File avogadro.spec of Package avogadro-qt4

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#
# spec file for package avogadro
#
# Copyright (c) 2016 SUSE LINUX GmbH, Nuernberg, Germany.
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
# upon. The license for this file, and modifications and additions to the
# file, is the same license as for the pristine package itself (unless the
# license for the pristine package is not an Open Source License, in which
# case the license is the MIT License). An "Open Source License" is a
# license that conforms to the Open Source Definition (Version 1.9)
# published by the Open Source Initiative.

# Please submit bugfixes or comments via http://bugs.opensuse.org/
#

Name:           avogadro-qt4
Version:        1.2.0
Release:        0
Summary:        A Molecular design tool
License:        GPL-2.0
Group:          Productivity/Scientific/Chemistry
Url:            http://avogadro.cc
Source0:        http://sourceforge.net/projects/avogadro/files/avogadro/%{version}/avogadro-%{version}.tar.gz
Source1:        avogadro.png
Source2:        baselibs.conf
# PATCH-FIX-UPSTREAM avogadro-1.1.0-avopkg-fix-echo.patch ledest@gmail.com
Patch1:         avogadro-1.1.0-avopkg-fix-echo.patch
Patch2:         avogadro-boost.patch
Patch3:         avogadro-opanbabel.patch
# PATCH-FIX-OPENSUSE don't use signbit() on non-float kkaempf@suse.de
Patch4:         0004-don-t-use-signbit-on-non-float.patch
# PATCH-FIX-OPENSUSE link with libm kkaempf@suse.de
Patch5:         0005-Link-with-libm.patch
# PATCH-FIX-UPSTREAM avogadro-port-to-eigen3.patch badshah400@gmail.com -- Cherry pick commits from upstream to get avogadro building with eigen3
Patch7:         avogadro-port-to-eigen3.patch

%if 0%{?suse_version} >= 1500
BuildRequires:  libboost_python-devel
%else
BuildRequires:  boost-devel
%endif
BuildRequires:  cmake
BuildRequires:  docbook-utils
BuildRequires:  fdupes
BuildRequires:  gcc-c++
%if 0%{?suse_version} > 1500 || 0%{?sle_version} >= 150400
# fails to build with latest glew, use an older one until it can be fixed
BuildRequires:  glew2_1-devel
%else
BuildRequires:  glew-devel
%endif
BuildRequires:  libopenbabel-devel >= 2.3.1
BuildRequires:  libqt4-devel >= 4.5.1
BuildRequires:  python-devel
BuildRequires:  python-numpy-devel
BuildRequires:  python-qt4-devel
BuildRequires:  python-sip-devel
BuildRequires:  pkgconfig(eigen3)
BuildRequires:  pkgconfig(glu)
BuildRequires:  pkgconfig(gl)
BuildRequires:  pkgconfig(x11)
BuildRequires:  pkgconfig(zlib)
Requires:       libavogadro1 = %{version}
Requires:       openbabel
Requires:       python-numpy
Requires:       python-sip
Provides:       avogadro = %{version}
Obsoletes:      avogadro < 1.90
# libmsym.so
Conflicts:      libmsym-devel

%description
Avogadro is an advanced molecular editor designed
for cross-platform use in computational chemistry,
molecular modeling, bioinformatics, materials science,
and related areas. It offers flexible rendering and
a powerful plugin architecture.

%package -n libavogadro1
Summary:        A Molecular design tool
Group:          Development/Libraries/C and C++
Provides:       libavogadro = %{version}-%{release}

%description -n libavogadro1
This package contains the shared libraries for Avogadro.

Avogadro is an advanced molecular editor designed
for cross-platform use in computational chemistry,
molecular modeling, bioinformatics, materials science,
and related areas. It offers flexible rendering and
a powerful plugin architecture.

%package -n avogadro-devel
Summary:        Development files for Avogadro
Group:          Development/Libraries/C and C++
Requires:       %{name} = %{version}
Conflicts:      libmsym-devel

%description -n avogadro-devel
This package contains files to develop applications using
Avogadros libraries.

%package -n python-avogadro
Summary:        A python wrapper to avogadro
Group:          Development/Languages/Python
Requires:       python-numpy
Requires:       python-sip

%description -n python-avogadro
This package contains the python wrapper to Avogadro.

