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.gitignore
View file @ ab9d5e8f
*DS_STORE
include/BALL/BALL.doc
contrib/*
*.o
......@@ -12,6 +13,7 @@ moc_*.C
*.aux
*.bbl
*.blg
*.qm
.Dependencies
lib/*
build/*
......@@ -30,9 +32,8 @@ source/libBALL.objects
source/libVIEW.objects
source/qt.version
include/BALL/VIEW/UIC/*
.idea
.project
.cproject
data/BALLView/translations/BALLView.de_DE.qm
data/BALLView/translations/BALLView.zh_TW.qm
source/TEST/data/SideChainPlacementProcessor_test_output_pre_1.pdb
CMakeLists.txt.user
CMakeLists.txt
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COPYRIGHT
View file @ ab9d5e8f
......@@ -3,8 +3,7 @@
bioinformatics.
Copyright (C) Andreas Hildebrandt, Oliver Kohlbacher, Hans-Peter
Lenhof, and others 1996-2012
Lenhof, Anna Katharina Hildebrandt, and others 1996-2012
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
......@@ -13,17 +12,17 @@
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library (BALL/source/LICENSE); if not, write
to the Free Software Foundation, Inc., 59 Temple Place, Suite 330,
Boston, MA 02111-1307 USA
License along with this library (LICENSE); if not, write to the
Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
Boston, MA 02110-1301 USA
You can contact the authors by electronic mail
Andreas Hildebrandt: Andreas.Hildebrandt@uni-mainz.de
Andreas Hildebrandt: andreas.hildebrandt@uni-mainz.de
Oliver Kohlbacher: oliver.kohlbacher@uni-tuebingen.de
......
ChangeLog
View file @ ab9d5e8f
BALL ChangeLog
BALL Changelog
The ChangeLog for BALL >= 1.3 can be found at the following URL:
http://ball-trac.bioinf.uni-sb.de/wiki/ReleaseNotes
The changelog for BALL releases >= 1.3 can be found here:
https://github.com/BALL-Project/ball/wiki/Release-Notes
Older ChangeLogs are located at the following URL:
http://www.ball-project.org/overview/version-history
Please note that these logs are just a list of highlights and by no means complete.
If you are interested in the full range of changes, see the commit log found here:
https://github.com/BALL-Project/ball/releases
source/APPLICATIONS/BALLVIEW/LICENSE → LICENSE
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GNU LESSER GENERAL PUBLIC LICENSE
Version 2.1, February 1999
GNU LESSER GENERAL PUBLIC LICENSE
Version 2.1, February 1999
Copyright (C) 1991, 1999 Free Software Foundation, Inc.
59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
......@@ -11,7 +10,7 @@
as the successor of the GNU Library Public License, version 2, hence
the version number 2.1.]
Preamble
Preamble
The licenses for most software are designed to take away your
freedom to share and change it. By contrast, the GNU General Public
......@@ -113,7 +112,7 @@ modification follow. Pay close attention to the difference between a
former contains code derived from the library, whereas the latter must
be combined with the library in order to run.
GNU LESSER GENERAL PUBLIC LICENSE
GNU LESSER GENERAL PUBLIC LICENSE
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License Agreement applies to any software library or other
......@@ -147,7 +146,7 @@ such a program is covered only if its contents constitute a work based
on the Library (independent of the use of the Library in a tool for
writing it). Whether that is true depends on what the Library does
and what the program that uses the Library does.
1. You may copy and distribute verbatim copies of the Library's
complete source code as you receive it, in any medium, provided that
you conspicuously and appropriately publish on each copy an
......@@ -433,7 +432,7 @@ decision will be guided by the two goals of preserving the free status
of all derivatives of our free software and of promoting the sharing
and reuse of software generally.
NO WARRANTY
NO WARRANTY
15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO
WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
......@@ -456,5 +455,5 @@ FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF
SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
DAMAGES.
