diff options
Diffstat (limited to 'extra/avogadro')
| -rw-r--r-- | extra/avogadro/PKGBUILD | 32 | ||||
| -rw-r--r-- | extra/avogadro/avogadro.install | 11 | ||||
| -rw-r--r-- | extra/avogadro/fix-boost.patch | 33 | ||||
| -rw-r--r-- | extra/avogadro/replace-qt4_automoc-with-qt4_wrap_cpp.patch | 778 |
4 files changed, 844 insertions, 10 deletions
diff --git a/extra/avogadro/PKGBUILD b/extra/avogadro/PKGBUILD index a30a4355e..aad64d103 100644 --- a/extra/avogadro/PKGBUILD +++ b/extra/avogadro/PKGBUILD @@ -1,30 +1,42 @@ -# $Id: PKGBUILD 132785 2011-07-26 07:29:20Z andrea $ -# Maintainer: Andrea Scarpino <andrea@archlinux.org> +# $Id: PKGBUILD 144043 2011-12-02 20:54:10Z ibiru $ +# Maintainer: +# Contributor: Andrea Scarpino <andrea@archlinux.org> # Contributor: Nick B <Shirakawasuna at gmail _dot_com> pkgname=avogadro pkgver=1.0.3 -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=('eigen' 'openbabel' 'python2-pyqt' 'boost-libs' 'glew' 'python2-numpy') +depends=('eigen2' 'openbabel' 'python2-pyqt' 'boost-libs' 'glew' 'python2-numpy') makedepends=('cmake' 'boost') -source=("http://downloads.sourceforge.net/${pkgname}/${pkgname}-${pkgver}.tar.bz2") -md5sums=('92c2702c1980f70fb6d87a1a58147911') +install=avogadro.install +source=("http://downloads.sourceforge.net/${pkgname}/${pkgname}-${pkgver}.tar.bz2" + 'replace-qt4_automoc-with-qt4_wrap_cpp.patch' + 'fix-boost.patch') +md5sums=('92c2702c1980f70fb6d87a1a58147911' + 'aec516daab066c15326a9681f8f15abc' + '46282e4709429447e44a0a54d51ad2ec') build() { - cd ${srcdir} + cd "${srcdir}"/${pkgname}-${pkgver} + patch -p1 -i "${srcdir}"/replace-qt4_automoc-with-qt4_wrap_cpp.patch + patch -p1 -i "${srcdir}"/fix-boost.patch + + cd "${srcdir}" mkdir build cd build cmake ../${pkgname}-${pkgver} \ -DCMAKE_BUILD_TYPE=Release \ - -DCMAKE_INSTALL_PREFIX=/usr + -DCMAKE_INSTALL_PREFIX=/usr \ + -DPYTHON_EXECUTABLE=/usr/bin/python2 \ + -DQT_MKSPECS_RELATIVE=share/qt/mkspecs make } package() { - cd ${srcdir}/build - make DESTDIR=${pkgdir} install + cd "${srcdir}/build" + make DESTDIR="${pkgdir}" install } diff --git a/extra/avogadro/avogadro.install b/extra/avogadro/avogadro.install new file mode 100644 index 000000000..2eaa60550 --- /dev/null +++ b/extra/avogadro/avogadro.install @@ -0,0 +1,11 @@ +post_install() { + update-desktop-database -q +} + +post_upgrade() { + post_install $1 +} + +post_remove() { + post_install $1 +} diff --git a/extra/avogadro/fix-boost.patch b/extra/avogadro/fix-boost.patch new file mode 100644 index 000000000..8fb53ef12 --- /dev/null +++ b/extra/avogadro/fix-boost.patch @@ -0,0 +1,33 @@ +--- 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/replace-qt4_automoc-with-qt4_wrap_cpp.patch b/extra/avogadro/replace-qt4_automoc-with-qt4_wrap_cpp.patch new file mode 100644 index 000000000..11f58a505 --- /dev/null +++ b/extra/avogadro/replace-qt4_automoc-with-qt4_wrap_cpp.patch @@ -0,0 +1,778 @@ +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 ¤t) +- { +- 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(¤tOBMol)) { +- 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 ¤t) ++ { ++ 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(¤tOBMol)) { ++ 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" |