%prep
%autosetup -p1 -n avogadro-%{version}
sed -i '/project/a add_definitions(-Dnullptr=NULL)' CMakeLists.txt

sed -i 's/find_package(OpenBabel2 REQUIRED)/find_package(OpenBabel3 REQUIRED)/' CMakeLists.txt
sed -i 's/OPENBABEL2_INCLUDE_DIR/OpenBabel3_INCLUDE_DIRS/' avogadro/src/CMakeLists.txt
sed -i 's/OPENBABEL2_LIBRARY_DIRS/OpenBabel3_LIBRARY_DIRS/' avogadro/src/CMakeLists.txt
sed -i 's/OPENBABEL2_LIBRARIES/OpenBabel3_LIBRARIES/' avogadro/src/CMakeLists.txt
sed -i 's/OPENBABEL2_LIBRARIES/OpenBabel3_LIBRARIES/' libavogadro/CMakeLists.txt
sed -i 's/OPENBABEL2_INCLUDE_DIR/OpenBabel3_INCLUDE_DIRS/' libavogadro/src/CMakeLists.txt
sed -i 's/OPENBABEL2_LIBRARY_DIRS/OpenBabel3_LIBRARY_DIRS/' libavogadro/src/CMakeLists.txt
sed -i 's/OPENBABEL2_LIBRARIES/OpenBabel3_LIBRARIES/' libavogadro/src/CMakeLists.txt

#sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\nnamespace std {\ntypedef decltype(nullptr) nullptr_t;\n}\n#endif' libavogadro/src/engines/bsdyengine.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/engines/bsdyengine.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/colors/elementcolor.cpp
sed -i '/openbabel\/atom.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/atom.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/animation.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/bond.h>' libavogadro/src/bond.cpp
sed -i '/mol.h/i #include <openbabel/atom.h>\n#include <openbabel/bond.h>\n#include <openbabel/obiter.h>' libavogadro/src/animation.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/elementdetail_p.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/elementitem_p.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/moleculefile.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/periodictableview.cpp
sed -i '/data.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/periodictablescene_p.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/chains.h>\n#include <openbabel/generic.h>' libavogadro/src/glwidget.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/elements.h>\n#include <openbabel/bond.h>\n#include <openbabel/ring.h>' libavogadro/src/molecule.cpp
sed -i '/mol.h/i #include <openbabel/atom.h>\n#include <openbabel/chains.h>' libavogadro/src/moleculefile.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/atom.h>' libavogadro/src/readfilethread_p.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/elements.h>' libavogadro/src/engines/wireengine.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/elements.h>' libavogadro/src/periodictableview.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/elements.h>' libavogadro/src/tools/drawtool.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/elements.h>' libavogadro/src/engines/labelengine.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/engines/cartoonengine.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/engines/hbondengine.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/elements.h>' libavogadro/src/engines/sphereengine.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/engines/stickengine.cpp
sed -i '/forcefield.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/elements.h>' libavogadro/src/tools/drawtool.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/generic.h>' libavogadro/src/tools/autoopttool.cpp
sed -i '/data.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/elements.h>' libavogadro/src/tools/zmatrixmodel.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/elements.h>' libavogadro/src/engines/qtaimengine.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/tools/aligntool.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/tools/autoopttool.h
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/tools/selectrotatetool.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/generic.h>\n#include <openbabel/obutil.h>' libavogadro/src/extensions/propmodel.cpp
#sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/generic.h>\n#include <openbabel/math/matrix3x3.h>\n#include <openbabel/math/vector3.h>\n#include <openbabel/elements.h>\n#include <openbabel/atom.h>' libavogadro/src/extensions/cartesianextension.h
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/generic.h>\n#include <openbabel/elements.h>\n#include <openbabel/atom.h>' libavogadro/src/extensions/cartesianextension.h
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/molecularpropextension.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/atom.h>\n#include <openbabel/bond.h>\n#include <openbabel/elements.h>\n#include <openbabel/generic.h>' libavogadro/src/extensions/propmodel.h
sed -i '/plugin.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/forcefielddialog.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/obiter.h>\n#include <openbabel/atom.h>' libavogadro/src/extensions/hydrogensextension.cpp
sed -i '/obconversion.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/forcefieldextension.h
sed -i '/forcefieldextension.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/forcefieldextension.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/invertchiralextension.cpp
sed -i '/mol.h/i #include <openbabel/generic.h>' libavogadro/src/extensions/propmodel.cpp
sed -i '/obconversion.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/insertfragmentdialog.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/atom.h>' libavogadro/src/extensions/selectextension.cpp
sed -i '/forcefield.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/constraintsmodel.h
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/internalcoord.h>\n#include <openbabel/bitvec.h>\n#include <openbabel/elements.h>\n#include <openbabel/data.h>' libavogadro/src/extensions/insertpeptideextension.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/insertcommand.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/insertfragmentextension.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/insertdnaextension.cpp
sed -i '/forcefield.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/conformersearchdialog.h
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/h2methylextension.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/animationextension.cpp
sed -i '/plugin.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/animationdialog.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/fileimportextension.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/obiter.h>\n#include <openbabel/atom.h>\n#include <openbabel/elements.h>' libavogadro/src/extensions/supercellextension.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/networkfetchextension.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/elements.h>' libavogadro/src/extensions/crystallography/avospglib.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/symmetry/symmetryextension.cpp
sed -i '/generic.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/crystallography/ceundo.h
sed -i '/generic.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/spectra/vibrationextension.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/spectra/vibrationwidget.cpp
sed -i '/generic.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/crystallography/crystallographyextension.cpp
sed -i '/generic.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/spectra/spectraextension.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/elements.h>' libavogadro/src/extensions/surfaces/vdwsurface.cpp
sed -i '/generic.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/elements.h>' libavogadro/src/extensions/crystallography/crystalpastedialog.h
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/spectra/spectradialog.h
sed -i '/generic.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/crystallography/crystalpastedialog.h
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/spectra/spectratype.h
sed -i '/generic.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/swcntbuilder/swcntbuilderextension.cpp
sed -i '/atom.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/swcntbuilder/avotubegen.cpp
sed -i '/generic.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/spectra/dos.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/quantuminput/inputfileextension.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/generic.h>' libavogadro/src/extensions/quantuminput/abinitinputdialog.cpp
sed -i '/generic.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/spectra/uv.cpp
sed -i '/generic.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/spectra/cd.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/spectra/raman.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/spectra/spectradialog.h
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/elements.h>' libavogadro/src/colors/residuecolor.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/orca/orcadata.h
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/elements.h>' libavogadro/src/extensions/quantuminput/daltoninputdialog.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif\n#include <openbabel/atom.h>\n#include <openbabel/elements.h>\n#include <openbabel/internalcoord.h>\n#include <openbabel/obiter.h>' libavogadro/src/extensions/quantuminput/gamessukinputdialog.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/colors/atomindexcolor.cpp
sed -i '/mol.h/i #ifndef _GXX_NULLPTR_T\n#define _GXX_NULLPTR_T\n#define nullptr NULL\n#endif' libavogadro/src/extensions/quantuminput/gamessextension.h

