Merge branch 'master' of gparabola:abslibre-mips64el

5 files changed, 70 insertions, 871 deletions

diff --git a/extra/avogadro/PKGBUILD b/extra/avogadro/PKGBUILD
index 39d1d61cc..9631d7030 100644
--- a/extra/avogadro/PKGBUILD
+++ b/extra/avogadro/PKGBUILD
@@ -1,32 +1,35 @@
-# $Id: PKGBUILD 176282 2013-01-28 16:48:15Z stephane $
+# $Id: PKGBUILD 181116 2013-03-31 19:16:38Z stephane $
 # Maintainer:
 # Contributor: Andrea Scarpino <andrea@archlinux.org>
 # Contributor: Nick B <Shirakawasuna at gmail _dot_com>
 
 pkgname=avogadro
 pkgver=1.1.0
-pkgrel=3
+pkgrel=4
 pkgdesc="An advanced molecular editor based on Qt"
 arch=('i686' 'x86_64' 'mips64el')
 url="http://avogadro.openmolecules.net/wiki/Main_Page"
 license=('GPL2')
 depends=('eigen2' 'openbabel' 'python2-pyqt' 'boost-libs' 'glew' 'python2-numpy')
-makedepends=('cmake' 'boost' 'doxygen' 'mesa')
+makedepends=('cmake' 'boost' 'doxygen' 'mesa-libgl')
 install=avogadro.install
 source=("http://downloads.sourceforge.net/${pkgname}/${pkgname}-${pkgver}.tar.bz2"
-	"avogadro-1.1.0-textrel.patch")
+        'boost153.patch')
 md5sums=('f4fbef5ffc69cc312b2316426c36a78d'
-	 '88c68540c0ccce7007e515f1b3fd03ed')
+         'aa2573f78d5dbd85b3cb79e08acde8ab')
 
 build() {
-  patch -Np0 -i ${srcdir}/avogadro-1.1.0-textrel.patch
+  cd ${pkgname}-${pkgver}
+  patch -p1 -i "${srcdir}"/boost153.patch
+  cd ../
+
   mkdir build
   cd build
   cmake ../${pkgname}-${pkgver} \
     -DCMAKE_BUILD_TYPE=Release \
     -DCMAKE_INSTALL_PREFIX=/usr \
     -DPYTHON_EXECUTABLE=/usr/bin/python2 \
-    -DQT_MKSPECS_RELATIVE=share/qt/mkspecs
+    -DQT_MKSPECS_RELATIVE=share/qt4/mkspecs
   make
 }
 
diff --git a/extra/avogadro/boost153.patch b/extra/avogadro/boost153.patch
new file mode 100644
index 000000000..fd8685974
--- /dev/null
+++ b/extra/avogadro/boost153.patch
@@ -0,0 +1,60 @@
+--- avogadro-1.1.0/libavogadro/src/pythonengine_p.h~	2013-03-29 12:46:16.306165881 +0000
++++ avogadro-1.1.0/libavogadro/src/pythonengine_p.h	2013-03-29 12:45:43.123089622 +0000
+@@ -27,7 +27,9 @@
+ 
+ #include <avogadro/global.h>
+ #include <avogadro/engine.h>
++#ifndef Q_MOC_RUN
+ #include <boost/python.hpp>
++#endif
+ 
+ namespace Avogadro {
+ 
+--- avogadro-1.1.0/libavogadro/src/pythonextension_p.h~	2013-03-29 12:46:32.156043085 +0000
++++ avogadro-1.1.0/libavogadro/src/pythonextension_p.h	2013-03-29 12:47:07.265771087 +0000
+@@ -29,7 +29,9 @@
+ #include <avogadro/extension.h>
+ #include <avogadro/primitive.h>
+ #include <avogadro/glwidget.h>
++#ifndef Q_MOC_RUN
+ #include <boost/python.hpp>
++#endif
+ 
+ #include <QWidget>
+ #include <QList>
+--- avogadro-1.1.0/libavogadro/src/pythontool_p.h~	2013-03-29 12:47:33.335569185 +0000
++++ avogadro-1.1.0/libavogadro/src/pythontool_p.h	2013-03-29 12:47:50.732101147 +0000
+@@ -27,7 +27,9 @@
+ 
+ #include <avogadro/global.h>
+ #include <avogadro/tool.h>
++#ifndef Q_MOC_RUN
+ #include <boost/python.hpp>
++#endif
+ 
+ #include <QObject>
+ #include <QAction>
+--- avogadro-1.1.0/libavogadro/src/pythoninterpreter.h~	2013-03-29 12:50:46.550738652 +0000
++++ avogadro-1.1.0/libavogadro/src/pythoninterpreter.h	2013-03-29 12:51:00.853961341 +0000
+@@ -26,7 +26,9 @@
+ #define PYTHONINTERPRETER_H
+ 
+ #include <avogadro/global.h>
++#ifndef Q_MOC_RUN
+ #include <boost/python.hpp>
++#endif
+ #include <avogadro/primitive.h>
+ #include <QString>
+ 
+--- avogadro-1.1.0/libavogadro/src/pythonscript.h~	2013-03-29 12:52:00.723488935 +0000
++++ avogadro-1.1.0/libavogadro/src/pythonscript.h	2013-03-29 12:52:11.676745364 +0000
+@@ -27,7 +27,9 @@
+ #define PYTHONSCRIPT_H
+ 
+ #include <avogadro/global.h>
++#ifndef Q_MOC_RUN
+ #include <boost/python.hpp>
++#endif
+ 
+ #include "pythonerror.h"
+ 
diff --git a/extra/avogadro/fix-boost.patch b/extra/avogadro/fix-boost.patch
deleted file mode 100644
index 8fb53ef12..000000000
--- a/extra/avogadro/fix-boost.patch
+++ /dev/null
@@ -1,33 +0,0 @@
---- avogadro-1.0.3/libavogadro/src/CMakeLists.txt~	2011-11-29 18:33:01.777291627 +0000
