Matt Thompson
Matt Thompson
> It would be even nicer to take out **kwargs so typos, etc. don't go unnoticed. +1 from me on moving from keyword arguments to named arguments
> Should there even be the possibility to have topology molecules without being part of a topology? I can't think of a use case for this. Nor any reason why...
I'm in support of this sort of change (#740). I think the last time I tried to implement this, I was somewhat intimidated but the number of places in the...
@Yoshanuikabundi please tag me or reach out to me directly if you have any questions or suggestions on integrating Interchange in this, including patches to other repos. I don't want...
My first-impression is that these new `Topology` methods should be standalone functions scoped to the notebook; I think we are getting close to the wire for significant changes to the...
> What are the dangers of just doing top.to_openmm() rather than interchange.to_openmm_topology()? Not a danger, but the toolkit's method does not include virtual sites (by design). Otherwise their behavior should...
There is another project [`retworkx`](https://github.com/Qiskit/retworkx/) that has some good benchmarks on distance/pair calculations and subgraph isomorphisms. It looks less mature that the graph-tool but they have a [JOSS paper](https://github.com/openjournals/joss-papers/blob/joss.03968/joss.03968/10.21105.joss.03968.pdf) in...
There's no compelling need in the existing toolkit functionality, but some part of the topology refactor would benefit from this. There's some amount of NetworkX graph isomorphism used in `Molecule.from_pdb`....
I think this has been fixed? ```python3 In [1]: from openff.toolkit.topology import Molecule Warning: Unable to load toolkit 'OpenEye Toolkit'. The Open Force Field Toolkit does not require the OpenEye...
The TODO two lines above seems quite relevant as a bit of debt 😅 . Relates somewhat to discussions around revamping the SMIRNOFF spec, particularly https://github.com/openforcefield/standards/issues/2#issuecomment-930133340. Requiring at least one...