sed -i '/mol.h/a #include <openbabel/parsmart.h>' libavogadro/src/extensions/quantuminput/gamessextension.cpp
sed -i '/mol.h/a #include <openbabel/elements.h>' libavogadro/src/engines/bsdyengine.cpp
sed -i 's/OpenBabel::etab./OpenBabel::OBElements::/' libavogadro/src/engines/bsdyengine.cpp
sed -i '/mol.h/a #include <openbabel/elements.h>' libavogadro/src/colors/elementcolor.cpp
#sed -i 's/OpenBabel::etab.GetRGB(atom->atomicNumber());/OpenBabel::OBElements::GetRGB(atom->atomicNumber())/' libavogadro/src/colors/elementcolor.cpp
sed -i 's/std::vector<double> rgb = OpenBabel::etab.GetRGB(atom->atomicNumber());/double r,g,b;\n      OpenBabel::OBElements::GetRGB(atom->atomicNumber(),\&r,\&g,\&b);/' libavogadro/src/colors/elementcolor.cpp
sed -i 's/rgb\[0\]/r/' libavogadro/src/colors/elementcolor.cpp
sed -i 's/rgb\[1\]/g/' libavogadro/src/colors/elementcolor.cpp
sed -i 's/rgb\[2\]/b/' libavogadro/src/colors/elementcolor.cpp
sed -i '/mol.h/a #include <openbabel/elements.h>' libavogadro/src/elementdetail_p.cpp
sed -i 's/std::vector<double> color = OpenBabel::etab.GetRGB(m_element);/double r,g,b;\n    OpenBabel::OBElements::GetRGB(m_element,\&r,\&g,\&b);/' libavogadro/src/elementdetail_p.cpp
sed -i 's/m_color.setRgbF(color\[0\], color\[1\], color\[2\]);/m_color.setRgbF(r, g, b);/' libavogadro/src/elementdetail_p.cpp
sed -i 's/OpenBabel::etab./OpenBabel::OBElements::/' libavogadro/src/elementdetail_p.cpp
sed -i '/mol.h/a #include <openbabel/elements.h>' libavogadro/src/elementitem_p.cpp
sed -i 's/std::vector<double> color = OpenBabel::etab.GetRGB(m_element);/double r,g,b;\n    OpenBabel::OBElements::GetRGB(m_element,\&r,\&g,\&b);/' libavogadro/src/elementitem_p.cpp
sed -i 's/m_color->setRgbF(color\[0\], color\[1\], color\[2\]);/m_color->setRgbF(r, g, b);/' libavogadro/src/elementitem_p.cpp
sed -i 's/OpenBabel::etab./OpenBabel::OBElements::/' libavogadro/src/elementitem_p.cpp
#TOCHECK
sed -i 's/obatom->SetImplicitValence/obatom->SetImplicitHCount/' libavogadro/src/molecule.cpp
sed -i 's/IsHydrogen()/GetAtomicNum() == OpenBabel::OBElements::Hydrogen/' libavogadro/src/molecule.cpp
sed -i 's/IsCarbon()/GetAtomicNum() == OpenBabel::OBElements::Carbon/' libavogadro/src/molecule.cpp
#TOCHECK
sed -i '/SetImplicitValencePerceived()/d' libavogadro/src/molecule.cpp
sed -i 's/OpenBabel::etab.GetSymbol/OpenBabel::OBElements::GetSymbol/' libavogadro/src/molecule.cpp
sed -i 's/KCAL_TO_KJ/OpenBabel::KCAL_TO_KJ/' libavogadro/src/molecule.cpp
sed -i '/mol.h()/a #include <openbabel/obfunctions.h>' libavogadro/src/molecule.cpp
sed -i '/default: \/\/ do nothing/a OpenBabel::OBAtomAssignTypicalImplicitHydrogens(obatom);' libavogadro/src/molecule.cpp
#sed -i '/mol.h/a #include <openbabel/obfunctions.h>' libavogadro/src/atom.cpp
#sed -i '/return obatom;/i OpenBabel::OBAtomAssignTypicalImplicitHydrogens(obatom);' libavogadro/src/atom.cpp
sed -i 's/mol.h/elements.h/' libavogadro/src/periodictableview.cpp
sed -i 's/etab.GetAtomicNum/OBElements::GetAtomicNum/' libavogadro/src/periodictableview.cpp
sed -i 's/OpenBabel::etab./OpenBabel::OBElements::/' libavogadro/src/engines/wireengine.cpp
sed -i 's/OpenBabel::etab./OpenBabel::OBElements::/' libavogadro/src/tools/drawtool.cpp
sed -i 's/OpenBabel::etab./OpenBabel::OBElements::/' libavogadro/src/engines/labelengine.cpp
sed -i 's/OpenBabel::etab./OpenBabel::OBElements::/' libavogadro/src/engines/sphereengine.cpp
sed -i '/using OpenBabel::etab/d' libavogadro/src/tools/zmatrixmodel.cpp
