[med-svn] [king] 02/05: Merge tag 'upstream/2.23.161103+dfsg'
Andreas Tille
tille at debian.org
Sun Dec 4 09:18:01 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository king.
commit 5f613bec46a7c5ace9081132893b2092ab813266
Merge: f95454e 40d8644
Author: Andreas Tille <tille at debian.org>
Date: Fri Dec 2 13:22:37 2016 +0100
Merge tag 'upstream/2.23.161103+dfsg'
Upstream version 2.23.161103+dfsg
chiropraxis/CHANGELOG.html | 15 +
chiropraxis/doc/tools-manual.pdf | Bin 76400 -> 75499 bytes
...s-manual.lyx => tools-manual-lyxformat-345.lyx} | 0
.../tools-manual.html.LyXconv/tools-manual.css | 121 +
.../tools-manual.html.LyXconv/tools-manual.html | 307 +
chiropraxis/doc/work/tools-manual.lyx | 82 +-
chiropraxis/doc/work/tools-manual.pdf | Bin 0 -> 75499 bytes
chiropraxis/resource/chiropraxis/buildnum.props | 4 +-
.../chiropraxis/kingtools/tools-manual.html | 608 +-
.../resource/chiropraxis/rotarama/Ramalyze.help | 2 +
.../chiropraxis/rotarama/rama/general.ndft | Bin 129687 -> 0 bytes
.../chiropraxis/rotarama/rama/glycine.ndft | Bin 129661 -> 0 bytes
.../resource/chiropraxis/rotarama/rama/prepro.ndft | Bin 129676 -> 0 bytes
.../chiropraxis/rotarama/rama/proline.ndft | Bin 129655 -> 0 bytes
.../chiropraxis/rotarama/rama/rama4-template.pdf | 1758 -----
.../resource/chiropraxis/rotarama/rota/asn.ndft | Bin 20786 -> 0 bytes
.../resource/chiropraxis/rotarama/rota/asp.ndft | Bin 10418 -> 0 bytes
.../resource/chiropraxis/rotarama/rota/cys.ndft | Bin 1477 -> 0 bytes
.../resource/chiropraxis/rotarama/rota/gln.ndft | Bin 364563 -> 0 bytes
.../resource/chiropraxis/rotarama/rota/glu.ndft | Bin 186363 -> 0 bytes
.../resource/chiropraxis/rotarama/rota/his.ndft | Bin 20786 -> 0 bytes
.../resource/chiropraxis/rotarama/rota/ile.ndft | Bin 20786 -> 0 bytes
.../resource/chiropraxis/rotarama/rota/leu.ndft | Bin 20808 -> 0 bytes
.../resource/chiropraxis/rotarama/rota/met.ndft | Bin 364563 -> 0 bytes
.../resource/chiropraxis/rotarama/rota/phetyr.ndft | Bin 10426 -> 0 bytes
.../resource/chiropraxis/rotarama/rota/ser.ndft | Bin 1477 -> 0 bytes
.../resource/chiropraxis/rotarama/rota/thr.ndft | Bin 1477 -> 0 bytes
.../resource/chiropraxis/rotarama/rota/trp.ndft | Bin 20786 -> 0 bytes
.../resource/chiropraxis/rotarama/rota/val.ndft | Bin 1477 -> 0 bytes
.../{rota/lys.ndft => rota8000/rota8000-arg.ndft} | Bin 6718540 -> 6718536 bytes
.../rotarama/rota8000/rota8000-asn.ndft | Bin 0 -> 20782 bytes
.../rotarama/rota8000/rota8000-asp.ndft | Bin 0 -> 10414 bytes
.../rotarama/rota8000/rota8000-cys.ndft | Bin 0 -> 1473 bytes
.../rotarama/rota8000/rota8000-gln.ndft | Bin 0 -> 364559 bytes
.../rotarama/rota8000/rota8000-glu.ndft | Bin 0 -> 186359 bytes
.../rotarama/rota8000/rota8000-his.ndft | Bin 0 -> 20782 bytes
.../rotarama/rota8000/rota8000-ile.ndft | Bin 0 -> 20782 bytes
.../rotarama/rota8000/rota8000-leu-clean.ndft | Bin 0 -> 20804 bytes
.../{rota/arg.ndft => rota8000/rota8000-lys.ndft} | Bin 6718540 -> 6718536 bytes
.../rotarama/rota8000/rota8000-met.ndft | Bin 0 -> 364559 bytes
.../rotarama/rota8000/rota8000-phetyr.ndft | Bin 0 -> 10422 bytes
.../{rota/pro.ndft => rota8000/rota8000-pro.ndft} | Bin 1477 -> 1473 bytes
.../rotarama/rota8000/rota8000-ser.ndft | Bin 0 -> 1473 bytes
.../rotarama/rota8000/rota8000-thr.ndft | Bin 0 -> 1473 bytes
.../rotarama/rota8000/rota8000-trp.ndft | Bin 0 -> 20782 bytes
.../rotarama/rota8000/rota8000-val.ndft | Bin 0 -> 1473 bytes
.../rotarama/rota8000/rotamer_names.props | 249 +
.../chiropraxis/sc/sidechain_angles_top8000.props | 404 ++
chiropraxis/resource/chiropraxis/version.props | 2 +-
.../src/chiropraxis/kingtools/BgKinRunner.java | 88 +-
.../src/chiropraxis/kingtools/PhiPsiWindow.java | 6 +-
.../chiropraxis/kingtools/SidechainRotator.java | 14 +-
.../src/chiropraxis/mc/AltConfShearFinder.java | 40 +-
.../src/chiropraxis/mc/AnisoOxygenSearch.java | 202 +-
