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avogadro ++pkgrel (and patches) for new boost

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This commit is contained in:
Drake 2012-01-16 00:35:03 +00:00
parent 549ac57ad7
commit cad34c7615
4 changed files with 829 additions and 5 deletions
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12
avogadro/PKGBUILD
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@ -3,12 +3,10 @@
#
# maintainer (x86_64): Giuseppe Calà <jiveaxe@gmail.com>
# include global config
source ../_buildscripts/${current_repo}-${_arch}-cfg.conf
pkgname=avogadro
pkgver=1.0.3
pkgrel=2
pkgrel=4
pkgdesc="An advanced molecular editor based on Qt"
arch=('i686' 'x86_64')
url="http://avogadro.openmolecules.net/wiki/Main_Page"
@ -19,9 +17,12 @@ source=("http://downloads.sourceforge.net/${pkgname}/${pkgname}-${pkgver}.tar.bz
md5sums=('92c2702c1980f70fb6d87a1a58147911')
build() {
cd "${srcdir}/${pkgname}-${pkgver}"
patch -p1 -i ../../replace-qt4_automoc-with-qt4_wrap_cpp.patch
patch -p1 -i ../../fix-boost.patch
cd ${srcdir}
mkdir build
mkdir -p build
cd build
# use the cmake module in system to enable python 2.7 support
@ -29,7 +30,8 @@ build() {
cmake ../${pkgname}-${pkgver} \
-DCMAKE_BUILD_TYPE=Release \
-DCMAKE_INSTALL_PREFIX=/usr
-DCMAKE_INSTALL_PREFIX=/usr \
-DQT_MKSPECS_RELATIVE=share/qt/mkspecs
make
}

11
avogadro/avogadro.install Normal file
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@ -0,0 +1,11 @@
post_install() {
update-desktop-database -q
}
post_upgrade() {
post_install $1
}
post_remove() {
post_install $1
}

33
avogadro/fix-boost.patch Normal file
View File

@ -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)

778
avogadro/replace-qt4_automoc-with-qt4_wrap_cpp.patch Normal file
View File

@ -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 &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"