sci-chemistry/ball: Drop old, fixes #485830, #505856

(Portage version: 2.2.10/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

11 files changed, 11 insertions, 2658 deletions

diff --git a/sci-chemistry/ball/ChangeLog b/sci-chemistry/ball/ChangeLog
index 86793ce83543..8ba4f0172e09 100644
--- a/sci-chemistry/ball/ChangeLog
+++ b/sci-chemistry/ball/ChangeLog
@@ -1,6 +1,16 @@
 # ChangeLog for sci-chemistry/ball
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ball/ChangeLog,v 1.13 2014/03/26 11:20:39 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ball/ChangeLog,v 1.14 2014/03/26 13:27:44 jlec Exp $
+
+  26 Mar 2014; Justin Lecher <jlec@gentoo.org> -ball-1.4.1-r1.ebuild,
+  -files/ball-1.4.1-Added-MAX_PENALTY-option-to-bond-order-assignment.patch,
+  -files/ball-1.4.1-Fix-compilation-of-FTPBondOrderStrategy-Fixes-451.patch,
+  -files/ball-1.4.1-Fix-compilation-of-Python-bindings-with-new-sip-vers.patch,
+  -files/ball-1.4.1-Fixed-a-bug-in-the-AssignBondOrderProcessor.patch,
+  -files/ball-1.4.1-Fixed-the-FPT-version-of-bond-order-assignment-2.patch,
+  -files/ball-1.4.1-gcc-4.7.patch, -files/ball-1.4.1-libsvm.patch,
+  -files/ball-1.4.1-pthread.patch, -files/ball-1.4.1-python.patch:
+  Drop old, fixes #485830, #505856
 
 *ball-1.4.2 (26 Mar 2014)
 
diff --git a/sci-chemistry/ball/ball-1.4.1-r1.ebuild b/sci-chemistry/ball/ball-1.4.1-r1.ebuild
deleted file mode 100644
index ba23080fc497..000000000000
--- a/sci-chemistry/ball/ball-1.4.1-r1.ebuild
+++ /dev/null
@@ -1,87 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ball/ball-1.4.1-r1.ebuild,v 1.7 2014/03/26 11:20:39 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_6,2_7} )
-
-inherit cmake-utils python-single-r1
-
-DESCRIPTION="Biochemical Algorithms Library"
-HOMEPAGE="http://www.ball-project.org/"
-SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="LGPL-2 GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cuda mpi +python sql test +threads +webkit"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	dev-cpp/eigen:3
-	dev-libs/boost
-	dev-qt/qtcore:4
-	dev-qt/qtgui:4
-	dev-qt/qtopengl:4
-	dev-qt/qttest:4
-	dev-qt/qtwebkit:4
-	media-libs/glew
-	sci-libs/fftw:3.0[threads?]
-	sci-libs/gsl
-	sci-libs/libsvm
-	sci-mathematics/lpsolve
-	virtual/opengl
-	x11-libs/libX11
-	cuda? ( dev-util/nvidia-cuda-toolkit )
-	mpi? ( virtual/mpi )
-	python? ( ${PYTHON_DEPS} )
-	sql? ( dev-qt/qtsql:4 )
-	webkit? ( dev-qt/qtwebkit:4 )"
-DEPEND="${RDEPEND}
-	dev-python/sip
-	sys-devel/bison
-	virtual/yacc"
-
-S="${WORKDIR}"/BALL
-
-PATCHES=(
-	"${FILESDIR}"/${P}-multilib.patch
-	"${FILESDIR}"/${P}-libsvm.patch
-	"${FILESDIR}"/${P}-pthread.patch
-	"${FILESDIR}"/${P}-python.patch
-	"${FILESDIR}"/${P}-missing-signed.patch
-	"${FILESDIR}"/${P}-gcc-4.7.patch
-	"${FILESDIR}"/${P}-BondOrder.xml.patch
-	"${FILESDIR}"/${P}-Fixed-the-FPT-version-of-bond-order-assignment-2.patch
-	"${FILESDIR}"/${P}-Added-MAX_PENALTY-option-to-bond-order-assignment.patch
-	"${FILESDIR}"/${P}-Fixed-a-bug-in-the-AssignBondOrderProcessor.patch
-	"${FILESDIR}"/${P}-Fix-compilation-of-Python-bindings-with-new-sip-vers.patch
-	)
-
-pkg_setup() {
-	use python && python-single-r1_pkg_setup
-}
-
-src_configure() {
-	local mycmakeargs=(
-		$(cmake-utils_use_use threads FFTW_THREADS)
-		$(cmake-utils_use cuda MT_ENABLE_CUDA)
-		$(cmake-utils_use mpi MT_ENABLE_MPI)
-		$(cmake-utils_use sql BALL_HAS_QTSQL)
-		$(cmake-utils_use_use webkit USE_QTWEBKIT)
-		$(cmake-utils_use python BALL_PYTHON_SUPPORT)
-	)
-	cmake-utils_src_configure
-	local i
-	for i in "${S}"/data/*; do
-		ln -sf "${i}" "${BUILD_DIR}"/source/TEST/ || die
-		ln -sf "${i}" "${S}"/source/TEST/ || die
-	done
-}
-
-src_compile() {
-	cmake-utils_src_compile
-	use test && cmake-utils_src_make build_tests
-}
diff --git a/sci-chemistry/ball/files/ball-1.4.1-Added-MAX_PENALTY-option-to-bond-order-assignment.patch b/sci-chemistry/ball/files/ball-1.4.1-Added-MAX_PENALTY-option-to-bond-order-assignment.patch
deleted file mode 100644
index 4af96b783cdb..000000000000
--- a/sci-chemistry/ball/files/ball-1.4.1-Added-MAX_PENALTY-option-to-bond-order-assignment.patch
+++ /dev/null
@@ -1,975 +0,0 @@
-From: Anna Dehof <anne@bioinf.uni-sb.de>
-Date: Mon, 26 Mar 2012 19:11:39 +0200
-Subject: Added MAX_PENALTY option to bond order assignment
-
----
- include/BALL/DATATYPE/GRAPH/treeWidth.h            |   28 +--
- .../STRUCTURE/BONDORDERS/FPTBondOrderStrategy.h    |   16 +-
- include/BALL/STRUCTURE/assignBondOrderProcessor.h  |   30 ++-
- source/APPLICATIONS/UTILITIES/assign_bond_orders.C |   34 +++-
- source/DATATYPE/GRAPH/treeWidth.C                  |    2 +-
- source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C |  199 +++++++++-----------
- source/STRUCTURE/assignBondOrderProcessor.C        |   44 +++--
- 7 files changed, 186 insertions(+), 167 deletions(-)
-
-diff --git a/include/BALL/DATATYPE/GRAPH/treeWidth.h b/include/BALL/DATATYPE/GRAPH/treeWidth.h
-index f7687ef..53ecffc 100644
---- a/include/BALL/DATATYPE/GRAPH/treeWidth.h
-+++ b/include/BALL/DATATYPE/GRAPH/treeWidth.h
-@@ -100,14 +100,14 @@ namespace BALL
- 
- 			typedef boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS,
- 																		  boost::property<boost::vertex_bag_content_t, std::set<OriginalVertexType>,
--																			boost::property<boost::vertex_bag_special_t, OriginalVertexType, 
--																			boost::property<boost::vertex_bag_type_t, int> > >, 
-+																			boost::property<boost::vertex_bag_special_t, OriginalVertexType,
-+																			boost::property<boost::vertex_bag_type_t, int> > >,
- 																	  boost::no_property> TreeDecompositionGraph;
- 
- 			typedef typename boost::graph_traits<TreeDecompositionGraph>::vertex_descriptor TreeDecompositionBag;
- 
- 			typedef boost::iterator_property_map<typename std::vector<TreeDecompositionBag>::iterator,
--							                             typename boost::property_map<TreeDecompositionGraph, boost::vertex_index_t>::type> 
-+							                             typename boost::property_map<TreeDecompositionGraph, boost::vertex_index_t>::type>
- 																					 TreeDecompositionParentMap;
- 			typedef boost::graph_as_tree<TreeDecompositionGraph, TreeDecompositionParentMap> TreeDecomposition;
- 
-@@ -131,7 +131,7 @@ namespace BALL
- 			class ComponentFilter_
- 			{
- 				public:
--					ComponentFilter_(ComponentMap cm, Position i) 
-+					ComponentFilter_(ComponentMap cm, Position i)
- 						: cm_(cm),
- 							component_(i)
- 					{ }
-@@ -144,7 +144,7 @@ namespace BALL
- 
- 				protected:
- 					ComponentMap  cm_;
--					Position      component_;	
-+					Position      component_;
- 			};
- 
- 			/** PropertyWriter for graphviz output.
-@@ -167,7 +167,7 @@ namespace BALL
- 			// TODO: would UndirectedGraph suffice here?
- 			MolecularGraph const* input_;
- 
--			std::vector<boost::shared_ptr<EditableGraph> > components_; 
-+			std::vector<boost::shared_ptr<EditableGraph> > components_;
- 
- 			std::vector<boost::shared_ptr<TreeDecomposition> >      nice_tree_decompositions_;
- 			std::vector<boost::shared_ptr<TreeDecompositionGraph> > nice_tree_decomposition_graphs_;
-@@ -201,7 +201,7 @@ namespace BALL
- 		 * @tparam Reducer the reducer which removes a vertex from the graph to reduce it's size
- 		 */
- 		template<class Criterion, class Reducer>
--		class GeneralLowerBoundAlgorithm 
-+		class GeneralLowerBoundAlgorithm
- 			: public UnaryFunctor<UndirectedGraph, Size>
- 		{
- 			public:
-@@ -284,7 +284,7 @@ namespace BALL
- 		 * @throw BALL::GRAPH::UnconnectedGraphException if called on unconnected graphs
- 		 */
- 		template<class Criterion>
--		class GreedyX 
-+		class GreedyX
- 			: public UnaryFunctor<UndirectedGraph, typename std::pair<
- 				std::vector<boost::graph_traits<typename UndirectedGraph::vertex_descriptor> >, Size> >
- 		{
-@@ -296,7 +296,7 @@ namespace BALL
- 		 * A criterium for GreedyFillIn which search for a vertex with
- 		 * minimum number of additional edges after eliminating
- 		 */
--		struct FillInHeuristic 
-+		struct FillInHeuristic
- 		{
- 			VertexType& operator() (UndirectedGraph& graph);
- 
-@@ -323,8 +323,8 @@ namespace BALL
- 				 */
- 				enum SIMPLICIAL_TYPE
- 				{
--					NOT_SIMPLICIAL, 
--					ALMOST_SIMPLICIAL, 
-+					NOT_SIMPLICIAL,
-+					ALMOST_SIMPLICIAL,
- 					IS_SIMPLICIAL
- 				};
- 
-@@ -484,7 +484,7 @@ namespace BALL
- 				TreeDecompositionBag buildJoin_(TreeDecompositionBag node, TreeDecompositionBag left,
- 				                                  TreeDecompositionBag right, bool do_forget);
- 
--				TreeDecompositionBag buildSingle_(TreeDecompositionBag node, int node_type, 
-+				TreeDecompositionBag buildSingle_(TreeDecompositionBag node, int node_type,
- 				                                    TreeDecompositionBag child);
- 
- 				TreeDecompositionBag buildLinkage_(TreeDecompositionBag node, TreeDecompositionBag child);
-@@ -492,8 +492,8 @@ namespace BALL
- 				TreeDecompositionBag linkWithIntroduceNodes_(TreeDecompositionContent parent_set, TreeDecompositionBag child);
- 				TreeDecompositionBag linkWithForgetNodes_   (TreeDecompositionContent parent_set, TreeDecompositionBag child);
- 
--				TreeDecompositionBag branch_(TreeDecompositionBag node, int node_type, 
--				                               typename std::vector<TreeDecompositionBag>::iterator begin, 
-+				TreeDecompositionBag branch_(TreeDecompositionBag node, int node_type,
-+				                               typename std::vector<TreeDecompositionBag>::iterator begin,
- 																			 typename std::vector<TreeDecompositionBag>::iterator end);
- 
- 				boost::shared_ptr<TreeDecomposition> tree_;
-diff --git a/include/BALL/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.h b/include/BALL/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.h
-index 55cef31..ba129b0 100644
---- a/include/BALL/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.h
-+++ b/include/BALL/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.h
-@@ -1117,6 +1117,11 @@ namespace BALL
- 					Size max_heap_size_;
- 
- 					/**
-+					 * The number of solutions produced so far.
-+					 */
-+					Size num_computed_solutions_;
-+
-+					/**
- 					 * current upperbound. This algorithm will just iterate solutions which are better than this upperbound;
- 					 */
- 					Penalty upper_bound_;
-@@ -1248,14 +1253,6 @@ namespace BALL
- 							                    Size solution_number, Penalty upper_bound = infinite_penalty);
- 
- 					/**
--					 * Construct a DPBackTrackingCombiner with the given FPTBondOrder and the number of solutions
--					 * @param bondAssignments vector with the bond assignments. Call #compute before constructing
--					 * @param solutionNumber the maximum number of solutions you want to backtrack
--					 */
--					DPBackTrackingCombiner_(std::vector<FPTBondOrderAssignment_>& bond_assignments, 
--					                        Size solution_number, Penalty upper_bound = infinite_penalty);
--
--					/**
- 					 * Copy constructor
- 					 */
- 					DPBackTrackingCombiner_(DPBackTrackingCombiner_ const& copy);
-@@ -1407,9 +1404,6 @@ namespace BALL
- 			 */
- 			std::vector<std::vector<int> > const* atom_to_block_;
- 
--			/// upper bound on the penalty values for which we compute solutions
--			Penalty upper_bound_;
--
- 			/**
- 			 * A shared pointer to the computing data, so that you can copy this instance without copying
- 			 * all the computing data
-diff --git a/include/BALL/STRUCTURE/assignBondOrderProcessor.h b/include/BALL/STRUCTURE/assignBondOrderProcessor.h
-index f8065d6..0d14af8 100644
---- a/include/BALL/STRUCTURE/assignBondOrderProcessor.h
-+++ b/include/BALL/STRUCTURE/assignBondOrderProcessor.h
-@@ -183,17 +183,35 @@ namespace BALL
- 
- 				/** the maximal number of solutions to compute
- 				 *
--				 *  If set to zero all optimal solutions will be computed.
-+				 *  If set to zero all optimal or all up to \link MAX_PENALTY MAX_PENALTY \endlink 
-+				 *  solutions will be computed.
- 				 *
--				 *  @see Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS
-+				 *  @see Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS 
-+				 *  @see Option::MAX_PENALTY
- 				 */
- 				static const char* MAX_NUMBER_OF_SOLUTIONS;
- 
--				/** compute also non-optimal solutions but not more than 
--				 *  \link MAX_NUMBER_OF_SOLUTIONS MAX_NUMBER_OF_SOLUTIONS \endlink solutions.
-+				/** the maximal penalty score allowed
-+				 *  
-+				 *  This option respects option \link MAX_NUMBER_OF_SOLUTIONS MAX_NUMBER_OF_SOLUTIONS \endlink
-+				 *  if specified.
- 				 *
-+				 *  If set to -1 this option will be ignored. 
-+				 *
-+				 *  @see Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS
- 				 *  @see Option::MAX_NUMBER_OF_SOLUTIONS
- 				 */
-+				static const char* MAX_PENALTY;
-+
-+				/** compute also sub-optimal solutions but not more than 
-+				 *  \link MAX_NUMBER_OF_SOLUTIONS MAX_NUMBER_OF_SOLUTIONS \endlink solutions.
-+				 *  
-+				 *  Alternatively \link Option::MAX_PENALTY  Option::MAX_PENALTY  \endlink
-+				 *  allows to specify a maximal penalty. 
-+				 *
-+				 *  @see Option::MAX_NUMBER_OF_SOLUTIONS 
-+				 *  @see Option::MAX_PENALTY
-+				 */
- 				static const char* COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS;
- 
- 				/** weighting of bond length penalties wrt valence penalties.
