1 files changed, 0 insertions, 191 deletions
diff --git a/sci-libs/chemkit/files/chemkit-0.1-unbundle.patch b/sci-libs/chemkit/files/chemkit-0.1-unbundle.patch
deleted file mode 100644
index e8c9d18dca6e..000000000000
--- a/sci-libs/chemkit/files/chemkit-0.1-unbundle.patch
+++ /dev/null
@@ -1,191 +0,0 @@
- CMakeLists.txt                              | 21 +++++++++++++++++++++
- src/plugins/chemjson/CMakeLists.txt         |  6 +++++-
- src/plugins/chemjson/chemjsonfileformat.cpp |  4 ++++
- src/plugins/cml/cmlfileformat.h             |  4 ++++
- src/plugins/inchi/CMakeLists.txt            |  4 +++-
- src/plugins/inchi/inchikeylineformat.cpp    |  4 ++++
- src/plugins/inchi/inchilineformat.cpp       |  4 ++++
- src/plugins/pdb/pdbmlfileformat.cpp         |  4 ++++
- src/plugins/xtc/CMakeLists.txt              |  9 +++++++--
- src/plugins/xtc/xtcfileformat.cpp           |  4 ++++
- 10 files changed, 60 insertions(+), 4 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index e531be4..622ea9d 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -55,6 +55,27 @@ configure_file(
- # export the Chemkit package
- export(PACKAGE Chemkit)
- 
-+option(USE_SYSTEM_INCHI "Use inchi installed in system" OFF)
-+option(USE_SYSTEM_JSONCPP "Use json cpp installed in system" OFF)
-+option(USE_SYSTEM_RAPIXML "Use rapidxml installed in system" OFF)
-+option(USE_SYSTEM_XDRF "Use xdrflib installed in system" OFF)
-+
-+if(USE_SYSTEM_INCHI)
-+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DSYSTEM_INCHI")
-+endif()
-+
-+if(USE_SYSTEM_JSONCPP)
-+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DSYSTEM_JSONCPP")
-+endif()
-+
-+if(USE_SYSTEM_RAPIDXML)
-+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DSYSTEM_RAPIDXML")
-+endif()
-+
-+if(USE_SYSTEM_XDRF)
-+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DSYSTEM_XDRF")
-+endif()
-+
- # build options
- option(CHEMKIT_WITH_GRAPHICS "Build the chemkit-graphics library." ON)
- option(CHEMKIT_WITH_IO "Build the chemkit-io library." ON)
-diff --git a/src/plugins/chemjson/CMakeLists.txt b/src/plugins/chemjson/CMakeLists.txt
-index 0e115b5..a5e6f48 100644
---- a/src/plugins/chemjson/CMakeLists.txt
-+++ b/src/plugins/chemjson/CMakeLists.txt
-@@ -10,7 +10,11 @@ set(SOURCES
-   chemjsonplugin.cpp
- )
- 
--aux_source_directory(../../3rdparty/jsoncpp/ JSONCPP_SOURCES)
-+if(NOT USE_SYSTEM_JSONCPP)
-+	aux_source_directory(../../3rdparty/jsoncpp/ JSONCPP_SOURCES)
-+else()
-+	target_link_libraries(chemjson jsoncpp)
-+endif()
- 
- add_chemkit_plugin(chemjson ${SOURCES} ${JSONCPP_SOURCES})
- target_link_libraries(chemjson ${CHEMKIT_LIBRARIES})
-diff --git a/src/plugins/chemjson/chemjsonfileformat.cpp b/src/plugins/chemjson/chemjsonfileformat.cpp
-index a0d271e..3cd5827 100644
---- a/src/plugins/chemjson/chemjsonfileformat.cpp
-+++ b/src/plugins/chemjson/chemjsonfileformat.cpp
-@@ -43,7 +43,11 @@
- #include <chemkit/molecule.h>
- #include <chemkit/moleculefile.h>
- 
-+#ifdef SYSTEM_JSONCPP
-+#include <jsoncpp/json/json.h>
-+#else
- #include "../../3rdparty/jsoncpp/json/json.h"
-+#endif
- 
- namespace {
- 
-diff --git a/src/plugins/cml/cmlfileformat.h b/src/plugins/cml/cmlfileformat.h
-index e813223..61a547d 100644
---- a/src/plugins/cml/cmlfileformat.h
-+++ b/src/plugins/cml/cmlfileformat.h
-@@ -38,7 +38,11 @@
- 
- #include <chemkit/moleculefileformat.h>
