# $Id: homology.pm,v 1.3 2003/06/10 09:33:20 letondal Exp $
# BioPerl module for Bio::Tools::Run::PiseApplication::homology
#
# Cared for by Catherine Letondal <letondal@pasteur.fr>
#
# For copyright and disclaimer see below.
#
# POD documentation - main docs before the code

=head1 NAME

Bio::Tools::Run::PiseApplication::homology

=head1 SYNOPSIS

  #

=head1 DESCRIPTION

Bio::Tools::Run::PiseApplication::homology

      Bioperl class for:

	homology	SCMF Homology Modelling Program (P. Koehl, M. Delarue)

	References:

		P. Koehl and M. Delarue. Nature Structural Biology. 2:163-169 (1995). 



      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/homology.html 
         for available values):


		homology (String)

		pdbfile (InFile)
			PDB data for the template protein
			pipe: pdbfile

		model_name (String)
			Name of the model protein to be built

		alignment (Sequence)
			Pairwise sequence alignment of template and model (MSF format preferred)
			pipe: readseq_ok_alig

		cycles (Float)
			Total number of cycles for SCMF refinement

		lambda (Float)
			Lambda for SCMF updates

=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/MailList.shtml  - 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
email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

=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/homology.html

=item *

Bio::Tools::Run::PiseApplication

=item *

Bio::Tools::Run::AnalysisFactory::Pise

=item *

Bio::Tools::Run::PiseJob

=back

=cut

#'
package Bio::Tools::Run::PiseApplication::homology;

use vars qw(@ISA);
use strict;
use Bio::Tools::Run::PiseApplication;

@ISA = qw(Bio::Tools::Run::PiseApplication);

=head2 new

 Title   : new()
 Usage   : my $homology = Bio::Tools::Run::PiseApplication::homology->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::homology 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 $homology = $factory->program('homology');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::homology.

=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/homology.pm

    $self->{COMMAND}   = "homology";
    $self->{VERSION}   = "5.a";
    $self->{TITLE}   = "homology";

    $self->{DESCRIPTION}   = "SCMF Homology Modelling Program";

    $self->{OPT_EMAIL}   = 0;

    $self->{AUTHORS}   = "P. Koehl, M. Delarue";

    $self->{REFERENCE}   = [

         "P. Koehl and M. Delarue. Nature Structural Biology. 2:163-169 (1995). ",
 ];

    $self->{_INTERFACE_STANDOUT} = undef;
    $self->{_STANDOUT_FILE} = undef;

    $self->{TOP_PARAMETERS}  = [ 
	"homology",
	"result_files",
	"pdb_file",
	"pdbfile",
	"model_name",
	"alignment",
	"cycles",
	"lambda",

    ];

    $self->{PARAMETERS_ORDER}  = [
	"homology",
	"result_files",
	"pdb_file",
	"pdbfile", 	# PDB data for the template protein
	"model_name", 	# Name of the model protein to be built
	"alignment", 	# Pairwise sequence alignment of template and model (MSF format preferred)
	"cycles", 	# Total number of cycles for SCMF refinement
	"lambda", 	# Lambda for SCMF updates

    ];

    $self->{TYPE}  = {
	"homology" => 'String',
	"result_files" => 'Results',
	"pdb_file" => 'Results',
	"pdbfile" => 'InFile',
	"model_name" => 'String',
	"alignment" => 'Sequence',
	"cycles" => 'Float',
	"lambda" => 'Float',

    };

    $self->{FORMAT}  = {
	"homology" => {
		"perl" => ' "homology.perl < params" ',
	},
	"result_files" => {
	},
	"pdb_file" => {
	},
	"pdbfile" => {
		"perl" => '"$value\\n"',
	},
	"model_name" => {
		"perl" => '"$value\\n"',
	},
	"alignment" => {
		"perl" => '"$value\\n"',
	},
	"cycles" => {
		"perl" => '"$value\\n"',
	},
	"lambda" => {
		"perl" => '"$value\\n"',
	},

    };

    $self->{FILENAMES}  = {
	"result_files" => 'params *.info *.proba *.frame *.log model*',
	"pdb_file" => '*.pdb',

    };

    $self->{SEQFMT}  = {
	"alignment" => [15],

    };

    $self->{GROUP}  = {
	"homology" => 0,
	"pdbfile" => 1,
	"model_name" => 2,
	"alignment" => 3,
	"cycles" => 5,
	"lambda" => 6,

    };

