CSB Toolbox Changelog
What's new in CSB Toolbox 1.2.1
Oct 8, 2013- csb.apps.buildhmm is now compatible with the latest HH-suite
- fixed a number of bugs
New in CSB Toolbox 1.2.0 (Oct 8, 2013)
- 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.
New in CSB Toolbox 1.1.0 (Oct 8, 2013)
- 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