-+++ avogadro-1.0.3/libavogadro/src/CMakeLists.txt	2011-11-29 18:33:23.480814612 +0000
-@@ -149,7 +149,7 @@
-   endforeach(P_ITEM ${PYTHON_SRCS})
- endif(NOT ENABLE_PYTHON OR NOT ALL_PYTHON_FOUND)
- 
--QT4_WRAP_CPP(libavogadro_MOC_SRCS ${libavogadro_MOC_HDRS})
-+QT4_WRAP_CPP(libavogadro_MOC_SRCS ${libavogadro_MOC_HDRS} OPTIONS -DBOOST_TT_HAS_OPERATOR_HPP_INCLUDED)
- 
- # you have to add link_directories before you add the target
- if(ENABLE_PYTHON AND ALL_PYTHON_FOUND)
---- avogadro-1.0.3/libavogadro/src/python/CMakeLists.txt~	2011-11-29 18:37:15.449506548 +0000
-+++ avogadro-1.0.3/libavogadro/src/python/CMakeLists.txt	2011-11-29 18:37:52.729831744 +0000
-@@ -11,7 +11,7 @@
- # use all cpp files in this directory
- FILE(GLOB wrapper_SRCS "*.cpp")
- 
--QT4_WRAP_CPP(MOC_SRCS moleculelist.h)
-+QT4_WRAP_CPP(MOC_SRCS moleculelist.h OPTIONS -DBOOST_TT_HAS_OPERATOR_HPP_INCLUDED)
- 
- ADD_LIBRARY(python-module MODULE ${wrapper_SRCS} ${MOC_SRCS})
- SET_TARGET_PROPERTIES(python-module PROPERTIES OUTPUT_NAME Avogadro)
---- avogadro-1.0.3/libavogadro/CMakeLists.txt~	2011-11-29 19:41:34.066938217 +0000
-+++ avogadro-1.0.3/libavogadro/CMakeLists.txt	2011-11-29 19:42:53.084320315 +0000
-@@ -18,7 +18,7 @@
-   # Assume all MOC stuff is in the headers, replace .cpp and use qt4_wrap_cpp
-   # We should probably scan the header to verify the Q_OBJECT macro is used
-   string(REPLACE ".cpp" ".h" hdr_list "${src_list}")
--  qt4_wrap_cpp(moc_files ${hdr_list})
-+  qt4_wrap_cpp(moc_files ${hdr_list} OPTIONS -DBOOST_TT_HAS_OPERATOR_HPP_INCLUDED)
-   # Now sort out the ui and qrc files, process them as appropriate
-   set(ui_plugin_files)
-   set(qrc_plugin_files)
diff --git a/extra/avogadro/fix-opengl-headers.patch b/extra/avogadro/fix-opengl-headers.patch
deleted file mode 100644
index e6e8bc3b5..000000000
--- a/extra/avogadro/fix-opengl-headers.patch
+++ /dev/null
@@ -1,53 +0,0 @@
---- avogadro-1.0.3/libavogadro/src/camera.cpp~	2012-02-27 18:35:52.109999585 +0000
-+++ avogadro-1.0.3/libavogadro/src/camera.cpp	2012-02-27 18:36:27.103053453 +0000
-@@ -25,6 +25,8 @@
- #include "camera.h"
- #include "glwidget.h"
- #include <avogadro/molecule.h>
-+#include <Eigen/LU>
-+#include <GL/glu.h>
- 
- using namespace Eigen;
- 
---- avogadro-1.0.3/libavogadro/src/glpainter_p.cpp~	2012-02-27 18:37:28.535894209 +0000
-+++ avogadro-1.0.3/libavogadro/src/glpainter_p.cpp	2012-02-27 18:37:46.912413557 +0000
-@@ -42,6 +42,7 @@
- #include <QColor>
- #include <QVarLengthArray>
- #include <Eigen/Geometry>
-+#include <GL/glu.h>
- 
- namespace Avogadro
- {
---- avogadro-1.0.3/libavogadro/src/glwidget.cpp~	2012-02-27 18:37:55.099014598 +0000
-+++ avogadro-1.0.3/libavogadro/src/glwidget.cpp	2012-02-27 18:38:30.805395066 +0000
-@@ -70,6 +70,8 @@
- 
- #include <openbabel/mol.h>
- 
-+#include <GL/glu.h>
-+
- using namespace OpenBabel;
- using namespace Eigen;
- 
---- avogadro-1.0.3/libavogadro/src/extensions/povpainter.cpp~	2012-02-27 18:36:53.646173944 +0000
-+++ avogadro-1.0.3/libavogadro/src/extensions/povpainter.cpp	2012-02-27 18:37:10.739370227 +0000
-@@ -36,6 +36,7 @@
- #include <QFile>
- #include <QDebug>
- #include <Eigen/Geometry>
-+#include <GL/glu.h>
- 
- namespace Avogadro
- {
---- avogadro-1.0.3/libavogadro/src/tools/selectrotatetool.cpp~	2012-02-27 18:38:47.491928000 +0000
-+++ avogadro-1.0.3/libavogadro/src/tools/selectrotatetool.cpp	2012-02-27 18:39:05.735115136 +0000
-@@ -44,6 +44,8 @@
- #include <QComboBox>
- #include <QDebug>
- 
-+#include <GL/glu.h>
-+
- using namespace std;
- using namespace OpenBabel;
- using namespace Eigen;
diff --git a/extra/avogadro/replace-qt4_automoc-with-qt4_wrap_cpp.patch b/extra/avogadro/replace-qt4_automoc-with-qt4_wrap_cpp.patch
deleted file mode 100644
index 11f58a505..000000000
--- a/extra/avogadro/replace-qt4_automoc-with-qt4_wrap_cpp.patch
+++ /dev/null
@@ -1,778 +0,0 @@
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/CMakeLists.txt avogadro-1.0.3-edit/libavogadro/src/CMakeLists.txt
