[med-svn] [python-csb] 02/03: Merge tag 'upstream/1.2.1+dfsg'

[Tomás Di Domenico]

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tdido-guest pushed a commit to branch master
in repository python-csb.

commit 40d5692cf56aa769a710a745e8497149ce5911dd
Merge: 57b16f8 de1f8cb
Author: Tomás Di Domenico <tdido at tdido.com.ar>
Date:   Wed Oct 9 20:09:09 2013 +0100

    Merge tag 'upstream/1.2.1+dfsg'
    
    Upstream version 1.2.1+dfsg

 PKG-INFO                                          |    2 +-
 csb/__init__.py                                   |    2 +-
 csb/apps/__init__.py                              |   10 +-
 csb/apps/buildhmm.py                              |   63 +-
 csb/apps/csfrag.py                                |  542 ++++++++
 csb/apps/hhfrag.py                                |  302 ++++-
 csb/apps/hhsearch.py                              |    5 +-
 csb/apps/precision.py                             |   30 +-
 csb/bio/fragments/__init__.py                     |  207 ++-
 csb/bio/fragments/rosetta.py                      |    4 +-
 csb/bio/io/clans.py                               |    5 +-
 csb/bio/io/cs.py                                  |  206 +++
 csb/bio/io/fasta.py                               |   16 +-
 csb/bio/io/hhpred.py                              |    2 +-
 csb/bio/io/noe.py                                 |  269 ++++
 csb/bio/io/wwpdb.py                               | 1096 +++++++++++----
 csb/bio/nmr/__init__.py                           | 1105 ++++++++++++++-
 csb/bio/nmr/resources/AtomConnectivity.xml        |  812 +++++++++++
 csb/bio/sequence/__init__.py                      |   21 +-
 csb/bio/sequence/alignment.py                     |  617 +++++++++
 csb/bio/structure/__init__.py                     |   52 +-
 csb/build.py                                      |   28 +-
 csb/io/__init__.py                                |    5 +
 csb/io/tsv.py                                     |   38 +-
 csb/numeric/__init__.py                           |   16 +-
 csb/numeric/integrators.py                        |   10 +-
 csb/statistics/__init__.py                        |    4 +-
 csb/statistics/samplers/__init__.py               |   12 +-
 csb/statistics/samplers/mc/__init__.py            |  838 +-----------
 csb/statistics/samplers/mc/multichain.py          | 1502 +++++++++++++++++++--
 csb/statistics/samplers/mc/neqsteppropagator.py   | 1239 +++++++++++++++++
 csb/statistics/samplers/mc/propagators.py         |   55 +-
 csb/statistics/samplers/mc/singlechain.py         |  311 ++++-
 csb/test/__init__.py                              |    2 +-
 csb/test/cases/bio/fragments/__init__.py          |   11 +-
 csb/test/cases/bio/hmm/__init__.py                |   11 +-
 csb/test/cases/bio/io/clans/__init__.py           |   24 +-
 csb/test/cases/bio/io/cs/__init__.py              |   87 ++
 csb/test/cases/bio/io/fasta/__init__.py           |    4 +-
 csb/test/cases/bio/io/noe/__init__.py             |  148 ++
 csb/test/cases/bio/io/wwpdb/__init__.py           |  194 ++-
 csb/test/cases/bio/nmr/__init__.py                |  348 ++++-
 csb/test/cases/bio/sequence/alignment/__init__.py |  196 +++
 csb/test/cases/bio/structure/__init__.py          |   29 +-
 csb/test/cases/core/__init__.py                   |   22 +-
 csb/test/cases/io/__init__.py                     |   87 +-
 csb/test/cases/numeric/__init__.py                |   59 +-
 csb/test/cases/statistics/samplers/__init__.py    |  728 +++++++++-
 csb/test/data/1d3z.regular.pdb                    |  342 ++---
 csb/test/data/2l01.v2.str                         |   31 +
 csb/test/data/2l01.v3.str                         |   45 +
 csb/test/data/Sparky.peaks                        |    5 +
 csb/test/data/Xeasy1.peaks                        |    9 +
 csb/test/data/Xeasy2.peaks                        |    8 +
 csb/test/data/csb.tsv                             |    2 +-
 csb/test/data/mapping.pdb                         |   12 +
 csb/test/data/mapping2.pdb                        |   10 +
 csb/test/data/mapping3.pdb                        |    9 +
 csb/test/data/modified.pdb                        |   16 +
 csb/test/data/modified2.pdb                       |   16 +
 csb/test/data/out.clans                           |   14 +-
 61 files changed, 10224 insertions(+), 1671 deletions(-)

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