sed -i 's/etab./OpenBabel::OBElements::/' libavogadro/src/tools/zmatrixmodel.cpp
sed -i 's/OpenBabel::etab./OpenBabel::OBElements::/' libavogadro/src/engines/qtaimengine.cpp
sed -i '/mol.h/a #include <openbabel/obiter.h>\n#include <openbabel/atom.h>\n#include <openbabel/bond.h>\n#include <openbabel/elements.h>' libavogadro/src/tools/selectrotatetool.cpp
sed -i 's/OpenBabel::etab./OpenBabel::OBElements::/' libavogadro/src/tools/selectrotatetool.cpp
sed -i 's/OpenBabel::etab./OpenBabel::OBElements::/' libavogadro/src/extensions/cartesianextension.cpp
#FIXME: handle iso again -- actually not necessary because GetAtomicNum() already handles D/T itself in OB 3.1
sed -i 's/GetAtomicNum(s.toStdString(), iso)/GetAtomicNum(s.toLatin1())/' libavogadro/src/extensions/cartesianextension.cpp
#FIXME: handle iso again -- actually not necessary because GetAtomicNum() already handles D/T itself in OB 3.1
sed -i 's/GetAtomicNum(_s.toStdString(), _iso)/GetAtomicNum(_s.toLatin1())/' libavogadro/src/extensions/cartesianextension.cpp
sed -i 's/OpenBabel::OBElements::GetName(atom->atomicNumber()).c_str()/OpenBabel::OBElements::GetName(atom->atomicNumber())/' libavogadro/src/extensions/cartesianextension.cpp
sed -i 's/OpenBabel::etab./OpenBabel::OBElements::/' libavogadro/src/extensions/propmodel.cpp
#TOCHECK
sed -i 's/GetValence()/GetExplicitDegree()/' libavogadro/src/extensions/propmodel.cpp
sed -i 's/etab./OpenBabel::OBElements::/' libavogadro/src/extensions/insertpeptideextension.cpp
#TOCHECK
sed -i 's/resdat.AssignBonds(obfragment, allAtoms);/resdat.AssignBonds(obfragment);/' libavogadro/src/extensions/insertpeptideextension.cpp
sed -i 's/etab./OBElements::/' libavogadro/src/extensions/supercellextension.cpp
sed -i 's/etab./OBElements::/' libavogadro/src/extensions/crystallography/avospglib.cpp
sed -i 's/etab./OBElements::/' libavogadro/src/extensions/crystallography/crystallographyextension.cpp
sed -i 's/etab./OBElements::/' libavogadro/src/extensions/surfaces/vdwsurface.cpp
sed -i 's/etab./OBElements::/' libavogadro/src/extensions/crystallography/crystalpastedialog.cpp
sed -i '/mol.h/a #include <openbabel/atom.h>\n#include <openbabel/elements.h>' libavogadro/src/extensions/spectra/nmr.cpp
sed -i 's/etab./OBElements::/' libavogadro/src/extensions/spectra/nmr.cpp
#TOCHECK
sed -i '/SetImplicitValencePerceived()/d' libavogadro/src/extensions/swcntbuilder/avotubegen.cpp
#TOCHECK
sed -i 's/obatom->SetImplicitValence/obatom->SetImplicitHCount/' libavogadro/src/extensions/swcntbuilder/avotubegen.cpp
#TOCHECK
sed -i 's/GetValence()/GetExplicitDegree()/' libavogadro/src/extensions/swcntbuilder/avotubegen.cpp
sed -i 's/std::vector<double> rgb = OpenBabel::etab.GetRGB( atom->atomicNumber() );/double r,g,b;\n      OpenBabel::OBElements::GetRGB( atom->atomicNumber(), \&r, \&g, \&b );/' libavogadro/src/colors/residuecolor.cpp
sed -i 's/rgb\[0\]/r/' libavogadro/src/colors/residuecolor.cpp
sed -i 's/rgb\[1\]/g/' libavogadro/src/colors/residuecolor.cpp
sed -i 's/rgb\[2\]/b/' libavogadro/src/colors/residuecolor.cpp
sed -i 's/etab./OBElements::/' libavogadro/src/extensions/quantuminput/daltoninputdialog.cpp
sed -i 's/etab./OBElements::/' libavogadro/src/extensions/quantuminput/gamessukinputdialog.cpp
sed -i '/mol.h/a #include <openbabel/elements.h>\n#include <openbabel/atom.h>\n#include <openbabel/internalcoord.h>\n#include <openbabel/obiter.h>' libavogadro/src/extensions/orca/orcainputdialog.cpp