---- avogadro-1.0.3/libavogadro/src/CMakeLists.txt	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/CMakeLists.txt	2011-11-29 18:49:58.520790652 +0100
-@@ -75,6 +75,42 @@
-   zmatrix.h
- )
- 
-+SET(libavogadro_MOC_HDRS
-+  animation.h
-+  atom.h
-+  bond.h
-+  color.h
-+  colorbutton.h
-+  colors/elementcolor.h
-+  cube.h
-+  elementdetail_p.h
-+  elementtranslator.h
-+  engine.h
-+  engines/bsdyengine.h
-+  extension.h
-+  fragment.h
-+  glwidget.h
-+  mesh.h
-+  molecule.h
-+  moleculefile.h
-+  moleculefile_p.h
-+  periodictablescene_p.h
-+  periodictableview.h
-+  plotwidget.h
-+  plugin.h
-+  pluginmanager.h
-+  primitive.h
-+  protein.h
-+  pythonengine_p.h
-+  pythonerror.h
-+  pythonextension_p.h
-+  pythontool_p.h
-+  residue.h
-+  tool.h
-+  toolgroup.h
-+  zmatrix.h
-+)
-+
- set(libavogadro_SRCS ${libavogadro_SRCS} ${libavogadro_UIS})
- # Also add in the qtiocompressor class
- #set(libavogadro_SRCS ${libavogadro_SRCS} ../qtiocompressor/qtiocompressor.cpp)
-@@ -113,7 +148,7 @@
-   endforeach(P_ITEM ${PYTHON_SRCS})
- endif(NOT ENABLE_PYTHON OR NOT ALL_PYTHON_FOUND)
- 
--qt4_automoc(${libavogadro_SRCS})
-+QT4_WRAP_CPP(libavogadro_MOC_SRCS ${libavogadro_MOC_HDRS})
- 
- # you have to add link_directories before you add the target
- if(ENABLE_PYTHON AND ALL_PYTHON_FOUND)
-@@ -149,7 +184,7 @@
-     COMMAND ${CMAKE_COMMAND} -E ${header_cmd} "${from}" "${to}")
- endforeach(headerFile ${libavogadro_HDRS})
- 
--add_library(avogadro SHARED ${libavogadro_SRCS} ${libavogadro_QM} ${pythontool_RC_SRCS})
-+add_library(avogadro SHARED ${libavogadro_SRCS} ${libavogadro_MOC_SRCS} ${libavogadro_QM} ${pythontool_RC_SRCS})
- set_target_properties(avogadro
-   PROPERTIES VERSION ${Avogadro_VERSION_FULL} SOVERSION 1 )
- target_link_libraries(avogadro ${AVO_LINK_LIBRARIES})
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/animation.cpp avogadro-1.0.3-edit/libavogadro/src/animation.cpp
---- avogadro-1.0.3/libavogadro/src/animation.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/animation.cpp	2011-11-29 18:48:47.967839537 +0100
-@@ -224,5 +224,3 @@
-   }
- 
- } // end namespace Avogadro
--
--#include "animation.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/atom.cpp avogadro-1.0.3-edit/libavogadro/src/atom.cpp
---- avogadro-1.0.3/libavogadro/src/atom.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/atom.cpp	2011-11-29 18:48:39.561218412 +0100
-@@ -293,5 +293,3 @@
-    }
- 
-  } // End namespace Avogadro
--
--#include "atom.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/bond.cpp avogadro-1.0.3-edit/libavogadro/src/bond.cpp
---- avogadro-1.0.3/libavogadro/src/bond.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/bond.cpp	2011-11-29 18:49:00.067773985 +0100
-@@ -166,5 +166,3 @@
-   }
- 
- } // End namespace Avogadro
--
--#include "bond.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/color.cpp avogadro-1.0.3-edit/libavogadro/src/color.cpp
---- avogadro-1.0.3/libavogadro/src/color.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/color.cpp	2011-11-29 18:49:05.207746140 +0100
-@@ -152,5 +152,3 @@
-     return "Generic Color";
-   }
- }
--
--#include "color.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/colorbutton.cpp avogadro-1.0.3-edit/libavogadro/src/colorbutton.cpp
---- avogadro-1.0.3/libavogadro/src/colorbutton.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/colorbutton.cpp	2011-11-29 18:49:11.987709410 +0100
-@@ -94,5 +94,3 @@
-   }
- 
- } // end namespace
--
--#include "colorbutton.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/colors/elementcolor.cpp avogadro-1.0.3-edit/libavogadro/src/colors/elementcolor.cpp
---- avogadro-1.0.3/libavogadro/src/colors/elementcolor.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/colors/elementcolor.cpp	2011-11-29 18:50:11.077389292 +0100
-@@ -63,7 +63,5 @@
- 
- }
- 
--#include "elementcolor.moc"
- //this is a static color plugin...
