openff-toolkit

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Move writer/reader formats into base class

1

Fixes #1832 and makes the structure of wrappers more uniform without breaking the API - [x] Tag issue being addressed - [ ] Add [tests](https://github.com/openforcefield/openff-toolkit/tree/main/openff/toolkit/_tests) - [ ] Update docstrings/[documentation](https://github.com/openforcefield/openff-toolkit/tree/main/docs),...

mattwthompson

`ToolkitWrapper` defines properties that point to attributes that are only ever defined in the derived classes. These properties point to "private" attributes so we might as well define them in...

mattwthompson

Add an API point to get a list of available charge methods

1

**Is your feature request related to a problem? Please describe.** Investigating the available charge methods often requires knowledge of how each toolkit wrapper is implemented, or inspecting the documentation. **Describe...

Yoshanuikabundi

**Is your feature request related to a problem? Please describe.** My machine has a 12-core/24 thread CPU. By default, antechamber spins up 24 threads to charge a molecule. I've found...

Yoshanuikabundi

`Topology.from_pdb(_additional_substructures=...` can use a LOT of memory

2

**Describe the bug** Trying to load a PDB of the new blockbuster drug semaglutide, a 31-residue polypeptide with two non-canonical residues, using the experimental `_additional_substructures` argument rapidly consumes memory. On...

Yoshanuikabundi

Current `Molecule` hashing is dangerous

2

**Is your feature request related to a problem? Please describe.** `Molecule.__hash__` uses (non-mapped) SMILES, which can cause hash collisions when otherwise identical molecules use different atom indices. This is almost...

mattwthompson

Allow Pydantic v2 in test environments

6

- [ ] Tag issue being addressed - [ ] Add [tests](https://github.com/openforcefield/openff-toolkit/tree/main/openff/toolkit/_tests) - [ ] Update docstrings/[documentation](https://github.com/openforcefield/openff-toolkit/tree/main/docs), if applicable - [ ] [Lint](https://open-forcefield-toolkit.readthedocs.io/en/latest/developing.html#style-guide) codebase - [ ] Update [changelog](https://github.com/openforcefield/openff-toolkit/blob/main/docs/releasehistory.rst)

mattwthompson

Do not require OpenMM for tests

2

Some users do not wish to download the CUDA toolkit to do things that don't require it. Much of the toolkit's API has been updated to accommodate this. The testing...

mattwthompson

Use paths in fixtures, allow writing molecules to paths

1

#740 - [ ] Tag issue being addressed - [ ] Add [tests](https://github.com/openforcefield/openff-toolkit/tree/main/openff/toolkit/_tests) - [ ] Update docstrings/[documentation](https://github.com/openforcefield/openff-toolkit/tree/main/docs), if applicable - [ ] [Lint](https://open-forcefield-toolkit.readthedocs.io/en/latest/developing.html#style-guide) codebase - [ ] Update [changelog](https://github.com/openforcefield/openff-toolkit/blob/main/docs/releasehistory.rst)

mattwthompson

Allow pytest 8

3

- [ ] Tag issue being addressed - [ ] Add [tests](https://github.com/openforcefield/openff-toolkit/tree/main/openff/toolkit/_tests) - [ ] Update docstrings/[documentation](https://github.com/openforcefield/openff-toolkit/tree/main/docs), if applicable - [ ] [Lint](https://open-forcefield-toolkit.readthedocs.io/en/latest/developing.html#style-guide) codebase - [ ] Update [changelog](https://github.com/openforcefield/openff-toolkit/blob/main/docs/releasehistory.rst)

mattwthompson