Skip to content

GitLab

Commit 2b9ebd85 authored by Antonio Rojas's avatar Antonio Rojas
Browse files

Add support for OpenBabel 3.x

parent a320c2eb
Hide whitespace changes
Inline Side-by-side
CMakeLists.txt
View file @ 2b9ebd85
......@@ -26,7 +26,10 @@ include(ECMSetupVersion)
find_package(Gettext REQUIRED)
find_package(PythonInterp REQUIRED)
find_package(PkgConfig)
find_package(OpenBabel2)
find_package(OpenBabel3 3.1)
if(NOT ${OpenBabel3_FOUND})
find_package(OpenBabel2)
endif()
find_package(AvogadroLibs)
find_package(Eigen3)
find_package(OCaml)
......@@ -37,9 +40,22 @@ check_include_files(ieeefp.h HAVE_IEEEFP_H)
# create configuration file
set(HAVE_FACILE ${LIBFACILE_FOUND})
set(HAVE_OPENBABEL3 ${OpenBabel3_FOUND})
set(HAVE_OPENBABEL2 ${OPENBABEL2_FOUND})
if(HAVE_OPENBABEL2 OR HAVE_OPENBABEL3)
set(HAVE_OPENBABEL 1)
endif()
set(HAVE_EIGEN ${EIGEN3_FOUND})
set(HAVE_AVOGADRO ${AvogadroLibs_FOUND})
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()
configure_file(
${CMAKE_CURRENT_SOURCE_DIR}/config-kalzium.h.cmake
${CMAKE_CURRENT_BINARY_DIR}/config-kalzium.h
......@@ -97,7 +113,7 @@ if(MSVC)
add_definitions(-DUSING_DYNAMIC_LIBS)
endif(MSVC)
if (OPENBABEL2_FOUND AND AvogadroLibs_FOUND AND EIGEN3_FOUND)
if (HAVE_OPENBABEL AND AvogadroLibs_FOUND AND EIGEN3_FOUND)
find_package(Qt5OpenGL ${QT_MIN_VERSION} REQUIRED)
find_package(KF5NewStuff REQUIRED)
# avoid compilerwarnings about redefinitions
......@@ -107,9 +123,9 @@ 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 AvogadroLibs_FOUND AND EIGEN3_FOUND)
else (HAVE_OPENBABEL AND AvogadroLibs_FOUND AND EIGEN3_FOUND)
message(STATUS "Kalzium molecular editor disabled")
endif (OPENBABEL2_FOUND AND AvogadroLibs_FOUND AND EIGEN3_FOUND)
endif (HAVE_OPENBABEL AND AvogadroLibs_FOUND AND EIGEN3_FOUND)
add_subdirectory(doc)
add_subdirectory(src)
......
compoundviewer/CMakeLists.txt
View file @ 2b9ebd85
include_directories(
${CMAKE_CURRENT_BINARY_DIR}/..
${EIGEN3_INCLUDE_DIR}
${OPENBABEL2_INCLUDE_DIR}
${OPENBABEL_INCLUDE_DIR}
${AvogadroLibs_INCLUDE_DIRS}
${PROJECT_SOURCE_DIR}/compoundviewer
)
......@@ -22,7 +22,7 @@ target_link_libraries(compoundviewer
Qt5::OpenGL
Qt5::Gui
Qt5::Widgets
${OPENBABEL2_LIBRARIES}
${OPENBABEL_LIBRARIES}
AvogadroQtGui
AvogadroQtOpenGL
AvogadroQtPlugins
......
compoundviewer/widgets/CMakeLists.txt
View file @ 2b9ebd85
......@@ -11,6 +11,6 @@ add_widget_files(kalziumui_PART_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/kalziumui.widge
add_library(kalziumuiwidgets MODULE ${kalziumui_PART_SRCS})
target_link_libraries(kalziumuiwidgets ${OPENBABEL2_LIBRARIES} Qt5::Designer KF5::Core)
target_link_libraries(kalziumuiwidgets ${OPENBABEL_LIBRARIES} Qt5::Designer KF5::Core)
install(TARGETS kalziumuiwidgets DESTINATION ${PLUGIN_INSTALL_DIR}/plugins/designer)
config-kalzium.h.cmake
View file @ 2b9ebd85
......@@ -4,6 +4,12 @@
/* Define to 1 if we have OpenBabel2 */
#cmakedefine HAVE_OPENBABEL2 1
/* Define to 1 if we have OpenBabel3 */
#cmakedefine HAVE_OPENBABEL3 1
/* Define to 1 if we have OpenBabel */
#cmakedefine HAVE_OPENBABEL 1
/* Define 1 if we have Eigen */
#cmakedefine HAVE_EIGEN 1
......
src/CMakeLists.txt
View file @ 2b9ebd85
......@@ -14,10 +14,10 @@ ecm_setup_version(${RELEASE_SERVICE_VERSION} VARIABLE_PREFIX KALZIUM VERSION_HEA
########### 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)
ki18n_wrap_ui(kalziumtools_SRCS
tools/obconverterwidget.ui
)
include_directories(SYSTEM ${OPENBABEL2_INCLUDE_DIR})
include_directories(SYSTEM ${OPENBABEL_INCLUDE_DIR})
if (EIGEN3_FOUND AND AvogadroLibs_FOUND)
......@@ -41,7 +41,7 @@ if (OPENBABEL2_FOUND)
