2 to mol1
  $mol2 ->rotate_translate(@transform);    #rotate and translate mol2
  $rmsd = $mol2 -> rmsd($mol1);            #compute the rmsd between mol2 and mol1
  $mol2 -> print("new.pdb");               #save the molecule to a file

DESCRIPTION ^

This module combines tools that are commonly used to analyze proteins and nucleic acids from a pdb file stuctures. The main benefits of using the module are its ability to parse and print out a pdb structure with minimum effort. However in addition to that it is possible to do structural alignments, RMSD calculations, atom editons, center of mass calculations, molecule editions and so forth. Both Atom objects and Molecule objects are defined within this module.

Methods for Atom objects

Methods for Molecule objects

SEE ALSO ^

http://www.pdb.org

AUTHOR ^

Raul Alcantara Aragon, <rulix@hotmail.com>

COPYRIGHT AND LICENSE ^

Copyright (C) 2012 by Raul Alcantara

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.12.3 or, at your option, any later version of Perl 5 you may have available.

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