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")