)
include_directories(${EIGEN3_INCLUDE_DIR})
endif (EIGEN3_FOUND AND AvogadroLibs_FOUND)
endif (OPENBABEL2_FOUND)
endif (HAVE_OPENBABEL)
## Kalzium calculator files
set(kalziumtools_SRCS
......@@ -150,8 +150,8 @@ target_link_libraries(kalzium
Qt5::Svg
science
)
if (OPENBABEL2_FOUND)
target_link_libraries(kalzium ${OPENBABEL2_LIBRARIES})
if (HAVE_OPENBABEL)
target_link_libraries(kalzium ${OPENBABEL_LIBRARIES})
if (EIGEN3_FOUND AND AvogadroLibs_FOUND)
target_link_libraries(kalzium
KF5::NewStuff
......@@ -163,7 +163,7 @@ if (OPENBABEL2_FOUND)
)
install(FILES kalzium.knsrc DESTINATION ${KDE_INSTALL_KNSRCDIR})
endif (EIGEN3_FOUND AND AvogadroLibs_FOUND)
endif (OPENBABEL2_FOUND)
endif (HAVE_OPENBABEL)
if (LIBFACILE_FOUND)
link_directories(${OCAMLC_DIR})
......
src/kalzium.cpp
View file @ 2b9ebd85
......@@ -37,7 +37,7 @@
#include "eqchemview.h"
#endif
#ifdef HAVE_OPENBABEL2
#ifdef HAVE_OPENBABEL
#if defined(HAVE_EIGEN) && defined(HAVE_AVOGADRO)
#include "tools/moleculeview.h"
#include <QGLFormat>
......@@ -197,7 +197,7 @@ void Kalzium::setupActions()
m_pOBConverterAction->setIcon(QIcon::fromTheme(QStringLiteral("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, &QAction::triggered, this, &Kalzium::slotOBConverter);
#ifndef HAVE_OPENBABEL2
#ifndef HAVE_OPENBABEL
m_pOBConverterAction->setEnabled(false);
#endif
......@@ -206,7 +206,7 @@ void Kalzium::setupActions()
m_pMoleculesviewer->setIcon(QIcon::fromTheme(QStringLiteral("kalzium_molviewer")));
m_pMoleculesviewer->setWhatsThis(i18nc("WhatsThis Help", "This tool allows you to view and edit 3D molecular structures."));
connect(m_pMoleculesviewer, &QAction::triggered, this, &Kalzium::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
......@@ -360,7 +360,7 @@ void Kalzium::slotRS()
void Kalzium::slotOBConverter()
{
#ifdef HAVE_OPENBABEL2
#ifdef HAVE_OPENBABEL
KOpenBabel * d = new KOpenBabel(this);
d->setAttribute(Qt::WA_DeleteOnClose);
d->show();
......@@ -369,7 +369,7 @@ 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()) {
QMessageBox::critical(Q_NULLPTR, i18n("Kalzium Error"), i18n("This system does not support OpenGL."));
......@@ -631,7 +631,7 @@ 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);
......
src/kalziumschemetype.cpp
View file @ 2b9ebd85
......@@ -25,6 +25,9 @@
#ifdef HAVE_OPENBABEL2
#include <openbabel/mol.h>
#endif
#ifdef HAVE_OPENBABEL3
#include <openbabel/elements.h>
#endif
#include <QBrush>
#include <QDebug>
......@@ -39,7 +42,7 @@ 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
}
......@@ -379,7 +382,7 @@ QList<legendPair> KalziumGroupsSchemeType::legendItems() const
return ll;
}
#ifdef HAVE_OPENBABEL2
#ifdef HAVE_OPENBABEL
///OpenBabel Color///
KalziumColorSchemeType::KalziumColorSchemeType()
: KalziumSchemeType()
......@@ -406,8 +409,15 @@ 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);
}
......
src/kalziumschemetype.h
View file @ 2b9ebd85
......@@ -230,7 +230,7 @@ private:
KalziumGroupsSchemeType();
};
#ifdef HAVE_OPENBABEL2
#ifdef HAVE_OPENBABEL
/**
* The scheme for color
*
......
src/main.cpp
View file @ 2b9ebd85
......@@ -144,7 +144,7 @@ int main(int argc, char **argv)
parser.process(app);
about.processCommandLine(&parser);
#if defined(HAVE_OPENBABEL2) && defined(HAVE_EIGEN) && defined(HAVE_AVOGADRO)
#if defined(HAVE_OPENBABEL) && defined(HAVE_EIGEN) && defined(HAVE_AVOGADRO)
parser.addOption(QCommandLineOption(QStringList() << QStringLiteral("m") << QStringLiteral("molecule"), i18n("Open the given molecule file"), QStringLiteral("file")));
#endif
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment