ProDy 1.10 Series¶
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 acceptEnsemble
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()
andextendAtomicData()
to slice more extend data based onSelection
or other types ofAtomic
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
andsdarray
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()
andshowAtomicMatrix()
functions to improve visualization.- Added an networkx option to
showTree()
so that the user can choose to usenetworkx
to visualize a given tree.
Ensemble and PDBEnsemble
- Associated an
MSA
object to thePDBEnsemble
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()
andparsePfamPDBs()
.
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.