foyer

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Precedence of bond/angle/dihedral definitions with and without wildcards

1

Dihedral terms (whether periodic or Ryckaert-Bellemans) are assigned such that those without wildcard characters are considered more specific than those containing wildcard characters, and are given precedence in assignment. Looking...

summeraz

Basically take this from the docs and turn it into something interactive: https://github.com/mosdef-hub/foyer/blob/master/docs/smarts.md#overriding-atomtypes

ctk3b

Currently it's only supported for atomtypes

ctk3b

ctk3b

updates: - [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v4.6.0)

pre-commit-ci[bot]

Clarify error in applying forcefield

1

### PR Summary: Slight change in error string to provide guidance to a user on how to resolve it. ### PR Checklist ------------ - [NA] Includes appropriate unit test(s) -...

jaclark5

Quickstart example fails

4

[Quickstart](https://github.com/mosdef-hub/foyer/blob/main/docs/source/getting_started/quickstart.rst#quickstart) example fails / is wrong / outdated : `mol = parmed.load("ethane.pdb")` - not `load`, but `load_file` Moreover, when using provided `ethane.pdb` molecule from `./docs/source/files/`, got the error: ``` Traceback...

iGulitch

Add ruff to pre-commit hooks

1

### PR Summary: This PR does the same as https://github.com/mosdef-hub/gmso/pull/819 in GMSO closes #572 ### PR Checklist ------------ - [ ] Includes appropriate unit test(s) - [ ] Appropriate docstring(s)...

chrisjonesBSU

Allowing automated atom typing for larger system(>=100 molecules) upon providing the exact coeff. for each atom,bond,angle,dihedral,impropers,etc. for it's smaller individual component( 1 molecule) .data file

1

**Describe the behavior you would like added to Foyer** A clear and concise description of what the proposed idea is. **Describe the solution you'd like** A clear and concise description...

amannsonii3

pydocstyle is no longer maintained, we should switch the pre-commit workflows over to [ruff](https://github.com/astral-sh/ruff). https://github.com/mosdef-hub/gmso/pull/819 for a starting point.

chrisjonesBSU