- Added :func:`.calcEnsembleENMs` to compute ENMs on each conformation of a
given ensemble to obtain an ensemble of modes.
- Added :class:`.ModeEnsemble` and :class:`.sdarray` classes as the basic
data types for signature dynamics.
- Added functions such as :func:`.calcSignatureSqFlucts`,
:func:`.calcSignatureCrossCorr`, :func:`.calcSignatureFractVariance` to extract signature dynamics.
- Added :func:`.calcEnsembleSpectralOverlaps` to obtain dynamical
overlaps/distances among the conformations in a given ensemble.
New Features:
Visualization
- Added :func:`.showAtomicLines` and :func:`.showAtomicMatrix` functions to
improve visualization.
- Added an networkx option to :func:`.showTree` so that the user can choose
to use :module:`~networkx` to visualize a given tree.
Ensemble and PDBEnsemble
- Associated an :class:`.MSA` object to the :class:`.PDBEnsemble` class.
- Added an pairwise option to :method:`.Ensemble.getRMSDs` to obtain an
RMSD table of every pair of conformations in the ensemble.
- Improved :method:`.Ensemble.setAtoms` for selecting a subset of
residues/atoms of the ensemble.
Databases and Web Services
- Added methods and classes for obtaining data from CATH and Dali.
- Added additional functions for Uniprot and Pfam such as
Bug Fixes and Improvement
- Fixed compatibility problems for Python 2 and 3.
- Improved the :func:`.saveModel` function to include class-specific features.
- Fixed a bug related to the :class:`.Atomgroup` addition method.
- Bug fixes to :class:`.NMA` classes.
- Fixed a problem with :class:`.MSA` indexing.
- Reorganized file structures and functions for consistency.
- Other bug fixes.