[med-svn] [python-csb] branch upstream updated (48ac2c6 -> de1f8cb)

[Tomás Di Domenico]

This is an automated email from the git hooks/post-receive script.

tdido-guest pushed a change to branch upstream
in repository python-csb.

      from  48ac2c6   Imported Upstream version 1.1.1
       new  de1f8cb   Imported Upstream version 1.2.1+dfsg

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 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(-)
 create mode 100644 csb/apps/csfrag.py
 create mode 100644 csb/bio/io/cs.py
 create mode 100644 csb/bio/io/noe.py
 create mode 100644 csb/bio/nmr/resources/AtomConnectivity.xml
 create mode 100644 csb/bio/sequence/alignment.py
 create mode 100644 csb/statistics/samplers/mc/neqsteppropagator.py
 create mode 100644 csb/test/cases/bio/io/cs/__init__.py
 create mode 100644 csb/test/cases/bio/io/noe/__init__.py
 create mode 100644 csb/test/cases/bio/sequence/alignment/__init__.py
 create mode 100644 csb/test/data/2l01.v2.str
 create mode 100644 csb/test/data/2l01.v3.str
 create mode 100644 csb/test/data/Sparky.peaks
 create mode 100644 csb/test/data/Xeasy1.peaks
 create mode 100644 csb/test/data/Xeasy2.peaks
 create mode 100644 csb/test/data/mapping.pdb
 create mode 100644 csb/test/data/mapping2.pdb
 create mode 100644 csb/test/data/mapping3.pdb
 create mode 100644 csb/test/data/modified.pdb
 create mode 100644 csb/test/data/modified2.pdb

-- 
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