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

PDBEnsemble

• Added the reweight option to ModeEnsemble to reweight the modes

based on matched eigenvalues.

• showSqFlucts() now plot color-coded square fluctuations using

domain information.

• Added calcSquareInnerProduct() for calculating the square inner

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:

• Added turbo option to calcEnsembleSpectralOverlaps() and

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

Bug Fixes and Improvements:

• writePDB() now can accept Ensemble as input.
• PY3K compatibility fixes.

1.10.7 (May 21, 2018)

New Features:

• Added overlay and gap option to showAtomicLines().

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.

1.10.4 (May 15, 2018)

• Minor fixes.

1.10.3 (May 14, 2018)

New Features:

• Added CATHDB for querying information from CATH database.
• Added sliceAtomicData() and extendAtomicData() to slice more extend data based on Selection or other types of Atomic objects.

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

• 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.