-@@ -227,6 +245,7 @@ namespace BALL
- 				static const String INIFile;
- 				static const int MAX_BOND_ORDER;
- 				static const int MAX_NUMBER_OF_SOLUTIONS;
-+				static const int MAX_PENALTY;
- 				static const bool COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS;
- 				static const float BOND_LENGTH_WEIGHTING;
- 				static const bool APPLY_FIRST_SOLUTION;
-@@ -716,6 +735,9 @@ namespace BALL
- 			// the max number of solutions to compute 
- 			int max_number_of_solutions_;
- 
-+			// the max penalty score 
-+			int max_penalty_;
-+
- 			// flag to indicate, whether also non-optimal solutions should be computed 
- 			bool compute_also_non_optimal_solutions_;
- 
-diff --git a/source/APPLICATIONS/UTILITIES/assign_bond_orders.C b/source/APPLICATIONS/UTILITIES/assign_bond_orders.C
-index cefef9b..7053baa 100644
---- a/source/APPLICATIONS/UTILITIES/assign_bond_orders.C
-+++ b/source/APPLICATIONS/UTILITIES/assign_bond_orders.C
-@@ -16,10 +16,10 @@ using namespace BALL;
- 
- int main(int argc, char** argv)
- {
--	if ((argc < 3) || (argc > 4))
-+	if (argc < 3)
- 	//	if (argc != 3)
- 	{
--		Log << "Usage:" << argv[0] << " <Molecule infile> <Molecule outfile> [num_sol]" << endl;
-+		Log << "Usage:" << argv[0] << " <Molecule infile> <Molecule outfile> [--num-sol=n] [--strategy=(fpt|a_star|ilp)] [--max-penalty=m]" << endl;
- 		return 1;
- 	}
- 
-@@ -49,24 +49,40 @@ int main(int argc, char** argv)
- 	//    set the options:
- 	//
- 	// the solution strategy (A*, ILP or FPT)
--	abop.options.set(AssignBondOrderProcessor::Option::ALGORITHM, AssignBondOrderProcessor::Algorithm::A_STAR);
-+	abop.options.set(AssignBondOrderProcessor::Option::ALGORITHM, AssignBondOrderProcessor::Algorithm::FPT);
- 
- 	// specify the inifile with the atomic valence penalties
- 	abop.options.set(AssignBondOrderProcessor::Option::INIFile, AssignBondOrderProcessor::Default::INIFile);
- 
- 	// options for considering bond length as well 
--	abop.options.setReal(AssignBondOrderProcessor::Option::BOND_LENGTH_WEIGHTING, 0);
--	abop.options.setReal(AssignBondOrderProcessor::Option::USE_FINE_PENALTY, true);
-+//	abop.options.setReal(AssignBondOrderProcessor::Option::BOND_LENGTH_WEIGHTING, 0);
-+//	abop.options.setReal(AssignBondOrderProcessor::Option::USE_FINE_PENALTY, true);
- 
- 	// the combination of the following two options causes the computation of all optimal solutions
- 	abop.options.setInteger(AssignBondOrderProcessor::Option::MAX_NUMBER_OF_SOLUTIONS, 0);
- 	abop.options.setBool(AssignBondOrderProcessor::Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS, false);
- 
--	if (argc == 4)
-+	if (argc > 3)
- 	{
--		Log << "  with compute fixed number (" << argv[3] << ") solutions" << endl;
--		abop.options.setInteger(AssignBondOrderProcessor::Option::MAX_NUMBER_OF_SOLUTIONS, String(argv[3]).toInt());
--		abop.options.setBool(AssignBondOrderProcessor::Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS, true);
-+		for (Index i=3; i<argc; ++i)
-+		{
-+			if (String(argv[i]).hasPrefix("--strategy"))
-+			{
-+				abop.options.set(AssignBondOrderProcessor::Option::ALGORITHM, String(argv[i]).getField(1, "="));
-+			}
-+			else if (String(argv[i]).hasPrefix("--num-sol"))
-+			{
-+				Log << "  with compute fixed number (" << argv[i] << ") solutions" << endl;
-+				abop.options.setInteger(AssignBondOrderProcessor::Option::MAX_NUMBER_OF_SOLUTIONS, String(argv[i]).getField(1, "=").toInt());
-+				abop.options.setBool(AssignBondOrderProcessor::Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS, true);
-+			}
-+			else if (String(argv[i]).hasPrefix("--max-penalty"))
-+			{
-+				abop.options.setInteger(AssignBondOrderProcessor::Option::MAX_PENALTY, String(argv[i]).getField(1, "=").toInt());
-+				abop.options.setBool(AssignBondOrderProcessor::Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS, true);
-+				Log << "  with maximum penalty (" <<  abop.options.getInteger(AssignBondOrderProcessor::Option::MAX_PENALTY) << ")" << endl;
-+			}
-+		}
- 	}
- 
- 	// define input and output properties
-diff --git a/source/DATATYPE/GRAPH/treeWidth.C b/source/DATATYPE/GRAPH/treeWidth.C
-index 7485305..cd0a879 100644
---- a/source/DATATYPE/GRAPH/treeWidth.C
-+++ b/source/DATATYPE/GRAPH/treeWidth.C
-@@ -12,7 +12,7 @@ namespace BALL
- 		// find all vertices in the current bag
- 		TreeDecompositionContent content = boost::get(boost::vertex_bag_content, *td_, v);
- 
--		for (typename TreeDecompositionContent::const_iterator tdc_it = content.begin(); tdc_it != content.end(); ++tdc_it)
-+		for (TreeDecompositionContent::const_iterator tdc_it = content.begin(); tdc_it != content.end(); ++tdc_it)
- 		{
- 			TreeWidth<MolecularGraph>::OriginalVertexType ov = *tdc_it;
- 			Atom const* atom = boost::get(boost::vertex_atom_ptr, *original_graph_, ov);
-diff --git a/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C b/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C
-index 42040e5..107823e 100644
---- a/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C
-+++ b/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C
-@@ -12,10 +12,6 @@ namespace BALL
- 	const FPTBondOrderStrategy::Penalty FPTBondOrderStrategy::infinite_penalty = 1e5;
- 	const FPTBondOrderStrategy::Valence FPTBondOrderStrategy::max_valence      = 8;
- 
--	String  FPTBondOrderStrategy::Option::UPPER_PENALTY_BOUND  = "upper_penalty_bound";
--
--	FPTBondOrderStrategy::Penalty FPTBondOrderStrategy::Default::UPPER_PENALTY_BOUND = infinite_penalty;
--
- 	FPTBondOrderStrategy::FPTBondOrderStrategy(AssignBondOrderProcessor* parent)
- 		: BondOrderAssignmentStrategy(parent)
- 	{
-@@ -33,15 +29,11 @@ namespace BALL
- 
- 	bool FPTBondOrderStrategy::readOptions(const Options& options)
- 	{
--		upper_bound_ = options.get(Option::UPPER_PENALTY_BOUND).toFloat();
--
- 		return true;
- 	}
- 
- 	void FPTBondOrderStrategy::setDefaultOptions()
- 	{
--		abop->options.setDefault(FPTBondOrderStrategy::Option::UPPER_PENALTY_BOUND,
--		                         FPTBondOrderStrategy::Default::UPPER_PENALTY_BOUND);
- 	}
- 
- 	void FPTBondOrderStrategy::init()
-@@ -64,16 +56,22 @@ namespace BALL
- 		std::vector<boost::shared_ptr<TreeDecomposition> > & ntds = computing_data_->tw->getNiceTreeDecompositions();
- 		std::vector<FPTBondOrderAssignment_*>& bond_assignments   = computing_data_->bond_assignments;
- 
-+		int max_penalty = abop->max_penalty_;
-+		if (max_penalty == -1)
-+			max_penalty = infinite_penalty;
-+		else
-+			max_penalty += 1;
-+
- 		bond_assignments.reserve(ntds.size());
- 		for (Position i = 0; i < ntds.size(); ++i)
- 		{
--			bond_assignments.push_back(new FPTBondOrderAssignment_(*this, ntds[i], upper_bound_));
--		  bond_assignments[i]->compute();
-+			bond_assignments.push_back(new FPTBondOrderAssignment_(*this, ntds[i], max_penalty));
-+		  Penalty result = bond_assignments[i]->compute();
- 		}
- 
- 		// initialize backtracking
- 		combiner_ = boost::shared_ptr<DPBackTrackingCombiner_>(
--		                   new DPBackTrackingCombiner_(bond_assignments, abop->max_number_of_solutions_, upper_bound_));
-+		                   new DPBackTrackingCombiner_(bond_assignments, abop->max_number_of_solutions_, max_penalty));
- 	}
- 
- 	boost::shared_ptr<BondOrderAssignment> FPTBondOrderStrategy::computeNextSolution()
-@@ -144,7 +142,7 @@ namespace BALL
- 			int penalty = (*penalties_)[start_index + position];
- 
- 			return (penalty < 0) ? infinite_penalty : static_cast<float>(penalty);
--		} 
-+		}
- 		else
- 		{
- 			return infinite_penalty;
-@@ -155,20 +153,20 @@ namespace BALL
- 	//*           DPConfig_                                                                               *
- 	//*****************************************************************************************************
- 
--	FPTBondOrderStrategy::DPConfig_::DPConfig_() 
--		: consumed_valences(0), 
-+	FPTBondOrderStrategy::DPConfig_::DPConfig_()
-+		: consumed_valences(0),
- 		  bond_assignments(0)
- 	{
- 	}
- 
--	FPTBondOrderStrategy::DPConfig_::DPConfig_(Size atoms, Size bonds) 
--		: consumed_valences(atoms, 0), 
-+	FPTBondOrderStrategy::DPConfig_::DPConfig_(Size atoms, Size bonds)
-+		: consumed_valences(atoms, 0),
- 		  bond_assignments(bonds, 0)
- 	{
- 	}
- 
--	FPTBondOrderStrategy::DPConfig_::DPConfig_(std::vector<Valence> const& v, std::vector<BondOrder> const& bo) 
--		: consumed_valences(v), 
-+	FPTBondOrderStrategy::DPConfig_::DPConfig_(std::vector<Valence> const& v, std::vector<BondOrder> const& bo)
-+		: consumed_valences(v),
- 		  bond_assignments(bo)
- 	{
- 	}
-@@ -258,12 +256,12 @@ namespace BALL
- 	//*           DPTable_                                                                                *
- 	//*****************************************************************************************************
- 
--	FPTBondOrderStrategy::DPTable_::DPTable_() 
-+	FPTBondOrderStrategy::DPTable_::DPTable_()
- 	  : table()
- 	{
- 	}
- 
--	FPTBondOrderStrategy::DPTable_::DPTable_(DPTable_ const& dptab) 
-+	FPTBondOrderStrategy::DPTable_::DPTable_(DPTable_ const& dptab)
- 		: table(dptab.table)
- 	{
- 	}
-@@ -345,7 +343,7 @@ namespace BALL
- 		if (insertion.second)
- 		{
- 			return true;
--		} 
-+		}
- 		else
- 		{
- 			if (insertion.first->second > penalty)
-@@ -353,7 +351,7 @@ namespace BALL
- 				insertion.first->second = penalty;
- 
- 				return true;
--			} 
-+			}
- 			else
- 			{
- 				return false;
-@@ -365,14 +363,14 @@ namespace BALL
- 	//*           AdditionalBagProperties_                                                                *
- 	//*****************************************************************************************************
- 
--	FPTBondOrderStrategy::AdditionalBagProperties_::AdditionalBagProperties_() 
--		: bonds(), 
--		  table(new DPTable_()) 
-+	FPTBondOrderStrategy::AdditionalBagProperties_::AdditionalBagProperties_()
-+		: bonds(),
-+		  table(new DPTable_())
- 	{
- 	}
- 
--	FPTBondOrderStrategy::AdditionalBagProperties_::AdditionalBagProperties_(AdditionalBagProperties_ const& copy) 
--		: bonds(copy.bonds), 
-+	FPTBondOrderStrategy::AdditionalBagProperties_::AdditionalBagProperties_(AdditionalBagProperties_ const& copy)
-+		: bonds(copy.bonds),
- 			table(new DPTable_(*copy.table))
- 	{
- 	}
-@@ -384,7 +382,7 @@ namespace BALL
- 
- 	FPTBondOrderStrategy::AdditionalBagProperties_& FPTBondOrderStrategy::AdditionalBagProperties_::operator=(AdditionalBagProperties_ const& copy)
- 	{
--		if (&copy != this) 
-+		if (&copy != this)
- 		{
- 			bonds = copy.bonds;
- 			table = new DPTable_(*copy.table);
-@@ -447,7 +445,7 @@ namespace BALL
- 				{
- 					throw Exception::NullPointer(__FILE__, __LINE__);
- 				}
--			case TreeWidth<MolecularGraph>::LEAF_BAG: 
-+			case TreeWidth<MolecularGraph>::LEAF_BAG:
- 				break;
- 			case TreeWidth<MolecularGraph>::END_BAG:
- 				if (boost::num_vertices(*molecule_) == 0 && (bag == root(*ntd_)))
-@@ -455,7 +453,7 @@ namespace BALL
- 					// empty molecule -> empty table
- 					bag_properties.table->insert(DPConfig_(), 0);
- 					return bag_properties.table;
--				} 
-+				}
- 				else
- 				{
- 					// else nice tree decomposition is damaged
-@@ -603,7 +601,7 @@ namespace BALL
- 		return bonds;
- 	}
- 
--	void FPTBondOrderStrategy::FPTBondOrderAssignment_::computeIntroduceBag(TreeDecompositionBag& bag, DPTable_& child, 
-+	void FPTBondOrderStrategy::FPTBondOrderAssignment_::computeIntroduceBag(TreeDecompositionBag& bag, DPTable_& child,
- 	                                                                        AdditionalBagProperties_& property)
- 	{
- 		typedef TreeWidth<MolecularGraph>::TreeDecompositionContent TreeDecompositionContent;
-@@ -614,7 +612,7 @@ namespace BALL
- 
- 		TreeDecompositionContent vertices = boost::get(boost::vertex_bag_content, *ntd_, bag);
- 		Size num_valences = vertices.size();
--		
-+
- 		std::vector<MolecularGraphTraits::EdgeType>& bonds = property.bonds;
- 		Size num_bonds = bonds.size();
- 
-@@ -654,7 +652,7 @@ namespace BALL
- 				{
- 					// remember the indizes of the new introduced bonds
- 					indices.push_back(vindex);
--				} 
-+				}
- 				else
- 				{
- 					conf.bond_assignments[vindex] = child_entry.first.get().bond_assignments[cindex++];
-@@ -662,7 +660,7 @@ namespace BALL
- 			}
- 
- 			// if there are any introduced bonds we have to fill them with each possible value
--			if (indices.size() > 0) 
-+			if (indices.size() > 0)
- 			{
- 				std::vector<int> bond_values(indices.size());
- 
-@@ -685,7 +683,7 @@ namespace BALL
- 						++current_index;
- 					}
- 				}
--			} 
-+			}
- 			else
- 			{
- 				table.insert(conf, child_entry.second);
-@@ -768,7 +766,7 @@ namespace BALL
- 		return parent_->getPenaltyFor_(forgotten_vertex, forgotten_valence) + child_row.second;
- 	}
- 
--	void FPTBondOrderStrategy::FPTBondOrderAssignment_::computeForgetBag(TreeDecompositionBag& bag, DPTable_& child, 
-+	void FPTBondOrderStrategy::FPTBondOrderAssignment_::computeForgetBag(TreeDecompositionBag& bag, DPTable_& child,
- 																					                             AdditionalBagProperties_& property)
- 	{
- 		typedef TreeWidth<MolecularGraph>::TreeDecompositionContent TreeDecompositionContent;
-@@ -795,7 +793,7 @@ namespace BALL
- 		}
- 	}
- 
--	void FPTBondOrderStrategy::FPTBondOrderAssignment_::computeRootBag(TreeDecompositionBag& bag, 
-+	void FPTBondOrderStrategy::FPTBondOrderAssignment_::computeRootBag(TreeDecompositionBag& bag,
- 	                                                                   DPTable_& child, AdditionalBagProperties_& bag_properties)
- 	{
- 		DPConfig_ empty(0, 0);
-@@ -816,7 +814,8 @@ namespace BALL
- 	}
- 
- 	void FPTBondOrderStrategy::FPTBondOrderAssignment_::computeJoinBag(TreeDecompositionBag& bag,
--                                  			DPTable_& left_child, DPTable_& right_child, AdditionalBagProperties_& property)
-+			                                                               DPTable_& left_child, DPTable_& right_child, 
-+																																		 AdditionalBagProperties_& property)
- 	{
- 		typedef TreeWidth<MolecularGraph>::TreeDecompositionContent TreeDecompositionContent;
- 
-@@ -1268,22 +1267,23 @@ namespace BALL
- 	//*           DPBackTracking_                                                                        *
- 	//*****************************************************************************************************
- 
--	FPTBondOrderStrategy::DPBackTracking_::DPBackTracking_(FPTBondOrderAssignment_& bond_assignment, Size max_num_solutions, 
--                                                         std::vector<MolecularGraphTraits::EdgeType> const& bonds, Penalty upper_bound) 
--		: bond_assignment_(&bond_assignment), 
--			current_state_(NULL), 
--			queue_(), 
--			max_num_solutions_(max_num_solutions), 
-+	FPTBondOrderStrategy::DPBackTracking_::DPBackTracking_(FPTBondOrderAssignment_& bond_assignment, Size max_num_solutions,
-+                                                         std::vector<MolecularGraphTraits::EdgeType> const& bonds, Penalty upper_bound)
