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gencoil(1) [debian man page]

GENCOIL(1)							   User Commands							GENCOIL(1)

NAME
gencoil - Generates a virtual coil suitable for sequence simulation in ODIN DESCRIPTION
gencoil: Generates a virtual coil suitable for sequence simulation in ODIN Usage and options: Generate a radially inhomogenous coil: gencoil -rad -n <inplane-size> -fov <FOV> -R <radial-inhomogeneity[%]> -o <Coil-file> Generate an array coil by rotating pre-existing image file: gencoil -rot -n <inplane-size> -fov <FOV> -nc <numof-rotated-subcoils> -i <input-image> -sl <selected-slice> -o <Coil-file> Generate an array coil consisting of simple loops: gencoil -arr -n <inplane-size> -nc <numof-rotated-loops> -fov <FOV> -R <array-radius> -o <Coil-file> Generate coil with a B1 gradient: gencoil -grad -n <inplane-size> -fov <FOV> -g <B1-gradient-endpoint> -o <Coil-file> Other options: -v <loglevel> or <component:loglevel> for debugging/tracing all components or a single component, respectively. Possible values for loglevel are: 0(noLog), 1(errorLog), 2(warningLog), 3(infoLog). -h, --help, -help, --version : Print help text or version information gencoil 1.8.5 March 2012 GENCOIL(1)

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Bio::Tools::Coil(3pm)					User Contributed Perl Documentation				     Bio::Tools::Coil(3pm)

NAME
Bio::Tools::Coil - parser for Coil output SYNOPSIS
use Bio::Tools::Coil my $parser = Bio::Tools::Coil->new(); while( my $sp_feat = $parser->next_result($file) ) { #do something #eg push @sp_feat, $sp_feat; } DESCRIPTION
Parser for Coil output FEEDBACK
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Support Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR
Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil originally written by Marc Sohrmann (ms2@sanger.ac.uk) Written in BioPipe by Balamurugan Kumarasamy <savikalpa@fugu-sg.org> # Please direct questions and support issues to <bioperl-l@bioperl.org> # Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org) APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ parse_results Title : parse_results Usage : obj->parse_results Function: Parses the coil output. Automatically called by next_result() if not yet done. Example : Returns : next_result Title : next_result Usage : while($feat = $coil->next_result($file)) { # do something } Function: Returns the next protein feature of the coil output file Returns : Args : _result Title : _result Usage : $feat = $obj->_result() Function: internal Example : Returns : _add_prediction Title : _add_prediction() Usage : $obj->_add_prediction($feat) Function: internal Example : Returns : _predictions_parsed Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE create_feature Title : create_feature Usage : obj->create_feature(\%feature) Function: Internal(not to be used directly) Returns : Args : _read_fasta Title : _read_fasta Usage : obj->_read_fasta($file) Function: Internal(not to be used directly) Returns : Args : perl v5.14.2 2012-03-02 Bio::Tools::Coil(3pm)

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