This document was edited Jul 2, 2019 by Rocco Moretti. This application was created and documented by Rocco Moretti, et al.

# Description of algorithm

Rosetta can take a number of different ways of specifying the chemical structure of a residue. Some of these (most noticably the Rosetta-specific params file format) aren't compatible with other programs.

The restype_converter application is able to take these inputs and convert them between formats.

# Limitations and Caveats

Rosetta's residue type outputting isn't necessarily comprehensive at this point. There's no guarantee that you're able to round-trip a given residue with the restype_converter application. (There's not even a guarantee that Rosetta will be able read the files which it output.)

That said, the params file output should be functionally complete and will likely round-trip, although there may be representational difference between a params file output and a params file input.

At this point, the PDB and SDF file output is mainly for atom/bond/coordinate information. It should be sufficient for getting something like a PyMol-readable file, though the usability for other cases may vary.

# Input

The restype_converter application does not make use of the standard Rosetta job distributor machinery, and as such doesn't obey normal input or output options.

By default, the converter works with full atom residue types. If you wish to work with centroid types, add the flag -in:file:centroid. (For centrot types, use -cenrot.)

The following options can be used to specify which residue types should be converted:

Option Description
-restype_convert:types A list of residue types names to take from the standard database. This can take patched names.
-restype_convert:name3 A list of three letter codes to take from the standard database. If more than one residue shares the same three letter code, all will be output. (Though it will likely not output patched types.)
-extra_res_fa A list of Rosetta Residue Params files to convert. (Not used with -in:file:centroid or -cenrot active.)
-extra_res_cen A list of Rosetta Residue Params files to convert. (Only used with -in:file:centroid active.)
-extra_res_mol A list of SDF/Mol files to convert. (Used in both centroid and fullatom.)
-extra_res_mmCIF A list of CIF formatted ligand files to convert. (Used in both centroid and fullatom.)

If you wish to load a residue type from the Rosetta-provided Chemical Components Dictionary file, simply prepend pdb_ to the three letter code, and use it with -restype_convert:types. (For example, to load the residue TTL from the CCD, pass -types pdb_TTL to the restype_convert application.)

# Output

By default, output will be in the current directory. You can control the path of the output with -out:path:all.

By default, files will be named with the full residue type name (including patches). You can use -out:prefix and -out:suffix to further decorate the output. (Currently there is no special handling of duplicate name detection.)

Output format is controlled by the following Boolean flags. (Multiple flags can be added to get multiple output formats from one run.)

Option Description Extension used
-out:pdb PDB format, single residue .pdb
-restype_convert:params_out Rosetta Residue Params file .params
-restype_convert:sdf_out SDF .sdf

(There's currently no mmCIF output available.)

# Command Lines

Sample command:

restype_convert.linuxgccrelease -restype_convert:types TRP:NtermProteinFull  -restype_convert:name3 CYS -extra_res_fa my_type.params -out:pdb -restype_convert:sdf_out 

# Example

See the integration test at rosetta/main/tests/integration/tests/restype_converter for an example.