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.