v0.2.1

Install Instructions

Online Installer

To play with the latest notebook, use this command to install the latest version of our packages:

conda env create openfe/openfe-notebooks
Then run:

conda activate openfe-notebooks
git clone https://github.com/OpenFreeEnergy/ExampleNotebooks.git openfe-example-notebooks
cd openfe-example-notebooks
git checkout april-2022
jupyter notebook openmm-rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb

Offline Installer

Download the relevant installer for your operating system and preferred python version.
We have attached the version of the example notebook that works with the latest release of openfe.

If you used our single file installer from the last release, download new-deps.tar.gz. Then activate the old environment before extracting and installing the packages with pip:

# Be sure the old environment is activated! 
mkdir new-deps && tar xzvf new-deps.tar.gz -C new-deps
pip install new-deps/*

Bug Fixes

Hotfix of results

v0.2

Initial release of relative free energy protocols

Alpha Release

What's Changed

• Initial skeleton by @dwhswenson in #21
• Add some changes requested in PR #21 by @IAlibay in #22
• Fix setup.cfg to include packages by @dwhswenson in #25
• Add base Scorer by @dwhswenson in #26
• atommapping implementation by @richardjgowers in #28
• Prevent CodeCov from running on forks, cron jobs by @dwhswenson in #27
• Convert to normal package; add utils; move errors to utils/errors by @dwhswenson in #32
• AtomMapper base classes by @dwhswenson in #30
• Remove Scorers by @dwhswenson in #33
• Molecule class by @dwhswenson in #39
• [WIP] Network container class by @dwhswenson in #40
• Add a simple coveragerc to ignore tests in reporting by @IAlibay in #44
• Tests for Network object by @dwhswenson in #43
• Add Versioneer by @mikemhenry in #45
• WIP: Lomap atommapper by @richardjgowers in #31
• suggested Network & Molecule changes by @richardjgowers in #46
• update AtomMapping type annotations by @richardjgowers in #48
• Set up basic mypy CI by @IAlibay in #50
• omit _version.py from coverage by @IAlibay in #53
• Proposed API change on AtomMapper by @dwhswenson in #56
• CLI Skeleton by @dwhswenson in #49
• network planning functions started by @richardjgowers in #41
• CLI for AtomMapping by @dwhswenson in #57
• added stubs for Molecule conversions by @richardjgowers in #58
• Molecule serialization/deserialization by @dwhswenson in #63
• Network Serialization by @dwhswenson in #64
• Docsdocsdocs by @richardjgowers in #66
• Skip running OE license check on PR by @mikemhenry in #71
• Add serialization test data script by @dwhswenson in #69
• Add support to get molecule name from _Name prop by @dwhswenson in #68
• Add support for CLI --mol to load SDF by @dwhswenson in #67
• Add visualization to AtomMapping by @mikemhenry in #60
• [WIP] Combine visualization with CLI by @dwhswenson in #72

Full Changelog: https://github.com/OpenFreeEnergy/openfe/commits/v0.1