END OF TERMS AND CONDITIONS
END OF TERMS AND CONDITIONS
MacOSX/BALLPackage/Applications/BALLView.app/Contents/Info.plist deleted 100644 → 0
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist SYSTEM "file://localhost/System/Library/DTDs/PropertyList.dtd">
<plist version="0.9">
<dict>
<key>CFBundleIconFile</key>
<string>BALLView.icns</string>
<key>CFBundlePackageType</key>
<string>APPL</string>
<key>CFBundleGetInfoString</key>
<string>Created by Qt/QMake</string>
<key>CFBundleSignature</key>
<string>ttxt</string>
<key>CFBundleExecutable</key>
<string>BALLView</string>
<key>LSEnvironment</key>
<dict>
<key>BALL_DATA_PATH</key>
<string>/Applications/BALLView.app/Contents/data</string>
<key>PYTHONPATH</key>
<string>/Applications/BALLView.app/Contents/Frameworks:$PYTHONPATH</string>
<key>LANG</key>
<string>en</string>
</dict>
<key>NOTE</key>
<string>Please, do NOT change this file -- It was generated by Qt/QMake.</string>
</dict>
</plist>
MacOSX/BALLPackage/Install_Resources/License.rtf deleted 100644 → 0
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MacOSX/BALLView-package-spnav.pmdoc/01ballview-contents.xml deleted 100644 → 0
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g="admin" p="33204"><mod>mode</mod></f><f n="TYR.db" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="U.db" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="VAL.db" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="ZN.db" o="root" g="admin" p="33204"><mod>mode</mod></f><mod>mode</mod></f><f n="graphics" o="root" g="admin" p="16893"><f n="assignBondOrders.png" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="colorize.png" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="cursor.png" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="delete.png" o="root" g="admin" p="33277"><mod>mode</mod></f><f n="down3.png" o="root" g="admin" p="33277"><mod>mode</mod></f><f n="download.png" o="root" g="admin" p="33277"><mod>mode</mod></f><f n="edit.png" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="element.png" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="focus.png" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="fullscreen.png" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="help.png" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="hydrogens.png" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="logo.png" o="root" g="admin" p="33277"><mod>mode</mod></f><f n="minimize.png" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="move.png" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="open.png" o="root" g="admin" p="33277"><mod>mode</mod></f><f n="picking.png" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="povray.png" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="pref.png" o="root" g="admin" p="33277"><mod>mode</mod></f><f n="pubchem.png" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="quickload.png" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="quicksave.png" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="revert.png" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="rotate.png" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="ruler.png" o="root" g="admin" 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n="structures" o="root" g="admin" p="16893"><f n="1A1F.pdb" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="alaala.dcd" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="AlaAla.hin" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="bpti.pdb" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="DB" o="root" g="admin" p="16893"><f n="create_database.sql" o="root" g="admin" p="33204"><mod>mode</mod></f><mod>mode</mod></f><f n="test.btf" o="root" g="admin" p="33277"><mod>mode</mod></f><mod>mode</mod></f><mod>mode</mod></f><f