solvation-analysis

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rdf_data not initialized properly when running solute.run()

6

I am using ase to convert an xdatcar file to a xyz and pdb file and reading it into the mda.Universe as you can see in the pdf attached [vertopal.com_5x_analysis.pdf](https://github.com/MDAnalysis/solvation-analysis/files/14887522/vertopal.com_5x_analysis.pdf)....

Caboomi

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...

orionarcher

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...

orionarcher

Similarly to what we do in the core library, finding the right RTD link is hard, so we can add an action to add the right link to the PR...

IAlibay

switch from conda incubator to micromamba action

1

Noticing that the conda builds are taking a long while, switching to micromamba will significantly speed CI up.

IAlibay

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...

orionarcher

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 -...

orionarcher

Should we allow custom functions for calculating solvation shells at the RDF step?

5

I am thinking that we might want to add more flexibility at the level above analysing the RDF itself. Ie, should we allow custom functions to calculate shells that don't...

hmacdope

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

6

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....

orionarcher