PENSA 0.2.2

Now includes subpackages in setup.

PENSA 0.2.1

New functionality:

• Distances reader based on MDAnalysis
• GPCR feature reader as an example for system-specific additions
• Tutorials for SSI and atom features

PENSA 0.2.0

New functionality:

• State-specific information
• Water features
• Atom features
• TICA
• Doc pages
• Tutorial using MOR traj. from GPCRmd

Major changes to existing functionality:

• The former modules are now sub-packages.
• The function get_features() was renamed to get_structure_features() to account for the fact that there are several feature types now.
• Torsion features are by default loaded in radians now. Cosine and sine can be obtained using the option cossin=True

Notes:

• Functionality and UI might still change in minor releases to streamline workflows!
• Documentation and tutorials do not cover all of the new functionality yet. We will update this step by step.

PENSA 0.1.2

Changelog:
Version 0.1.2 ...

• now provides feature names as a list of strings. No more .describe() is necessary.
• corrects the behavior of option bin_width in relative_entropy_analysis(). So far, this option falsely did not have any effect. To retain the old behavior, use bin_width=None, bin_num=10, which are also the new default options.
• removes the obsolete bin_width option in Kolmogorov-Smirnov analysis (this was just a copy-paste artifact)
• fixes the previously undefined variables in reporting of relative_entropy_analysis().
• adds the first tests for pytest (only a dummy for now) and test data.
• adds axis labels for PC comparison and feature correlations.
• adds a tutorial that uses GPCRmd simulations of a mu-opioid receptor.

PENSA 0.1.1

Functionality:

• preprocessing
• featurization
• feature comparison via relative entropy
• feature comparison via Kolmogorov-Smirnov statistic
• projection on combined principal components
• clustering combined ensembles

Add-ons:

• example python scripts
• visualization script for VMD
• bash script tutorial
• Jupyter notebook tutorial