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kalzium4
Add-support-for-OpenBabel-3.x.patch
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File Add-support-for-OpenBabel-3.x.patch of Package kalzium4
From 2b9ebd854d85fa1e092c766e149e16ac18019496 Mon Sep 17 00:00:00 2001 From: Antonio Rojas <arojas@archlinux.org> Date: Wed, 6 Jan 2021 09:41:41 +0000 Subject: [PATCH] Add support for OpenBabel 3.x --- CMakeLists.txt | 24 ++++++++++++++++++++---- compoundviewer/CMakeLists.txt | 4 ++-- compoundviewer/widgets/CMakeLists.txt | 2 +- config-kalzium.h.cmake | 6 ++++++ src/CMakeLists.txt | 16 ++++++++-------- src/kalzium.cpp | 12 ++++++------ src/kalziumschemetype.cpp | 14 ++++++++++++-- src/kalziumschemetype.h | 2 +- src/main.cpp | 2 +- 9 files changed, 57 insertions(+), 25 deletions(-) diff --git a/KalziumConfigureChecks.cmake b/KalziumConfigureChecks.cmake index 889bcfbc..96162801 100644 --- a/KalziumConfigureChecks.cmake +++ b/KalziumConfigureChecks.cmake @@ -3,7 +3,10 @@ include(CheckFunctionExists) macro_optional_find_package(OCaml) macro_optional_find_package(Libfacile) -macro_optional_find_package(OpenBabel2) +macro_optional_find_package(OpenBabel3 3.1) +if(NOT ${OpenBabel3_FOUND}) + macro_optional_find_package(OpenBabel2) +endif() macro_optional_find_package(Eigen3) macro_optional_find_package(Avogadro 1.0.0 NO_MODULE) @@ -13,10 +16,22 @@ check_include_files(ieeefp.h HAVE_IEEEFP_H) check_include_files(ieeefp.h HAVE_IEEEFP_H) macro_bool_to_01(LIBFACILE_FOUND HAVE_FACILE) +macro_bool_to_01(OpenBabel3_FOUND HAVE_OPENBABEL3) macro_bool_to_01(OPENBABEL2_FOUND HAVE_OPENBABEL2) +if(HAVE_OPENBABEL2 OR HAVE_OPENBABEL3) + set(HAVE_OPENBABEL 1) +endif() macro_bool_to_01(EIGEN3_FOUND HAVE_EIGEN) macro_bool_to_01(Avogadro_FOUND HAVE_AVOGADRO) +if(HAVE_OPENBABEL3) + set(OPENBABEL_INCLUDE_DIR ${OpenBabel3_INCLUDE_DIRS}) + set(OPENBABEL_LIBRARIES ${OpenBabel3_LIBRARIES}) +elseif(HAVE_OPENBABEL2) + set(OPENBABEL_INCLUDE_DIR ${OPENBABEL2_INCLUDE_DIR}) + set(OPENBABEL_LIBRARIES ${OPENBABEL2_LIBRARIES}) +endif() + # at the end, output the configuration configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/config-kalzium.h.cmake @@ -25,7 +28,7 @@ configure_file( macro_log_feature(OCAML_FOUND "OCaml" "OCaml is needed by Kalzium for the Equation Solver" "http://caml.inria.fr/" FALSE "" "") macro_log_feature(LIBFACILE_FOUND "LibFacile" "libfacile is needed by Kalzium for the Equation Solver." "http://www.recherche.enac.fr/log/facile/" FALSE "" "") -macro_log_feature(OPENBABEL2_FOUND "OpenBabel2" "OpenBabel is needed by Kalzium for the 3D-molecule viewer" "http://openbabel.sourceforge.net/" FALSE "2.2" "") +macro_log_feature(HAVE_OPENBABEL "OpenBabel" "OpenBabel is needed by Kalzium for the 3D-molecule viewer" "http://openbabel.sourceforge.net/" FALSE "2.2" "") macro_log_feature(EIGEN3_FOUND "Eigen3" "A generic C++ template library for dense and sparse matrices" "http://eigen.tuxfamily.org" FALSE "3.0.0" "") macro_log_feature(Avogadro_FOUND "Avogadro" "Advanced