Associated data and scripts, including the glycan conformer table.

Please see README for a full description of each component. Briefly, these include the following scripts: create_substituted_JD.py—Used to create substituted job description file for rosetta_scripts_jd3; create_symmetry_mates.py—This was used to create symmetry mates with a 12 A radius; density_build_example.xml—An an example of a main job definition file before being substituted for each glycan; density_build_example_substituted.xml—Substituted version; glycan_bm_plots.py—Tools used for plotting all benchmark experiments from Rosetta JSON files.; glycan_conformer_table.txt—The resultant glycan conformer table used in Rosetta and benchmarked against; glycan_tree_relax.xml—Main script used for de novo benchmarking.; glycan_tree_relax_dens.xml—Main script used for density building.; glycan_tree_relax_with_solvation.xml—Script used for running the GTM with explicit waters; glycan_water_mediated_hbonds.xml—Script for calculating water mediated hydrogen bonds; pdb_roots_density_sym.txt—Benchmark glycan list used for create_substituted_JD.py; refine_with_map_dih2.xml—Script used for refining input structures into the rosetta energy function using density.
(ZIP)