- //Q_EXPORT_PLUGIN2(elementcolor, Avogadro::ElementColorFactory)
--
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/cube.cpp avogadro-1.0.3-edit/libavogadro/src/cube.cpp
---- avogadro-1.0.3/libavogadro/src/cube.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/cube.cpp	2011-11-29 18:50:26.357306516 +0100
-@@ -322,5 +322,3 @@
-   }
- 
- } // End namespace Avogadro
--
--#include "cube.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/elementdetail_p.cpp avogadro-1.0.3-edit/libavogadro/src/elementdetail_p.cpp
---- avogadro-1.0.3/libavogadro/src/elementdetail_p.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/elementdetail_p.cpp	2011-11-29 18:50:37.680578505 +0100
-@@ -132,5 +132,3 @@
-   }
- 
- } // End namespace Avogadro
--
--#include "elementdetail_p.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/elementtranslator.cpp avogadro-1.0.3-edit/libavogadro/src/elementtranslator.cpp
---- avogadro-1.0.3/libavogadro/src/elementtranslator.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/elementtranslator.cpp	2011-11-29 18:50:48.160521729 +0100
-@@ -401,5 +401,3 @@
-   }
- 
- } // End namespace Avogadro
--
--#include "elementtranslator.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/engine.cpp avogadro-1.0.3-edit/libavogadro/src/engine.cpp
---- avogadro-1.0.3/libavogadro/src/engine.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/engine.cpp	2011-11-29 18:50:54.397154610 +0100
-@@ -377,5 +377,3 @@
-       return m_molecule->bonds();
-   }
- }
--
--#include "engine.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/engines/bsdyengine.cpp avogadro-1.0.3-edit/libavogadro/src/engines/bsdyengine.cpp
---- avogadro-1.0.3/libavogadro/src/engines/bsdyengine.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/engines/bsdyengine.cpp	2011-11-29 18:51:18.733689435 +0100
-@@ -442,7 +442,5 @@
-   }
- 
- }
--
--#include "bsdyengine.moc"
- // This is a static engine...
- // Q_EXPORT_PLUGIN2( bsdyengine, Avogadro::BSDYEngineFactory )
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/extension.cpp avogadro-1.0.3-edit/libavogadro/src/extension.cpp
---- avogadro-1.0.3/libavogadro/src/extension.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/extension.cpp	2011-11-29 18:51:56.360152261 +0100
-@@ -80,5 +80,3 @@
-   }
- 
- }
--
--#include "extension.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/fragment.cpp avogadro-1.0.3-edit/libavogadro/src/fragment.cpp
---- avogadro-1.0.3/libavogadro/src/fragment.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/fragment.cpp	2011-11-29 18:52:01.906788880 +0100
-@@ -82,5 +82,3 @@
-   }
- 
- } // End namespace Avogadro
--
--#include "fragment.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/glwidget.cpp avogadro-1.0.3-edit/libavogadro/src/glwidget.cpp
---- avogadro-1.0.3/libavogadro/src/glwidget.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/glwidget.cpp	2011-11-29 18:52:14.346721486 +0100
-@@ -1966,5 +1966,3 @@
-     d->updateCache = true;
-   }
- }
--
--#include "glwidget.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/mesh.cpp avogadro-1.0.3-edit/libavogadro/src/mesh.cpp
---- avogadro-1.0.3/libavogadro/src/mesh.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/mesh.cpp	2011-11-29 18:52:23.033341093 +0100
-@@ -231,5 +231,3 @@
-   }
- 
- } // End namespace Avogadro
--
--#include "mesh.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/molecule.cpp avogadro-1.0.3-edit/libavogadro/src/molecule.cpp
---- avogadro-1.0.3/libavogadro/src/molecule.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/molecule.cpp	2011-11-29 18:52:33.573283993 +0100
-@@ -1575,5 +1575,3 @@
-   }
- 
- } // End namespace Avogadro
--
--#include "molecule.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/moleculefile.cpp avogadro-1.0.3-edit/libavogadro/src/moleculefile.cpp
---- avogadro-1.0.3/libavogadro/src/moleculefile.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/moleculefile.cpp	2011-11-29 18:56:26.728687548 +0100
-@@ -22,23 +22,14 @@
-   02110-1301, USA.