n="Frameworks" o="root" g="admin" p="16893"><f n="BALLmodule.so" o="root" g="admin" p="33277"><mod>mode</mod></f><f n="libBALL.dylib" o="root" g="admin" p="33277"><mod>mode</mod></f><f n="libboost_iostreams-xgcc40-mt-1_37.dylib" o="root" g="admin" p="33277"><mod>mode</mod></f><f n="libboost_system-xgcc40-mt-1_37.dylib" o="root" g="admin" p="33277"><mod>mode</mod></f><f n="libboost_thread-xgcc40-mt-1_37.dylib" o="root" g="admin" 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p="16893"><mod>mode</mod></f><f n="Versions" o="root" g="admin" p="16893"><f n="4" o="root" g="admin" p="16893"><f n="QtTest" o="root" g="admin" p="33277"><mod>mode</mod></f><mod>mode</mod></f><mod>mode</mod></f><mod>mode</mod></f><f n="QtXml.framework" o="root" g="admin" p="16893"><f n="Resources" o="root" g="admin" p="16893"><mod>mode</mod></f><f n="Versions" o="root" g="admin" p="16893"><f n="4" o="root" g="admin" p="16893"><f n="QtXml" o="root" g="admin" p="33277"><mod>mode</mod></f><mod>mode</mod></f><mod>mode</mod></f><mod>mode</mod></f><f n="sip.so" o="root" g="admin" p="33277"><mod>mode</mod></f><mod>mode</mod></f><f n="Info.plist" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="MacOS" o="root" g="admin" p="16893"><f n="BALLView" o="root" g="admin" p="33277"><mod>mode</mod></f><mod>mode</mod></f><f n="PkgInfo" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="PlugIns" o="root" g="admin" p="16893"><f n="accessible" o="root" g="admin" p="16893"><f n="libqtaccessiblewidgets.dylib" o="root" g="admin" p="33277"><mod>mode</mod></f><mod>mode</mod></f><f n="codecs" o="root" g="admin" p="16893"><f n="libqcncodecs.dylib" o="root" g="admin" p="33277"><mod>mode</mod></f><f n="libqjpcodecs.dylib" o="root" g="admin" p="33277"><mod>mode</mod></f><f n="libqkrcodecs.dylib" o="root" g="admin" p="33277"><mod>mode</mod></f><f n="libqtwcodecs.dylib" o="root" g="admin" p="33277"><mod>mode</mod></f><mod>mode</mod></f><f n="imageformats" o="root" g="admin" p="16893"><f n="libqgif.dylib" o="root" g="admin" p="33277"><mod>mode</mod></f><f n="libqico.dylib" o="root" g="admin" p="33277"><mod>mode</mod></f><f n="libqjpeg.dylib" o="root" g="admin" p="33277"><mod>mode</mod></f><f n="libqmng.dylib" o="root" g="admin" p="33277"><mod>mode</mod></f><f n="libqtiff.dylib" o="root" g="admin" p="33277"><mod>mode</mod></f><mod>mode</mod></f><f n="sqldrivers" o="root" g="admin" p="16893"><f n="libqsqlite.dylib" o="root" g="admin" p="33277"><mod>mode</mod></f><f n="libqsqlodbc.dylib" o="root" g="admin" p="33277"><mod>mode</mod></f><mod>mode</mod></f><mod>mode</mod></f><f n="Resources" o="root" g="admin" p="16893"><f n="BALLView.icns" o="root" g="admin" p="33204"><mod>mode</mod></f><f n="qt.conf" o="root" g="admin" p="33204"><mod>mode</mod></f><mod>mode</mod></f><mod>mode</mod></f><mod>mode</mod></f></pkg-contents>
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<pkgref spec="1.12" uuid="D8CAA537-F61F-4560-8FCB-DD433FBFE642"><config><identifier>org.ballview.ballview13Beta2.ballview.pkg</identifier><version>2</version><description></description><post-install type="none"/><requireAuthorization/><installFrom relative="true" includeRoot="true">BALLPackage/Applications/BALLView.app</installFrom><installTo relocatable="true">/Applications</installTo><flags><followSymbolicLinks/></flags><packageStore type="internal"></packageStore><mod>parent</mod><mod>version</mod><mod>includeRoot</mod><mod>installFrom.isRelativeType</mod><mod>installTo</mod></config><contents><file-list>01ballview-contents.xml</file-list><component id="org.ballview.ballview13Beta2.ballview.pkg.ballviewapp" path="/Users/andreas/BALL_devel/MacOSX/BALLPackage/Applications/BALLView.app" isRelocatable="true"><locator-info><token title="pkmk-token-2"/></locator-info></component><filter>/CVS$</filter><filter>/\.svn$</filter><filter>/\.cvsignore$</filter><filter>/\.cvspass$</filter><filter>/\.DS_Store$</filter></contents></pkgref>