chiropraxis/src/chiropraxis/mc/BackrubPioneer.java | 66 +-
chiropraxis/src/chiropraxis/mc/ShearFit.java | 237 +-
chiropraxis/src/chiropraxis/mc/ShearPioneer.java | 96 +-
chiropraxis/src/chiropraxis/mc/SheetBuilder2.java | 1624 +++++
.../src/chiropraxis/mc/SheetResiduePair.java | 395 ++
chiropraxis/src/chiropraxis/rotarama/Ramalyze.java | 70 +-
chiropraxis/src/chiropraxis/rotarama/Rotalyze.java | 3 +-
chiropraxis/src/chiropraxis/rotarama/Rotamer.java | 87 +-
.../src/chiropraxis/sc/SidechainAngles2.java | 2 +-
driftwood/CHANGELOG.html | 5 +
driftwood/resource/driftwood/buildnum.props | 4 +-
driftwood/resource/driftwood/version.props | 2 +-
driftwood/src/driftwood/moldb2/Disulfide.java | 10 +
driftwood/src/driftwood/moldb2/Disulfides.java | 6 +
driftwood/src/driftwood/moldb2/Model.java | 9 +-
driftwood/src/driftwood/moldb2/ModelState.java | 38 +-
driftwood/src/driftwood/moldb2/PdbDisulfides.java | 9 +-
driftwood/src/driftwood/moldb2/PdbReader.java | 106 +-
.../driftwood/moldb2/PdbSecondaryStructure.java | 12 +-
driftwood/src/driftwood/moldb2/PdbWriter.java | 76 +-
driftwood/src/driftwood/moldb2/Residue.java | 134 +-
.../src/driftwood/moldb2/SecondaryStructure.java | 17 +-
extratools/CHANGELOG.html | 6 +
extratools/resource/META-INF/services/king.Plugin | 1 +
extratools/resource/extratools/buildnum.props | 4 +-
extratools/resource/extratools/version.props | 2 +-
extratools/resource/king/king_prefs | 1 +
.../resource/king/tool/postkin/sc-connect.props | 6 +-
.../tool/data_analysis/HighDimSliderPlugin.java | 19 +
.../src/king/tool/data_analysis/PlottingTool.java | 11 +-
extratools/src/king/tool/export/PdbExport.java | 259 +
extratools/src/king/tool/loops/HighLowSliders.java | 14 +-
.../src/king/tool/postkin/KinFudgerTool.java | 45 +-
.../src/king/tool/postkin/PointComparator.java | 77 +-
extratools/src/king/tool/util/KinUtil.java | 35 +-
king/CHANGELOG.html | 12 +
king/README.md | 7 +
king/build.xml | 95 +-
king/doc/king-manual.pdf | Bin 246002 -> 299383 bytes
...ng-manual.lyx => king-manual-lyxformat-345.lyx} | 0
.../work/king-manual.html.LyXconv/king-manual.css | 148 +
.../work/king-manual.html.LyXconv/king-manual.html | 1721 +++++
king/doc/work/king-manual.lyx | 7239 ++++++++++----------
king/probe | Bin 0 -> 501136 bytes
king/resource/king/buildnum.props | 4 +-
king/resource/king/html/king-manual.css | 148 +
king/resource/king/html/king-manual.html | 3488 +++++-----
king/resource/king/images/king-logo.2016.gif | Bin 0 -> 9038 bytes
king/resource/king/images/king-logo.2016.png | Bin 0 -> 42223 bytes
king/resource/king/version.props | 2 +-
king/src/king/BasicTool.java | 2 +-
king/src/king/JoglCanvas.java | 48 +-
king/src/king/KinCanvas.java | 4 +-
king/src/king/KingMain.java | 1 +
king/src/king/ToolBox.java | 2 +-
king/src/king/ToolServices.java | 2 +-
king/src/king/UIMenus.java | 2 +-
king/src/king/core/KGroup.java | 54 +-
king/src/king/core/KList.java | 4 +-
king/src/king/core/Kinemage.java | 15 +-
king/src/king/io/KinfileParser.java | 30 +-
king/src/king/io/KinfileWriter.java | 3 +
king/src/king/painters/JoglEngine3D.java | 84 +-
king/src/king/painters/JoglPainter.java | 16 +-
king/src/king/tool/draw/DrawingTool.java | 2 +-
king/src/king/tool/edmap/EDMapPlotter.java | 14 +-
king/src/king/tool/edmap/EDMapWindow.java | 253 +-
king/work/king-logo.2016.psd | Bin 0 -> 185822 bytes
king/work/mageosX.icns | Bin 0 -> 53163 bytes
molikin/CHANGELOG.html | 9 +-
molikin/resource/molikin/buildnum.props | 4 +-
molikin/src/molikin/RibbonPrinter.java | 19 +-
molikin/src/molikin/StickPrinter.java | 60 +-
molikin/src/molikin/Util.java | 85 +-
.../src/molikin/crayons/AltConfNetworkCrayon.java | 118 +
molikin/src/molikin/crayons/RotaramaCrayon.java | 4 +-
molikin/src/molikin/logic/BallAndStickLogic.java | 48 +-
131 files changed, 13149 insertions(+), 7988 deletions(-)
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