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.IX Title "Bio::Tools::Run::Coil 3pm"
.TH Bio::Tools::Run::Coil 3pm 2024-03-12 "perl v5.38.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH NAME
Bio::Tools::Run::Coil \- wrapper for ncoils program
.SH SYNOPSIS
.IX Header "SYNOPSIS"
.Vb 2
\&  # Build a Coil factory
\&  my $factory = Bio::Tools::Run::Coil\->new($params);
\&
\&  # Pass the factory a Bio::Seq object
\&  # @feats is an array of Bio::SeqFeature::Generic objects
\&  my @feats = $factory\->run($seq);
.Ve
.SH DESCRIPTION
.IX Header "DESCRIPTION"
This module is a wrapper for the \fBncoils\fR program available via
<http://www.russell.embl\-heidelberg.de/coils/coils.tar.gz> for predicting 
coiled coils in protein sequences.
.PP
By default it looks for an executable called \fIncoils\fR and data/parameter files
in the directory specified by the \fICOILSDIR\fR environmental variable.
.SH REFERENCES
.IX Header "REFERENCES"
Lupas, van Dyke & Stock, 
\&\fIPredicting coiled coils from protein sequences\fR, 
Science \fB252\fR:1162\-1164, 1991.
.PP
Lupas, A.,
\&\fIPrediction and Analysis of Coiled-Coil Structures\fR,
Meth. Enzymology \fB266\fR:513\-525, 1996.
.SH FEEDBACK
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS Support
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.
.SS "Reporting Bugs"
.IX Subsection "Reporting Bugs"
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH AUTHORS
.IX Header "AUTHORS"
.Vb 2
\& Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil
\& originally written by Marc Sohrmann (ms2@sanger.ac.uk)
\&
\& Written in BioPipe by Balamurugan Kumarasamy <savikalpa@fugu\-sg.org>
.Ve
.PP
# Please direct questions and support issues to <bioperl\-l@bioperl.org> 
#
 Cared for by the Fugu Informatics team (fuguteam@fugu\-sg.org)
.SH APPENDIX
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS program_name
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $factory>program_name()
\& Function: holds the program name 
\& Returns:  string 
\& Args    : None
.Ve
.SS program_dir
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : $factory\->program_dir(@params)
\& Function: returns the program directory, obtained from ENV variable. 
\& Returns:  string 
\& Args    :
.Ve
.SS new
.IX Subsection "new"
.Vb 5
\& Title   : new
\& Usage   : $coil\->new(@params)
\& Function: creates a new Coil factory
\& Returns:  Bio::Tools::Run::Coil
\& Args    :
.Ve
.SS predict_protein_features
.IX Subsection "predict_protein_features"
.Vb 5
\& Title   :   predict_protein_features()
\& Usage   :   DEPRECATED. Use $obj\->run instead. 
\& Function:   Runs Coil and creates an array of featrues
\& Returns :   An array of Bio::SeqFeature::Generic objects
\& Args    :   A Bio::PrimarySeqI
.Ve
.SS run
.IX Subsection "run"
.Vb 5
\& Title   :   run
\& Usage   :   $obj\->run($seq)
\& Function:   Runs Coil and creates an array of featrues
\& Returns :   An array of Bio::SeqFeature::Generic objects
\& Args    :   A Bio::PrimarySeqI, or a Fasta filename.
.Ve
.SS _input
.IX Subsection "_input"
.Vb 5
\& Title   :   _input
\& Usage   :   obj\->_input($seqFile)
\& Function:   Internal(not to be used directly)
\& Returns :
\& Args    :
.Ve
.SS _run
.IX Subsection "_run"
.Vb 5
\& Title   :   _run
\& Usage   :   $obj\->_run()
\& Function:   Internal(not to be used directly)
\& Returns :   An array of Bio::SeqFeature::Generic objects
\& Args    :
.Ve
.SS _writeSeqFile
.IX Subsection "_writeSeqFile"
.Vb 5
\& Title   :   _writeSeqFile
\& Usage   :   obj\->_writeSeqFile($seq)
\& Function:   Internal(not to be used directly)
\& Returns :
\& Args    :
.Ve