---
name: "RG::Reprof"
section: "3pm"
platform: "linux"
package: "librg-reprof-bundle-perl"
version: "1.0.1-9"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/RG::Reprof"
---

# RG::Reprof(3pm)

protein secondary structure and accessibility predictor

## 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/\>