Lily Wang

[Request] Isotopic smiles

5

**Is your feature request related to a problem? Please describe.** A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] `Molecule.from_smiles("[13C]").to_smiles()` does not roundtrip...

[Request] More explicit function signature in Molecule.is_isomorphic_with

3

**Is your feature request related to a problem? Please describe.** A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] It's quite easy to...

Consolidate TopologyAttrs with consistent meanings

6

TopologyAttrs are a bit of a mess right now, and the documentation is not up-to-date. This is a list of some inconsistencies I found. ## atomiccharge The GAMESS parser uses...

VirtualSiteType.inPlaneAngle and outOfPlaneAngle._unit is None

2

**Describe the bug** Despite the code appearing to do otherwise, both `VirtualSiteType.inPlaneAngle._unit` and `VirtualSiteType.outOfPlaneAngle._unit` is `None`. Other unit-ed attributes, like `VirtualSiteType.distance`, don't have this issue. I'm not sure if this...

**Is your feature request related to a problem? Please describe.** Add code that "normalizes" unusual SMARTS patterns. This came up recently in both Lorenzo's parameter analysis and at https://github.com/MobleyLab/FreeSolv/issues/51 ....

Indexing error for two-atom molecules

2

Noticed while using Espaloma to assign charges to a batch of molecules -- as far as I can tell, any 2-atom molecule results in an indexing error when trying to...

runcuda.sh overwrites environment variables

3

Targets involving workqueue seem to wrap commands in `data/runcuda.sh`. This unfortunately overwrites variables in the local environment, trying to load quite an old version of CUDA (4/5), if the hostname...

**Is your feature request related to a problem? Please describe.** When assigning partial charges with OpenEye, conformers are generated via the toolkit API using OpenEye: https://github.com/openforcefield/openff-toolkit/blob/f79f48bef13a997619c4391ca6c800806238237a/openff/toolkit/utils/openeye_wrapper.py#L2456-L2461 @ntBre and I have...

oemol.GetConfs() consuming large amount of memory even when no conformers are present

4

**Describe the bug** Not a bug per se, but could impact on toolkit usability for large molecules -- while debugging https://github.com/openforcefield/openff-nagl/issues/101 I saw that converting molecules to and from OpenEye...

Benchmark guessers with asv

2

We should benchmark the changes made in https://github.com/MDAnalysis/mdanalysis/pull/3753/files/a946156f440e0ec7714854723a201f4d4b941526#r1550099795 .