    $self->{BY_GROUP_PARAMETERS}  = [
	"homology",
	"result_files",
	"pdb_file",
	"pdbfile",
	"model_name",
	"alignment",
	"cycles",
	"lambda",

    ];

    $self->{SIZE}  = {

    };

    $self->{ISHIDDEN}  = {
	"homology" => 1,
	"result_files" => 0,
	"pdb_file" => 0,
	"pdbfile" => 0,
	"model_name" => 0,
	"alignment" => 0,
	"cycles" => 0,
	"lambda" => 0,

    };

    $self->{ISCOMMAND}  = {
	"homology" => 1,
	"result_files" => 0,
	"pdb_file" => 0,
	"pdbfile" => 0,
	"model_name" => 0,
	"alignment" => 0,
	"cycles" => 0,
	"lambda" => 0,

    };

    $self->{ISMANDATORY}  = {
	"homology" => 0,
	"result_files" => 0,
	"pdb_file" => 0,
	"pdbfile" => 1,
	"model_name" => 1,
	"alignment" => 1,
	"cycles" => 1,
	"lambda" => 1,

    };

    $self->{PROMPT}  = {
	"homology" => "",
	"result_files" => "",
	"pdb_file" => "",
	"pdbfile" => "PDB data for the template protein",
	"model_name" => "Name of the model protein to be built",
	"alignment" => "Pairwise sequence alignment of template and model (MSF format preferred)",
	"cycles" => "Total number of cycles for SCMF refinement",
	"lambda" => "Lambda for SCMF updates",

    };

    $self->{ISSTANDOUT}  = {
	"homology" => 0,
	"result_files" => 0,
	"pdb_file" => 0,
	"pdbfile" => 0,
	"model_name" => 0,
	"alignment" => 0,
	"cycles" => 0,
	"lambda" => 0,

    };

    $self->{VLIST}  = {

    };

    $self->{FLIST}  = {

    };

    $self->{SEPARATOR}  = {

    };

    $self->{VDEF}  = {
	"model_name" => 'model',
	"cycles" => '30',
	"lambda" => '0.1',

    };

    $self->{PRECOND}  = {
	"homology" => { "perl" => '1' },
	"result_files" => { "perl" => '1' },
	"pdb_file" => { "perl" => '1' },
	"pdbfile" => { "perl" => '1' },
	"model_name" => { "perl" => '1' },
	"alignment" => { "perl" => '1' },
	"cycles" => { "perl" => '1' },
	"lambda" => { "perl" => '1' },

    };

    $self->{CTRL}  = {

    };

    $self->{PIPEOUT}  = {

    };

    $self->{WITHPIPEOUT}  = {

    };

    $self->{PIPEIN}  = {
	"pdbfile" => {
		 "pdbfile" => '1',
	},
	"alignment" => {
		 "readseq_ok_alig" => '1',
	},

    };

    $self->{WITHPIPEIN}  = {

    };

    $self->{ISCLEAN}  = {
	"homology" => 0,
	"result_files" => 0,
	"pdb_file" => 0,
	"pdbfile" => 0,
	"model_name" => 0,
	"alignment" => 0,
	"cycles" => 0,
	"lambda" => 0,

    };

    $self->{ISSIMPLE}  = {
	"homology" => 0,
	"result_files" => 0,
	"pdb_file" => 0,
	"pdbfile" => 1,
	"model_name" => 1,
	"alignment" => 1,
	"cycles" => 0,
	"lambda" => 0,

    };

    $self->{PARAMFILE}  = {
	"pdbfile" => "params",
	"model_name" => "params",
	"alignment" => "params",
	"cycles" => "params",
	"lambda" => "params",

    };

    $self->{COMMENT}  = {
	"model_name" => [
		"The file named MODEL.pdb will contain the model protein coordinates (where MODEL is the chosen name of the model).",
	],
	"alignment" => [
		"The template correspond to the molecule described in the PDB data, the model is the molecule whose structure is to be be computed.",
		"You must provide an alignment in this order:",
		"1st sequence: template",
		"2nd sequence: protein to model",
	],
	"cycles" => [
		"30 or 40 should be enough most of the time.",
	],
	"lambda" => [
		"Enter 0.1 or 0.2",
	],

    };

    $self->{SCALEMIN}  = {

    };

    $self->{SCALEMAX}  = {

    };

    $self->{SCALEINC}  = {

    };

    $self->{INFO}  = {

    };

# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/homology.pm



    $self->_init_params(@params);

    return $self;
}



1; # Needed to keep compiler happy