-+		: bond_assignment_(&bond_assignment),
-+			current_state_(NULL),
-+			queue_(),
-+			max_num_solutions_(max_num_solutions),
- 			bonds_(&bonds),
--			bags_(boost::shared_ptr<std::vector<TreeDecompositionBag> >(new std::vector<TreeDecompositionBag>)), 
--			max_heap_size_(max_num_solutions), 
-+			bags_(boost::shared_ptr<std::vector<TreeDecompositionBag> >(new std::vector<TreeDecompositionBag>)),
-+			max_heap_size_(1e6),
-+			num_computed_solutions_(0),
- 			upper_bound_(upper_bound)
- 	{
- 		// order bags in preorder
- 		if (bond_assignment.ntd_ == NULL)
- 		{
- 			throw Exception::NullPointer(__FILE__, __LINE__);
--		} 
-+		}
- 		else
- 		{
- 			bags_->reserve(boost::num_vertices(bond_assignment.ntd_->_g));
-@@ -1303,14 +1303,15 @@ namespace BALL
- 		}
- 	}
- 
--	FPTBondOrderStrategy::DPBackTracking_::DPBackTracking_(DPBackTracking_ const& copy) 
--	 : bond_assignment_(copy.bond_assignment_), 
--		 current_state_(NULL), 
-+	FPTBondOrderStrategy::DPBackTracking_::DPBackTracking_(DPBackTracking_ const& copy)
-+	 : bond_assignment_(copy.bond_assignment_),
-+		 current_state_(NULL),
- 		 queue_(),
--		 max_num_solutions_(copy.max_num_solutions_), 
--		 bonds_(copy.bonds_), 
--		 bags_(copy.bags_), 
-+		 max_num_solutions_(copy.max_num_solutions_),
-+		 bonds_(copy.bonds_),
-+		 bags_(copy.bags_),
- 		 max_heap_size_(copy.max_heap_size_),
-+		 num_computed_solutions_(copy.num_computed_solutions_),
- 		 upper_bound_(copy.upper_bound_)
- 	{
- 		if (copy.current_state_ != NULL)
-@@ -1345,6 +1346,7 @@ namespace BALL
- 			bonds_ = copy.bonds_;
- 			bags_ = copy.bags_;
- 			max_heap_size_ = copy.max_heap_size_;
-+			num_computed_solutions_ = copy.num_computed_solutions_;
- 			upper_bound_ = copy.upper_bound_;
- 		}
- 
-@@ -1365,6 +1367,7 @@ namespace BALL
- 
- 		std::vector<BackTrackingState_*> copy(queue_.begin(), queue_.end());
- 		queue_.clear();
-+		num_computed_solutions_ = 0;
- 
- 		for (std::vector<BackTrackingState_*>::iterator iter = copy.begin(); iter != copy.end(); ++iter)
- 		{
-@@ -1372,7 +1375,7 @@ namespace BALL
- 		}
- 	}
- 
--	bool FPTBondOrderStrategy::DPBackTracking_::StateComparator_::operator() (BackTrackingState_ const * left, 
-+	bool FPTBondOrderStrategy::DPBackTracking_::StateComparator_::operator() (BackTrackingState_ const * left,
- 	                                                                          BackTrackingState_ const * right) const
- 	{
- 		return *left < *right;
-@@ -1397,7 +1400,7 @@ namespace BALL
- 		if (order < properties.size())
- 		{
- 			return properties[order];
--		} 
-+		}
- 		else
- 		{
- 			throw Exception::IndexOverflow(__FILE__, __LINE__, static_cast<Index>(order), properties.size());
-@@ -1426,12 +1429,12 @@ namespace BALL
- 
- 	bool FPTBondOrderStrategy::DPBackTracking_::hasMoreSolutions() const
- 	{
--		return (!queue_.empty() && (max_heap_size_ > 0));
-+		return (!queue_.empty() && (!max_num_solutions_ || (num_computed_solutions_ <= max_num_solutions_)));
- 	}
- 
- 	void FPTBondOrderStrategy::DPBackTracking_::nextSolution()
- 	{
--		if (queue_.empty() || max_heap_size_ == 0)
-+		if (queue_.empty() || max_heap_size_ == 0 || ((max_num_solutions_ > 0) && (num_computed_solutions_ > max_num_solutions_)))
- 		{
- 			throw Exception::OutOfRange(__FILE__, __LINE__);
- 		}
-@@ -1444,7 +1447,7 @@ namespace BALL
- 		std::multiset<BackTrackingState_*, StateComparator_>::iterator first = queue_.begin();
- 		current_state_ = *first;
- 		queue_.erase(first);
--		--max_heap_size_;
-+		++num_computed_solutions_;
- 
- 		TreeDecomposition& tree = *bond_assignment_->ntd_;
- 
-@@ -1469,7 +1472,7 @@ namespace BALL
- 				{
- 					TreeDecomposition::children_iterator c_2 = c_i;
- 					++c_2;
--					visitJoin(*current_state_, bag, getTable(boost::get(boost::vertex_index, tree, *c_i)), 
-+					visitJoin(*current_state_, bag, getTable(boost::get(boost::vertex_index, tree, *c_i)),
- 																				getTable(boost::get(boost::vertex_index, tree, *c_2)));
- 					break;
- 				}
-@@ -1769,7 +1772,7 @@ namespace BALL
- 		if (d < bonds_->size())
- 		{
- 			return d;
--		} 
-+		}
- 		else
- 		{
- 			throw Exception::IndexOverflow(__FILE__, __LINE__, static_cast<Index>(d), bonds_->size());
-@@ -1795,7 +1798,7 @@ namespace BALL
- 
- 	bool FPTBondOrderStrategy::DPBackTracking_::isSolutionNeeded(Penalty penalty)
- 	{
--		if (max_heap_size_ == 0) {return false;}
-+		if (max_heap_size_ == 0 || ((max_num_solutions_ > 0) && (num_computed_solutions_ > max_num_solutions_))) {return false;}
- 		if (queue_.size() >= max_heap_size_) {return Maths::isLess(penalty, upper_bound_);}
- 		return Maths::isLessOrEqual(penalty, upper_bound_);
- 	}
-@@ -1846,7 +1849,7 @@ namespace BALL
- 		if (queue_.empty() || max_heap_size_ == 0)
- 		{
- 			return FPTBondOrderStrategy::infinite_penalty;
--		} 
-+		}
- 		else
- 		{
- 			return (*queue_.begin())->assignment.penalty;
-@@ -1857,25 +1860,25 @@ namespace BALL
- 	//*           DPBackTrackingCombiner_                                                                 *
- 	//*****************************************************************************************************
- 
--	FPTBondOrderStrategy::DPBackTrackingCombiner_::DPBackTrackingCombiner_(DPBackTrackingCombiner_ const& copy) 
--		: backtrackers_(copy.deepCopyOfBacktrackers_()), 
-+	FPTBondOrderStrategy::DPBackTrackingCombiner_::DPBackTrackingCombiner_(DPBackTrackingCombiner_ const& copy)
-+		: backtrackers_(copy.deepCopyOfBacktrackers_()),
- 		  priority_queue_(copy.priority_queue_),
--			component_solutions_(copy.component_solutions_), 
-+			component_solutions_(copy.component_solutions_),
- 			assignment_(copy.assignment_),
--			solution_number_(copy.solution_number_), 
--			optimum_(copy.optimum_), 
-+			solution_number_(copy.solution_number_),
-+			optimum_(copy.optimum_),
- 			upper_bound_(copy.upper_bound_)
- 	{
- 	}
- 
--	FPTBondOrderStrategy::DPBackTrackingCombiner_::DPBackTrackingCombiner_(std::vector<FPTBondOrderAssignment_*>& bond_assignments, 
--		                                                                     Size solution_number, Penalty upper_bound) 
--		: backtrackers_(), 
--		  priority_queue_(), 
-+	FPTBondOrderStrategy::DPBackTrackingCombiner_::DPBackTrackingCombiner_(std::vector<FPTBondOrderAssignment_*>& bond_assignments,
-+		                                                                     Size solution_number, Penalty upper_bound)
-+		: backtrackers_(),
-+		  priority_queue_(),
- 			component_solutions_(bond_assignments.size()),
--			assignment_(), 
--			solution_number_(solution_number), 
--			optimum_(FPTBondOrderStrategy::infinite_penalty), 
-+			assignment_(),
-+			solution_number_(solution_number),
-+			optimum_(FPTBondOrderStrategy::infinite_penalty),
- 			upper_bound_(upper_bound)
- 	{
- 		if (bond_assignments.empty())
-@@ -1897,7 +1900,7 @@ namespace BALL
- 		FPTBondOrderStrategy::EdgeComparator_ ec(&graph);
- 		std::sort(sorted_edges.begin(), sorted_edges.end(), ec);
- 
--		for (std::vector<FPTBondOrderAssignment_*>::const_iterator iter  = bond_assignments.begin(); 
-+		for (std::vector<FPTBondOrderAssignment_*>::const_iterator iter  = bond_assignments.begin();
- 		                                                           iter != bond_assignments.end();   ++iter)
- 		{
- 			backtrackers_.push_back(new DPBackTracking_(**iter, solution_number_, sorted_edges, upper_bound_));
-@@ -1906,39 +1909,6 @@ namespace BALL
- 		initialize_();
- 	}
- 
--	FPTBondOrderStrategy::DPBackTrackingCombiner_::DPBackTrackingCombiner_(std::vector<FPTBondOrderAssignment_>& bond_assignments, 
--		                                             Size solution_number, Penalty upper_bound) 
--		: backtrackers_(), 
--		  priority_queue_(), 
--			component_solutions_(bond_assignments.size()),
--			assignment_(), 
--			solution_number_(solution_number), 
--			optimum_(FPTBondOrderStrategy::infinite_penalty), 
--			upper_bound_(upper_bound)
--	{
--		backtrackers_.reserve(bond_assignments.size());
--
--		MolecularGraph& graph = *bond_assignments[0].molecule_;
--		sorted_edges.reserve(boost::num_edges(graph));
--
--		BGL_FORALL_EDGES(edge_it, graph, MolecularGraph)
--		{
--			sorted_edges.push_back(edge_it);
--		}
--
--		// sort bonds - the second vertex could be in false order
--		FPTBondOrderStrategy::EdgeComparator_ ec(&graph);
--		std::sort(sorted_edges.begin(), sorted_edges.end(), ec);
--
--		for (std::vector<FPTBondOrderAssignment_>::iterator iter  = bond_assignments.begin(); 
--		                                                    iter != bond_assignments.end();   ++iter)
--		{
--			backtrackers_.push_back(new DPBackTracking_(*iter, solution_number_, sorted_edges, upper_bound_));
--		}
--
--		initialize_();
--	}
--
- 	FPTBondOrderStrategy::DPBackTrackingCombiner_::~DPBackTrackingCombiner_()
- 	{
- 		clear();
-@@ -1946,14 +1916,14 @@ namespace BALL
- 
- 	void FPTBondOrderStrategy::DPBackTrackingCombiner_::clear()
- 	{
--		for (std::vector<DPBackTracking_*>::iterator iter  = backtrackers_.begin(); 
-+		for (std::vector<DPBackTracking_*>::iterator iter  = backtrackers_.begin();
- 		                                             iter != backtrackers_.end();   ++iter)
- 		{
- 			delete *iter;
- 		}
- 	}
- 
--	FPTBondOrderStrategy::DPBackTrackingCombiner_& 
-+	FPTBondOrderStrategy::DPBackTrackingCombiner_&
- 	FPTBondOrderStrategy::DPBackTrackingCombiner_::operator = (DPBackTrackingCombiner_ const& copy)
- 	{
- 		if (this != &copy)
-@@ -1972,7 +1942,7 @@ namespace BALL
- 		return *this;
- 	}
- 
--	std::pair<Size, FPTBondOrderStrategy::Penalty> 
-+	std::pair<Size, FPTBondOrderStrategy::Penalty>
- 	FPTBondOrderStrategy::DPBackTrackingCombiner_::getNextMinimumBackTracker_() const
- 	{
- 		if (backtrackers_.size() == 1)
-@@ -2034,7 +2004,7 @@ namespace BALL
- 				assignment_ = ass;
- 
- 				return;
--			} 
-+			}
- 			else
- 			{
- 				throw Exception::OutOfRange(__FILE__, __LINE__);
-@@ -2061,7 +2031,7 @@ namespace BALL
- 			assignment_ = priority_queue_.top();
- 
- 			priority_queue_.pop();
--		} 
-+		}
- 		else
- 		{
- 			throw Exception::OutOfRange(__FILE__, __LINE__);
-@@ -2151,7 +2121,7 @@ namespace BALL
- 		return assignment_;
- 	}
- 
--	std::vector<FPTBondOrderStrategy::DPBackTracking_*> 
-+	std::vector<FPTBondOrderStrategy::DPBackTracking_*>
- 	FPTBondOrderStrategy::DPBackTrackingCombiner_::deepCopyOfBacktrackers_() const
- 	{
- 		std::vector<DPBackTracking_*> ts;
-@@ -2166,5 +2136,4 @@ namespace BALL
- 		return ts;
- 	}
- 
--
- }
-diff --git a/source/STRUCTURE/assignBondOrderProcessor.C b/source/STRUCTURE/assignBondOrderProcessor.C
-index f8acc4f..9863a54 100644
---- a/source/STRUCTURE/assignBondOrderProcessor.C
-+++ b/source/STRUCTURE/assignBondOrderProcessor.C
-@@ -108,6 +108,9 @@ namespace BALL
- 	const char* AssignBondOrderProcessor::Option::MAX_NUMBER_OF_SOLUTIONS = "max_number_of_solutions";
- 	const int  AssignBondOrderProcessor::Default::MAX_NUMBER_OF_SOLUTIONS = 10;
- 
-+	const char* AssignBondOrderProcessor::Option::MAX_PENALTY = "max_penalty_score";
-+	const int  AssignBondOrderProcessor::Default::MAX_PENALTY = -1;
-+
- 	const char* AssignBondOrderProcessor::Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS = "compute_also_non_optimal_solutions";
- 	const bool  AssignBondOrderProcessor::Default::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS = false;
- 
-@@ -148,6 +151,7 @@ namespace BALL
- 			max_bond_order_(),
- 			alpha_(),
- 			max_number_of_solutions_(),
-+			max_penalty_(-1),
- 			compute_also_non_optimal_solutions_(),
- 			add_missing_hydrogens_(),
- 			compute_also_connectivity_(),
-@@ -237,13 +241,14 @@ namespace BALL
- 			ret &= s_it->second->readOptions(options);
- 		}
- 
--		max_bond_order_ = options.getInteger(Option::MAX_BOND_ORDER);
--		alpha_ = options.getReal(Option::BOND_LENGTH_WEIGHTING);
--		max_number_of_solutions_ = options.getInteger(Option::MAX_NUMBER_OF_SOLUTIONS);
-+		max_bond_order_            = options.getInteger(Option::MAX_BOND_ORDER);
-+		alpha_                     = options.getReal(Option::BOND_LENGTH_WEIGHTING);
-+		max_number_of_solutions_   = options.getInteger(Option::MAX_NUMBER_OF_SOLUTIONS);
-+		max_penalty_               = options.getInteger(Option::MAX_PENALTY);
- 		compute_also_non_optimal_solutions_ = options.getBool(Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS);
--		add_missing_hydrogens_ = options.getBool(Option::ADD_HYDROGENS);
-+		add_missing_hydrogens_     = options.getBool(Option::ADD_HYDROGENS);
- 		compute_also_connectivity_ = options.getBool(Option::COMPUTE_ALSO_CONNECTIVITY);
--		use_fine_penalty_ = options.getBool(Option::USE_FINE_PENALTY);
-+		use_fine_penalty_          = options.getBool(Option::USE_FINE_PENALTY);
- 
- 		if (max_bond_order_ <= 0)
- 		{
-@@ -257,6 +262,12 @@ namespace BALL
- 				          << " : Error in options! Please check the option Option::MAX_NUMBER_OF_SOLUTIONS."  << endl;
- 			ret = false;
- 		}
-+		if (max_penalty_ < -1)
-+		{
-+			Log.error() << __FILE__ << " " << __LINE__
-+				          << " : Error in options! Please check the option Option::MAX_PENALTY."  << endl;
-+			ret = false;
-+		}
- 		if ((alpha_ < 0) || ((alpha_ > 1)))
- 		{
- 			Log.error() << __FILE__ << " " << __LINE__
-@@ -280,14 +291,13 @@ namespace BALL
- 						|| (options.getBool(Option::OVERWRITE_SELECTED_BONDS)  == true)
- 						|| (options.getBool(Option::OVERWRITE_SINGLE_BOND_ORDERS) == false)
- 						|| (options.getBool(Option::OVERWRITE_DOUBLE_BOND_ORDERS) == false)
--						|| (options.getBool(Option::OVERWRITE_TRIPLE_BOND_ORDERS) == false)
--						|| (options.getInteger(Option::MAX_NUMBER_OF_SOLUTIONS) == 0))
-+						|| (options.getBool(Option::OVERWRITE_TRIPLE_BOND_ORDERS) == false) )
- 			 )
- 		{
- 			Log.error() << __FILE__ << " " << __LINE__
- 				          << " : Error in options! FPT cannot be used with these options." << endl
--									<< " Switch to solution strategy ASTAR by setting Option::ALGORITHM to Algorithm::ASTAR." << endl;
--
-+									<< " Consider switch to solution strategy ASTAR by setting Option::ALGORITHM to Algorithm::ASTAR." << endl
-+									<< " Abort." << endl;
- 			ret = false;
- 		}
- 
-@@ -328,6 +338,7 @@ cout << " \t Penalty file " << options[Option::Option::INIFile] << endl;
- cout << " \t alpha: " << options[Option::BOND_LENGTH_WEIGHTING] << endl;
- cout << " \t max bond order: " << options[Option::MAX_BOND_ORDER] << endl;
- cout << " \t max number of solutions " << options[Option::MAX_NUMBER_OF_SOLUTIONS] << endl;
-+cout << " \t max penalty " << options[Option::MAX_PENALTY] << endl;
- cout << " \t compute also non-optimal solutions: " << options.getBool(Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS) << endl;
- cout << " \t compute also connectivity: " << options.getBool(Option::COMPUTE_ALSO_CONNECTIVITY) << endl;
- cout << " \t connectivity cutoff: " << options[Option::CONNECTIVITY_CUTOFF] << endl;
-@@ -354,7 +365,7 @@ cout << endl;
- 			// check the options
- 
- 			// What kind of composite do we have?
