Automated Dihedral Analysis

.github/workflows/ci.yaml

@@ -76,7 +76,6 @@ jobs:
     - name: Install pybol (fixture staging tool)
       run: |
          python -m pip install pybol
-
     - name: Install GROMACS (${{ matrix.gromacs-version }})
       run: |
          micromamba install 'gromacs==${{ matrix.gromacs-version }}' pocl

.gitignore

@@ -12,3 +12,6 @@ dist
 doc/examples/benzene/Equilibrium/
 .coverage
 coverage.xml
+*.lock
+*.npz
+dir.csv

CHANGES

@@ -5,7 +5,7 @@ CHANGES for MDPOW
 Add summary of changes for each release. Use ISO 8061 dates. Reference
 GitHub issues numbers and PR numbers.
 
-2022-??-??    0.9.0
+2023-??-??    0.9.0
 cadeduckworth, orbeckst, VOD555
 
 Changes
@@ -19,7 +19,14 @@ Changes
 * _prepare_universe and _conclude_universe removed from 
   EnsembleAnalysis.run() method, no longer needed (per comments, #199)
 * added support for Python 3.10
-* dropped testing on Python 3.6 
+* dropped testing on Python 3.6
+
+Enhancements
+
+* new workflows module (PR #217)
+* new automated dihedral analysis workflow (detect dihedrals with SMARTS,
+  analyze with EnsembleAnalysis, and generate seaborn violinplots)
+  PR #217)
 
 Fixes
 

devtools/conda-envs/test_env.yaml

@@ -15,9 +15,11 @@ dependencies:
 - numkit
 - gromacswrapper
 - alchemlyb <2
+- rdkit
+- seaborn
 
   # Testing
 - pytest
 - pytest-pep8
 - pytest-cov
-- codecov  
+- codecov

doc/requirements.txt

@@ -6,3 +6,6 @@ pyyaml
 GromacsWrapper>=0.5.1
 alchemlyb
 mdanalysis
+rdkit
+seaborn
+matplotlib

doc/sphinx/source/analysis.txt

@@ -20,12 +20,11 @@ all FEP simulations. They then make data available (typically, as a
 :class:`pandas.DataFrame`).
 
 .. toctree::
-   :maxdepth: 1
+   :maxdepth: 2
 
    analysis/solvation
    analysis/dihedral
 
-
 .. _framework:   
 
 Ensemble Analysis Framework
@@ -45,10 +44,9 @@ in more detail in [Lescoulie2021]_.
 .. toctree::
    :maxdepth: 1
 
-   analysis/ensemble_analysis	      
+   analysis/ensemble_analysis
    analysis/ensemble
 
-
 References
 ----------
 .. [Lescoulie2021] A. Lescoulie, "SPIDAL Summer REU 2021: Upgrading MDPOW and

doc/sphinx/source/conf.py

@@ -244,6 +244,10 @@
                        'https://numpy.org/doc/stable/': None,
                        'https://docs.scipy.org/doc/scipy/reference/': None,
                        'https://gromacswrapper.readthedocs.io/en/latest': None,
+                       'https://docs.mdanalysis.org/stable/': None,
+                       'https://www.rdkit.org/docs/': None,
+                       'https://pandas.pydata.org/docs/': None,
+                       'https://seaborn.pydata.org': None,
                    }
 
 
@@ -255,5 +259,4 @@
 # This value selects what content will be inserted into the main body of an autoclass directive.
 # "class", "init", "both"
 autoclass_content = "both"
-
-
+automodule_content = "both"

doc/sphinx/source/index.txt

@@ -139,7 +139,8 @@ For current issues and open feature requests please look through the
    scripts
    equil
    fep
-   analysis   
+   analysis
+   workflows
    utilities
    forcefields