SimonBoothroyd

**Describe what you are trying to achieve** The documentation for `OptimizationRecord.trajectory` states: > trajectory (List[ObjectId], Optional) – The list of Molecule Id’s the Optimization procedure generated at each step of...

**Is your feature request related to a problem? Please describe.** The `ResultRecord.get_molecule()` function currently checks for a client before checking to see if the molecule is already cached. This means...

vdW handler overwrites v-site charge increments

5

**Describe the bug** The vdW handler currently sets the charges of all atoms to be zero, including those that have had their charge re-distributed by a virtual site. **To Reproduce**...

vdW switch width not used

5

**Describe the bug** This `vdWHandler` exposes a `switch_width` property but as far as I can tell this doesn't get used anywhere in the code. **To Reproduce** ``` from openff.toolkit.topology import...

Deprecate charge_from_molecules kwarg

6

**Is your feature request related to a problem? Please describe.** It might be a good idea to begin thinking about deprecating the `charge_from_molecules` kwarg that is currently accepted by the...

**Is your feature request related to a problem? Please describe.** It would be useful to be able to determine which atoms in a molecule are topologically symmetrical for applications such...

LibraryCharge handler slow SMARTS matching

8

**Describe the bug** I've come across a couple of cases where the library change handler SMARTS matching code hangs when attempting to match a full molecule SMILES. This is likely...

Store which atoms have undefined stereochemistry

2

**Is your feature request related to a problem? Please describe.** It with be useful if the toolkit tracked (or added a method to find) which atoms / bonds in a...

RDKit `from_smiles` allows implicit H smiles when explicit H is True

1

**Describe the bug** The RDKit toolkit wrapper does not [raise the expected exception](https://github.com/openforcefield/openff-toolkit/blob/a0bcb3b1b763718d01ed0bdb0e359b766b302561/openff/toolkit/utils/toolkits.py#L3389-L3395) when creating a molecule from `'[NH+:1]([C@:2]([C:3](=[O:4])[O-:10])([C:5]([C:6]([C:7]([C:8]([NH+:9]([H:22])[H:23])([H:20])[H:21])([H:18])[H:19])([H:16])[H:17])([H:14])[H:15])[H:13])([H:11])[H:12]'` when the `explicit_hydrogens` option is set to true. This allows some...

Canonically order molecule before conformer generation

1

**Is your feature request related to a problem? Please describe.** The ordering of a molecule can affect which conformers are generated for it using OE (and probably also RDKit). This...