Bio::Tools::Run::PiseApplication::confmat.3pm

Langue: en

Autres versions - même langue

Version: 2008-11-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Tools::Run::PiseApplication::confmat

SYNOPSIS

   #
 
 

DESCRIPTION

Bio::Tools::Run::PiseApplication::confmat
       Bioperl class for:
 
         confmat Side chain packing optimization on a given main chain template for protein PDB files (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/confmat.html 
          for available values):
 
 
                 confmat (String)
 
                 pdbfile (InFile)
                         PDB file
                         pipe: pdbfile
 
                 bridge_file (InFile)
                         Disulphide bridges file
 
                 generic_name (String)
                         Generic name of output files
 
                 cycles (Integer)
                         Number of cycles you want to perform
 
                 logfile (OutFile)
 
 

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 (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/confmat.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
Bio::Tools::Run::PiseJob

new

  Title   : new()
  Usage   : my $confmat = Bio::Tools::Run::PiseApplication::confmat->new($location, $email, @params);
  Function: Creates a Bio::Tools::Run::PiseApplication::confmat 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 $confmat = $factory->program('confmat');
  Example : -
  Returns : An instance of Bio::Tools::Run::PiseApplication::confmat.