Seth Axen

Alternatively, `mpi4py.futures.MPICommExecutor` is a child of `concurrent.futures.Executor`, so we could perhaps just use `Executor` API functions to support all 4 modes. I don't see a `SequentialExecutor` or `SerialExecutor` anywhere, so...

The most comprehensive benchmarks we've run with E3FP are in Table S3 and Figure S10 of the [supplement](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6075869/bin/NIHMS909954-supplement-Supporting_Information.pdf) of the paper. I've included them below: The code that ran these...

Regarding storage sizes, I haven't run any benchmarks in this area. E3FP's default storage approach is described [here](https://e3fp.readthedocs.io/en/latest/usage/fingerprints/storage.html). Since it's just a light wrapper of a `scipy.sparse.csr_matrix`, its performance will...

@PARODBE sorry for the late reply. There's insufficient information here for me to replicate the issue. At the bare minimum, please provide a minimum code example including SMILES or a...

Hi, I'm very sorry for the late reply to this issue. I was only partially able to reproduce the error: ```julia >>> import e3fp. >>> from e3fp.pipeline import fprints_from_mol, confs_from_smiles...

Looking at the latest code coverage, most code has corresponding tests, except for conformer generation (which is difficult to test anyways) and pipeline methods. Once pipeline tests are written, this...

Hi @PARODBE, sorry for the late reply. The folding occurs by splitting the fingerprint vector into 2 vectors of identical length and OR-ing them. Hence it decreases the size by...

I agree, we should have a more informative error, but loading the previously generated conformers probably isn't a good idea. The main purpose of the values file is to write...

Somewhat related to this issue, conformer energies are now stored in SDF files (see d9c3b1a). HDF5 file capabilities are still present for when one wants all energies stored in a...

No, it would be a separate workflow. See for example the one linked above. So it would not alter the time it takes to run the current test suite, and...