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

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.