OpenFreeEnergy/gufe

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core data models of the Open Free Energy ecosystem

Stars: 45
Forks: 13
Open beginner issues: 0
Indexed issues: 115
Avg merge: 2d 11h
Merged PRs (30d): 3

Dominant language: Python
License: MIT
Last GitHub push: Sep 2, 2026
Latest indexed: Sep 19, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: good first issue

Beginner friendly Everything

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115 open issues indexed

rename fixture names for clarity Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

OpenFreeEnergy/gufe#836 · Opened Sep 17, 2026
`ProteinMembraneComponent` serialization/deserialization is incredibly slow Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

OpenFreeEnergy/gufe#835 · 1 comment · Opened Sep 8, 2026
Add `.offxml` to small molecule force field settings entry. Open

OpenFreeEnergy/gufe#833 · 1 assignee · Opened Sep 1, 2026
Should `SmallMoleculeComponent` pull charges from a mol2 input Open

Difficulty 4/5 3-5 days Newbie friendliness 50/100

OpenFreeEnergy/gufe#828 · Opened Aug 21, 2026
add AtomMappingScorer type Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

OpenFreeEnergy/gufe#790 · Opened May 27, 2026
Add convenience method to get the difference in formal charge between two SmallMoleculeComponents Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

OpenFreeEnergy/gufe#783 · 2 comments · Opened Apr 17, 2026
Assign `mapping` a default value of None in `Protocol.validate` Open

OpenFreeEnergy/gufe#782 · 1 comment · 1 assignee · Opened Apr 17, 2026
ProtocolUnitResult should have a reference to the ProtocolUnit that created it Open

Difficulty 5/5 Over a week Newbie friendliness 42/100

OpenFreeEnergy/gufe#781 · 2 comments · Opened Apr 16, 2026
try using pixi Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

OpenFreeEnergy/gufe#776 · 1 comment · Opened Mar 31, 2026
Network-wide validation Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

OpenFreeEnergy/gufe#763 · 2 reactions · Opened Mar 18, 2026
expose select test fixtures in the api Open

OpenFreeEnergy/gufe#756 · 2 comments · 1 assignee · Opened Mar 4, 2026
Need a contributors guide Open

OpenFreeEnergy/gufe#749 · 1 comment · 1 assignee · Opened Feb 25, 2026
interrogate pre-commit hook doesn't work when using `pixi` Open

Difficulty 1/5 Under an hour Newbie friendliness 55/100

OpenFreeEnergy/gufe#747 · 1 comment · Opened Feb 24, 2026
weekly test of minimal deps Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

OpenFreeEnergy/gufe#746 · 1 reaction · Opened Feb 23, 2026
Cache the density property on ExplicitPDBComponent? Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

OpenFreeEnergy/gufe#735 · Opened Feb 12, 2026
Count molecules method for `SolvatedPDBComponent` Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

OpenFreeEnergy/gufe#734 · Opened Feb 12, 2026
add callback argument to validation method(s) Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

OpenFreeEnergy/gufe#733 · Opened Feb 11, 2026
`GufeTokenizable`s cannot contain a dictionary with other `GufeTokenizable`s as keys Open

bug module-tokenization

OpenFreeEnergy/gufe#714 · 1 comment · 1 reaction · 1 assignee · Opened Jan 23, 2026
Direct serialization of `GufeTokenizable` attributes holding `GufeKey` instances produces false round tripping Open

module-tokenization serialization

OpenFreeEnergy/gufe#713 · 1 comment · 1 assignee · Opened Jan 22, 2026
`GufeTokenizable` definitions containing other `GufeTokenizable` objects inside a `tuple` produces confusing exception Open

OpenFreeEnergy/gufe#711 · 1 comment · 1 assignee · Opened Jan 16, 2026
CONECT records cannot be parsed for systems with >100k atoms Open

OpenFreeEnergy/gufe#702 · 1 comment · 3 assignees · Opened Jan 7, 2026
update PdbxContainers.py Open