sed -i 's/etab./OBElements::/' libavogadro/src/extensions/orca/orcainputdialog.cpp
sed -i '/mol.h/a #include <openbabel/elements.h>\n#include <openbabel/atom.h>\n#include <openbabel/obiter.h>\n#include <openbabel/internalcoord.h>' libavogadro/src/extensions/quantuminput/gaussianinputdialog.cpp
sed -i 's/etab./OBElements::/' libavogadro/src/extensions/quantuminput/gaussianinputdialog.cpp
sed -i '/mol.h/a #include <openbabel/elements.h>' libavogadro/src/extensions/quantuminput/gamessinputdata.cpp
sed -i 's/etab./OBElements::/' libavogadro/src/extensions/quantuminput/gamessinputdata.cpp
sed -i '/mol.h/a #include <openbabel/obiter.h>\n#include <openbabel/atom.h>' libavogadro/src/extensions/quantuminput/molproinputdialog.cpp
sed -i '/mol.h/a #include <openbabel/elements.h>\n#include <openbabel/internalcoord.h>' libavogadro/src/extensions/quantuminput/molproinputdialog.cpp
sed -i 's/etab./OBElements::/' libavogadro/src/extensions/quantuminput/molproinputdialog.cpp
sed -i '/mol.h/a #include <openbabel/elements.h>\n#include <openbabel/atom.h>\n#include <openbabel/internalcoord.h>\n#include <openbabel/obiter.h>' libavogadro/src/extensions/quantuminput/mopacinputdialog.cpp
sed -i '/using OpenBabel::etab/d' libavogadro/src/extensions/quantuminput/mopacinputdialog.cpp
sed -i 's/OpenBabel::etab./OpenBabel::OBElements::/' libavogadro/src/extensions/quantuminput/mopacinputdialog.cpp
sed -i 's/etab./OpenBabel::OBElements::/' libavogadro/src/extensions/quantuminput/mopacinputdialog.cpp
sed -i '/mol.h/a #include <openbabel/elements.h>\n#include <openbabel/math/vector3.h>\n#include <openbabel/atom.h>\n#include <openbabel/generic.h>' libavogadro/src/extensions/orca/orcaanalysedialog.cpp
sed -i 's/etab./OpenBabel::OBElements::/' libavogadro/src/extensions/orca/orcaanalysedialog.cpp
sed -i '/mol.h/a #include <openbabel/elements.h>\n#include <openbabel/atom.h>\n#include <openbabel/internalcoord.h>\n#include <openbabel/obiter.h>' libavogadro/src/extensions/quantuminput/nwcheminputdialog.cpp
sed -i 's/etab./OBElements::/' libavogadro/src/extensions/quantuminput/nwcheminputdialog.cpp
sed -i '/mol.h/a #include <openbabel/elements.h>' libavogadro/src/extensions/quantuminput/psi4inputdialog.cpp
sed -i 's/etab./OBElements::/' libavogadro/src/extensions/quantuminput/psi4inputdialog.cpp
sed -i '/mol.h/a #include <openbabel/elements.h>' libavogadro/src/colors/smartscolor.cpp
sed -i 's/std::vector<double> rgb = OpenBabel::etab.GetRGB(atom->atomicNumber());/double r,g,b;\n      OpenBabel::OBElements::GetRGB(atom->atomicNumber(),\&r,\&g,\&b);/' libavogadro/src/colors/smartscolor.cpp
sed -i 's/rgb\[0\]/r/' libavogadro/src/colors/smartscolor.cpp
sed -i 's/rgb\[1\]/g/' libavogadro/src/colors/smartscolor.cpp
sed -i 's/rgb\[2\]/b/' libavogadro/src/colors/smartscolor.cpp
sed -i '/mol.h/a #include <openbabel/elements.h>\n#include <openbabel/atom.h>\n#include <openbabel/internalcoord.h>\n#include <openbabel/obiter.h>' libavogadro/src/extensions/quantuminput/qcheminputdialog.cpp
sed -i 's/OpenBabel::etab./OpenBabel::OBElements::/' libavogadro/src/extensions/quantuminput/qcheminputdialog.cpp
sed -i 's/etab./OpenBabel::OBElements::/' libavogadro/src/extensions/quantuminput/qcheminputdialog.cpp
sed -i '/mol.h/a #include <openbabel/elements.h>' libavogadro/src/extensions/quantuminput/lammpsinputdialog.cpp
sed -i 's/etab./OpenBabel::OBElements::/' libavogadro/src/extensions/quantuminput/lammpsinputdialog.cpp

