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

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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.bioperl.org/ Catherine Letondal (letondal@pasteur.fr) 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. This software is provided "as is" without warranty of any kind. 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.