- 
-+#ifdef SYSTEM_RAPIDXML
-+#include <rapidxml/rapidxml.hpp>
-+#else
- #include "../../3rdparty/rapidxml/rapidxml.hpp"
-+#endif
- 
- class CmlFileFormat : public chemkit::MoleculeFileFormat
- {
-diff --git a/src/plugins/inchi/CMakeLists.txt b/src/plugins/inchi/CMakeLists.txt
-index 2b25d9b..5f45f8a 100644
---- a/src/plugins/inchi/CMakeLists.txt
-+++ b/src/plugins/inchi/CMakeLists.txt
-@@ -7,7 +7,9 @@ set(SOURCES
-   inchiplugin.cpp
- )
- 
--aux_source_directory(../../3rdparty/inchi/ IUPAC_INCHI_SOURCES)
-+if(NOT USE_SYSTEM_INCHI)
-+	aux_source_directory(../../3rdparty/inchi/ IUPAC_INCHI_SOURCES)
-+endif()
- 
- add_chemkit_plugin(inchi ${SOURCES} ${IUPAC_INCHI_SOURCES})
- target_link_libraries(inchi ${CHEMKIT_LIBRARIES})
-diff --git a/src/plugins/inchi/inchikeylineformat.cpp b/src/plugins/inchi/inchikeylineformat.cpp
-index 2682f95..cec0a17 100644
---- a/src/plugins/inchi/inchikeylineformat.cpp
-+++ b/src/plugins/inchi/inchikeylineformat.cpp
-@@ -38,7 +38,11 @@
- #include <boost/format.hpp>
- 
- #include "inchilineformat.h"
-+#ifdef SYSTEM_INCHI
-+#include <inchi_api.h>
-+#else
- #include "../../3rdparty/inchi/inchi_api.h"
-+#endif
- 
- InchiKeyLineFormat::InchiKeyLineFormat()
-     : chemkit::LineFormat("inchikey")
-diff --git a/src/plugins/inchi/inchilineformat.cpp b/src/plugins/inchi/inchilineformat.cpp
-index 5b9bc42..ea5977c 100644
---- a/src/plugins/inchi/inchilineformat.cpp
-+++ b/src/plugins/inchi/inchilineformat.cpp
-@@ -42,7 +42,11 @@
- 
- #include <boost/algorithm/string.hpp>
- 
-+#ifdef SYSTEM_INCHI
-+#include <inchi_api.h>
-+#else
- #include "../../3rdparty/inchi/inchi_api.h"
-+#endif
- 
- #include <chemkit/atom.h>
- #include <chemkit/bond.h>
-diff --git a/src/plugins/pdb/pdbmlfileformat.cpp b/src/plugins/pdb/pdbmlfileformat.cpp
-index 081a4ec..2ca4269 100644
---- a/src/plugins/pdb/pdbmlfileformat.cpp
-+++ b/src/plugins/pdb/pdbmlfileformat.cpp
-@@ -35,7 +35,11 @@
- 
- #include "pdbmlfileformat.h"
- 
-+#ifdef SYSTEM_RAPIDXML
-+#include <rapidxml/rapidxml.hpp>
-+#else
- #include "../../3rdparty/rapidxml/rapidxml.hpp"
-+#endif
- 
- #include <chemkit/atom.h>
- #include <chemkit/polymer.h>
-diff --git a/src/plugins/xtc/CMakeLists.txt b/src/plugins/xtc/CMakeLists.txt
-index 98d8ba7..8c09e64 100644
---- a/src/plugins/xtc/CMakeLists.txt
-+++ b/src/plugins/xtc/CMakeLists.txt
-@@ -13,7 +13,12 @@ set(SOURCES
-   xtcplugin.cpp
- )
- 
--aux_source_directory(../../3rdparty/xdrf/ XDRF_SOURCES)
-+
-+if(USE_SYSTEM_XDRF)
-+	find_library(XDRF_LIBRARY NAMES xdrfile libxdrfile)
-+else()
-+	aux_source_directory(../../3rdparty/xdrf/ XDRF_SOURCES)
-+endif()
- 
- add_chemkit_plugin(xtc ${SOURCES} ${XDRF_SOURCES})
--target_link_libraries(xtc ${CHEMKIT_LIBRARIES} ${Boost_LIBRARIES})
-+target_link_libraries(xtc ${CHEMKIT_LIBRARIES} ${Boost_LIBRARIES} ${XDRF_LIBRARY} )
-diff --git a/src/plugins/xtc/xtcfileformat.cpp b/src/plugins/xtc/xtcfileformat.cpp
-index 0f00cb6..f8659ca 100644
---- a/src/plugins/xtc/xtcfileformat.cpp
-+++ b/src/plugins/xtc/xtcfileformat.cpp
-@@ -47,7 +47,11 @@
- #include <chemkit/trajectoryframe.h>
- #include <chemkit/cartesiancoordinates.h>
- 
-+#ifdef SYSTEM_XDRF
-+#include <xdrfile/xdrfile.h>
-+#else
- #include "../../3rdparty/xdrf/xdrf.h"
-+#endif
- 
- XtcFileFormat::XtcFileFormat()
-     : chemkit::TrajectoryFileFormat("xtc")