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Bio::Tools::Run::PiseApplication::stride.3pm
Langue: en
Version: 2005-10-09 (mandriva - 01/05/08)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::Tools::Run::PiseApplication::strideSYNOPSIS
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DESCRIPTION
Bio::Tools::Run::PiseApplication::strideBioperl 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)
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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
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- http://bioweb.pasteur.fr/seqanal/interfaces/stride.html
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- Bio::Tools::Run::PiseApplication
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- Bio::Tools::Run::AnalysisFactory::Pise
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- 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.
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