-  **********************************************************************/
- 
--#include "moleculefile.h"
-+#include "moleculefile_p.h"
- 
- #include <avogadro/molecule.h>
- 
--#include <QFile>
- #include <QFileInfo>
--#include <QStringList>
--#include <QThread>
- #include <QDebug>
- #include <QPointer>
- 
--#include <openbabel/mol.h>
--#include <openbabel/obconversion.h>
--
--// Included in obconversion.h
--//#include <iostream>
--
- namespace Avogadro {
- 
-   using OpenBabel::OBConversion;
-@@ -578,164 +569,6 @@
-     return false;
-   }
- 
--  class ReadFileThread : public QThread
--  {
--    //    Q_OBJECT 
--
--    public:
--      ReadFileThread(MoleculeFile *moleculeFile) : m_moleculeFile(moleculeFile)
--      {
--      }
--      
--      void addConformer(const OpenBabel::OBMol &conformer)
--      {
--        unsigned int numAtoms = conformer.NumAtoms();
--        std::vector<Eigen::Vector3d> *coords = new std::vector<Eigen::Vector3d>(numAtoms);
--        for (unsigned int i = 0; i < numAtoms; ++i)
--          coords->push_back(Eigen::Vector3d(conformer.GetAtom(i+1)->GetVector().AsArray()));
--        m_moleculeFile->m_conformers.push_back(coords);
--      }
--
--      void detectConformers(unsigned int c, const OpenBabel::OBMol &first, const OpenBabel::OBMol &current)
--      {
--        if (!c) {
--          // this is the first molecule read
--          m_moleculeFile->setConformerFile(true);
--          addConformer(current);
--          return;
--        }
--
--        if (!m_moleculeFile->isConformerFile())
--          return;
--
--        // as long as we are not sure if this really is a 
--        // conformer/trajectory file, add the conformers
--        addConformer(current);
--
--        // performance: check only certain molecule 1-10,20,50
--        switch (c) {
--          case 1:
--          case 2:
--          case 3:
--          case 4:
--          case 5:
--          case 6:
--          case 7:
--          case 8:
--          case 9:
--          case 10:
--          case 20:
--          case 50:
--            break;
--          default:
--            return;
--        }
--
--        if (first.NumAtoms() != current.NumAtoms()) {
--          m_moleculeFile->setConformerFile(false);
--          m_moleculeFile->m_conformers.clear();
--          return;
--        }
--
--        for (unsigned int i = 0; i < first.NumAtoms(); ++i) {
--          OpenBabel::OBAtom *firstAtom = first.GetAtom(i+1);
--          OpenBabel::OBAtom *currentAtom = current.GetAtom(i+1);
--          if (firstAtom->GetAtomicNum() != currentAtom->GetAtomicNum()) {
--            m_moleculeFile->setConformerFile(false);
--            m_moleculeFile->m_conformers.clear();
--            return;
--          }    
--        }
--      }
--
--      void run()
--      {
--        // Check that the file can be read from disk
--        if (!MoleculeFile::canOpen(m_moleculeFile->m_fileName, QFile::ReadOnly | QFile::Text)) {
--          // Cannot read the file
--          m_moleculeFile->m_error.append(QObject::tr("File %1 cannot be opened for reading.")
--                                         .arg(m_moleculeFile->m_fileName));
--          return;
--        }
-- 
--        // Construct the OpenBabel objects, set the file type
--        OpenBabel::OBConversion conv;
--        OpenBabel::OBFormat *inFormat;
--        if (!m_moleculeFile->m_fileType.isEmpty() && !conv.SetInFormat(m_moleculeFile->m_fileType.toAscii().data())) {
--          // Input format not supported
--          m_moleculeFile->m_error.append(
--              QObject::tr("File type '%1' is not supported for reading.").arg(m_moleculeFile->m_fileType));
--          return;
--        } else {
--          inFormat = conv.FormatFromExt(m_moleculeFile->m_fileName.toAscii().data());
--          if (!inFormat || !conv.SetInFormat(inFormat)) {
--            // Input format not supported
--            m_moleculeFile->m_error.append(QObject::tr("File type for file '%1' is not supported for reading.")
--                                           .arg(m_moleculeFile->m_fileName));
--            return;
--          }
--        }
--
--        // set any options
--        if (!m_moleculeFile->m_fileOptions.isEmpty()) {
--          foreach(const QString &option,
--              m_moleculeFile->m_fileOptions.split('\n', QString::SkipEmptyParts)) {
--            conv.AddOption(option.toAscii().data(), OBConversion::INOPTIONS);
--          }
--        }
--
--        // Now attempt to read the molecule in
--        ifstream ifs;
--        ifs.open(m_moleculeFile->m_fileName.toLocal8Bit()); // This handles utf8 file names etc
--        if (!ifs) // Should not happen, already checked file could be opened
--          return;
--      
--        // read all molecules
--        OpenBabel::OBMol firstOBMol, currentOBMol;
--        unsigned int c = 0;
--        conv.SetInStream(&ifs);
--        m_moleculeFile->streamposRef().push_back(ifs.tellg());
--        while (ifs.good() && conv.Read(&currentOBMol)) {
--          if (!c)
--            firstOBMol = currentOBMol;
--
--          if (c > 20 && !m_moleculeFile->isConformerFile())
--            m_moleculeFile->setFirstReady(true);
--
--          // detect conformer/trajectory files
--          detectConformers(c, firstOBMol, currentOBMol);
--          // store information about molecule
--          m_moleculeFile->streamposRef().push_back(ifs.tellg());
--          m_moleculeFile->titlesRef().append(currentOBMol.GetTitle());
--          // increment count
--          ++c;
--        }
--        m_moleculeFile->streamposRef().pop_back();
--
--        // signle molecule files are not conformer files
--        if (c == 1) {
--          m_moleculeFile->setConformerFile(false);
--          m_moleculeFile->m_conformers.clear();
--        }
--
--        // check for empty titles
--        for (int i = 0; i < m_moleculeFile->titlesRef().size(); ++i) {
--          if (!m_moleculeFile->titlesRef()[i].isEmpty())
--            continue;
--
--          QString title;
--          if (m_moleculeFile->isConformerFile())
--            title = tr("Conformer %1").arg(i+1);
--          else
--            title = tr("Molecule %1").arg(i+1);
--        
--          m_moleculeFile->titlesRef()[i] = title;
--        }
--      }
--
--      MoleculeFile *m_moleculeFile;
--  }; // end ReadFileThread class
--
-   MoleculeFile* MoleculeFile::readFile(const QString &fileName,
-       const QString &fileType, const QString &fileOptions, bool wait)
-   {
-@@ -794,6 +627,3 @@
-   }
- 
- } // end namespace Avogadro
--
--#include "moleculefile.moc"
--
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/moleculefile_p.h avogadro-1.0.3-edit/libavogadro/src/moleculefile_p.h
---- avogadro-1.0.3/libavogadro/src/moleculefile_p.h	1970-01-01 01:00:00.000000000 +0100
-+++ avogadro-1.0.3-edit/libavogadro/src/moleculefile_p.h	2011-11-29 18:57:43.108273764 +0100
-@@ -0,0 +1,202 @@
-+/**********************************************************************
-+  MoleculeFile - Class representing molecule file.
