Matt Thompson

Add uniform, automated linting

2

I find it difficult to read some changesets in this project, owing largely to things like long lines and inconsistent text wrapping. Enter (standard set of tools). The https://pre-commit.ci/ would...

## Description Taking a stab at using the new APIs - I may not get back to this for a minute so feel free to grab any of these changes...

Update versioneer

4

```shell $ pip install versioneer $ versioneer install ``` magic and then everything works in Python 3.12 (surely)

```python3 import espaloma from openff.toolkit.topology import Molecule molecule = Molecule.from_smiles("CCO") graph = espaloma.Graph(molecule) espaloma_model = espaloma.get_model("latest") espaloma_model(graph.heterograph) espaloma.graphs.deploy.openmm_system_from_graph( graph, forcefield="openff-2.1.0", ) ``` ```python AssertionError Traceback (most recent call last) Cell...

Do not use `numpy.asfarray` which is removed in 2.0

1

https://numpy.org/devdocs/release/2.0.0-notes.html#numpy-2-0-python-api-removals ``` $ git checkout upstream/master && ruff check --preview --select NPY201 . --exclude tools HEAD is now at b395fd4b Replace &> run.log with > run.log 2>&1 (dash compatible) src/molecule.py:3173:22:...

From Slack

The toolkit stores the header of `antechamber -L` as the AmberTools version for provenance and reporting, but in odd versions these two dffier: ``` $ antechamber -L | head -n2...

Add method for deleting conformer(s)

4

**Is your feature request related to a problem? Please describe.** There's no (public) method for deleting conformers. `Molecule.generate_conformers` will overwrite conformers, but in some other use cases one might want...

**Is your feature request related to a problem? Please describe.** Users, especially those adapting OpenFF tools and force fields outside of conventional drug discovery applications, commonly use large molecules for...