--			// Do we have a molecule? (Nothingelse is allowed)
-+			// Do we have a molecule? (Nothing else is allowed)
- 			if (RTTI::isKindOf<Molecule>(ac))
- 			{
- 				// Store the AtomContainer
-@@ -517,7 +528,7 @@ cout << "preassignPenaltyClasses_:" << preassignPenaltyClasses_() << " precomput
- #ifdef BALL_HAS_LPSOLVE
- 						strategy = strategies_["ILP"].get();
- #else
--						Log.error() << "Error: BALL was configured without lpsolve support! Try A_STAR instead!" <<
-+						Log.error() << "Error: BALL was configured without lpsolve support! Try A_STAR or FPT instead!" <<
- 												__FILE__ << " " << __LINE__<< std::endl;
- 
- 						return Processor::ABORT;
-@@ -552,16 +563,20 @@ cout << "preassignPenaltyClasses_:" << preassignPenaltyClasses_() << " precomput
- 						solutions_.push_back(*solution);
- 
- 						// Do we have to find more solutions?
--						bool found_another = true;
--						bool last_sol_is_optimal = true;
-+						bool found_another        = true;
-+						bool last_sol_is_optimal  = true;
-+						bool consider_max_penalty = (max_penalty_ > -1);
-+						double last_penalty       = getTotalPenalty(0);
- 
- 						while (    found_another
- 						        && ((getNumberOfComputedSolutions() < max_number_of_solutions_) || (!max_number_of_solutions_))
- 						        && (last_sol_is_optimal || (compute_also_non_optimal_solutions_))
-+										&& ((last_penalty <= max_penalty_) || (!consider_max_penalty))
- 						      )
- 						{
- 							found_another = computeNextSolution(options.getBool(Option::APPLY_FIRST_SOLUTION));
- 							last_sol_is_optimal &= (fabs(getTotalPenalty(0) - getTotalPenalty(solutions_.size()-1)) < 1.e-4);
-+							last_penalty  = getTotalPenalty(solutions_.size()-1);
- 						}
- #if defined DEBUG_TIMER		
- 					timer_.stop();
-@@ -1206,6 +1221,9 @@ cout << " ~~~~~~~~ added hydrogen dump ~~~~~~~~~~~~~~~~" << endl;
- 		options.setDefaultInteger(AssignBondOrderProcessor::Option::MAX_NUMBER_OF_SOLUTIONS,
- 		                          AssignBondOrderProcessor::Default::MAX_NUMBER_OF_SOLUTIONS);
- 
-+		options.setDefaultInteger(AssignBondOrderProcessor::Option::MAX_PENALTY,
-+		                          AssignBondOrderProcessor::Default::MAX_PENALTY);
-+
- 		options.setDefaultBool(AssignBondOrderProcessor::Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS,
- 		                       AssignBondOrderProcessor::Default::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS);
- 
diff --git a/sci-chemistry/ball/files/ball-1.4.1-Fix-compilation-of-FTPBondOrderStrategy-Fixes-451.patch b/sci-chemistry/ball/files/ball-1.4.1-Fix-compilation-of-FTPBondOrderStrategy-Fixes-451.patch
deleted file mode 100644
index 40b4b252fa48..000000000000
--- a/sci-chemistry/ball/files/ball-1.4.1-Fix-compilation-of-FTPBondOrderStrategy-Fixes-451.patch
+++ /dev/null
@@ -1,138 +0,0 @@
-From: Anna Dehof <anne@bioinf.uni-sb.de>
-Date: Fri, 8 Jun 2012 19:28:12 +0200
-Subject: Fix compilation of FTPBondOrderStrategy (Fixes #451)
-
-This patch is due to Daniel Stoeckel.
----
- source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C |   33 +++++++++++---------
- 1 file changed, 18 insertions(+), 15 deletions(-)
-
-diff --git a/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C b/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C
-index 6572d96..98adf98 100644
---- a/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C
-+++ b/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C
-@@ -322,7 +322,7 @@ namespace BALL
- 			}
- 		}
- 
--		return *best;
-+		return DPConstRow_(boost::reference_wrapper<DPConfig_ const>(best->first), best->second);
- 	}
- 
- 	FPTBondOrderStrategy::Penalty FPTBondOrderStrategy::DPTable_::operator[](FPTBondOrderStrategy::DPConfig_ const& config) const
-@@ -601,6 +601,9 @@ namespace BALL
- 
- 		return bonds;
- 	}
-+	
-+#define	convertToCRow(tmp)\
-+		std::make_pair(boost::reference_wrapper<const DPConfig_>((tmp).first), (tmp).second)
- 
- 	void FPTBondOrderStrategy::FPTBondOrderAssignment_::computeIntroduceBag(TreeDecompositionBag& bag, DPTable_& child,
- 	                                                                        AdditionalBagProperties_& property)
-@@ -621,7 +624,7 @@ namespace BALL
- 		// copy with n new bondvalue-columns with different values
- 		for (DPTable_::const_iterator iter = child.begin(); iter != child.end(); ++iter)
- 		{
--			DPConstRow_ child_entry = *iter;
-+			DPConstRow_ child_entry = convertToCRow(*iter);
- 			DPConfig_ conf(num_valences, num_bonds);
- 
- 			Size vindex = 0;
-@@ -786,7 +789,7 @@ namespace BALL
- 
- 		for (DPTable_::const_iterator entry_iterator = child.begin(); entry_iterator != child.end(); ++entry_iterator)
- 		{
--			Penalty entry_penalty(forgetInnerVertexIn(bag, *entry_iterator, new_entry, child_property.bonds, forgotten_index));
-+			Penalty entry_penalty(forgetInnerVertexIn(bag, convertToCRow(*entry_iterator), new_entry, child_property.bonds, forgotten_index));
- 			if (entry_penalty < upper_bound_)
- 			{
- 				property.table->insert(new_entry, entry_penalty);
-@@ -803,7 +806,7 @@ namespace BALL
- 		Penalty min_penalty = FPTBondOrderStrategy::infinite_penalty;
- 		for (DPTable_::const_iterator iter = child.begin(); iter != child.end(); ++iter)
- 		{
--			min_penalty = std::min(min_penalty, forgetInnerVertexIn(bag, *iter, empty, empty_list, 0));
-+			min_penalty = std::min(min_penalty, forgetInnerVertexIn(bag, convertToCRow(*iter), empty, empty_list, 0));
- 
- 			if (Maths::isEqual(0, min_penalty))
- 			{
-@@ -830,14 +833,14 @@ namespace BALL
- 		// insert each entry of the left child into a DPJoinMap
- 		for (DPTable_::const_iterator left_iter = left_child.begin(); left_iter != left_child.end(); ++left_iter)
- 		{
--			DPConstRow_ left_entry = *left_iter;
-+			DPConstRow_ left_entry = convertToCRow(*left_iter);
- 			map.insert(std::pair<DPConfig_ const*, Penalty> (left_entry.first.get_pointer(), left_entry.second));
- 		}
- 
- 		// find for each entry of the right child's table appropiate entries in the DPJoinMap (which have the same bondvalues)
- 		for (DPTable_::const_iterator r_iter = right_child.begin(); r_iter != right_child.end(); ++r_iter)
- 		{
--			DPConstRow_ right_entry = *r_iter;
-+			DPConstRow_ right_entry = convertToCRow(*r_iter);
- 			DPConfig_ const* right_conf = right_entry.first.get_pointer();
- 
- 			std::pair<DPJoinMap_::const_iterator, DPJoinMap_::const_iterator> matching_range(map.equal_range(right_conf));
-@@ -1602,7 +1605,7 @@ namespace BALL
- 		// insert possible antecessors in vectors
- 		for (DPTable_::const_iterator iter = left_table.begin(); iter != left_table.end(); ++iter)
- 		{
--			DPConstRow_ antecessor = *iter;
-+			DPConstRow_ antecessor = convertToCRow(*iter);
- 			if (comp.compare(&successor, antecessor.first.get_pointer()) == 0)
- 			{
- 				left_entries.push_back(iter);
-@@ -1611,7 +1614,7 @@ namespace BALL
- 
- 		for (DPTable_::const_iterator iter = right_table.begin(); iter != right_table.end(); ++iter)
- 		{
--			DPConstRow_ antecessor = *iter;
-+			DPConstRow_ antecessor = convertToCRow(*iter);
- 			if (comp.compare(&successor, antecessor.first.get_pointer()) == 0)
- 			{
- 				right_entries.push_back(iter);
-@@ -1623,10 +1626,10 @@ namespace BALL
- 
- 		for (std::vector<DPTable_::const_iterator>::const_iterator left = left_entries.begin(); left != left_entries.end(); ++left)
- 		{
--			DPConstRow_ left_entry = **left;
-+			DPConstRow_ left_entry = convertToCRow(**left);
- 			for (std::vector<DPTable_::const_iterator>::const_iterator right = right_entries.begin(); right != right_entries.end(); ++right)
- 			{
--				DPConstRow_ right_entry = **right;
-+				DPConstRow_ right_entry = convertToCRow(**right);
- 
- 				// check sum of valences
- 				bool correct_valences = true;
-@@ -1657,8 +1660,8 @@ namespace BALL
- 
- 		Penalty best_penalty = best.first->second + best.second->second;
- 
--		DPConstRow_ left  = *best.first;
--		DPConstRow_ right = *best.second;
-+		DPConstRow_ left  = convertToCRow(*best.first);
-+		DPConstRow_ right = convertToCRow(*best.second);
- 
- 		extendState(state, left.first, 0);
- 		++state.index;
-@@ -1668,8 +1671,8 @@ namespace BALL
- 		{
- 			DPPairIt_ entry = *iter;
- 
--			DPConstRow_ left  = *entry.first;
--			DPConstRow_ right = *entry.second;
-+			DPConstRow_ left  = convertToCRow(*entry.first);
-+			DPConstRow_ right = convertToCRow(*entry.second);
- 
- 			Penalty add_penalty = (left.second + right.second) - best_penalty;
- 			if (isSolutionNeeded(state.assignment.penalty + add_penalty))
-@@ -1720,7 +1723,7 @@ namespace BALL
- 		// check for each row entry: is it a possible anteccessor?
- 		for (DPTable_::iterator iter = table.begin(); iter != table.end(); ++iter)
- 		{
--			Penalty pen  = bond_assignment_->forgetInnerVertexIn(bag, *iter, test_entry, child_bonds, forgotten_index);
-+			Penalty pen  = bond_assignment_->forgetInnerVertexIn(bag, convertToCRow(*iter), test_entry, child_bonds, forgotten_index);
- 
- 			if (pen < FPTBondOrderStrategy::infinite_penalty && test_entry == successor)
- 			{
diff --git a/sci-chemistry/ball/files/ball-1.4.1-Fix-compilation-of-Python-bindings-with-new-sip-vers.patch b/sci-chemistry/ball/files/ball-1.4.1-Fix-compilation-of-Python-bindings-with-new-sip-vers.patch
deleted file mode 100644
index 38b3ba0dab1b..000000000000
--- a/sci-chemistry/ball/files/ball-1.4.1-Fix-compilation-of-Python-bindings-with-new-sip-vers.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-From: Andreas Hildebrandt <andreas.hildebrandt@uni-mainz.de>
-Date: Wed, 15 Aug 2012 00:12:49 +0200
-Subject: Fix compilation of Python bindings with new sip versions.
-
-For some reason, sip does not like static members of the same type as the class.
-In this case, a varget_... - method is generated with the wrong arguments
-(unnamed parameter which should be called "sipSelf"). This patch works around
-it.