molecular editor" "http://avogadro.openmolecules.net" FALSE "1.0" "") macro_log_feature(CHEMICAL_MIME_DATA_FOUND "Chemical mime data" "Needed to open CML molecules from the file manager" "http://chemical-mime.sourceforge.net/" FALSE "" "") diff --git a/CMakeLists.txt b/CMakeLists.txt index 889bcfbc..96162801 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -35,7 +35,7 @@ kde4_no_enable_final(kalzium) include(KalziumConfigureChecks.cmake) -if (OPENBABEL2_FOUND AND Avogadro_FOUND AND EIGEN3_FOUND) +if (HAVE_OPENBABEL AND Avogadro_FOUND AND EIGEN3_FOUND) # avoid compilerwarnings about redefinitions # todo: use check_function_exits() ? message(STATUS "Kalzium molecular editor enabled") @@ -43,9 +43,9 @@ if (OPENBABEL2_FOUND AND AvogadroLibs_FOUND AND EIGEN3_FOUND) add_definitions(-DHAVE_SNPRINTF -DHAVE_STRCASECMP -DHAVE_STRNCASECMP) endif (WIN32) add_subdirectory(compoundviewer) -else (OPENBABEL2_FOUND AND Avogadro_FOUND AND EIGEN3_FOUND) +else (HAVE_OPENBABEL AND Avogadro_FOUND AND EIGEN3_FOUND) message(STATUS "Kalzium molecular editor disabled") -endif (OPENBABEL2_FOUND AND Avogadro_FOUND AND EIGEN3_FOUND) +endif (HAVE_OPENBABEL AND Avogadro_FOUND AND EIGEN3_FOUND) add_subdirectory(doc) add_subdirectory(src) diff --git a/compoundviewer/CMakeLists.txt b/compoundviewer/CMakeLists.txt index db367a7d..3fd2c42b 100644 --- a/compoundviewer/CMakeLists.txt +++ b/compoundviewer/CMakeLists.txt @@ -3,7 +3,7 @@ include_directories( ${CMAKE_CURRENT_BINARY_DIR}/.. ${EIGEN3_INCLUDE_DIR} - ${OPENBABEL2_INCLUDE_DIR} + ${OPENBABEL_INCLUDE_DIR} ) set( compoundviewer_SRCS @@ -16,7 +16,7 @@ target_link_libraries(compoundviewer kde4_add_library(compoundviewer SHARED ${compoundviewer_SRCS}) target_link_libraries(compoundviewer - ${OPENBABEL2_LIBRARIES} + ${OPENBABEL_LIBRARIES} ${QT_QTOPENGL_LIBRARY} ${KDE4_KDEUI_LIBS} avogadro diff --git a/compoundviewer/widgets/CMakeLists.txt b/compoundviewer/widgets/CMakeLists.txt index 7658056c..a1e54204 100644 --- a/compoundviewer/widgets/CMakeLists.txt +++ b/compoundviewer/widgets/CMakeLists.txt @@ -11,6 +11,6 @@ kde4_add_widget_files(kalziumui_PART_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/kalziumui. kde4_add_plugin(kalziumuiwidgets ${kalziumui_PART_SRCS}) -target_link_libraries(kalziumuiwidgets ${OPENBABEL2_LIBRARIES} ${QT_QTDESIGNER_LIBRARY} ${KDE4_KDECORE_LIBS}) +target_link_libraries(kalziumuiwidgets ${OPENBABEL_LIBRARIES} ${QT_QTDESIGNER_LIBRARY} ${KDE4_KDECORE_LIBS}) install(TARGETS kalziumuiwidgets DESTINATION ${PLUGIN_INSTALL_DIR}/plugins/designer) diff --git a/config-kalzium.h.cmake b/config-kalzium.h.cmake index f834d57d..99862809 100644 --- a/config-kalzium.h.cmake +++ b/config-kalzium.h.cmake @@ -4,6 +4,12 @@ /* Define to 1 if we have OpenBabel2 */ #cmakedefine HAVE_OPENBABEL2 1 +/* Define to 1 if we have OpenBabel3 */ +#cmakedefine HAVE_OPENBABEL3 1 + +/* Define to 1 if we have OpenBabel */ +#cmakedefine HAVE_OPENBABEL 1 + /* Define 1 if we have Eigen */ #cmakedefine HAVE_EIGEN 1 diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 30c34133..a4cd86df 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -10,10 +10,10 @@ include_directories( ########### next target ############### -# The tools can only be built when OpenBabel2 is found. -# The moleculeviewer needs not only OpenBabel2 but also Eigen2 and Avogadro, +# The tools can only be built when OpenBabel is found. +# The moleculeviewer needs not only OpenBabel but also Eigen and Avogadro, # so there is a nested if-check. -if (OPENBABEL2_FOUND) +if (HAVE_OPENBABEL) set(kalziumtools_SRCS tools/obconverter.cpp ) @@ -25,7 +25,7 @@ if (OPENBABEL2_FOUND) kde4_add_ui_files(kalziumtools_SRCS tools/obconverterwidget.ui ) - include_directories(${OPENBABEL2_INCLUDE_DIR}) + include_directories(${OPENBABEL_INCLUDE_DIR}) if (EIGEN3_FOUND AND Avogadro_FOUND) @@ -37,7 +37,7 @@ if (OPENBABEL2_FOUND) ) include_directories(${EIGEN3_INCLUDE_DIR}) endif (EIGEN3_FOUND AND Avogadro_FOUND) -endif (OPENBABEL2_FOUND) +endif (HAVE_OPENBABEL) ## Kalzium calculator files set(kalziumtools_SRCS @@ -135,12 +135,12 @@ target_link_libraries(kalzium target_link_libraries(kalzium ${KDE4_KHTML_LIBRARY} ${KDE4_KNEWSTUFF3_LIBS} ${KDE4_KUNITCONVERSION_LIBS} ${QT_QTSCRIPT_LIBRARY} ${QT_QTDECLARATIVE_LIBRARY} science) -if (OPENBABEL2_FOUND) - target_link_libraries(kalzium ${OPENBABEL2_LIBRARIES}) +if (HAVE_OPENBABEL) + target_link_libraries(kalzium ${OPENBABEL_LIBRARIES}) if (EIGEN3_FOUND AND Avogadro_FOUND) target_link_libraries(kalzium ${QT_QTOPENGL_LIBRARY} compoundviewer avogadro) endif (EIGEN3_FOUND AND Avogadro_FOUND) -endif (OPENBABEL2_FOUND) +endif (HAVE_OPENBABEL) if (LIBFACILE_FOUND) link_directories(${OCAMLC_DIR}) diff --git a/src/kalzium.cpp b/src/kalzium.cpp index 065780ea..4de4c8fa 100644 --- a/src/kalzium.cpp +++ b/src/kalzium.cpp @@ -39,7 +39,7 @@ #include "eqchemview.h" #endif -#ifdef HAVE_OPENBABEL2 +#ifdef HAVE_OPENBABEL #if defined(HAVE_EIGEN) && defined(HAVE_AVOGADRO) #include "tools/moleculeview.h" #endif @@ -203,7 +203,7 @@ void Kalzium::setupActions() m_pOBConverterAction->setIcon(KIcon("edit-copy")); m_pOBConverterAction->setWhatsThis(i18nc("WhatsThis Help", "With this tool, you can convert files containing chemical data between various file formats.")); connect(m_pOBConverterAction, SIGNAL(triggered()), this, SLOT(slotOBConverter())); -#ifndef HAVE_OPENBABEL2 +#ifndef HAVE_OPENBABEL m_pOBConverterAction->setEnabled(false); #endif @@ -212,7 +212,7 @@ void Kalzium::setupActions() m_pMoleculesviewer->setIcon(KIcon("kalzium_molviewer")); m_pMoleculesviewer->setWhatsThis(i18nc("WhatsThis Help", "This tool allows you to view and edit 3D molecular structures.")); connect(m_pMoleculesviewer, SIGNAL(triggered()), this, SLOT(slotMoleculeviewer())); -#if !defined(HAVE_OPENBABEL2) || !defined(HAVE_EIGEN) || !defined(HAVE_AVOGADRO) +#if !defined(HAVE_OPENBABEL) || !defined(HAVE_EIGEN) || !defined(HAVE_AVOGADRO) m_pMoleculesviewer->setEnabled(false); #endif @@ -367,7 +367,7 @@ void Kalzium::slotRS() void