CSB 1.2.5

This is a maintenance release, which resolves a few minor compatibility issues with numpy and Python 3.6.

CSB 1.2.3

Added compatibility with the Anaconda python distribution.

CSB 1.2.2

Minor bug fixes and improvements.

HHfrag 2.1

HHfrag-2.1.zip

This is the second official release of the HHfrag software, as described in:

• HHfrag: HMM-based fragment detection using HHpred. Bioinformatics (2011)
• Confidence-guided local structure prediction with HHfrag. PLOS ONE (2013)

This release contains all supporting database files and documentation required to run the program. HHfrag is part of CSB, so no source code is included in this package. If you are looking for the source code, please navigate to CSB, package csb.apps.hhfrag. Download the matching CSB release from here:

csb-1.2.1.tar.gz

This is a minor maintenance release:

• csb.apps.buildhmm is now compatible with the latest HH-suite
• fixed a number of bugs

For more information and installation instructions please refer to the README files included in the release packages.

CSB 1.2.0

New features and API changes

csb.bio.io.wwpdb:

• New, highly granular AbstractStructureParser model. It is now possible to create customized PDB parsers with minimal effort, maximazing code reuse.
• Robust mapping of PDB ATOM records. PDB parsers can now switch to a failsafe sequence alignment-based strategy when needed. All PDB structures are therefore parsable in this release.

csb.bio.structure:

• New property: Residue.is_modified - to distinguish between canonical and modified residues.
• New property: Residue.label - stores the original PDB label of modified residues.

csb.bio.sequence.alignment:

• Added an extensible sequence alignment object model.
• Implemented local and global alignment.

csb.bio.nmr:

• Added support for chemical shifts, NOE spectra and contact maps.

csb.bio.io.cs, csb.bio.io.noe:

• Implemented basic chemical shift and NOE parsers.

Apps

• csfrag: compile libraries of analogous fragments using chemical shifts (new app).
• hhfrag: use CSfrag libraries for gap filling.
• hhfrag: perform prediction of torsion angles from fragment centroids.

CSB 1.1.0

New features and API changes:

csb.bio.structure Refactored DisorderedAtom with a standard implementation of the proxy pattern
csb.bio.structure Refactored AbstractEntity, Atom and DisorderedAtom:

• renamed AbstractEntity.list_coordinates() to get_coordinates()
• renamed Atom.temperature to bfactor
• implemented DisorderedAtom.find()
csb.statistics Added support for the Gumbel distributions
  csb.statistics Renamed the llambda parameter of InverseGaussian to scale
csb.statistics Proper parameter validation of probability density objects
  csb.statistics Implemented a ML estimator for InverseGaussian
csb.test.cases.statistics Replaced all functional tests with proper unit test cases
  csb.statistics.samplers Added full temperature support for MC sampling algorithms
  csb.test csb.test.Case.assertWithinDelta was deprecated and removed
  csb.build Refactored RevisionHandler and added support for Mercurial repositories

Bug fixes:

csb.bio.structure DisorderedAtom.residue is None for alternate != 'A'
csb.bio.io.wwpdb AbstractStructureParser.parse_models() crashes for X-ray structures
csb.bio.hmm ProfileHMM.segment() fails when the A3M alignment in the profile contains duplicate identifiers
csb.statistics csb.statistics.pdf.InverseGaussian.llambda returns wrong value
csb.numeric csb.numeric.integrators: FastLeapFrog gives faulty results when only one integration step is performed
csb.numeric csb.numeric.polar crashes on python 3.1
csb.bio.io.clans ClansParser does not tolerate malformatted colorarr descriptions
csb.bio.io.clans ClansParser does not parse seqgroup property 'hide=1' correctly
csb.bio.io.clans ClansParser crashes on files created by newest CLANS version
csb.bio.io.clans ClansParser sets Clans.entries to a list while it should be a ClansEntryCollection

CSB 1.0.0

First stable release.