-+
-+  Copyright (C) 2009 Marcus Hanwell, Tim Vandermeersch
-+
-+  This file is part of the Avogadro molecular editor project.
-+  For more information, see <http://avogadro.openmolecules.net/>
-+
-+  Avogadro is free software; you can redistribute it and/or modify
-+  it under the terms of the GNU General Public License as published by
-+  the Free Software Foundation; either version 2 of the License, or
-+  (at your option) any later version.
-+
-+  Avogadro 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 General Public License for more details.
-+
-+  You should have received a copy of the GNU General Public License
-+  along with this program; if not, write to the Free Software
-+  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
-+  02110-1301, USA.
-+ **********************************************************************/
-+
-+#ifndef MOLECULEFILE_P_H
-+#define MOLECULEFILE_P_H
-+
-+#include "moleculefile.h"
-+
-+#include <openbabel/mol.h>
-+#include <openbabel/obconversion.h>
-+
-+#include <QFile>
-+#include <QStringList>
-+#include <QThread>
-+
-+namespace Avogadro {
-+
-+  using OpenBabel::OBConversion;
-+  using std::ifstream;
-+
-+class ReadFileThread : public QThread
-+{
-+      Q_OBJECT
-+
-+  public:
-+    ReadFileThread(MoleculeFile *moleculeFile) : m_moleculeFile(moleculeFile)
-+    {
-+    }
-+
-+    void addConformer(const OpenBabel::OBMol &conformer)
-+    {
-+      unsigned int numAtoms = conformer.NumAtoms();
-+      std::vector<Eigen::Vector3d> *coords = new std::vector<Eigen::Vector3d>(numAtoms);
-+      for (unsigned int i = 0; i < numAtoms; ++i)
-+        coords->push_back(Eigen::Vector3d(conformer.GetAtom(i+1)->GetVector().AsArray()));
-+      m_moleculeFile->m_conformers.push_back(coords);
-+    }
-+
-+    void detectConformers(unsigned int c, const OpenBabel::OBMol &first, const OpenBabel::OBMol &current)
-+    {
-+      if (!c) {
-+        // this is the first molecule read
-+        m_moleculeFile->setConformerFile(true);
-+        addConformer(current);
-+        return;
-+      }
-+
-+      if (!m_moleculeFile->isConformerFile())
-+        return;
-+
-+      // as long as we are not sure if this really is a
-+      // conformer/trajectory file, add the conformers
-+      addConformer(current);
-+
-+      // performance: check only certain molecule 1-10,20,50
-+      switch (c) {
-+        case 1:
-+        case 2:
-+        case 3:
-+        case 4:
-+        case 5:
-+        case 6:
-+        case 7:
-+        case 8:
-+        case 9:
-+        case 10:
-+        case 20:
-+        case 50:
-+          break;
-+        default:
-+          return;
-+      }
-+
-+      if (first.NumAtoms() != current.NumAtoms()) {
-+        m_moleculeFile->setConformerFile(false);
-+        m_moleculeFile->m_conformers.clear();
-+        return;
-+      }
-+
-+      for (unsigned int i = 0; i < first.NumAtoms(); ++i) {
-+        OpenBabel::OBAtom *firstAtom = first.GetAtom(i+1);
-+        OpenBabel::OBAtom *currentAtom = current.GetAtom(i+1);
-+        if (firstAtom->GetAtomicNum() != currentAtom->GetAtomicNum()) {
-+          m_moleculeFile->setConformerFile(false);
-+          m_moleculeFile->m_conformers.clear();
-+          return;
-+        }
-+      }
-+    }
-+
-+    void run()
-+    {
-+      // Check that the file can be read from disk
-+      if (!MoleculeFile::canOpen(m_moleculeFile->m_fileName, QFile::ReadOnly | QFile::Text)) {
-+        // Cannot read the file
-+        m_moleculeFile->m_error.append(QObject::tr("File %1 cannot be opened for reading.")