----
- source/PYTHON/EXTENSIONS/BALL/PTE_.sip |    2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/source/PYTHON/EXTENSIONS/BALL/PTE_.sip b/source/PYTHON/EXTENSIONS/BALL/PTE_.sip
-index 4589e92..3e5f8ff 100644
---- a/source/PYTHON/EXTENSIONS/BALL/PTE_.sip
-+++ b/source/PYTHON/EXTENSIONS/BALL/PTE_.sip
-@@ -61,7 +61,7 @@ class Element
-    //friend ostream& operator << (ostream& s, const Element&);
-    bool isUnknown() const;
- 
--	 static Element UNKNOWN;
-+	 Element UNKNOWN;
-  };
- 
- class PTE_
diff --git a/sci-chemistry/ball/files/ball-1.4.1-Fixed-a-bug-in-the-AssignBondOrderProcessor.patch b/sci-chemistry/ball/files/ball-1.4.1-Fixed-a-bug-in-the-AssignBondOrderProcessor.patch
deleted file mode 100644
index 813c9369bdac..000000000000
--- a/sci-chemistry/ball/files/ball-1.4.1-Fixed-a-bug-in-the-AssignBondOrderProcessor.patch
+++ /dev/null
@@ -1,271 +0,0 @@
-From: Anna Dehof <anne@bioinf.uni-sb.de>
-Date: Fri, 27 Apr 2012 18:41:52 +0200
-Subject: Fixed a bug in the AssignBondOrderProcessor
-
----
- .../STRUCTURE/BONDORDERS/bondOrderAssignment.h     |    2 +-
- source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C |   13 +++--
- source/STRUCTURE/assignBondOrderProcessor.C        |   27 +++++++----
- source/TEST/AssignBondOrderProcessor_test.C        |   50 +++++++++++++++-----
- 4 files changed, 67 insertions(+), 25 deletions(-)
-
-diff --git a/include/BALL/STRUCTURE/BONDORDERS/bondOrderAssignment.h b/include/BALL/STRUCTURE/BONDORDERS/bondOrderAssignment.h
-index 57adc41..f8aab75 100644
---- a/include/BALL/STRUCTURE/BONDORDERS/bondOrderAssignment.h
-+++ b/include/BALL/STRUCTURE/BONDORDERS/bondOrderAssignment.h
-@@ -68,7 +68,7 @@ namespace BALL
- 			float total_charge;
- 			int node_expansions;
- 			int queue_size;
--			
-+
- 			AtomContainer* ac;
- 	};
- }
-diff --git a/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C b/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C
-index 107823e..6572d96 100644
---- a/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C
-+++ b/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C
-@@ -108,7 +108,8 @@ namespace BALL
- 		}
- 		else
- 		{
--		/*	Log.info() << "AssignBondOrderProcessor: strategy FPT does not support computeNextSolution(). " << endl
-+			// since we return a pointer, nothing to do here
-+			/*	Log.info() << "AssignBondOrderProcessor: strategy FPT does not support computeNextSolution(). " << endl
- 								 << "Please use the options Option::MAX_NUMBER_OF_SOLUTIONS or Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS " << endl
- 								 << "to compute additional solutions." << endl; */
- 		}
-@@ -1429,12 +1430,12 @@ namespace BALL
- 
- 	bool FPTBondOrderStrategy::DPBackTracking_::hasMoreSolutions() const
- 	{
--		return (!queue_.empty() && (!max_num_solutions_ || (num_computed_solutions_ <= max_num_solutions_)));
-+		return (!queue_.empty() && (!max_num_solutions_ || (num_computed_solutions_ < max_num_solutions_)));
- 	}
- 
- 	void FPTBondOrderStrategy::DPBackTracking_::nextSolution()
- 	{
--		if (queue_.empty() || max_heap_size_ == 0 || ((max_num_solutions_ > 0) && (num_computed_solutions_ > max_num_solutions_)))
-+		if (queue_.empty() || (max_heap_size_ == 0) || ((max_num_solutions_ > 0) && (num_computed_solutions_ > max_num_solutions_)))
- 		{
- 			throw Exception::OutOfRange(__FILE__, __LINE__);
- 		}
-@@ -1987,7 +1988,9 @@ namespace BALL
- 
- 	bool FPTBondOrderStrategy::DPBackTrackingCombiner_::hasMoreSolutions() const
- 	{
--		return (!priority_queue_.empty() || (getNextMinimumBackTracker_().second) < upper_bound_);
-+		std::pair<Size, Penalty> next_min = getNextMinimumBackTracker_();
-+
-+		return (backtrackers_[next_min.first]->hasMoreSolutions() && (!priority_queue_.empty() || (next_min.second) < upper_bound_));
- 	}
- 
- 	void FPTBondOrderStrategy::DPBackTrackingCombiner_::nextSolution()
-@@ -2014,7 +2017,7 @@ namespace BALL
- 		// compute next minimal Solution
- 		std::pair<Size, Penalty> next_min = getNextMinimumBackTracker_();
- 
--		if (next_min.second < upper_bound_ && (priority_queue_.empty() || next_min.second < priority_queue_.top().penalty))
-+		if ((next_min.second < upper_bound_) && (priority_queue_.empty() || (next_min.second < priority_queue_.top().penalty)))
- 		{
- 			DPBackTracking_& min_back_tracker = *backtrackers_[next_min.first];
- 
-diff --git a/source/STRUCTURE/assignBondOrderProcessor.C b/source/STRUCTURE/assignBondOrderProcessor.C
-index 9863a54..9443fb8 100644
---- a/source/STRUCTURE/assignBondOrderProcessor.C
-+++ b/source/STRUCTURE/assignBondOrderProcessor.C
-@@ -295,8 +295,20 @@ namespace BALL
- 			 )
- 		{
- 			Log.error() << __FILE__ << " " << __LINE__
--				          << " : Error in options! FPT cannot be used with these options." << endl
--									<< " Consider switch to solution strategy ASTAR by setting Option::ALGORITHM to Algorithm::ASTAR." << endl
-+				          << " : Error in options! FPT cannot be used with these option(s): ";
-+			if (options.getReal(Option::BOND_LENGTH_WEIGHTING) > 0.)
-+				Log.error() << "BOND_LENGTH_WEIGHTING ";
-+			if (options.getBool(Option::ADD_HYDROGENS))
-+				Log.error() << "ADD_HYDROGENS ";
-+			if (options.getBool(Option::COMPUTE_ALSO_CONNECTIVITY))
-+				Log.error() << "COMPUTE_ALSO_CONNECTIVITY ";
-+			if (options.getBool(Option::OVERWRITE_SELECTED_BONDS))
-+				Log.error() << "OVERWRITE_SELECTED_BONDS ";
-+			if (!options.getBool(Option::OVERWRITE_SINGLE_BOND_ORDERS))
-+				Log.error() << "OVERWRITE_SINGLE_BOND_ORDERS ";
-+			Log.error() << endl;
-+
-+			Log.error() << " Consider switch to solution strategy ASTAR by setting Option::ALGORITHM to Algorithm::ASTAR." << endl
- 									<< " Abort." << endl;
- 			ret = false;
- 		}
-@@ -321,8 +333,8 @@ namespace BALL
- 
- #ifdef DEBUG 
- cout << "  OPTIONS:" << endl;
--cout << " \t Algorithm: " <<  options[Option::Option::ALGORITHM] << endl;
--cout << " \t Heuristic: " <<  options[Option::Option::HEURISTIC] << endl;
-+cout << " \t Algorithm: " <<  options[Option::ALGORITHM] << endl;
-+cout << " \t Heuristic: " <<  options[Option::HEURISTIC] << endl;
- 
- cout << " \t Overwrite bonds (single, double, triple, selected):"
- 		 << options.getBool(Option::OVERWRITE_SINGLE_BOND_ORDERS) << " "
-@@ -334,7 +346,7 @@ cout << " \t Overwrite bonds (single, double, triple, selected):"
- cout << " \t Add hydrogens : " << options.getBool(Option::ADD_HYDROGENS) << endl;
- cout << " \t Use fine penalty : " << options.getBool(Option::USE_FINE_PENALTY) << endl;
- cout << " \t Kekulizer: " << options.getBool(Option::KEKULIZE_RINGS)  << endl;
--cout << " \t Penalty file " << options[Option::Option::INIFile] << endl;
-+cout << " \t Penalty file " << options[Option::INIFile] << endl;
- cout << " \t alpha: " << options[Option::BOND_LENGTH_WEIGHTING] << endl;
- cout << " \t max bond order: " << options[Option::MAX_BOND_ORDER] << endl;
- cout << " \t max number of solutions " << options[Option::MAX_NUMBER_OF_SOLUTIONS] << endl;
-@@ -549,7 +561,7 @@ cout << "preassignPenaltyClasses_:" << preassignPenaltyClasses_() << " precomput
- 					boost::shared_ptr<BondOrderAssignment> solution = strategy->computeNextSolution();
- 
- 					// Do we have a solution? 
--					if (!solution)
-+					if (!solution || !solution->valid)
- 					{
- 						Log.info() << "AssignBondOrderProcessor: No valid bond order assignment found!" << endl;
- #if defined DEBUG_TIMER					
-@@ -1237,7 +1249,6 @@ cout << " ~~~~~~~~ added hydrogen dump ~~~~~~~~~~~~~~~~" << endl;
- 		                       AssignBondOrderProcessor::Default::APPLY_FIRST_SOLUTION);
- 	}
- 
--
- 	bool AssignBondOrderProcessor::apply(Position i)
- 	{
- 		bool result = false;
-@@ -1370,7 +1381,7 @@ cout << " ~~~~~~~~ added hydrogen dump ~~~~~~~~~~~~~~~~" << endl;
- 
- 		boost::shared_ptr<BondOrderAssignment> solution = strategy->computeNextSolution();
- 
--		if (solution)
-+		if (solution && solution->valid)
- 		{
- 			solutions_.push_back(*solution);
- 			found_a_sol = true;
-diff --git a/source/TEST/AssignBondOrderProcessor_test.C b/source/TEST/AssignBondOrderProcessor_test.C
-index 6dfafcc..fdf92d1 100644
---- a/source/TEST/AssignBondOrderProcessor_test.C
-+++ b/source/TEST/AssignBondOrderProcessor_test.C
-@@ -201,6 +201,8 @@ RESULT
- 
- 
- CHECK(check Options for consistency)
-+	Log.error().disableOutput();
-+
- 	AssignBondOrderProcessor testbop;
- 	testbop.setDefaultOptions();
- 	TEST_EQUAL(testbop.hasValidOptions(), true)
-@@ -208,21 +210,17 @@ CHECK(check Options for consistency)
- 	testbop.setDefaultOptions();
- 	testbop.options.set(AssignBondOrderProcessor::Option::ALGORITHM, AssignBondOrderProcessor::Algorithm::FPT);
- 	testbop.options.set(AssignBondOrderProcessor::Option::ADD_HYDROGENS, true);
--
- 	TEST_EQUAL(testbop.hasValidOptions(), false)
- 
- 	testbop.setDefaultOptions();
- 	testbop.options.set(AssignBondOrderProcessor::Option::ALGORITHM, AssignBondOrderProcessor::Algorithm::FPT);
- 	testbop.options.set(AssignBondOrderProcessor::Option::OVERWRITE_SELECTED_BONDS, true);
--
- 	TEST_EQUAL(testbop.hasValidOptions(), false)
- 
- 	testbop.setDefaultOptions();
- 	testbop.options.set(AssignBondOrderProcessor::Option::ALGORITHM, AssignBondOrderProcessor::Algorithm::FPT);
- 	testbop.options.set(AssignBondOrderProcessor::Option::MAX_NUMBER_OF_SOLUTIONS, 0);
--
--	TEST_EQUAL(testbop.hasValidOptions(), false)
--
-+	TEST_EQUAL(testbop.hasValidOptions(), true)
- 
- 	testbop.setDefaultOptions();
- 	testbop.options.set(AssignBondOrderProcessor::Option::ALGORITHM, AssignBondOrderProcessor::Algorithm::FPT);
-@@ -230,9 +228,8 @@ CHECK(check Options for consistency)
- 	testbop.options.set(AssignBondOrderProcessor::Option::OVERWRITE_SINGLE_BOND_ORDERS, true);
- 	testbop.options.set(AssignBondOrderProcessor::Option::COMPUTE_ALSO_CONNECTIVITY, true);
- 	testbop.options.set(AssignBondOrderProcessor::Option::MAX_NUMBER_OF_SOLUTIONS, 0);
--
- 	TEST_EQUAL(testbop.hasValidOptions(), false)
--
-+	Log.error().enableOutput();
- RESULT
- 
- ///////////////////////  ALGORITHMS     //////////////////////
-@@ -841,10 +838,11 @@ CHECK(getTotalPenalty(Position i) and operator() FPT single solution)
- 	System sys2;
- 	MOL2File mol_in2(BALL_TEST_DATA_PATH(AssignBondOrderProcessor_test_AN06.mol2), std::ios::in);
- 	mol_in2 >> sys2;
-+	TEST_EQUAL(testbop.getNumberOfComputedSolutions(), 10)
-+
- 	sys2.apply(testbop);
- 	TEST_REAL_EQUAL(testbop.getTotalPenalty(0), 2.f)//0.00625) 
- 
--
- 	System sys3;
- 	MOL2File mol_in3(BALL_TEST_DATA_PATH(AssignBondOrderProcessor_test_BEWCUB.mol2), std::ios::in);
- 	mol_in3 >> sys3;
-@@ -856,6 +854,7 @@ CHECK(getTotalPenalty(Position i) and operator() FPT single solution)
- 	MOL2File mol15(BALL_TEST_DATA_PATH(AssignBondOrderProcessor_test_CUDJAM_sol_5.mol2), std::ios::in);
- 	mol15 >> sys15;
- 	sys15.apply(testbop);
-+
- 	TEST_REAL_EQUAL(testbop.getTotalPenalty(1), 2.f ) //0.0015528 )
- 	TEST_REAL_EQUAL(testbop.getTotalPenalty(2), 5.f ) //0.00388199)
- 	TEST_REAL_EQUAL(testbop.getTotalPenalty(3), 7.f ) //0.00543478)
-@@ -904,6 +903,34 @@ CHECK(getTotalPenalty(Position i) and operator() FPT single solution)
- 
- RESULT
- 
-+CHECK(operator() FPT vs A*)
-+	AssignBondOrderProcessor testbop_a;
-+	testbop_a.options.set(AssignBondOrderProcessor::Option::ALGORITHM,AssignBondOrderProcessor::Algorithm::A_STAR);
-+	testbop_a.options.setBool(AssignBondOrderProcessor::Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS, true);
-+
-+	AssignBondOrderProcessor testbop_fpt;
-+	testbop_fpt.options.set(AssignBondOrderProcessor::Option::ALGORITHM,AssignBondOrderProcessor::Algorithm::FPT);
-+	testbop_fpt.options.setBool(AssignBondOrderProcessor::Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS, true);
-+
-+	System sys4;
-+	MOL2File mol4(BALL_TEST_DATA_PATH(AssignBondOrderProcessor_test_CITSED10_sol_6.mol2), std::ios::in);
-+	mol4 >> sys4;
-+	sys4.apply(testbop_a);
-+	sys4.apply(testbop_fpt);
-+	TEST_REAL_EQUAL(testbop_a.getNumberOfComputedSolutions(), testbop_fpt.getNumberOfComputedSolutions())
-+
-+	TEST_REAL_EQUAL(testbop_a.getTotalPenalty(0), testbop_fpt.getTotalPenalty(0)) //1.f )
-+	TEST_REAL_EQUAL(testbop_a.getTotalPenalty(1), testbop_fpt.getTotalPenalty(1)) //1.f )
-+	TEST_REAL_EQUAL(testbop_a.getTotalPenalty(2), testbop_fpt.getTotalPenalty(2)) //32.f)
-+	TEST_REAL_EQUAL(testbop_a.getTotalPenalty(3), testbop_fpt.getTotalPenalty(3)) //34.f)
-+	TEST_REAL_EQUAL(testbop_a.getTotalPenalty(4), testbop_fpt.getTotalPenalty(4)) //34.f)
-+	TEST_REAL_EQUAL(testbop_a.getTotalPenalty(5), testbop_fpt.getTotalPenalty(5)) //34.f)
-+	TEST_REAL_EQUAL(testbop_a.getTotalPenalty(6), testbop_fpt.getTotalPenalty(6)) //66.f)
-+	TEST_REAL_EQUAL(testbop_a.getTotalPenalty(7), testbop_fpt.getTotalPenalty(7)) //66.f)
-+	TEST_REAL_EQUAL(testbop_a.getTotalPenalty(8), testbop_fpt.getTotalPenalty(8)) //67.f)
-+
-+RESULT
-+
- 
- CHECK(getTotalCharge(Position i))
- 	// This feature is experimental!! 
-@@ -1023,7 +1050,7 @@ CHECK(computeNextSolution() using ILP)
- 	MOL2File mol_in(BALL_TEST_DATA_PATH(AssignBondOrderProcessor_test_AN06.mol2), std::ios::in);
- 	mol_in >> sys;
- 	sys.apply(testbop);
--	TEST_EQUAL(testbop.getNumberOfComputedSolutions(),1)
-+	TEST_EQUAL(testbop.getNumberOfComputedSolutions(), 1)
- 	TEST_REAL_EQUAL(testbop.getTotalPenalty(0), 2.f)//0.00625)// 2.)
