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 (email@example.com)
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
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.
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.
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.
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.
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.
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.)
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.
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.