CustomStringValueMetric

Added by Vikram K. Mulligan (vmulligan@flatironinstitute.org) on 29 June 2022.

Table of Contents

- CustomStringValueMetric
- See also

Description

The CustomStringValueMetric allows a user to add an arbitrary string, indexed by a label, to a pose. The value will be written out in the PDB file, or can be accessed by metrics that access strings. This also provides a means for storing strings that are not produced by metrics in PyRosetta or from Rosetta C++, as well as for passing strings from the commandline to store in poses.

Example with custom strings set from commandline

<ROSETTASCRIPTS>
	<SIMPLE_METRICS>
            <CustomStringValueMetric name="pose_annotation" value="%%external_val%%" />
	</SIMPLE_METRICS>
	<PROTOCOLS>
            <Add metrics="my_metric" />
	</PROTOCOLS>
</ROSETTASCRIPTS>

~/Rosetta/main/source/src/rosetta_scripts.default.linuxgccrelease -parser:protocol my_script.xml -script_vars external_val=high_quality_pose -in:file:s first_file.pdb
~/Rosetta/main/source/src/rosetta_scripts.default.linuxgccrelease -parser:protocol my_script.xml -script_vars external_val=poor_quality_pose -in:file:s second_file.pdb

The above would produce two outputs. In the first case, the pose annotation "high_quality_pose" would be stored in the first pose, and in the second, the pose annotation "low_quality_pose" would be stored in the second. This could be useful in cases in which external software (molecular dynamics programs, other molecular modelling packages, deep learning models, etc.) is used to perform some qualitative analysis on a pose, but one wishes Rosetta to be able to read the annotation produced.

Full options (auto-generated documentation)

Autogenerated Tag Syntax Documentation:

A metric for caching an arbitrary, user-defined string in a pose.

References and author information for the CustomStringValueMetric simple metric:

CustomStringValueMetric SimpleMetric's author(s): Vikram K. Mulligan, Systems Biology Group, Center for Computational Biology, Flatiron Institute [vmulligan@flatironinstitute.org]

<CustomStringValueMetric name="(&string;)" custom_type="(&string;)"
        value="(&string;)" />

custom_type: Allows multiple configured SimpleMetrics of a single type to be called in a single RunSimpleMetrics and SimpleMetricFeatures. The custom_type name will be added to the data tag in the scorefile or features database.
value: The custom string to cache in the pose.

CustomStringValueMetric