Ref #25
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Ref #25
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***Refactor MonitoringPlotter class initialization and visualization*** ***Generate report data for labels and observable data
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Description
Previously, we have created openMM topology using the openff toolkit. Since this involves calculating the partial charges with AM1-BCC (which we don't need for running simulations with NNP), this introduced a large computational overhead that we can avoid.
This PR moves to generating the openMM topology using PDB files with roundtrips through rdkit. This change had a few unintended consequences, therefore this PR has a lot of other, minor changes to the overall package structure.
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