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# $Id: stride.pm,v 1.6 2006/07/04 22:23:35 mauricio Exp $
# BioPerl module for Bio::Tools::Run::PiseApplication::stride
#
# Cared for by Catherine Letondal <letondal@pasteur.fr>
#
# For copyright and disclaimer see below.
#
# POD documentation - main docs before the code
HideShow 114 lines of Pod
=head1 NAME
Bio::Tools::Run::PiseApplication::stride
=head1 SYNOPSIS
  #
=head1 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)
=head1 FEEDBACK
=head2 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
=head2 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/
=head1 AUTHOR
Catherine Letondal (letondal@pasteur.fr)
=head1 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.
=head1 DISCLAIMER
This software is provided "as is" without warranty of any kind.
=head1 SEE ALSO
=over
=item *
http://bioweb.pasteur.fr/seqanal/interfaces/stride.html
=item *
Bio::Tools::Run::PiseApplication
=item *
Bio::Tools::Run::AnalysisFactory::Pise
=item *
Bio::Tools::Run::PiseJob
=back
=cut
#'
package Bio::Tools::Run::PiseApplication::stride;
use vars qw(@ISA);
use strict;
use Bio::Tools::Run::PiseApplication;
@ISA = qw(Bio::Tools::Run::PiseApplication);
HideShow 14 lines of Pod
=head2 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 = $factory->program('stride');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::stride.
=cut
sub new {
    my ($class, $location, $email, @params) = @_;
    my $self = $class->SUPER::new($location, $email);
# -- begin of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/stride.pm
    $self->{COMMAND}   = "stride";
    $self->{VERSION}   = "5.a";
    $self->{TITLE}   = "STRIDE";
    $self->{DESCRIPTION}   = "Protein secondary structure assignment from atomic coordinates";
    $self->{OPT_EMAIL}   = 0;
    $self->{AUTHORS}   = "D. Frishman & P. Argos";
    $self->{REFERENCE}   = [
         "Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins. 1995 Dec;23(4):566-79.",
 ];
    $self->{_INTERFACE_STANDOUT} = undef;
    $self->{_STANDOUT_FILE} = undef;
    $self->{TOP_PARAMETERS}  = [ 
        "stride",
        "pdbfile",
        "pdbid",
        "control",
        "output",
        "molscript_file",
        "outfile",
    ];
    $self->{PARAMETERS_ORDER}  = [
        "stride",
        "pdbfile",      # PDB File
        "pdbid",        # or you can instead enter a PDB id.
        "control",      # Control parameters
        "read_chain",   # Read only these chains (-r)
        "process_chain",        # Process only these chains (-c)
        "output",       # Output parameters
        "molscript",    # Generate a Molscript file (-m)
        "ss_only",      # Report secondary structure summary Only (-o)
        "hydrogen",     # Report Hydrogen bonds (-h)
        "fasta",        # Generate SeQuence file in FASTA format (-q)
        "molscript_file",
        "outfile",
    ];
    $self->{TYPE}  = {
        "stride" => 'String',
        "pdbfile" => 'InFile',
        "pdbid" => 'String',
        "control" => 'Paragraph',
        "read_chain" => 'String',
        "process_chain" => 'String',
        "output" => 'Paragraph',
        "molscript" => 'Switch',
        "ss_only" => 'Switch',
        "hydrogen" => 'Switch',
        "fasta" => 'Switch',
        "molscript_file" => 'Results',
        "outfile" => 'Results',
    };
    $self->{FORMAT}  = {
        "stride" => {
                "perl" => '"stride"',
        },
        "pdbfile" => {
                "perl" => '($pdbid) ? " $pdbid.pdb" : " $value"',
        },
        "pdbid" => {
                "perl" => '(($pdbid =~ tr/A-Z/a-z/) || $value)? "cat `pdbloc $pdbid` > $pdbid.pdb ; " : "" ',
        },
        "control" => {
        },
        "read_chain" => {
                "perl" => '($value)? " -r$value" : "" ',
        },
        "process_chain" => {
                "perl" => '($value)? " -c$value" : "" ',
        },
        "output" => {
        },
        "molscript" => {
                "perl" => ' ($value)? " -m$pdbfile.mol" : "" ',
        },
        "ss_only" => {
                "perl" => ' ($value)? " -o":""',
        },
        "hydrogen" => {
                "perl" => ' ($value)? " -h" : "" ',
        },
        "fasta" => {
                "perl" => ' ($value)? " -q" : "" ',
        },
        "molscript_file" => {
        },
        "outfile" => {
        },
    };
    $self->{FILENAMES}  = {
        "molscript_file" => '*.mol',
        "outfile" => '*.out',
    };
    $self->{SEQFMT}  = {
    };
    $self->{GROUP}  = {
        "stride" => 0,
        "pdbfile" => 10,
        "pdbid" => -10,
        "read_chain" => 1,
        "process_chain" => 1,
        "molscript" => 1,
        "ss_only" => 1,
        "hydrogen" => 1,
        "fasta" => 1,
    };
    $self->{BY_GROUP_PARAMETERS}  = [
        "pdbid",
        "stride",
        "molscript_file",
        "control",
        "output",
        "outfile",
        "process_chain",
        "molscript",
        "ss_only",
        "hydrogen",
        "fasta",
        "read_chain",
        "pdbfile",
    ];
    $self->{SIZE}  = {
    };
    $self->{ISHIDDEN}  = {
        "stride" => 1,
        "pdbfile" => 0,
        "pdbid" => 0,