- 	TEST_EQUAL(testbop.computeNextSolution(), true)
- 	TEST_REAL_EQUAL(testbop.getTotalPenalty(1), 32.f)//0.1)//32.)
-@@ -1091,9 +1118,10 @@ CHECK(computeNextSolution() using FPT)
- 	MOL2File mol_in(BALL_TEST_DATA_PATH(AssignBondOrderProcessor_test_AN06.mol2), std::ios::in);
- 	mol_in >> sys;
- 	sys.apply(testbop);
--	TEST_EQUAL(testbop.getNumberOfComputedSolutions(),1)
-+	TEST_EQUAL(testbop.getNumberOfComputedSolutions(), 1)
- 	TEST_REAL_EQUAL(testbop.getTotalPenalty(0), 2.f)//0.00625)// 2.)
--	TEST_EQUAL(testbop.computeNextSolution(), false)
-+	bool test = testbop.computeNextSolution();
-+	TEST_EQUAL(test, false)
- 
- RESULT
- 
diff --git a/sci-chemistry/ball/files/ball-1.4.1-Fixed-the-FPT-version-of-bond-order-assignment-2.patch b/sci-chemistry/ball/files/ball-1.4.1-Fixed-the-FPT-version-of-bond-order-assignment-2.patch
deleted file mode 100644
index c5d3fddb1b89..000000000000
--- a/sci-chemistry/ball/files/ball-1.4.1-Fixed-the-FPT-version-of-bond-order-assignment-2.patch
+++ /dev/null
@@ -1,444 +0,0 @@
- include/BALL/DATATYPE/GRAPH/graphAlgorithms.h      |   7 +-
- include/BALL/DATATYPE/GRAPH/treeWidth.h            |  44 ++++++-
- include/BALL/DATATYPE/GRAPH/treeWidth.iC           | 145 +++++++++++++--------
- source/DATATYPE/GRAPH/treeWidth.C                  |  24 ++++
- source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C |  12 +-
- 5 files changed, 161 insertions(+), 71 deletions(-)
-
-diff --git a/include/BALL/DATATYPE/GRAPH/graphAlgorithms.h b/include/BALL/DATATYPE/GRAPH/graphAlgorithms.h
-index d10de34..5e218ff 100644
---- a/include/BALL/DATATYPE/GRAPH/graphAlgorithms.h
-+++ b/include/BALL/DATATYPE/GRAPH/graphAlgorithms.h
-@@ -25,7 +25,7 @@ namespace boost
- 	enum vertex_orig_ptr_t { vertex_orig_ptr };
- 
- 	enum edge_bond_ptr_t { edge_bond_ptr };
--	enum edge_orig_ptr_t   { edge_orig_ptr   };
-+	enum edge_orig_ptr_t { edge_orig_ptr   };
- 
- 	BOOST_INSTALL_PROPERTY(vertex, atom_ptr);
- 	BOOST_INSTALL_PROPERTY(vertex, orig_ptr);
-@@ -150,7 +150,7 @@ namespace BALL
- 			{
- 				bi = ai; ++bi;
- 				for (; bi != ai_end; ++bi)
--					if (!boost::edge(*ai, *bi, graph).second)
-+					if (*bi != *ai && !boost::edge(*ai, *bi, graph).second)
- 						boost::add_edge(*ai, *bi, graph);
- 			}
- 
-@@ -179,7 +179,6 @@ namespace BALL
- 
- 				typedef typename boost::property_traits<typename boost::property_map<UndirectedGraph, boost::edge_all_t>::type>::value_type EdgeProperties;
- 				
--				EdgeProperties ep = boost::get(boost::edge_all_t(), graph, boost::edge(vertex, *ai, graph).first) ;
- 				result.getEdgeProperties().push_back(boost::get(boost::edge_all_t(), graph, boost::edge(vertex, *ai, graph).first));
- 
- 				bi = ai; ++bi;
-@@ -189,7 +188,7 @@ namespace BALL
- 					{
- 						boost::add_edge(*ai, *bi, graph);
- 						result.getEdges().push_back(std::make_pair(boost::get(boost::vertex_index, graph, *ai),
--						                                                     boost::get(boost::vertex_index, graph, *bi)));
-+						                                                      boost::get(boost::vertex_index, graph, *bi)));
- 					}
- 				}
- 			}
-diff --git a/include/BALL/DATATYPE/GRAPH/treeWidth.h b/include/BALL/DATATYPE/GRAPH/treeWidth.h
-index dc7cdc5..f7687ef 100644
---- a/include/BALL/DATATYPE/GRAPH/treeWidth.h
-+++ b/include/BALL/DATATYPE/GRAPH/treeWidth.h
-@@ -30,10 +30,12 @@
- #include <map>
- #include <set>
- #include <vector>
-+#include <iostream>
- 
- #include <boost/graph/connected_components.hpp>
- #include <boost/graph/filtered_graph.hpp>
- #include <boost/graph/graph_as_tree.hpp>
-+#include <boost/graph/graphviz.hpp>
- #include <boost/graph/copy.hpp>
- 
- namespace boost
-@@ -91,7 +93,7 @@ namespace BALL
- 				END_BAG
- 			};
- 
--			typedef typename GRAPH::GraphTraits<UndirectedGraph>::EditableGraph EditableGraph;
-+			typedef typename GRAPH::GraphTraits<UndirectedGraph>::EditableGraph      EditableGraph;
- 			typedef typename boost::graph_traits<UndirectedGraph>::vertex_descriptor OriginalVertexType;
- 
- 			typedef std::set<OriginalVertexType> TreeDecompositionContent;
-@@ -111,6 +113,16 @@ namespace BALL
- 
- 			TreeWidth(UndirectedGraph const& input);
- 
-+			/** Compute the tree width of a given tree decomposition.
-+			 *  This function iterates over all nodes in the graph to determine the tree width,
-+			 *  i.e., the (maximum number of vertices over all bags) - 1 
-+			 */
-+			static Size computeTreeWidth(TreeDecomposition const& td);
-+
-+			/** Write a tree decomposition in graphviz format.
-+			 */
-+			void writeGraphvizFile(std::ostream& out, TreeDecomposition const& td);
-+
- 			std::vector<boost::shared_ptr<EditableGraph> >& getComponents() { return components_; }
- 			std::vector<boost::shared_ptr<TreeDecomposition> >& getNiceTreeDecompositions()   { return nice_tree_decompositions_; }
- 
-@@ -120,25 +132,44 @@ namespace BALL
- 			{
- 				public:
- 					ComponentFilter_(ComponentMap cm, Position i) 
--						: cm_(&cm),
-+						: cm_(cm),
- 							component_(i)
- 					{ }
- 
- 					template <typename Vertex>
- 					bool operator() (const Vertex& e) const 
- 					{
--						return ((*cm_)[e] == component_);
-+						return ((cm_)[e] == component_);
- 					}
- 
- 				protected:
--					ComponentMap* cm_;
-+					ComponentMap  cm_;
- 					Position      component_;	
- 			};
- 
-+			/** PropertyWriter for graphviz output.
-+			 */
-+			class BagContentWriter 
-+			{
-+				public:
-+					BagContentWriter(TreeDecomposition const* td, UndirectedGraph const* original_graph)
-+					  : td_(td),
-+						  original_graph_(original_graph)
-+					{ }
-+
-+					void operator() (std::ostream& out, const TreeDecompositionBag& v) const;
-+
-+				protected:
-+					TreeDecomposition const* td_;
-+					UndirectedGraph   const* original_graph_;
-+			};
-+
-+			// TODO: would UndirectedGraph suffice here?
- 			MolecularGraph const* input_;
-+
- 			std::vector<boost::shared_ptr<EditableGraph> > components_; 
- 
--			std::vector<boost::shared_ptr<TreeDecomposition> >    nice_tree_decompositions_;
-+			std::vector<boost::shared_ptr<TreeDecomposition> >      nice_tree_decompositions_;
- 			std::vector<boost::shared_ptr<TreeDecompositionGraph> > nice_tree_decomposition_graphs_;
- 	};
- 
-@@ -397,6 +428,9 @@ namespace BALL
- 				 * The bitset remembers the eliminated vertices without an ordering.
- 				 */
- 				BitSet buildBitset() const;
-+
-+			protected:
-+				std::map<int, VertexType> index_to_vertex_;
- 		};
- 
- 		/**
-diff --git a/include/BALL/DATATYPE/GRAPH/treeWidth.iC b/include/BALL/DATATYPE/GRAPH/treeWidth.iC
-index 633e588..99f14cf 100644
---- a/include/BALL/DATATYPE/GRAPH/treeWidth.iC
-+++ b/include/BALL/DATATYPE/GRAPH/treeWidth.iC
-@@ -68,6 +68,34 @@ namespace BALL
- 		}
- 	}
- 
-+	template <class UndirectedGraph>
-+	Size TreeWidth<UndirectedGraph>::computeTreeWidth(TreeDecomposition const& td)
-+	{
-+		Size result = 1;
-+
-+		BGL_FORALL_VERTICES_T(current_vertex, td._g, UndirectedGraph)
-+		{
-+			result = std::max((Size)(boost::get(boost::vertex_bag_content, td, current_vertex).size()), result);
-+		}
-+
-+		return result - 1;
-+	}
-+
-+	template <class UndirectedGraph>
-+	void TreeWidth<UndirectedGraph>::writeGraphvizFile(std::ostream& out, TreeDecomposition const& td)
-+	{
-+		boost::write_graphviz(out, td._g, BagContentWriter(&td, input_));
-+	}
-+
-+	template <>
-+	void TreeWidth<MolecularGraph>::BagContentWriter::operator() (std::ostream& out, const TreeDecompositionBag& v) const;
-+
-+	template <class UndirectedGraph>
-+	void TreeWidth<UndirectedGraph>::BagContentWriter::operator() (std::ostream& out, const TreeDecompositionBag& v) const
-+	{
-+		out << "[label=\"" << boost::get(boost::vertex_index, *td_, v) << "\"]";
-+	}
-+
- 	// *****************************************************************************************
- 	// * TreeWidthImplementation                                                               *
- 	// *****************************************************************************************
-@@ -322,8 +350,9 @@ namespace BALL
- 		if (boost::out_degree(vertex, graph_) <= 1)
- 			return IS_SIMPLICIAL;
- 
--		VertexType* n1 = NULL;
--		VertexType* n2 = NULL;
-+		VertexType n1 = VertexType();
-+		VertexType n2 = VertexType();
-+		bool found_unconnected = false;
- 
- 		typename boost::graph_traits<UndirectedGraph>::adjacency_iterator a_i, a_j, ai_end;
- 
-@@ -337,20 +366,21 @@ namespace BALL
- 
- 				if (!boost::edge(i, j, graph_).second)
- 				{
--					if (!n1)
-+					if (!found_unconnected)
- 					{
--						n1 = &i;
--						n2 = &j;
-+						n1 = i;
-+						n2 = j;
-+						found_unconnected = true;
- 					} 
--					else if (i == *n1 || i == *n2)
-+					else if (i == n1 || i == n2)
- 					{
--						n1 = &i;
--						n2 = &i;
-+						n1 = i;
-+						n2 = i;
- 					} 
--					else if (j == *n1 || j == *n2)
-+					else if (j == n1 || j == n2)
- 					{
--						n1 = &j;
--						n2 = &j;
-+						n1 = j;
-+						n2 = j;
- 					} 
- 					else
- 					{
-@@ -376,11 +406,10 @@ namespace BALL
- 	{
- 		Size nxt = cstate.permutation.size();
- 
--		std::map<int, VertexType> index_to_vertex;
- 		BGL_FORALL_VERTICES_T(current_vertex, graph_, UndirectedGraph)
- 		{
- 			Size index = boost::get(boost::vertex_index, graph_, current_vertex);
--			index_to_vertex[index] = current_vertex;
-+			index_to_vertex_[index] = current_vertex;
- 			SIMPLICIAL_TYPE simplicial(isSimplicial(current_vertex));
- 			if (simplicial == IS_SIMPLICIAL || simplicial == ALMOST_SIMPLICIAL)
- 			{
-@@ -388,14 +417,13 @@ namespace BALL
- 			}
- 		}
- 
--	
--		for (typename std::vector<Size>::const_iterator st_iter = cstate.permutation.begin() + nxt; 
--				st_iter != cstate.permutation.end(); ++st_iter)
-+		for (typename std::vector<Size>::const_iterator st_iter  = cstate.permutation.begin() + nxt; 
-+				                                            st_iter != cstate.permutation.end(); 
-+																										++st_iter)
- 		{
--			VertexType vertex = index_to_vertex[*st_iter];
-+			VertexType vertex = index_to_vertex_[*st_iter];
- 			cstate.g = std::max(cstate.g, (Size)boost::out_degree(vertex, graph_));
- 			cstate.f = std::max(cstate.f, cstate.g);
--
- 			GRAPH::eliminateVertex(vertex, graph_);
- 		}
- 	}
-@@ -459,55 +487,62 @@ namespace BALL
- 			{
- 				upper_bound = nstate.f;
- 				state.permutation = nstate.permutation;
--				state.permutation.push_back(0);
-+				BGL_FORALL_VERTICES_T(v, graph_, UndirectedGraph) // yes, it is only one, but still...