sed -i '/mol.h/a #include <openbabel/elements.h>' avogadro/src/primitiveitemmodel.cpp
sed -i 's/etab./OBElements::/' avogadro/src/primitiveitemmodel.cpp
sed -i '/mol.h/a #include <openbabel/elements.h>\n#include <openbabel/generic.h>' avogadro/src/mainwindow.cpp

sed -i 's/etab.GetNumberOfElements()/119/' avogadro/src/mainwindow.cpp
sed -i 's/etab./OBElements::/' avogadro/src/mainwindow.cpp
#FIXME: handle iso again -- actually not necessary because GetAtomicNum() already handles D/T itself in OB 3.1
sed -i 's/GetAtomicNum(name.c_str(), iso)/GetAtomicNum(name.c_str())/' avogadro/src/mainwindow.cpp
sed -i 's/GetName(i).c_str()/GetName(i)/' avogadro/src/mainwindow.cpp
sed -i '/mol.h/a #include <openbabel/elements.h>' avogadro/src/projectdelegates/atomdelegate.cpp
sed -i 's/etab./OBElements::/' avogadro/src/projectdelegates/atomdelegate.cpp

%build
%cmake \
	-DBoost_NO_BOOST_CMAKE=ON \
	-DINSTALL_LIB_DIR=%{_libdir} \
	-DINSTALL_CMAKE_DIR=%{_libdir}/cmake/libmsym \
	-DENABLE_GLSL=ON \
	-DENABLE_UPDATE_CHECKER=OFF \
	-DENABLE_ZMATRIX_TOOL=ON \
	-DENABLE_PYTHON=ON \
	-DPYTHON_EXECUTABLE=%{_bindir}/python2 \
	-DCMAKE_BUILD_TYPE=RelWithDebInfo

