This document was created September 2017 by Andrew Leaver-Fay. The parse_rosetta_script application is maintained by Brian Kuhlman's lab. Send questions to (bkuhlman@email.unc.edu)

# Code and Demo

The "entry-point" code for the parse_rosetta_script application lives in src/protocols/rosetta_scripts/RosettaScriptsParser.cc, however, it relies on the schemas defined by hundreds of Movers, Filters, ResidueSelectors, TaskOperations, etc that are distributed throughout the code base.

A demo for the use of this application lives in the Rosetta/rosetta_scripts_scripts/testing/parse_all_scripts.py -- this script will run the parse_rosetta_script application against all of the scripts listed in Rosetta/rosetta_scripts_scripts/scripts_to_parse.py

# References

The original rosetta_scripts paper was published in the following paper:

Fleishman, Sarel J., et al. "RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite." PloS one 6.6 (2011): e20161.

# Application purpose

The purpose of this application is to test an XML script written for the rosetta_scripts application to ensure that it is valid according to Rosetta's internally-generated XML Schema and to then test if all of the objects that are defined within this XML script can be constructed -- in particular, if all of their parse_my_tag methods succeed. If the script passes these two tests, then the application will print a brief success message and exit with a 0 exit status -- if either steps fail, it will print any error message that had been generated, and exit with a non-zero exit status.

# Algorithm

The script loads in the XML file, expanding all xi:include tags that it encounters, and replacing all script-vars variables that it finds. It constructs the schema for rosetta_scripts and validates the input XML file against the schema. If this step succeeds, then it constructs all of the Mover/Filter/ResidueSelector/ScoreFunction/TaskOperation/etc. objects that are specified in the XML file and calls all of their parse-my-tag / parse-tag methods.

# Limitations

This application does not execute a rosetta script, it merely verifies that it could be executed.

In the case of the MultiplePoseMover, where an entire protocol is embedded beneath the <MultiplePoseMover...> tag, the construction of the embedded Movers/Filters/etc. does not take place until the MultiplePoseMover's apply method is invoked. This script does not invoke the apply method of any Mover, and so it cannot guarantee that the embedded Movers/Filters/etc. can be correctly instantiated. It will, at least, ensure that the embedded Movers/Filters/etc. are valid according to Rosetta's internally-generated schema.

# Input Files

The principle input files for this application are XML files. One XML file may include another XML file using an <xi:include href="filename"> tag. This allows you to reuse elements in multiple scripts withut duplication.

In addition to the input XML files, the Movers/Filters/etc. which are created as a result of tags in those XML files, may also read from input files. Some of these Movers/Filters/etc. will read from the input files during the parse-my-tag / parse-tag functions that are invoked, but many delay the file read until their apply function is called. In this application, their apply functions are not called.

# Options

There are two principle command-line arguments to use with rosetta_scripts and rosetta-scripts-like applications (such as this one)

-parser:protocol <xml-filename>                         The script that will be read and whose tags will be turned into Rosetta objects
-parser:script_vars <ws-sep-varname-equals-value-pairs> The input XML file(s) may contain variables that can then be replaced with other
values from the command line. These variables should be enclosed in double % symbols.
E.g. <SomeTag value="%%myvariable%%"/>. The variable in the previous XML element named
myvariable can be replaced with a particular value, e.g. 10.3 by having the script_vars
flag on the command line: --parser:script_vars myvariable=10.3
You may have as many variables as you would like; each variable should be separated by
whitespace (i.e. the ws-sep part; it is white-space-separated). The variable name an
the value you wish to assign should be separated by an equals sign. Valid variable names
include any alpha-numeric strings and may contain underscores; they should not contain
consecutive percent symbols. Alternatively, you may include the script_vars option multiple
times on the command line, giving a different variable=value pair for each instance.


There are many other flags that this application and that other rosetta-scripts-related applications will use as the objects that they construct are initialized. (In general, we frown on objects that are initialized using rosetta_scripts from accessing the command line, but not all developers have been careful in ensuring that their Movers/Filters/etc. avoid using the command line.)

# Tips

You can use the -parser:info <tag-name> option with the rosetta_scripts application to print out XML-schema information and associated documentation text for a particular Tag with the requested tag-name if you find that one Mover/Filter/etc. is not parsing.

# Expected Outputs

Exits with a brief success message if the input script can be parsed and with a zero exit status; exits with a detailed error message and a non-zero exit status otherwise.

# Post Processing

No post-processing