pdb2pka/SConscript           | 9 ++++++++-
 pdb2pka/substruct/SConscript | 6 ++++++
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/pdb2pka/SConscript b/pdb2pka/SConscript
index 583cdc5..6c30011 100644
--- a/pdb2pka/SConscript
+++ b/pdb2pka/SConscript
@@ -1,4 +1,11 @@
 Import('env')
+import os
+
+env['CCFLAGS'].extend(os.environ['CXXFLAGS'].split())
+env['LINKFLAGS'].extend(os.environ['LDFLAGS'].split())
+env['CXX'] = os.environ['CXX']
+env['LINK'] = os.environ['CXX']
+
 
 if env['REBUILD_SWIG']:
     pyc = env.LoadableModule('_pMC_mult', ['pMC_mult.cpp', 'pMC_mult.i'])
@@ -9,4 +16,4 @@ Default(pyc)
     
 algorithms_module = SConscript('substruct/SConscript')
 
-Return('pyc algorithms_module')
\ No newline at end of file
+Return('pyc algorithms_module')
diff --git a/pdb2pka/substruct/SConscript b/pdb2pka/substruct/SConscript
index 7dbcdb0..56fb577 100644
--- a/pdb2pka/substruct/SConscript
+++ b/pdb2pka/substruct/SConscript
@@ -1,7 +1,13 @@
 import distutils
 import numpy
+import os
 Import('env')
 
+env['CCFLAGS'].extend(os.environ['CXXFLAGS'].split())
+env['LINKFLAGS'].extend(os.environ['LDFLAGS'].split())
+env['CXX'] = os.environ['CXX']
+env['LINK'] = os.environ['CXX']
+
 env.Append(CPPPATH=[distutils.sysconfig.get_python_inc(), numpy.get_include()])
 
 algorithms_pyc = env.LoadableModule('Algorithms', ['Algorithms.cpp'])