/ 
bioperl-run-1.5.2_005-RC
/ Bio::Tools::Run::PiseApplication::decorate

NAME

Bio::Tools::Run::PiseApplication::decorate

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::decorate

      Bioperl class for:

	decorate	Side chain packing optimization of a new sequence on a given template main chain. (P. Koehl, M. Delarue)

	References:

		P. Koehl et M. Delarue. J. Mol. Biol. 239:249-275 (1994)



      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/decorate.html 
         for available values):


		decorate (String)

		pdbfile (InFile)
			PDB data for the template backbone
			pipe: pdbfile

		alignment (Sequence)
			Pairwise sequence alignment of template and model (MSF format required) PLEASE GIVE THE ALIGNEMENT IN THIS ORDER !  PDB Seq.(#1) vs Target Seq. (#2)
			pipe: readseq_ok_alig

		generic_name (String)
			Generic name of output files

		cycles (Integer)
			Total number of cycles you want to perform

		lambda (Float)
			Lambda factor for convergence

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

http://bugzilla.open-bio.org/

AUTHOR

Catherine Letondal (letondal@pasteur.fr)

COPYRIGHT

Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

SEE ALSO

  • http://bioweb.pasteur.fr/seqanal/interfaces/decorate.html

  • Bio::Tools::Run::PiseApplication

  • Bio::Tools::Run::AnalysisFactory::Pise

  • Bio::Tools::Run::PiseJob

new

Title   : new()
Usage   : my $decorate = Bio::Tools::Run::PiseApplication::decorate->new($location, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::decorate object.
          This method should not be used directly, but rather by 
          a Bio::Tools::Run::AnalysisFactory::Pise instance.
          my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
          my $decorate = $factory->program('decorate');
Example : -
Returns : An instance of Bio::Tools::Run::PiseApplication::decorate.