%cmake_build

%install
%cmake_install

mkdir -p %{buildroot}/%{_datadir}/qt4/mkspecs/
mv %{buildroot}%{_prefix}/features %{buildroot}/%{_datadir}/qt4/mkspecs/
# Create the system menu entry
mkdir -p %{buildroot}%{_datadir}/applications
cat > %{buildroot}%{_datadir}/applications/avogadro.desktop << EOF
[Desktop Entry]
Name=Avogadro
Comment=%{summary}
GenericName=Avogadro
Exec=avogadro
Icon=avogadro
Terminal=0
Categories=KDE;Education;Chemistry;
Type=Application
X-SuSE-translate=false
EOF

# icon
install -D -m644 %{SOURCE1} %{buildroot}%{_datadir}/pixmaps/avogadro.png
%fdupes %{buildroot}%{_datadir}/libavogadro/shaders/
%fdupes %{buildroot}%{_datadir}/avogadro/

%post -n libavogadro1 -p /sbin/ldconfig

%postun -n libavogadro1 -p /sbin/ldconfig

%files
%doc AUTHORS README
%license COPYING
%{_mandir}/man1/avogadro.1.gz
%{_mandir}/man1/avopkg.1.gz
%{_bindir}/avogadro
%{_bindir}/avopkg
%{_bindir}/qube
%dir %{_datadir}/libavogadro
%{_datadir}/libavogadro/shaders/
%{_datadir}/avogadro
%{_datadir}/pixmaps/*.png
%{_datadir}/applications/avogadro.desktop
#plugins not libraries
%{_libdir}/libmsym.so
%dir %{_libdir}/avogadro
%dir %{_libdir}/avogadro/1_2
%dir %{_libdir}/avogadro/1_2/colors
%dir %{_libdir}/avogadro/1_2/engines
%dir %{_libdir}/avogadro/1_2/extensions
%dir %{_libdir}/avogadro/1_2/tools
%{_libdir}/avogadro/1_2/*/*.so
%dir %{_datadir}/libavogadro/engineScripts
%dir %{_datadir}/libavogadro/extensionScripts
%{_datadir}/libavogadro/engineScripts/wireframe.py
%{_datadir}/libavogadro/extensionScripts/example.py

%files -n avogadro-devel
%dir %{_includedir}/avogadro
%{_includedir}/avogadro/*.h
%dir %{_includedir}/libmsym
%{_includedir}/libmsym/*.h
%dir %{_libdir}/cmake/libmsym
%{_libdir}/cmake/libmsym/*.cmake
%dir %{_libdir}/avogadro/1_2/cmake
%{_libdir}/libavogadro.so
%{_libdir}/libavogadro_OpenQube.so
%{_libdir}/avogadro/1_2/cmake/*
%{_libdir}/avogadro/1_2/*.cmake
%{_libdir}/avogadro/*.cmake
%{_libdir}/pkgconfig/*.pc
%{_datadir}/qt4/mkspecs/features/avogadro.prf

%files -n libavogadro1
%{_libdir}/*.so.*

%files -n python-avogadro
# installed with python support
%{python2_sitearch}/Avogadro.so

%changelog

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File avogadro.spec of Package avogadro-qt4 (Revision b1d36fd762d6c085b39011b3378bf289)

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