A repository of host-guest complexes available for benchmarking force fields used in the OpenFF-Evaluator program.
Taproom includes the following host-guest complexes (126 in total) with YAML files containing information necessary to perform free energy calculation using the attach-pull-release (APR) method.
alpha-cyclodextrin:- host key =
acd - Data set from Rekharsky et al. - 22 host-guest complexes
- host key =
beta-cyclodextrin:- host key =
bcd - Data set from Rekharsky et al. - 21 host-guest complexes
- bCD--R-rimantadine from SAMPL7
- host key =
cucurbit[7]uril:- host key =
cb7 - SAMPL3 - 2 host-guest complexes (G8 and G9)
- SAMPL4 - 14 host-guest complexes
- A1, A2, A5, B2, B5, B11 from Moghaddam et al.
- 1 host-guest complex from Kim et al.
- host key =
cucurbit[8]uril:octa-acid:tetra-endo-methyl octa-acid:
This module is designed to be lightweight and have minimal dependencies. As such, the simplest way to use these benchmarks is to clone this repository and run python setup.py develop. After installation, taproom.benchmarks is exposed as an entry point, and available to other Python modules. The dictionary host_guest_systems contains YAML-formatted "instructions" that can be used to simulate the host-guest complexes. The dictionary host_guest_measurements contains YAML-formatted experimental data, curated from public literature.
The following snippet can be used to expose the installed benchmarks.
import importlib.metadata
def _get_installed_benchmarks():
_installed_benchmarks = {}
for entry_point in importlib.metadata.entry_points(group="taproom.benchmarks"):
_installed_benchmarks[entry_point.name] = entry_point.load()
return _installed_benchmarks
host_guest_benchmarks = _get_installed_benchmarks()
host_guest_systems = host_guest_benchmarks["host_guest_systems"]
host_guest_measurements = host_guest_benchmarks["host_guest_measurements"]For information on the YAML formatting, see Schema.md.
MIT. See License for more information.
Copyright (c) 2023, Open Force Field Consortium
- David R. Slochower
- Simon Boothroyd
- Katy Kellett
- Jeffry Setiadi