openff-toolkit
openff-toolkit copied to clipboard
openforcefield
The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
**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,...
**Describe the bug** Passing a PDB with residues with insertion codes such as what is demonstrated below leads to a squashed residue rather than two individual ones: ``` ATOM 2601...
This PR updates the showcase to use all the new magic in the toolkit and interchange. It will no longer use Parmed and OpenMM force fields. It also includes performance...
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...
**Description** I have recently ported over my workflow to use openff.toolkit instead of the old openforcefield module. This is meant to take in a small molecule mol2 file and a...
**Describe the bug** `Molecule.enumerate_stereoisomers()` fails on some molecules with the OpenEye toolkit backend. **To Reproduce** Here is an example: ```python >>> from openff.toolkit.topology import Molecule >>> mol = Molecule.from_smiles('C1CN2C3CC4CC(C3)CC(C4)C2=N1', allow_undefined_stereo=True)...
- [ ] 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)
### 1: Get approval from Jeff Wagner (or current [product owner](https://github.com/openforcefield/status)) to release main "as is" ### 2: Create a new release on GitHub, following this template: https://github.com/openforcefield/openff-toolkit/releases/new #### Tag...
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)
To improve ease of packaging and reduce dependency size, it would be good to use a minimal build of OpenMM. This build would just be used to produce openMM-format systems...
Metadata
Owner
Metadata
The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io