        "control" => 0,
        "read_chain" => 0,
        "process_chain" => 0,
        "output" => 0,
        "molscript" => 0,
        "ss_only" => 0,
        "hydrogen" => 0,
        "fasta" => 0,
        "molscript_file" => 0,
        "outfile" => 0,
    };
    $self->{ISCOMMAND}  = {
        "stride" => 1,
        "pdbfile" => 0,
        "pdbid" => 0,
        "control" => 0,
        "read_chain" => 0,
        "process_chain" => 0,
        "output" => 0,
        "molscript" => 0,
        "ss_only" => 0,
        "hydrogen" => 0,
        "fasta" => 0,
        "molscript_file" => 0,
        "outfile" => 0,
    };
    $self->{ISMANDATORY}  = {
        "stride" => 0,
        "pdbfile" => 0,
        "pdbid" => 0,
        "control" => 0,
        "read_chain" => 0,
        "process_chain" => 0,
        "output" => 0,
        "molscript" => 0,
        "ss_only" => 0,
        "hydrogen" => 0,
        "fasta" => 0,
        "molscript_file" => 0,
        "outfile" => 0,
    };
    $self->{PROMPT}  = {
        "stride" => "",
        "pdbfile" => "PDB File",
        "pdbid" => "or you can instead enter a PDB id.",
        "control" => "Control parameters",
        "read_chain" => "Read only these chains (-r)",
        "process_chain" => "Process only these chains (-c)",
        "output" => "Output parameters",
        "molscript" => "Generate a Molscript file (-m)",
        "ss_only" => "Report secondary structure summary Only (-o)",
        "hydrogen" => "Report Hydrogen bonds (-h)",
        "fasta" => "Generate SeQuence file in FASTA format (-q)",
        "molscript_file" => "",
        "outfile" => "",
    };
    $self->{ISSTANDOUT}  = {
        "stride" => 0,
        "pdbfile" => 0,
        "pdbid" => 0,
        "control" => 0,
        "read_chain" => 0,
        "process_chain" => 0,
        "output" => 0,
        "molscript" => 0,
        "ss_only" => 0,
        "hydrogen" => 0,
        "fasta" => 0,
        "molscript_file" => 0,
        "outfile" => 0,
    };
    $self->{VLIST}  = {
        "control" => ['read_chain','process_chain',],
        "output" => ['molscript','ss_only','hydrogen','fasta',],
    };
    $self->{FLIST}  = {
    };
    $self->{SEPARATOR}  = {
    };
    $self->{VDEF}  = {
        "molscript" => '0',
        "ss_only" => '0',
        "hydrogen" => '0',
        "fasta" => '0',
    };
    $self->{PRECOND}  = {
        "stride" => { "perl" => '1' },
        "pdbfile" => { "perl" => '1' },
        "pdbid" => { "perl" => '1' },
        "control" => { "perl" => '1' },
        "read_chain" => { "perl" => '1' },
        "process_chain" => { "perl" => '1' },
        "output" => { "perl" => '1' },
        "molscript" => { "perl" => '1' },
        "ss_only" => { "perl" => '1' },
        "hydrogen" => { "perl" => '1' },
        "fasta" => { "perl" => '1' },
        "molscript_file" => {
                "perl" => '$molscript',
        },
        "outfile" => { "perl" => '1' },
    };
    $self->{CTRL}  = {
        "pdbfile" => {
                "perl" => {
                        '! ($pdbid || $pdbfile)' => "You must enter either the PDB data or the PDB id",
                },
        },
    };
    $self->{PIPEOUT}  = {
        "outfile" => {
                 '1' => "stride_outfile",
        },
    };
    $self->{WITHPIPEOUT}  = {
    };
    $self->{PIPEIN}  = {
    };
    $self->{WITHPIPEIN}  = {
    };
    $self->{ISCLEAN}  = {
        "stride" => 0,
        "pdbfile" => 0,
        "pdbid" => 0,
        "control" => 0,
        "read_chain" => 0,
        "process_chain" => 0,
        "output" => 0,
        "molscript" => 0,
        "ss_only" => 0,
        "hydrogen" => 0,
        "fasta" => 0,
        "molscript_file" => 0,
        "outfile" => 0,
    };
    $self->{ISSIMPLE}  = {
        "stride" => 1,
        "pdbfile" => 1,
        "pdbid" => 1,
        "control" => 0,
        "read_chain" => 0,
        "process_chain" => 0,
        "output" => 0,
        "molscript" => 0,
        "ss_only" => 0,
        "hydrogen" => 0,
        "fasta" => 0,
        "molscript_file" => 0,
        "outfile" => 0,
    };
    $self->{PARAMFILE}  = {
    };
    $self->{COMMENT}  = {
        "read_chain" => [
                "Example: AB",
                "=> calculate secondary structure assignment for chains A and B only.",
        ],
        "process_chain" => [
                "Process only chains Id1, Id2 ...etc. Secondary structure assignment will be produced only for these chains, but other chains that are present will be taken into account while calculating residue accessible surface and detecting inter-chain hydrogen bonds and, possibly, interchain beta-sheets. By default all protein chains read are processed.",
                "Examples: ",
                "Process only = ABC and Read only = C",
                "=> calculate secondary structure assignment for chain C in the presence of chains A and B.",
        ],
    };
    $self->{SCALEMIN}  = {
    };
    $self->{SCALEMAX}  = {
    };
    $self->{SCALEINC}  = {
    };
    $self->{INFO}  = {
    };
# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/stride.pm
    $self->_init_params(@params);
    return $self;
}
1; # Needed to keep compiler happy