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csb-1.1.0

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Downloads: 72
Change Set: cbb5fb53ad27
Released: Aug 6, 2012
Updated: Nov 26, 2012 by kalev
Dev status: Stable Help Icon

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Source Code csb-1.1.0
source code, 5862K, uploaded Aug 6, 2012 - 72 downloads

Release Notes

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

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