[med-svn] [r-cran-bio3d] branch upstream updated (1953330 -> dc60a34)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository r-cran-bio3d.

      from  1953330   New upstream version 2.3-1
       new  dc60a34   New upstream version 2.3-3

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:
 DESCRIPTION                   |   6 +-
 MD5                           |  71 ++++++++--------
 R/atom.select.pdb.R           |  14 +++-
 R/atom2ele.R                  |  65 ++++++++++++--
 R/cnapath.R                   |   4 +-
 R/community.aln.R             |   6 ++
 R/get.pdb.R                   |  14 ++--
 R/hmmer.R                     |  10 +++
 R/pdbs2sse.R                  |  42 ++++++++--
 R/plot.blast.R                |   2 +-
 R/plot.dmat.R                 |  14 ++--
 R/plot.matrix.loadings.R      |  86 ++++++++++---------
 R/plot.pca.scree.R            |   2 +-
 R/read.cif.R                  |   2 +-
 R/read.pdb.R                  |   2 +-
 R/uniprot.R                   |  26 +++++-
 build/vignette.rds            | Bin 203 -> 203 bytes
 inst/doc/bio3d_vignettes.html | 191 ++++++++++++++++++++++++++++++++++--------
 man/atom.select.Rd            |   4 +-
 man/atom2ele.Rd               |  16 ++--
 man/bio3d.package.Rd          |   4 +-
 man/cna.Rd                    |   6 +-
 man/cnapath.Rd                |   6 ++
 man/community.aln.Rd          |   7 +-
 man/community.tree.Rd         |   5 ++
 man/identify.cna.Rd           |   5 ++
 man/layout.cna.Rd             |   5 ++
 man/mustang.Rd                |   6 ++
 man/network.amendment.Rd      |   7 +-
 man/plot.cna.Rd               |  11 +--
 man/plot.matrix.loadings.Rd   |   4 +-
 man/plot.pca.Rd               |   2 +-
 man/print.cna.Rd              |   5 ++
 man/prune.cna.Rd              |   5 ++
 man/vmd.cna.Rd                |   5 ++
 src/init.c                    |  28 +++++++
 src/read_cif.cpp              |  14 ++--
 37 files changed, 522 insertions(+), 180 deletions(-)
 create mode 100644 src/init.c

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