Orion Cohen

water from

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- [x] I believe this to be a bug with Open Babel - [ ] This is a feature request ## Environment Information Open Babel version: 3.1.1 Operating system and...

change equality comparison operation to `as_dict`

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## Summary The current equality operation for InputSet's will fail if `InputSet.inputs` has mutable values. This happens often because InputSet is designed to support `InputFile`s as `inputs`. I have changed...

A builder for classical md workflows

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This PR implements an `ElectrolyteBuilder` class for analysis of trajectories generated by atomate2.openmm. The core `ElectrolyteBuilder` class is supported by a variety of utility functions that interact with `MDAnalysis` and...

I am in the process of adding linting (#103) that will supersede the pep8speaks plugin. I unfortunately do not have administrative permissions to disable it. @IAlibay or @hmacdope would you...

Currently, if a molecule is included as a solvent but isn't in any solvation shells, it will not be included in various dataframes and dictionaries that tabulate results. This leads...

Installing from source in a fresh directory with this code: ``` >>> git clone [email protected]:MDAnalysis/solvation-analysis.git >>> cd solvation-analysis >>> pip install -e . ``` Yields an install that yields version...

This is split off from PR #78 to address two points the consistency and formatting of the documentation. Todos: - [ ] closely read over all documentation for errors -...

Add save() and load() method to solution.

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This important functionality is currently missing. As is, users would need to rerun their analysis. There should be methods to serialize and load a solution object in a single file....

Atomate2 OpenMM integration & broader classical MD framework

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Developed by @xperrylinn and @orionarcher ## Summary This PR builds out support for OpenMM with a framework that could be extended to support other MD codes. Namely LAMMPS, Amber, and...

Simpler molecule graph support + performance enhancement to XRD plot

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## Features This PR implements two completely separate features: 1. It cleans up the support for MoleculeGraphs in structure.py 2. It vectorizes the XRD implementation to improve performance 30x For...