ProDy 1.10 Series

1.10 (Apr 30, 2019)

Signature Dynamics

• Added calcEnsembleENMs() to compute ENMs on each conformation of a

given ensemble to obtain an ensemble of modes.

• Added ModeEnsemble and sdarray classes as the basic

data types for signature dynamics.

• Added functions such as calcSignatureSqFlucts(),

calcSignatureCrossCorr(), calcSignatureFractVariance() to extract signature dynamics.

• Added calcEnsembleSpectralOverlaps() to obtain dynamical

overlaps/distances among the conformations in a given ensemble.

New Features:

Visualization

• Added showAtomicLines() and showAtomicMatrix() functions to

improve visualization.

• Added an networkx option to showTree() so that the user can choose

to use :module:`~networkx` to visualize a given tree.

Ensemble and PDBEnsemble

• Associated an MSA object to the 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

queryUniprot() and parsePfamPDBs().

Bug Fixes and Improvement

• Fixed compatibility problems for Python 2 and 3.
• Improved the saveModel() function to include class-specific features.
• Fixed a bug related to the Atomgroup addition method.
• Bug fixes to NMA classes.
• Fixed a problem with MSA indexing.
• Reorganized file structures and functions for consistency.
• Other bug fixes.