Matt Thompson

Improve default .gitignore defaults for common IDEs

9

Some IDEs store settings in folders that are not automatically `.gitignore`'d here. The three IDEs I know of that computational chemistry-ish developers use are * VS Code - `.vscode/`, handled...

Defer loading modules used only in `compat.upcast_types`

2

Work in progress. I will rebase #1491 or something similar into this as well. ``` In [1]: >>> import sys ...: >>> from pint import UnitRegistry ...: >>> 'pandas' in...

Slow import times due to always importing optional packages

3

Hi, thanks to the developers and maintainers for creating and supporting this software. I've noticed some slow (> 1 second) import times and used Tuna to isolate it as the...

Can't serialize to JSON

5

**Describe the bug** I wanted to save a collection to disk in order to avoid needing to downloads a large dataset every time I ran a test or re-started a...

`ForceField` allows multiple parameters to have the same SMIRKS patterns

18

**Describe the bug** The toolkit's force field class allows multiple parameters within the same handler to have the same SMIRKS patterns. While it may seem like a strange use case,...

Re-introduce compatible openmmforcefields

3

Release ~~0.11.1~~ 0.11.2 of `openmmforcefields` introduces a **backwards-compatible** fix for the new toolkit APIs. This PR attempts to re-introduce the examples that depend on it. - [ ] Tag issue...

Update virtual site notebook

4

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

Add `vdWHandler.long_range_dispersion`

2

Pending https://github.com/openforcefield/standards/pull/40 - [ ] Tag issue being addressed - [x] 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 - [x] [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)

Raise exception when processing molecule with radical electrons

2

Here's a block to add to the changelog, keeping it out of the tree to make merges easier: ``` - [PR #1236](https://github.com/openforcefield/openff-toolkit/pull/1236) raises [`RadicalsNotSupportedError`](openff.toolkit.utils.exceptions.RadicalsNotSupportedError) when [`Molecule.from_openeye`](openff.toolkit.topology.Molecule.from_openeye), [`Molecule.from_rdkit`](openff.toolkit.topology.Molecule.from_rdkit), [`Molecule.from_smiles`](openff.toolkit.topology.Molecule.from_smiles), or similar...

`OpenEyeToolkitWrapper.to_file` writes PDB files with no CONECT records

2

**Describe the bug** A `Molecule` written to a PDB file **includes** CONECT records when OpenEye Toolkits are **not** available but **excludes** them when they **are**. This can lead to surprising...