-+				{
-+					state.permutation.push_back(boost::get(boost::vertex_index, graph_, v));
-+				}
- 			}
- 		} 
- 		else
- 		{
--			std::map<int, VertexType> index_to_vertex;
-+			index_to_vertex_.clear();
- 			BGL_FORALL_VERTICES_T(v, graph_, UndirectedGraph)
- 			{
--				index_to_vertex[boost::get(boost::vertex_index, graph_, v)] = v;
-+				index_to_vertex_[boost::get(boost::vertex_index, graph_, v)] = v;
- 			}
- 
- 			for (typename std::vector<Size>::iterator viter = greedy_solution.first.begin(); 
- 					viter != greedy_solution.first.end(); ++viter)
- 			{
--				VertexType& vertex = index_to_vertex[*viter];
--				Size degree = boost::out_degree(vertex, graph_);
--
--				GRAPH::UndoEliminateOperation<UndirectedGraph> elimination(graph_, vertex);
--
--				QuickBBState xstate(nstate);
--				xstate.g = std::max(nstate.g, degree);
--				xstate.permutation.push_back(boost::get(boost::vertex_index, graph_, vertex));
--
--				BitSet bitset(buildBitset());
--
--				Size lower_bound = L()(graph_);
--				xstate.h = lower_bound;
--				xstate.f = max(xstate.g, lower_bound);
--
--				if (xstate.f >= upper_bound)
--				{
--					elimination.undo();
--
--					continue;
--				}
--
--				MapPos entry(visitedSubgraphs.insert(MapEntry(bitset, xstate.f)));
--
--				if (entry.second)
--				{
--					branchAndBound(xstate);
--				} 
--				else if ((entry.first)->second > xstate.f)
-+				if (index_to_vertex_.find(*viter) != index_to_vertex_.end())
- 				{
--					entry.first->second = xstate.f;
--					branchAndBound(xstate);
-+					VertexType& vertex = index_to_vertex_[*viter];
-+					Size degree = boost::out_degree(vertex, graph_);
-+
-+					GRAPH::UndoEliminateOperation<UndirectedGraph> elimination = GRAPH::eliminateVertexUndoable(vertex, graph_);
-+
-+					QuickBBState xstate(nstate);
-+					xstate.g = std::max(nstate.g, degree);
-+					xstate.permutation.push_back(*viter);
-+
-+					BitSet bitset(buildBitset());
-+
-+					Size lower_bound = L()(graph_);
-+					xstate.h = lower_bound;
-+					xstate.f = max(xstate.g, lower_bound);
-+
-+					if (xstate.f >= upper_bound)
-+					{
-+						VertexType vertex_replace = elimination.undo();
-+						index_to_vertex_[*viter] = vertex_replace;
-+						continue;
-+					}
-+
-+					MapPos entry(visitedSubgraphs.insert(MapEntry(bitset, xstate.f)));
-+
-+					if (entry.second)
-+					{
-+						branchAndBound(xstate);
-+					} 
-+					else if ((entry.first)->second > xstate.f)
-+					{
-+						entry.first->second = xstate.f;
-+						branchAndBound(xstate);
-+					}
-+
-+					VertexType vertex_replace = elimination.undo();
-+					index_to_vertex_[*viter] = vertex_replace;
- 				}
--
--				elimination.undo();
- 			}
- 		}
- 	}
-@@ -687,7 +722,7 @@ namespace BALL
- 	typename TreeWidth<OriginalGraphType>::TreeDecompositionBag
- 	TreeWidthImplementation<UndirectedGraph>::TreeDecompositionBuilder<OriginalGraphType>::buildRoot_(TreeDecompositionBag child)
- 	{
--		TreeDecompositionBag last_vertex;
-+		TreeDecompositionBag last_vertex = TreeDecompositionBag();
- 
-     TreeDecompositionContent content = boost::get(boost::vertex_bag_content, *nice_tree_, child);
- 
-diff --git a/source/DATATYPE/GRAPH/treeWidth.C b/source/DATATYPE/GRAPH/treeWidth.C
-index 981605d..7485305 100644
---- a/source/DATATYPE/GRAPH/treeWidth.C
-+++ b/source/DATATYPE/GRAPH/treeWidth.C
-@@ -1 +1,25 @@
- #include <BALL/DATATYPE/GRAPH/treeWidth.h>
-+
-+#include <BALL/KERNEL/atom.h>
-+
-+namespace BALL
-+{
-+	template <>
-+	void TreeWidth<MolecularGraph>::BagContentWriter::operator() (std::ostream& out, const TreeDecompositionBag& v) const
-+	{
-+		out << "[label=\"";
-+
-+		// find all vertices in the current bag
-+		TreeDecompositionContent content = boost::get(boost::vertex_bag_content, *td_, v);
-+
-+		for (typename TreeDecompositionContent::const_iterator tdc_it = content.begin(); tdc_it != content.end(); ++tdc_it)
-+		{
-+			TreeWidth<MolecularGraph>::OriginalVertexType ov = *tdc_it;
-+			Atom const* atom = boost::get(boost::vertex_atom_ptr, *original_graph_, ov);
-+
-+			out << atom->getFullName() << " (" << atom << ") " << "\\n";
-+		}
-+
-+		out << "\"]";
-+	}
-+}
-diff --git a/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C b/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C
-index 4f872ae..c708535 100644
---- a/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C
-+++ b/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C
-@@ -68,7 +68,7 @@ namespace BALL
- 		for (Position i = 0; i < ntds.size(); ++i)
- 		{
- 			bond_assignments.push_back(new FPTBondOrderAssignment_(*this, ntds[i], upper_bound_));
--		  Penalty result = bond_assignments[i]->compute();
-+		  bond_assignments[i]->compute();
- 		}
- 
- 		// initialize backtracking
-@@ -650,8 +650,8 @@ namespace BALL
- 			{
- 				Edge e = *it;
- 
--				MolecularGraphTraits::VertexType source = boost::source(*it, *molecule_);
--				MolecularGraphTraits::VertexType target = boost::target(*it, *molecule_);
-+				MolecularGraphTraits::VertexType source = boost::source(e, *molecule_);
-+				MolecularGraphTraits::VertexType target = boost::target(e, *molecule_);
- 
- 				if (iv == source || iv == target)
- 				{
-@@ -1893,8 +1893,7 @@ namespace BALL
- 
- 		BGL_FORALL_EDGES(edge_it, graph, MolecularGraph)
- 		{
--			if (boost::source(edge_it, graph) < boost::target(edge_it, graph))
--				sorted_edges.push_back(edge_it);
-+			sorted_edges.push_back(edge_it);
- 		}
- 
- 		// sort bonds - the second vertex could be in false order
-@@ -1927,8 +1926,7 @@ namespace BALL
- 
- 		BGL_FORALL_EDGES(edge_it, graph, MolecularGraph)
- 		{
--			if (boost::source(edge_it, graph) < boost::target(edge_it, graph))
--				sorted_edges.push_back(edge_it);
-+			sorted_edges.push_back(edge_it);
- 		}
- 
- 		// sort bonds - the second vertex could be in false order
diff --git a/sci-chemistry/ball/files/ball-1.4.1-gcc-4.7.patch b/sci-chemistry/ball/files/ball-1.4.1-gcc-4.7.patch
deleted file mode 100644
index 6ab98729a83e..000000000000
--- a/sci-chemistry/ball/files/ball-1.4.1-gcc-4.7.patch
+++ /dev/null
@@ -1,592 +0,0 @@
- include/BALL/COMMON/global.h                       | 26 +++++------
- include/BALL/COMMON/hash.h                         | 36 +++++++--------
- include/BALL/DATATYPE/bitVector.h                  |  2 +-
- include/BALL/DATATYPE/hashMap.h                    |  9 +---
- include/BALL/DATATYPE/string.h                     | 11 +++--
- include/BALL/DATATYPE/string.iC                    |  5 ++
- include/BALL/SYSTEM/binaryFileAdaptor.h            | 53 +++++++++++-----------
- source/COMMON/exception.C                          |  6 +--
- source/COMMON/hash.C                               |  2 +-
- source/COMMON/init.C                               |  4 +-
- source/COMMON/logStream.C                          |  6 +--
- source/COMMON/version.C                            |  2 +-
- source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C | 41 +++++++++--------
- source/STRUCTURE/kekulizer.C                       |  8 ++--
- source/TEST/INIFile_test.C                         |  8 ++--
- source/TEST/ParameterSection_test.C                |  2 +-
- 16 files changed, 114 insertions(+), 107 deletions(-)
-
-diff --git a/include/BALL/COMMON/global.h b/include/BALL/COMMON/global.h
-index 11d9246..02c81c6 100644
---- a/include/BALL/COMMON/global.h
-+++ b/include/BALL/COMMON/global.h
-@@ -9,7 +9,7 @@
- #	include <BALL/CONFIG/config.h>
- #endif
- 
--#include <limits.h>
-+#include <limits>
- #include <time.h>
- 
- #ifdef BALL_HAS_BASETSD_H
-@@ -223,28 +223,28 @@ namespace BALL
- 		ASCII__SEMICOLON        = ';'
- 	};
- 
--	static const Distance INVALID_DISTANCE = INT_MIN;
--	static const Distance DISTANCE_MIN = (INT_MIN + 1);
--	static const Distance DISTANCE_MAX = INT_MAX;
-+	static const Distance INVALID_DISTANCE = std::numeric_limits<Distance>::max();
-+	static const Distance DISTANCE_MIN = (std::numeric_limits<Distance>::min() + 1);
-+	static const Distance DISTANCE_MAX = std::numeric_limits<Distance>::max();
- 
--	static const Handle INVALID_HANDLE = INT_MAX;
-+	static const Handle INVALID_HANDLE = std::numeric_limits<Handle>::max();
- 	static const Handle HANDLE_MIN = 0 ;
--	static const Handle HANDLE_MAX = INT_MAX - 1;
-+	static const Handle HANDLE_MAX = std::numeric_limits<Handle>::max() - 1;
- 
- 	static const Index INVALID_INDEX = -1;
- 	static const Index INDEX_MIN = 0;
--	static const Index INDEX_MAX = INT_MAX;
-+	static const Index INDEX_MAX = std::numeric_limits<Index>::max();
- 
--	static const Position INVALID_POSITION = INT_MAX;
-+	static const Position INVALID_POSITION = std::numeric_limits<Position>::max();
- 	static const Position POSITION_MIN = 0;
--	static const Position POSITION_MAX = INT_MAX - 1;
-+	static const Position POSITION_MAX = std::numeric_limits<Position>::max() - 1;
- 
- #	undef SIZE_MAX
--	static const Size INVALID_SIZE = INT_MAX;
-+	static const Size INVALID_SIZE = std::numeric_limits<Size>::max();
- 	static const Size SIZE_MIN = 0;
--	static const Size SIZE_MAX = INT_MAX - 1;
--	
--	
-+	static const Size SIZE_MAX = std::numeric_limits<Size>::max() - 1;
-+
-+
- }
- 
- #endif // BALL_COMMON_GLOBAL_H
-diff --git a/include/BALL/COMMON/hash.h b/include/BALL/COMMON/hash.h
-index 8d45df3..ebb9a55 100644
---- a/include/BALL/COMMON/hash.h
-+++ b/include/BALL/COMMON/hash.h
-@@ -15,24 +15,6 @@
- 
- namespace BALL 
- {
--	/**	General Hash Function Template.
--			This template function provides a simple wrapper
--			for the specialized hash functions. It facilitates their use 
--			in STL hash associative containers which expect a <b>Hasher</b>
--			class as template parameter.
--	\ingroup Common
--	*/
--  template <typename T>
--  class HashFunction
--  {
--    public:
--		
--		HashIndex operator () (const T& t) const
--    {
--      return Hash(t);
--		}
--	};
--
- 	/**	@name Specialized Hash Functions.
- 	*/
- 	//@{
-@@ -105,6 +87,24 @@ namespace BALL
- 
- 	//@}
- 
-+	/**	General Hash Function Template.
-+			This template function provides a simple wrapper
-+			for the specialized hash functions. It facilitates their use 
-+			in STL hash associative containers which expect a <b>Hasher</b>
-+			class as template parameter.
-+	\ingroup Common
-+	*/
-+  template <typename T>
-+  class HashFunction
-+  {
-+    public:
-+		
-+		HashIndex operator () (const T& t) const
-+    {
-+      return Hash(t);
-+		}
-+	};
-+
- } // namespace BALL
- 
- #endif // BALL_COMMON_HASH_H
-diff --git a/include/BALL/DATATYPE/bitVector.h b/include/BALL/DATATYPE/bitVector.h
-index 991f08e..dc7ead6 100644
---- a/include/BALL/DATATYPE/bitVector.h
-+++ b/include/BALL/DATATYPE/bitVector.h
-@@ -18,7 +18,7 @@
- #endif
- 
- 
--#include <string.h>
-+#include <cstring>
- 
- #define BALL_BLOCK_BITS 8
- #define BALL_BLOCK_MASK (BALL_BLOCK_BITS - 1)
-diff --git a/include/BALL/DATATYPE/hashMap.h b/include/BALL/DATATYPE/hashMap.h
-index 329db2b..f185b8c 100644
---- a/include/BALL/DATATYPE/hashMap.h
-+++ b/include/BALL/DATATYPE/hashMap.h
-@@ -236,7 +236,7 @@ namespace BALL
- 	template <class Key, class T>
- 	const T& HashMap<Key, T>::operator [] (const Key& key) const
- 	{
--		ConstIterator it = find(key);
-+		ConstIterator it = this->find(key);
- 		if (it == Base::end())
- 		{
- 			throw IllegalKey(__FILE__, __LINE__);
-@@ -272,12 +272,7 @@ namespace BALL
- 	T& HashMap<Key, T>::operator [] (const Key& key)
- 		
- 	{
--		Iterator it = find(key);
--		if (it == Base::end())
--		{
--			it = insert(ValueType(key, T())).first;
--		}
--		return it->second;
-+		return BALL_MAP_NAME::operator[] (key);
- 	}
- 
- } // namespace BALL
-diff --git a/include/BALL/DATATYPE/string.h b/include/BALL/DATATYPE/string.h
-index 1172180..aa11c35 100644
---- a/include/BALL/DATATYPE/string.h
-+++ b/include/BALL/DATATYPE/string.h
-@@ -27,10 +27,10 @@
- #endif
- 
- #include <string>
--#include <ctype.h>
--#include <errno.h>
--#include <stdlib.h>
--#include <string.h>
-+#include <cctype>
-+#include <cerrno>
-+#include <cstdlib>
-+#include <cstring>
- #include <iostream>
- #include <vector>
- 
-@@ -155,6 +155,9 @@ namespace BALL
- 		/// STL string copy constructor
- 		String(const string& string);
- 
-+		/// Copy constructor
-+		String(const String& s);
-+
- #ifdef BALL_STD_STRING_HAS_RVALUE_REFERENCES
- 		/// Move constructor
- 		String(String&& s);
-diff --git a/include/BALL/DATATYPE/string.iC b/include/BALL/DATATYPE/string.iC
-index b255849..c347588 100644
---- a/include/BALL/DATATYPE/string.iC
-+++ b/include/BALL/DATATYPE/string.iC
-@@ -8,6 +8,11 @@ String::String()
- {
- }
- 
-+BALL_INLINE String::String(const String& s)
-+	: string(s)
-+{
-+}
-+
- #ifdef BALL_STD_STRING_HAS_RVALUE_REFERENCES
- BALL_INLINE
- String::String(String&& s)
-diff --git a/include/BALL/SYSTEM/binaryFileAdaptor.h b/include/BALL/SYSTEM/binaryFileAdaptor.h
-index 64f0f5d..6488e18 100644
---- a/include/BALL/SYSTEM/binaryFileAdaptor.h
-+++ b/include/BALL/SYSTEM/binaryFileAdaptor.h
-@@ -10,6 +10,33 @@
- 
- namespace BALL
- {
-+	/** Coping with endianness. This function swaps the bytes of a variable
-+			of type T if this type is of size 2n.
-+	*/
-+	template <typename T>
-+	void swapBytes(T& t)
-+	{
-+		if (sizeof(T) % 2 != 0)
-+		{
-+			Log.error() << "Cannot swap types of uneven size." << std::endl;
-+			return;
-+		}
-+
-+		char* tmp = reinterpret_cast<char*>(&t);
-+		std::reverse(tmp, tmp + sizeof(T));
-+	}
-+
-+	//In the following some specialisations of swapBytes are provided for efficiency reasons
-+	//These should also cover BALL types like Size, Position and Index
-+	template<> BALL_EXPORT void swapBytes(unsigned short&);
-+	template<> BALL_EXPORT void swapBytes(short&);
-+	template<> BALL_EXPORT void swapBytes(unsigned int&);
-+	template<> BALL_EXPORT void swapBytes(int&);
-+	template<> BALL_EXPORT void swapBytes(unsigned long&);
-+	template<> BALL_EXPORT void swapBytes(long&);
-+	template<> BALL_EXPORT void swapBytes(float&);
-+	template<> BALL_EXPORT void swapBytes(double&);
-+
- 	/**
- 	 * Helper class for data conversion.
- 	 * BinaryFileAdaptors are used to read and write binary data from and to
-@@ -152,32 +179,6 @@ namespace BALL
- 		return is;
- 	}
- 
--	/** Coping with endianness. This function swaps the bytes of a variable
--			of type T if this type is of size 2n.
