Merge pull request #105 from MDAnalysis/0.4

Enhanced plotting and visualization.
MDAnalysis · May 9, 2024 · c9957d6 · c9957d6
2 parents c7022aa + e485c5c
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diff --git a/README.md b/README.md
@@ -15,13 +15,11 @@ SolvationAnalysis
 ---
 
 Solvation analysis implements a robust, cohesive, and fast set of methods
-for analyzing the solvation structure of a liquid. It seamlessly integrates with
-[MDAnalysis](https://www.mdanalysis.org/), making use of the core AtomGroup
-and Universe data structures to parse solvation information. If you are interested
-in understanding the solvation structure of a liquid, this package is for you!
+for analyzing the solvation structure of a liquid. It integrates with
+[MDAnalysis](https://www.mdanalysis.org/) to seamlessly calculate, query,
+and visualize solvation information.
 
-
-Find documentation and tutorials on [readthedocs].
+Find documentation and tutorials on [readthedocs](https://solvation-analysis.readthedocs.io/en/latest/).
 
 ### Installing SolvationAnalysis
 
@@ -35,6 +33,23 @@ pip install solvation-analysis
 conda install -c conda-forge solvation_analysis
 ```
 
+### Solvation Analysis Summarized
+
+![summary](docs/tutorials/images/summary_figure.png)
+
+
+### Visualization
+
+With just a few lines of code, solvation analysis can calculate detailed
+properties within and between solvent systems. A few examples are shown below.
+
+![solvation_analysis.plotting.compare_coordination_numbers](docs/tutorials/images/coordination_plot.png)
+
+![solvation_analysis.plotting.plot_speciation](docs/tutorials/images/speciation_plot.png)
+
+![solvation_analysis.plotting.plot_rdfs](docs/tutorials/images/rdf_plot.png)
+
+
 ### Contributing
 
 Contributions, both issues and PRs, are welcome. If you'd like to contribute, we ask that you

diff --git a/docs/getting_started.ipynb b/docs/getting_started.ipynb
@@ -16,6 +16,7 @@
     "- Multi Atom Solutes: generalize to solutes with many atoms\n",
     "- Visualization: use `nglview` to visualize structures\n",
     "- Residence and Networking: calculate residence times and solute-solvent networks\n",
+    "- Plotting and Comparing: generate illustrative plots of solvation properties\n",
     "- RDF Fitting: See how solvation-analysis finds solvation cutoffs\n",
     "\n",
     "For a full catalog of the properties calculated, read through the API documentation. Solvation-analysis is a powerful tool that calculates a wide range of properties, but it will take some time to master. If you ever have any questions, or encounter any bugs, please raise an issue on [GitHub](https://github.com/MDAnalysis/solvation-analysis).\n"

diff --git a/docs/tutorials/basics_tutorial.ipynb b/docs/tutorials/basics_tutorial.ipynb
diff --git a/docs/tutorials/images/coordination_plot.png b/docs/tutorials/images/coordination_plot.png
diff --git a/docs/tutorials/images/rdf_plot.png b/docs/tutorials/images/rdf_plot.png
diff --git a/docs/tutorials/images/speciation_plot.png b/docs/tutorials/images/speciation_plot.png
diff --git a/docs/tutorials/images/summary_figure.png b/docs/tutorials/images/summary_figure.png
diff --git a/docs/tutorials/plotting_tutorial.ipynb b/docs/tutorials/plotting_tutorial.ipynb
diff --git a/solvation_analysis/_column_names.py b/solvation_analysis/_column_names.py
@@ -29,4 +29,4 @@
 NETWORKED = "networked"
 
 # for speciation
-COUNT = "count"
+COUNT = "fraction"
diff --git a/solvation_analysis/coordination.py b/solvation_analysis/coordination.py
@@ -49,7 +49,7 @@ class Coordination:
     Parameters
     ----------
     solvation_data : pandas.DataFrame
-        The solvation data frame output by Solute.
+        The solvation dataframe output by Solute.
     n_frames : int
         The number of frames in solvation_data.
     n_solutes : int

diff --git a/solvation_analysis/pairing.py b/solvation_analysis/pairing.py
@@ -43,7 +43,7 @@ class Pairing:
     Parameters
     ----------
     solvation_data : pandas.DataFrame
-        The solvation data frame output by Solute.
+        The solvation dataframe output by Solute.
     n_frames : int
         The number of frames in solvation_data.
     n_solutes : int