OpenFreeEnergy/gufe#697 · 1 assignee · Opened Dec 19, 2025
add viz functionality to `ExplicitMoleculeComponent` Open

OpenFreeEnergy/gufe#692 · 1 assignee · Opened Dec 11, 2025
[Discussions] How we define endstates Open

OpenFreeEnergy/gufe#686 · 5 assignees · Opened Dec 1, 2025
ChemicalSystem should not have the same Component multiple times. Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

OpenFreeEnergy/gufe#685 · Opened Nov 25, 2025
investigate arm64 platform differences Open

bug

OpenFreeEnergy/gufe#680 · 1 assignee · Opened Nov 19, 2025
drop/reduce openmm dependency Open

OpenFreeEnergy/gufe#662 · 1 comment · 2 assignees · Opened Oct 22, 2025
Change repr for quantities Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

OpenFreeEnergy/gufe#655 · Opened Oct 21, 2025
Mapping should default to None in Protocol methods Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

OpenFreeEnergy/gufe#643 · Opened Oct 14, 2025
wrap pydantic errors for better usability Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

OpenFreeEnergy/gufe#641 · Opened Oct 10, 2025
review all high-level docstrings Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

OpenFreeEnergy/gufe#628 · Opened Oct 1, 2025
Add `AtomMappingScorer` class Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

OpenFreeEnergy/gufe#624 · 1 comment · Opened Sep 19, 2025
handle str options more thoroughly in settings Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

OpenFreeEnergy/gufe#609 · Opened Sep 3, 2025
use pydantic `Field` instead of inline docstrings Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

OpenFreeEnergy/gufe#603 · Opened Aug 20, 2025
mypy: fix missing imports from rdkit allchem Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

OpenFreeEnergy/gufe#592 · Opened Jul 22, 2025
apply pyupgrade linting Open

OpenFreeEnergy/gufe#588 · 1 assignee · Opened Jul 18, 2025
Add how-to doc for creating a new AtomMapper Open

OpenFreeEnergy/gufe#582 · 1 assignee · Opened Jul 2, 2025
Add how-to doc for defining a new AtomMapping Open

OpenFreeEnergy/gufe#581 · 2 comments · 2 assignees · Opened Jul 2, 2025
Add how-to doc for defining a new ComponentMapping Open

OpenFreeEnergy/gufe#580 · 1 comment · 1 assignee · Opened Jul 2, 2025
Add `merge` method for ProteinComponent Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/gufe#568 · 5 comments · 1 reaction · Opened Jun 17, 2025
Use atom serial number in ion error message Open

priority-low

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

OpenFreeEnergy/gufe#546 · Opened Apr 28, 2025
clean up public API Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

OpenFreeEnergy/gufe#528 · 1 comment · Opened Apr 15, 2025
Add how-to doc for defining an entirely new `GufeTokenizable` Open

docs-developer priority:medium

OpenFreeEnergy/gufe#527 · 2 assignees · Opened Apr 15, 2025
Vendored files need better process Open

OpenFreeEnergy/gufe#518 · 2 comments · 1 reaction · 2 assignees · Opened Mar 28, 2025
Identify all `DeprecationWarning`s present; drop in release v2.0 Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

OpenFreeEnergy/gufe#513 · Opened Mar 18, 2025
Validate default value for Settings models Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/gufe#491 · 2 comments · 2 reactions · Opened Feb 25, 2025
Add "base" Settings classes Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/gufe#490 · 2 comments · Opened Feb 25, 2025
Remove use and definitions of `serialize_numpy` and `deserialize_numpy` from `gufe.molhashing` Open

OpenFreeEnergy/gufe#487 · 2 reactions · 1 assignee · Opened Feb 18, 2025
Developer documentation overhaul Open

OpenFreeEnergy/gufe#486 · 1 assignee · Opened Feb 18, 2025
Allow for ProteinComponent (or really any "multi-molecule" Component) to be converted to either an Interchange object or an OpenFF Topology Open

OpenFreeEnergy/gufe#476 · 2 comments · 1 assignee · Opened Feb 1, 2025

OpenFreeEnergy/gufe

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