ExternalPackerResultLoader

Author: Vikram K. Mulligan (vmulligan@flatironinstitute.org) Page created 22 December 2018.

Table of Contents

Description

The ExternalPackerResultLoader takes as input a packer problem file containing information about an input pose, a set of rotamers for that pose, the one-body energy for each rotamer, and the two-body energies for each interacting rotamer pair, an a second file defining a packer solution, and uses these to reconstruct a pose with the solution threaded onto it. Note that this mover discards the input pose. This mover is intended to be used in conjunction with the InteractionGraphSummaryMetric, which generates descriptions of packing problems, and with external annealers or optimizers. It permits Rosetta to set up a packing problem using the Rosetta energy function, an external annealer or optimizer to find the ideal solution, and Rosetta to rebuild the pose with the externally-found solution so that additional refinement operations may be carried out.

Options

Autogenerated Tag Syntax Documentation:

This mover allows a solution to a packer problem to be imported from an external file. This allows Rosetta to communicate with external optimization packages, and provides a means of visualizing the result easily.

<ExternalPackerResultLoader name="(&string;)"
        packer_problem_definition_file="(&string;)"
        solution_definition_file="(&string;)" />

packer_problem_definition_file: The file from which a description of the packer problem will be loaded.
solution_definition_file: The file from which the solution to the packer problem will be loaded.

Input formats

Packer problem input format

The packer problem input format must match the output format for the InteractionGraphSummaryMetric. Please see the documentation for the InteractionGraphSummaryMetric for details. Note that the full output (including pose and rotamer geometry information) is needed.

Packer solution input format

The packer solution file must be formatted as a series of lines, one for each designable position in the packer problem, each with two whitespace-separated columns. The first must specify the sequence position in the pose, and the second must specify the rotamer index selected for that sequence position as a solution to the packer problem. No designable residue's sequence position may be repeated. So, for example, if positions 3, 5, and 6 in a pose are designable, and rotamer indices 7, 14, and 3 at these positions, respectively, were chosen as the optimal solutions to a packing problem, the file would look like this:

3     7
5     14
6     3

This file format is intended to be easy for external annealers to be programmed to write.

ExternalPackerResultLoader