openff-fragmenter

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Use xtb for the WBO

2

At the free energy workshop, it was mentioned that Cresset is now using xtb to calculate the WBO for fragmentation as they do not have access to openeye. This seems...

jthorton

Fragmentation issue because of stereochem when the bond involves Sulfur

3

Hi, I bumped into the following issue while processing this sulfoxide compound ("O=S(c1ccc(Nc2nc(OCC3CCCCC3)c4c([nH]cn4)n2)cc1)C"). Dissecting the code looks like it builds fragments around all rotatable bonds without issue but raises the...

rvkrishnan30

Provide a way to map from `WBOFragmenter` input molecule to parent molecule

1

### Summary Many users probably want to follow specific atoms/bonds through the fragmentation process. However, as a result of performing canonicalization of input molecules, there's no way to map from...

j-wags

Calculating AM1 WBOs can fail for several reasons. Some are: 1. Missing BCC parameters 2. Missing stereochemistry 3. Total charge does not equal formal charge. The current workaround is just...

ChayaSt

The chirality of some fragments flip with respect to the chirality in the parent molecule.

ChayaSt

Use new Pydantic v1 backdoor

1

## Description https://docs.pydantic.dev/latest/changelog/#v11018-2024-08-22 ## Todos Notable points that this PR has either accomplished or will accomplish. - [ ] Use new Pydantic v1 backdoor ## Status - [ ] Ready...

mattwthompson

GPU-Omega warning

1

I get this warning when using the fragmenter, despite GPU-Omega working on my end: ``` from openff.toolkit.topology import Molecule from openff.fragmenter.fragment import WBOFragmenter from openeye import oeomega tor_opts = oeomega.OETorDriveOptions()...

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