-+                                       .arg(m_moleculeFile->m_fileName));
-+        return;
-+      }
-+
-+      // Construct the OpenBabel objects, set the file type
-+      OpenBabel::OBConversion conv;
-+      OpenBabel::OBFormat *inFormat;
-+      if (!m_moleculeFile->m_fileType.isEmpty() && !conv.SetInFormat(m_moleculeFile->m_fileType.toAscii().data())) {
-+        // Input format not supported
-+        m_moleculeFile->m_error.append(
-+            QObject::tr("File type '%1' is not supported for reading.").arg(m_moleculeFile->m_fileType));
-+        return;
-+      } else {
-+        inFormat = conv.FormatFromExt(m_moleculeFile->m_fileName.toAscii().data());
-+        if (!inFormat || !conv.SetInFormat(inFormat)) {
-+          // Input format not supported
-+          m_moleculeFile->m_error.append(QObject::tr("File type for file '%1' is not supported for reading.")
-+                                         .arg(m_moleculeFile->m_fileName));
-+          return;
-+        }
-+      }
-+
-+      // set any options
-+      if (!m_moleculeFile->m_fileOptions.isEmpty()) {
-+        foreach(const QString &option,
-+            m_moleculeFile->m_fileOptions.split('\n', QString::SkipEmptyParts)) {
-+          conv.AddOption(option.toAscii().data(), OBConversion::INOPTIONS);
-+        }
-+      }
-+
-+      // Now attempt to read the molecule in
-+      ifstream ifs;
-+      ifs.open(m_moleculeFile->m_fileName.toLocal8Bit()); // This handles utf8 file names etc
-+      if (!ifs) // Should not happen, already checked file could be opened
-+        return;
-+
-+      // read all molecules
-+      OpenBabel::OBMol firstOBMol, currentOBMol;
-+      unsigned int c = 0;
-+      conv.SetInStream(&ifs);
-+      m_moleculeFile->streamposRef().push_back(ifs.tellg());
-+      while (ifs.good() && conv.Read(&currentOBMol)) {
-+        if (!c)
-+          firstOBMol = currentOBMol;
-+
-+        if (c > 20 && !m_moleculeFile->isConformerFile())
-+          m_moleculeFile->setFirstReady(true);
-+
-+        // detect conformer/trajectory files
-+        detectConformers(c, firstOBMol, currentOBMol);
-+        // store information about molecule
-+        m_moleculeFile->streamposRef().push_back(ifs.tellg());
-+        m_moleculeFile->titlesRef().append(currentOBMol.GetTitle());
-+        // increment count
-+        ++c;
-+      }
-+      m_moleculeFile->streamposRef().pop_back();
-+
-+      // signle molecule files are not conformer files
-+      if (c == 1) {
-+        m_moleculeFile->setConformerFile(false);
-+        m_moleculeFile->m_conformers.clear();
-+      }
-+
-+      // check for empty titles
-+      for (int i = 0; i < m_moleculeFile->titlesRef().size(); ++i) {
-+        if (!m_moleculeFile->titlesRef()[i].isEmpty())
-+          continue;
-+
-+        QString title;
-+        if (m_moleculeFile->isConformerFile())
-+          title = tr("Conformer %1").arg(i+1);
-+        else
-+          title = tr("Molecule %1").arg(i+1);
-+
-+        m_moleculeFile->titlesRef()[i] = title;
-+      }
-+    }
-+
-+    MoleculeFile *m_moleculeFile;
-+};
-+
-+} // end namespace Avogadro
-+
-+#endif // MOLECULEFILE_P_H
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/periodictablescene_p.cpp avogadro-1.0.3-edit/libavogadro/src/periodictablescene_p.cpp
---- avogadro-1.0.3/libavogadro/src/periodictablescene_p.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/periodictablescene_p.cpp	2011-11-29 18:52:50.259860261 +0100
-@@ -213,5 +213,3 @@
-   }
- 
- } // End namespace Avogadro
--
--#include "periodictablescene_p.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/periodictableview.cpp avogadro-1.0.3-edit/libavogadro/src/periodictableview.cpp
---- avogadro-1.0.3/libavogadro/src/periodictableview.cpp     2011-11-29 19:30:25.130970122 +0000
-+++ avogadro-1.0.3-edit/libavogadro/src/periodictableview.cpp        2011-11-29 18:52:50.259860261 +0100
-@@ -69,4 +69,3 @@
- 
- } // End namespace Avogadro
- 
--#include "periodictableview.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/plotwidget.cpp avogadro-1.0.3-edit/libavogadro/src/plotwidget.cpp
---- avogadro-1.0.3/libavogadro/src/plotwidget.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/plotwidget.cpp	2011-11-29 18:53:09.389756626 +0100
-@@ -27,7 +27,6 @@
-  **********************************************************************/
- 
- #include "plotwidget.h"
--#include "plotwidget.moc"
- 
- #include <math.h>
- #include <QDebug>
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/plugin.cpp avogadro-1.0.3-edit/libavogadro/src/plugin.cpp
---- avogadro-1.0.3/libavogadro/src/plugin.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/plugin.cpp	2011-11-29 18:53:16.016387394 +0100
-@@ -65,5 +65,3 @@
-   }
- 
- } // end namespace Avogadro
--
--#include "plugin.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/pluginmanager.cpp avogadro-1.0.3-edit/libavogadro/src/pluginmanager.cpp