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<pkmkdoc spec="1.12"><properties><title>BALLView 1.3 beta2</title><build>/Users/andreas/Desktop/BALLView 1.3 beta2.mpkg</build><organization>org.ballview</organization><userSees ui="easy"/><min-target os="2"/><domain anywhere="true"/></properties><distribution><versions min-spec="1.000000"/><scripts></scripts></distribution><contents><choice title="BALLView" id="choice18" starts_selected="true" starts_enabled="true" starts_hidden="false"><pkgref id="org.ballview.ballview13Beta2.ballview.pkg"/></choice></contents><resources bg-scale="none" bg-align="topleft"><locale lang="English"><resource relative="true" mod="true" type="background">BALLPackage/Install_Resources/background.jpg</resource><resource relative="true" mod="true" type="license">BALLPackage/Install_Resources/License.rtf</resource><resource relative="true" mod="true" type="welcome">BALLPackage/Install_Resources/Welcome.rtf</resource><resource mime-type="text/rtf" kind="embedded" type="conclusion"><![CDATA[{\rtf1\ansi\ansicpg1252\cocoartf949\cocoasubrtf460
{\fonttbl\f0\fnil\fcharset0 LucidaGrande;}
{\colortbl;\red255\green255\blue255;}
\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\ql\qnatural\pardirnatural
\f0\fs26 \cf0 NOTE: if you chose to install BALLView on a non-standard volume, you may have to edit the variables\
\
\b BALL_DATA_PATH
\b0 \
\
and\
\
\b PYTHONPATH\
\b0 \
in\
\
\b BALLView.app/Contents/Info.plist\
\b0 \
to point to the correct install location!}]]></resource></locale></resources><flags/><postinstall><action id="com.apple.packagemaker.actions.showfile"><value>org.ballview.ballview13Beta2.ballview.pkg.ballviewapp</value><type>component</type></action></postinstall><item type="file">01ballview.xml</item><mod>postinstallActions.actions</mod><mod>properties.title</mod></pkmkdoc>
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist SYSTEM "file://localhost/System/Library/DTDs/PropertyList.dtd">
<plist version="0.9">
<dict>
<key>CFBundleIconFile</key>
<string>BALLView.icns</string>
<key>CFBundlePackageType</key>
<string>APPL</string>
<key>CFBundleGetInfoString</key>
<string>Created by Qt/QMake</string>
<key>CFBundleSignature</key>
<string>ttxt</string>
<key>CFBundleExecutable</key>
<string>BALLView</string>
<key>LSEnvironment</key>
<dict>
<key>BALL_DATA_PATH</key>
<string>/Applications/BALLView.app/Contents/data</string>
<key>PYTHONPATH</key>
<string>/Applications/BALLView.app/Contents/Frameworks:$PYTHONPATH</string>
<key>LANG</key>
<string>en</string>
</dict>
<key>NOTE</key>
<string>Please, do NOT change this file -- It was generated by Qt/QMake.</string>
</dict>
</plist>
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#!/bin/bash
## This script finds all .dylibs in a given directory, lists their dynamic load dependencies,
## tries to detect them in the same directory hierarchy, and, if found, prepares their load
## dependencies for bundling
search_path=$1
for lib in $(find "$search_path" -name \*.dylib -o -name \*.so); do
for cur_name in $(otool -L $lib | awk '{if (NR >= 2) print $1}' | grep -v @executable_path); do
cur_base_name=$(basename $cur_name)
in_bundle_name=$(find "$search_path" -name $cur_base_name)
in_bundle_base_name=$(echo "$in_bundle_name" | sed "s_^.*/Contents/\(.*\)_\1_g")
if [ -n "$in_bundle_name" -a -f "$in_bundle_name" ]; then
target=$in_bundle_name
a=$(readlink $target);
if test $a; then
target=$a
fi;
if [ "$cur_base_name" == "$(basename $lib)" ]; then
install_name_tool -id @executable_path/../Frameworks/$(basename $target) $lib
else
install_name_tool -change $cur_name @executable_path/../$in_bundle_base_name $lib
fi
fi
done;
done