ProDy 1.10 Series

1.10.11 (Oct 25, 2019)

New Features:

  • Added calcDynamicFlexiblityIndex().
  • Added “related_entries” to PDB header.
  • Enabled RTB to take a customized Hessian as input.
  • Added numEntries to NMA, Mode, and ModeSet objects.

Bug Fixes and Improvements:

  • Added a keyword argument to mapChainByChain() to allow user-defined

correspondence of chain IDs between the target and the mobile.

  • Compatibility and bug fixes for various functions.
  • Fixed compilation error on MacOS if a user-installed gcc is present.
  • Consistency fixes.
  • Added new modules and functions for handling angles, dihedrals, impropers,

cross-terms, non-bonded exclusions, hydrogen bond donor and acceptor information from PSF files and including them in AtomGroup.

1.10.10 (May 9, 2019)

Bug Fixes and Improvements:

  • Compatibility fix for the RTB module on Windows.
  • Fixed compilation error on MacOS.
  • Consistency fixes.

1.10.9 (May 2, 2019)

New Features:

  • Added a method option to pairModes() to use other solvers for the

linear assignment problem.

  • Added functions for handling user-defined data for Ensemble and


  • Added the reweight option to ModeEnsemble to reweight the modes

based on matched eigenvalues.

domain information.

product between two square fluctuations.

  • Allowed parseHiC() to automatically identify and read bindary hic files.

Bug Fixes and Improvements:

  • Fixes to parsePDB() for compatibility with large PDB files.
  • Fixes and improvements to membrane ANM functions for faster computation.
  • PY3K compatibility fixes.

1.10.8 (Sept 18, 2018)

New Features:

matchModes(). Both options allow speed-up about 40%.

Bug Fixes and Improvements:

1.10.7 (May 21, 2018)

New Features:

Bug Fixes and Improvements:

  • Reorganized MechStiff functions. Now MechStiff functions are moved out from

the ANM class, and get... were renamed to calc...

  • Fixed a problem that an error will be raised when searching a sequence

against Pfam.

  • PY3K compatibility fixes.

1.10.3 (May 14, 2018)

New Features:

Bug Fixes and Improvements:

  • Switched to Python Wheel for distributing on Windows. This will allow Windows users to pip install prody.
  • Fixed a error when compiling C++ extensions on MacOS.
  • Various bug fixes according to issues proposed on the GitHub.

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

New Features:


Ensemble and PDBEnsemble

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.