ProDy 1.10 Series

1.10.2 (May 2, 2018)

  • Minor fixes.

1.10.1 (May 1, 2018)

  • Added the function sliceAtomicData for slicing data based on slicing atoms.
  • Updated the documentation for making a release.
  • Other documentation and minor fixes.

1.10 (Apr 30, 2018)

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 networkx to visualize a given tree.

Ensemble and PDBEnsemble

  • Associated an MSA object to the PDBEnsemble class.
  • Added an pairwise option to Ensemble.getRMSDs() to obtain an

RMSD table of every pair of conformations in the ensemble.

  • Improved 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 Improvements

  • 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.