NAME

       RG::Reprof::Reprof - protein secondary structure and accessibility predictor

SYNOPSIS

       use RG::Reprof::Reprof;

DESCRIPTION

       See module commented source for further details.

   Methods
       OBJ RG::Reprof::Reprof->new( model_dir => PATH )
           Default model_dir: /tmp/lkajan/root/share/reprof.

           Returns new instance of RG::Reprof::Reprof.

       int $OBJ->run( input_file => PATH, out_file => PATH, mutation_file => PATH,
       specific_models => hashref, output_func => coderef )
           out_file may be a directory.
           mutation_file may be undefined.
           specific_models may be undefined.
               This is a hash of model and feature files with 'model_name' keys like:

                {
                  'fub_model' => '/path/to/model_file',
                  'fub_features' => '/path/to/features_file'
                }

               Check the module source for the list for model names.

           void output_func( out_file, sec_pred, acc_pred, sequence ) - function to call when
           output is ready.
               If undefined, the built-in write_output() function is called that prints results
               to one or more files.  The following positional parameters are passed to this
               function:

               out_file
                   Output file name.

               sec_pred
                   Secondary structure prediction, see source for details.

               acc_pred
                   Accessibility prediction, see source for details.

               sequence
                   Reference to array of residues of input sequence (e.g. [ 'M', 'A', 'G', ... ]
                   ).

AUTHOR

       Original version by Peter Hoenigschmid <hoenigschmid@rostlab.org> and Burkhard Rost.

       Some perl module work and documentation by Laszlo Kajan <lkajan@rostlab.org>.

SEE ALSO

       <http://rostlab.org/>