Kalzium::slotOBConverter() { -#ifdef HAVE_OPENBABEL2 +#ifdef HAVE_OPENBABEL KOpenBabel * d = new KOpenBabel(this); d->setAttribute(Qt::WA_DeleteOnClose); d->show(); @@ -376,7 +376,7 @@ void Kalzium::slotOBConverter() MoleculeDialog *Kalzium::slotMoleculeviewer() { -#if defined(HAVE_OPENBABEL2) && defined(HAVE_EIGEN) && defined(HAVE_AVOGADRO) +#if defined(HAVE_OPENBABEL) && defined(HAVE_EIGEN) && defined(HAVE_AVOGADRO) if (!QGLFormat::hasOpenGL()) { KMessageBox::error(0, i18n("This system does not support OpenGL."), i18n("Kalzium Error")); @@ -638,7 +638,7 @@ Kalzium::~Kalzium() void Kalzium::loadMolecule(const QString &moleculeFile) { -#if defined(HAVE_OPENBABEL2) && defined(HAVE_EIGEN) && defined(HAVE_AVOGADRO) +#if defined(HAVE_OPENBABEL) && defined(HAVE_EIGEN) && defined(HAVE_AVOGADRO) MoleculeDialog *d = slotMoleculeviewer(); if (d) { d->loadMolecule(moleculeFile); diff --git a/src/kalziumschemetype.cpp b/src/kalziumschemetype.cpp index bf516bc7..acb39acf 100644 --- a/src/kalziumschemetype.cpp +++ b/src/kalziumschemetype.cpp @@ -25,6 +25,9 @@ #ifdef HAVE_OPENBABEL2 #include <openbabel/mol.h> #endif +#ifdef HAVE_OPENBABEL3 +#include <openbabel/elements.h> +#endif #include <QBrush> @@ -40,7 +43,7 @@ KalziumSchemeTypeFactory::KalziumSchemeTypeFactory() m_schemes << KalziumIconicSchemeType::instance(); m_schemes << KalziumFamilySchemeType::instance(); m_schemes << KalziumGroupsSchemeType::instance(); - #ifdef HAVE_OPENBABEL2 + #ifdef HAVE_OPENBABEL m_schemes << KalziumColorSchemeType::instance(); #endif } @@ -380,7 +383,7 @@ QList<legendPair> KalziumGroupsSchemeType::legendItems() const return ll; } -#ifdef HAVE_OPENBABEL2 +#ifdef HAVE_OPENBABEL ///OpenBabel Color/// KalziumColorSchemeType::KalziumColorSchemeType() : KalziumSchemeType() @@ -407,8 +410,15 @@ QBrush KalziumColorSchemeType::elementBrush(int el) const { QColor c; +#ifdef HAVE_OPENBABEL2 std::vector<double> color = OpenBabel::etab.GetRGB(el); c.setRgbF(color[0], color[1], color[2]); +#endif +#ifdef HAVE_OPENBABEL3 + double red, green, blue; + OpenBabel::OBElements::GetRGB(el, &red, &green, &blue); + c.setRgbF(red, green, blue); +#endif return QBrush(c); } diff --git a/src/kalziumschemetype.h b/src/kalziumschemetype.h index c4bb4085..e1a91e10 100644 --- a/src/kalziumschemetype.h +++ b/src/kalziumschemetype.h @@ -230,7 +230,7 @@ private: KalziumGroupsSchemeType(); }; -#ifdef HAVE_OPENBABEL2 +#ifdef HAVE_OPENBABEL /** * The scheme for color * diff --git a/src/main.cpp b/src/main.cpp index c1bfd59c..e0686716 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -75,7 +75,7 @@ int main(int argc, char **argv) KCmdLineArgs::init(argc, argv, &about); KCmdLineOptions options; -#if defined(HAVE_OPENBABEL2) && defined(HAVE_EIGEN) && defined(HAVE_AVOGADRO) +#if defined(HAVE_OPENBABEL) && defined(HAVE_EIGEN) && defined(HAVE_AVOGADRO) options.add("molecule <file>", ki18n("Open the given molecule file")); #endif KCmdLineArgs::addCmdLineOptions(options); -- GitLab
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