---- avogadro-1.0.3/libavogadro/src/pluginmanager.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/pluginmanager.cpp	2011-11-29 18:53:23.569679807 +0100
-@@ -784,5 +784,3 @@
-   }
- 
- }
--
--#include "pluginmanager.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/primitive.cpp avogadro-1.0.3-edit/libavogadro/src/primitive.cpp
---- avogadro-1.0.3/libavogadro/src/primitive.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/primitive.cpp	2011-11-29 18:53:29.139649631 +0100
-@@ -77,5 +77,3 @@
-   }
- 
- }
--
--#include "primitive.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/protein.cpp avogadro-1.0.3-edit/libavogadro/src/protein.cpp
---- avogadro-1.0.3/libavogadro/src/protein.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/protein.cpp	2011-11-29 18:53:37.952935219 +0100
-@@ -978,5 +978,3 @@
-   }
- 
- } // End namespace Avogadro
--
--#include "protein.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/python/CMakeLists.txt avogadro-1.0.3-edit/libavogadro/src/python/CMakeLists.txt
---- avogadro-1.0.3/libavogadro/src/python/CMakeLists.txt	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/python/CMakeLists.txt	2011-11-29 18:58:02.354836165 +0100
-@@ -11,9 +11,9 @@
- # use all cpp files in this directory
- FILE(GLOB wrapper_SRCS "*.cpp")
- 
--qt4_automoc(moleculelist.cpp)
-+QT4_WRAP_CPP(MOC_SRCS moleculelist.h)
- 
--ADD_LIBRARY(python-module MODULE ${wrapper_SRCS})
-+ADD_LIBRARY(python-module MODULE ${wrapper_SRCS} ${MOC_SRCS})
- SET_TARGET_PROPERTIES(python-module PROPERTIES OUTPUT_NAME Avogadro)
- SET_TARGET_PROPERTIES(python-module PROPERTIES PREFIX "")
- if (WIN32)
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/python/moleculelist.cpp avogadro-1.0.3-edit/libavogadro/src/python/moleculelist.cpp
---- avogadro-1.0.3/libavogadro/src/python/moleculelist.cpp     2011-11-29 19:26:07.562214311 +0100
-+++ avogadro-1.0.3-edit/libavogadro/src/python/moleculelist.cpp      2011-11-29 19:26:14.538843182 +0100
-@@ -70,4 +70,3 @@
- 
- }
- 
--#include "moleculelist.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/pythonengine_p.cpp avogadro-1.0.3-edit/libavogadro/src/pythonengine_p.cpp
---- avogadro-1.0.3/libavogadro/src/pythonengine_p.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/pythonengine_p.cpp	2011-11-29 18:53:45.492894371 +0100
-@@ -289,5 +289,3 @@
- 
- 
- }
--
--#include "pythonengine_p.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/pythonerror.cpp avogadro-1.0.3-edit/libavogadro/src/pythonerror.cpp
---- avogadro-1.0.3/libavogadro/src/pythonerror.cpp     2011-11-29 19:24:26.949426045 +0100
-+++ avogadro-1.0.3-edit/libavogadro/src/pythonerror.cpp      2011-11-29 19:24:41.176015640 +0100
-@@ -112,4 +112,3 @@
- 
- } // namespace
- 
--#include "pythonerror.moc"
-
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/pythonextension_p.cpp avogadro-1.0.3-edit/libavogadro/src/pythonextension_p.cpp
---- avogadro-1.0.3/libavogadro/src/pythonextension_p.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/pythonextension_p.cpp	2011-11-29 18:53:54.082847836 +0100
-@@ -340,5 +340,3 @@
-   }
- 
- }
--
--#include "pythonextension_p.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/pythontool_p.cpp avogadro-1.0.3-edit/libavogadro/src/pythontool_p.cpp
---- avogadro-1.0.3/libavogadro/src/pythontool_p.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/pythontool_p.cpp	2011-11-29 18:54:02.269470152 +0100
-@@ -344,5 +344,3 @@
-   }
- 
- }
--
--#include "pythontool_p.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/residue.cpp avogadro-1.0.3-edit/libavogadro/src/residue.cpp
---- avogadro-1.0.3/libavogadro/src/residue.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/residue.cpp	2011-11-29 18:54:14.316071557 +0100
-@@ -160,6 +160,3 @@
-   }
- 
- } // End namespace Avogadro
--
-- #include "residue.moc"
--
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/tool.cpp avogadro-1.0.3-edit/libavogadro/src/tool.cpp
---- avogadro-1.0.3/libavogadro/src/tool.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/tool.cpp	2011-11-29 18:55:05.515794184 +0100
-@@ -117,5 +117,3 @@
-   }
- 
- } // end namespace Avogadro
--
--#include "tool.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/toolgroup.cpp avogadro-1.0.3-edit/libavogadro/src/toolgroup.cpp
---- avogadro-1.0.3/libavogadro/src/toolgroup.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/toolgroup.cpp	2011-11-29 18:55:11.699094018 +0100
-@@ -206,5 +206,3 @@
-   }
- 
- } // end namespace Avogadro
--
--#include "toolgroup.moc"
-diff -U 3 -H -d -r -N -- avogadro-1.0.3/libavogadro/src/zmatrix.cpp avogadro-1.0.3-edit/libavogadro/src/zmatrix.cpp
---- avogadro-1.0.3/libavogadro/src/zmatrix.cpp	2011-04-25 07:22:18.000000000 +0200
-+++ avogadro-1.0.3-edit/libavogadro/src/zmatrix.cpp	2011-11-29 18:55:17.209064168 +0100
-@@ -149,5 +149,3 @@
- 
- 
- } // End namespace Avogadro
--
--#include "zmatrix.moc"