/ 
bioperl-run-1.4
/ Bio::Tools::Run::PiseApplication::stride

NAME

Bio::Tools::Run::PiseApplication::stride

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::stride

      Bioperl class for:

	STRIDE	Protein secondary structure assignment from atomic coordinates (D. Frishman & P. Argos)

	References:

		Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins. 1995 Dec;23(4):566-79.



      Parameters: 

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


		stride (String)

		pdbfile (InFile)
			PDB File

		pdbid (String)
			or you can instead enter a PDB id.

		read_chain (String)
			Read only these chains (-r)

		process_chain (String)
			Process only these chains (-c)

		molscript (Switch)
			Generate a Molscript file (-m)

		ss_only (Switch)
			Report secondary structure summary Only (-o)

		hydrogen (Switch)
			Report Hydrogen bonds (-h)

		fasta (Switch)
			Generate SeQuence file in FASTA format (-q)

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/MailList.shtml  - 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 email or the web:

bioperl-bugs@bioperl.org
http://bioperl.org/bioperl-bugs/

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/stride.html

  • Bio::Tools::Run::PiseApplication

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

  • Bio::Tools::Run::PiseJob

new

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