spyrmsd
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RMeli
📐 Symmetry-corrected RMSD in Python
As we discussed in #105: here is my first shot at implementation of RMSD functions with multicore and timeout functionalities. For now, I kept the `rmsd_timeout` function public, however we...
The performance of `spyrmsd` seems to have been mis-represented in a recent pre-print: * [Canonized then Minimized RMSD for Three-Dimensional Structures](https://arxiv.org/abs/2405.00339) * https://github.com/JerryJohnsonLee/CanonizedRMSD/issues/8 This is likely due to the poor...
Molecular graphs are currently matched taking into account the connectivity and the elements (#10). There should be an option that allows users to match according to bond order as well....
* Most of the information is redundant * `pip install -e .[openbabel]` and similar do not work (optional dependencies) * Trying to add [optional dependencies](https://peps.python.org/pep-0631/#optional-dependencies) to `pyproject.toml` results in `flit_core.config.ConfigError:...
The [installation documentation](https://spyrmsd.readthedocs.io/en/develop/installation.html) has not been updated as much as the README and needs to be re-worked. The same goes for the tutorial, where `rustworkx` does not appear.
PR #113 introduced parallelisation of `rmsdwrapper`, with the goal of providing a very useful timeout functionality (to avoid hangs in pathological cases where graph isomorphism takes a very long time)....