Merge pull request #4473 from RosettaCommons/jadolfbr/glycan_benchmarking3
# WaterMediatedHbondMetric
A metric to measure hydrogen bonds between a set of residues that are water-mediated.
Docs: https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/SimpleMetrics/simple_metric_pages/WaterMediatedHbondMetric
## DEPTH:
We only traverse a depth of 1 by default. Make sure to set the -ignore_waters flag to false in order to have Rosetta include the HOH residues.
## SELECTION:
If one residue selector is given, will calculate bridged waters between residues of the selection and all [OTHER] residues, otherwise it will calculate bridges between one selection and another.
If NO SELECTION is give, will report ALL bridged hbonds in a pose [by default without self-water-self hbonds].
## HBOND:
Since these are bridged hbonds, and h-bond networks can be rather complex, the numbers
reported here are the unique h-bond paths from sele1 to sele2. If you give only a single residue selector, these are bridged hbonds from sele1 to OTHER residues in sele1.
By default we do not include mediated hbonds back on itself, but this is an option.
## TIPS:
It is generally recommended to repack the waters using the OptH TaskOperation before input into this metric, especially if only Oxygens were present. Using the option -include_vrt false will keep all waters present in the resulting structure. Use the option -corrections::water::wat_rot_sampling 10 to decrease the angle of sampling from a default of 30 to 10. This will result in many more rotamers, but will improve networks.
Hydration shells can be calculated by passing selection1 as all waters in the pose, selection2 as the protein or chain, and then reporting only a single depth (with max_depth at 0 and 1 for the first and second shell waters."
# HbondMetric
A metric to report the total h-bonds residues from a selection to all [OTHER] residues, or from a set of residues to another set of residues. If No selection is given, will report ALL vs ALL.
Docs: https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/SimpleMetrics/simple_metric_pages/HbondMetric
## Tips:
Use the SummaryMetric to get total hbonds of a selection or total number of residues having some number of hbonds. . See the WaterMediatedBridgedHBondMetric for water-mediated h-bonds.
By default does not report self-self hbonds
# Etc
- Added unit tests for both metrics
- Fixed glycan integration tests
- Add deprecated warning for -1 option in `test/run.py` as it will say subtests pass even though they don't.