--	*/
--	template <typename T>
--	void swapBytes(T& t)
--	{
--		if (sizeof(T) % 2 != 0)
--		{
--			Log.error() << "Cannot swap types of uneven size." << std::endl;
--			return;
--		}
--
--		char* tmp = reinterpret_cast<char*>(&t);
--		std::reverse(tmp, tmp + sizeof(T));
--	}
--
--	//In the following some specialisations of swapBytes are provided for efficiency reasons
--	//These should also cover BALL types like Size, Position and Index
--	template<> BALL_EXPORT void swapBytes(unsigned short&);
--	template<> BALL_EXPORT void swapBytes(short&);
--	template<> BALL_EXPORT void swapBytes(unsigned int&);
--	template<> BALL_EXPORT void swapBytes(int&);
--	template<> BALL_EXPORT void swapBytes(unsigned long&);
--	template<> BALL_EXPORT void swapBytes(long&);
--	template<> BALL_EXPORT void swapBytes(float&);
--	template<> BALL_EXPORT void swapBytes(double&);
- } //namespace BALL
- 
- #ifndef BALL_NO_INLINE_FUNCTIONS
-diff --git a/source/COMMON/exception.C b/source/COMMON/exception.C
-index e7855ce..464f971 100644
---- a/source/COMMON/exception.C
-+++ b/source/COMMON/exception.C
-@@ -9,10 +9,10 @@
- #include <iostream>
- #include <typeinfo>
- #include <exception>
--#include <stdio.h>
--#include <stdlib.h>	// for getenv in terminate()
-+#include <cstdio>
-+#include <cstdlib>	// for getenv in terminate()
- #include <sys/types.h>
--#include <signal.h> // for SIGSEGV and kill
-+#include <csignal> // for SIGSEGV and kill
- 
- #ifdef BALL_HAS_UNISTD_H
- #	include <unistd.h> // fot getpid
-diff --git a/source/COMMON/hash.C b/source/COMMON/hash.C
-index 0d81493..ffe75de 100644
---- a/source/COMMON/hash.C
-+++ b/source/COMMON/hash.C
-@@ -72,7 +72,7 @@ namespace BALL
- 		Index index = 0;
- 		Index temp_index;
- 
--#		define BALL_BITS_IN_HASHVALUE_   (sizeof(Index) * CHAR_BIT)
-+#		define BALL_BITS_IN_HASHVALUE_   (sizeof(Index) * std::numeric_limits<unsigned char>::digits)
- #		define BALL_THREE_QUARTERS_      ((Index)((BALL_BITS_IN_HASHVALUE_ * 3) / 4))
- #		define BALL_ONE_EIGHTH_          ((Index)(BALL_BITS_IN_HASHVALUE_ / 8))
- #		define BALL_HIGH_BITS_           (~((Index)(~0) >> BALL_ONE_EIGHTH_))
-diff --git a/source/COMMON/init.C b/source/COMMON/init.C
-index d426756..856fe68 100644
---- a/source/COMMON/init.C
-+++ b/source/COMMON/init.C
-@@ -4,8 +4,8 @@
- 
- #include <BALL/COMMON/init.h>
- 
--#include <locale.h>
--#include <stdlib.h>
-+#include <clocale>
-+#include <cstdlib>
- 
- namespace BALL
- {
-diff --git a/source/COMMON/logStream.C b/source/COMMON/logStream.C
-index 12b9184..0340e24 100644
---- a/source/COMMON/logStream.C
-+++ b/source/COMMON/logStream.C
-@@ -26,9 +26,9 @@ namespace BALL
- 	// at this point, it is not yet possible to
- 	// include BALL/COMMON/limits.h (which were a 
- 	// much nicer solution...). Ugly header dependencies...
--	const int LogStreamBuf::MIN_LEVEL = INT_MIN;
--	const int LogStreamBuf::MAX_LEVEL = INT_MAX;
--	const Time LogStreamBuf::MAX_TIME = INT_MAX;
-+	const int LogStreamBuf::MIN_LEVEL = std::numeric_limits<int>::min();
-+	const int LogStreamBuf::MAX_LEVEL = std::numeric_limits<int>::max();
-+	const Time LogStreamBuf::MAX_TIME = std::numeric_limits<Time>::max();
- 
- 	LogStreamBuf::LogStreamBuf() 
- 		: std::streambuf(),
-diff --git a/source/COMMON/version.C b/source/COMMON/version.C
-index 1a0987b..15c9d87 100644
---- a/source/COMMON/version.C
-+++ b/source/COMMON/version.C
-@@ -12,7 +12,7 @@ namespace BALL
- {
- 	const char* VersionInfo::getVersion() 
- 	{
--		return BALL_RELEASE_STRING " ("__DATE__", " __TIME__ ")";
-+		return BALL_RELEASE_STRING " (" __DATE__ ", " __TIME__ ")";
- 	}
- 
- 	int VersionInfo::getMinorRevision()
-diff --git a/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C b/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C
-index 89a1f68..4f872ae 100644
---- a/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C
-+++ b/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C
-@@ -323,7 +323,7 @@ namespace BALL
- 			}
- 		}
- 
--		return *best;
-+		return DPConstRow_(boost::reference_wrapper<DPConfig_ const>(best->first), best->second);
- 	}
- 
- 	FPTBondOrderStrategy::Penalty FPTBondOrderStrategy::DPTable_::operator[](FPTBondOrderStrategy::DPConfig_ const& config) const
-@@ -602,6 +602,9 @@ namespace BALL
- 
- 		return bonds;
- 	}
-+	
-+#define	convertToCRow(tmp)\
-+		std::make_pair(boost::reference_wrapper<const DPConfig_>((tmp).first), (tmp).second)
- 
- 	void FPTBondOrderStrategy::FPTBondOrderAssignment_::computeIntroduceBag(TreeDecompositionBag& bag, DPTable_& child, 
- 	                                                                        AdditionalBagProperties_& property)
-@@ -622,7 +625,7 @@ namespace BALL
- 		// copy with n new bondvalue-columns with different values
- 		for (DPTable_::const_iterator iter = child.begin(); iter != child.end(); ++iter)
- 		{
--			DPConstRow_ child_entry = *iter;
-+			DPConstRow_ child_entry = convertToCRow(*iter);
- 			DPConfig_ conf(num_valences, num_bonds);
- 
- 			Size vindex = 0;
-@@ -787,7 +790,7 @@ namespace BALL
- 
- 		for (DPTable_::const_iterator entry_iterator = child.begin(); entry_iterator != child.end(); ++entry_iterator)
- 		{
--			Penalty entry_penalty(forgetInnerVertexIn(bag, *entry_iterator, new_entry, child_property.bonds, forgotten_index));
-+			Penalty entry_penalty(forgetInnerVertexIn(bag, convertToCRow(*entry_iterator), new_entry, child_property.bonds, forgotten_index));
- 			if (entry_penalty < upper_bound_)
- 			{
- 				property.table->insert(new_entry, entry_penalty);
-@@ -804,7 +807,7 @@ namespace BALL
- 		Penalty min_penalty = FPTBondOrderStrategy::infinite_penalty;
- 		for (DPTable_::const_iterator iter = child.begin(); iter != child.end(); ++iter)
- 		{
--			min_penalty = std::min(min_penalty, forgetInnerVertexIn(bag, *iter, empty, empty_list, 0));
-+			min_penalty = std::min(min_penalty, forgetInnerVertexIn(bag, convertToCRow(*iter), empty, empty_list, 0));
- 
- 			if (Maths::isEqual(0, min_penalty))
- 			{
-@@ -830,17 +833,17 @@ namespace BALL
- 		// insert each entry of the left child into a DPJoinMap
- 		for (DPTable_::const_iterator left_iter = left_child.begin(); left_iter != left_child.end(); ++left_iter)
- 		{
--			DPConstRow_ left_entry = *left_iter;
--			map.insert(pair<DPConfig_ const*, Penalty> (left_entry.first.get_pointer(), left_entry.second));
-+			DPConstRow_ left_entry = convertToCRow(*left_iter);
-+			map.insert(std::pair<DPConfig_ const*, Penalty> (left_entry.first.get_pointer(), left_entry.second));
- 		}
- 
- 		// find for each entry of the right child's table appropiate entries in the DPJoinMap (which have the same bondvalues)
- 		for (DPTable_::const_iterator r_iter = right_child.begin(); r_iter != right_child.end(); ++r_iter)
- 		{
--			DPConstRow_ right_entry = *r_iter;
-+			DPConstRow_ right_entry = convertToCRow(*r_iter);
- 			DPConfig_ const* right_conf = right_entry.first.get_pointer();
- 
--			pair<DPJoinMap_::const_iterator, DPJoinMap_::const_iterator> matching_range(map.equal_range(right_conf));
-+			std::pair<DPJoinMap_::const_iterator, DPJoinMap_::const_iterator> matching_range(map.equal_range(right_conf));
- 
- 			for (DPJoinMap_::const_iterator match  = matching_range.first;
- 					                            match != matching_range.second; ++match)
-@@ -1441,7 +1444,7 @@ namespace BALL
- 			delete current_state_;
- 		}
- 
--		multiset<BackTrackingState_*, StateComparator_>::iterator first = queue_.begin();
-+		std::multiset<BackTrackingState_*, StateComparator_>::iterator first = queue_.begin();
- 		current_state_ = *first;
- 		queue_.erase(first);
- 		--max_heap_size_;
-@@ -1598,7 +1601,7 @@ namespace BALL
- 		// insert possible antecessors in vectors
- 		for (DPTable_::const_iterator iter = left_table.begin(); iter != left_table.end(); ++iter)
- 		{
--			DPConstRow_ antecessor = *iter;
-+			DPConstRow_ antecessor = convertToCRow(*iter);
- 			if (comp.compare(&successor, antecessor.first.get_pointer()) == 0)
- 			{
- 				left_entries.push_back(iter);
-@@ -1607,7 +1610,7 @@ namespace BALL
- 
- 		for (DPTable_::const_iterator iter = right_table.begin(); iter != right_table.end(); ++iter)
- 		{
--			DPConstRow_ antecessor = *iter;
-+			DPConstRow_ antecessor = convertToCRow(*iter);
- 			if (comp.compare(&successor, antecessor.first.get_pointer()) == 0)
- 			{
- 				right_entries.push_back(iter);
-@@ -1619,10 +1622,10 @@ namespace BALL
- 
- 		for (std::vector<DPTable_::const_iterator>::const_iterator left = left_entries.begin(); left != left_entries.end(); ++left)
- 		{
--			DPConstRow_ left_entry = **left;
-+			DPConstRow_ left_entry = convertToCRow(**left);
- 			for (std::vector<DPTable_::const_iterator>::const_iterator right = right_entries.begin(); right != right_entries.end(); ++right)
- 			{
--				DPConstRow_ right_entry = **right;
-+				DPConstRow_ right_entry = convertToCRow(**right);
- 
- 				// check sum of valences
- 				bool correct_valences = true;
-@@ -1653,8 +1656,8 @@ namespace BALL
- 
- 		Penalty best_penalty = best.first->second + best.second->second;
- 
--		DPConstRow_ left  = *best.first;
--		DPConstRow_ right = *best.second;
-+		DPConstRow_ left  = convertToCRow(*best.first);
-+		DPConstRow_ right = convertToCRow(*best.second);
- 
- 		extendState(state, left.first, 0);
- 		++state.index;
-@@ -1664,8 +1667,8 @@ namespace BALL
- 		{
- 			DPPairIt_ entry = *iter;
- 
--			DPConstRow_ left  = *entry.first;
--			DPConstRow_ right = *entry.second;
-+			DPConstRow_ left  = convertToCRow(*entry.first);
-+			DPConstRow_ right = convertToCRow(*entry.second);
- 
- 			Penalty add_penalty = (left.second + right.second) - best_penalty;
- 			if (isSolutionNeeded(state.assignment.penalty + add_penalty))
-@@ -1716,7 +1719,7 @@ namespace BALL
- 		// check for each row entry: is it a possible anteccessor?
- 		for (DPTable_::iterator iter = table.begin(); iter != table.end(); ++iter)
- 		{
--			Penalty pen  = bond_assignment_->forgetInnerVertexIn(bag, *iter, test_entry, child_bonds, forgotten_index);
-+			Penalty pen  = bond_assignment_->forgetInnerVertexIn(bag, convertToCRow(*iter), test_entry, child_bonds, forgotten_index);
- 
- 			if (pen < FPTBondOrderStrategy::infinite_penalty && test_entry == successor)
- 			{
-@@ -1783,7 +1786,7 @@ namespace BALL
- 		{
- 			while (queue_.size() > max_heap_size_)
- 			{
--				multiset<BackTrackingState_*, StateComparator_>::iterator pos = queue_.end();
-+				std::multiset<BackTrackingState_*, StateComparator_>::iterator pos = queue_.end();
- 				--pos;
- 				delete *pos;
- 				queue_.erase(pos);
-diff --git a/source/STRUCTURE/kekulizer.C b/source/STRUCTURE/kekulizer.C
-index d1f4e78..c277091 100644
---- a/source/STRUCTURE/kekulizer.C
-+++ b/source/STRUCTURE/kekulizer.C
-@@ -266,7 +266,7 @@ void Kekuliser::dump()
- 			Log.error() << partner->getName() << " ";
- 		}
- 		Log.error() << "  " << current_penalty_;
--		if (lowest_penalty_ != INT_MAX) Log.error() << " + " << lowest_penalty_;
-+		if (lowest_penalty_ != std::numeric_limits<int>::max()) Log.error() << " + " << lowest_penalty_;
- 		Log.error() << std::endl;
- 	}
- }
-@@ -415,11 +415,11 @@ bool Kekuliser::fixAromaticRings_()
- #endif
- 
- 		solutions_.clear();
--		lowest_penalty_ = INT_MAX;
-+		lowest_penalty_ = std::numeric_limits<int>::max();
- 		current_penalty_ = 0;
- 		fixAromaticSystem_(0);
- 		// test could be changed to achieve at most a given max value:
--		if (lowest_penalty_ < INT_MAX) 
-+		if (lowest_penalty_ < std::numeric_limits<int>::max())
- 		{
- 			if (lowest_penalty_ == 0)
- 			{
-@@ -765,7 +765,7 @@ void Kekuliser::applySolution_(Position pos)
- // return the best solution
- Position Kekuliser::calculateDistanceScores_()
- {
--	float best_score = INT_MAX;
-+	float best_score = std::numeric_limits<int>::max();
- 	Size best_solution = 0;
- 
- 	for (Position solp = 0; solp < solutions_.size(); solp++)
-diff --git a/source/TEST/INIFile_test.C b/source/TEST/INIFile_test.C
-index 1f59d2c..cf37841 100644
---- a/source/TEST/INIFile_test.C
-+++ b/source/TEST/INIFile_test.C
-@@ -198,10 +198,10 @@ CHECK(bool appendLine(const String& section_name, const String& line))
- 	
- 	CAPTURE_OUTPUT_LEVEL(2000)
- 		TEST_EQUAL(ini.appendLine("Section9", "GAU"), false)
--	COMPARE_OUTPUT("In INIFile "BALL_TEST_DATA_PATH(INIFile_test.ini)" , error while appending line: GAU . Illegal section-name: Section9\n")
-+	COMPARE_OUTPUT("In INIFile " BALL_TEST_DATA_PATH(INIFile_test.ini)" , error while appending line: GAU . Illegal section-name: Section9\n")
- 	CAPTURE_OUTPUT_LEVEL(2000)
- 		TEST_EQUAL(ini.appendLine("Section2", "[AU"), false)	
--	COMPARE_OUTPUT("In INIFile "BALL_TEST_DATA_PATH(INIFile_test.ini)" , error while appending line: [AU . Illegal section-name: Section2\n")
-+	COMPARE_OUTPUT("In INIFile " BALL_TEST_DATA_PATH(INIFile_test.ini)" , error while appending line: [AU . Illegal section-name: Section2\n")
- 	TEST_EQUAL(ini.appendLine("Section3", "test1 = 123"), true)	
- 	TEST_EQUAL(*ini.getLine(9), "test1 = 123")
- 	TEST_EQUAL(ini.getNumberOfLines(), 11)
-@@ -403,13 +403,13 @@ CHECK(bool appendSection(const String& section))
- 	TEST_EQUAL(ini.hasSection(ini.HEADER), true)
- 	CAPTURE_OUTPUT_LEVEL(2000)
- 		TEST_EQUAL(ini.appendSection(ini.HEADER), false)
--		const char* output = "INIFile::appendSection: "BALL_TEST_DATA_PATH(INIFile_test.ini)" , while adding section: '#HEADER!' already exists.\n";
-+		const char* output = "INIFile::appendSection: " BALL_TEST_DATA_PATH(INIFile_test.ini)" , while adding section: '#HEADER!' already exists.\n";
- 	COMPARE_OUTPUT(output)
-   TEST_EQUAL(ini.getNumberOfLines(), 10)
- 
-   CAPTURE_OUTPUT_LEVEL(2000)
- 		TEST_EQUAL(ini.appendSection("Section1"), false)
--	COMPARE_OUTPUT("INIFile::appendSection: "BALL_TEST_DATA_PATH(INIFile_test.ini)" , while adding section: 'Section1' already exists.\n")
-+	COMPARE_OUTPUT("INIFile::appendSection: " BALL_TEST_DATA_PATH(INIFile_test.ini)" , while adding section: 'Section1' already exists.\n")
-   TEST_EQUAL(ini.getNumberOfLines(), 10)
- 	TEST_EQUAL(ini.hasSection("Section1"), true)
- 
-diff --git a/source/TEST/ParameterSection_test.C b/source/TEST/ParameterSection_test.C
-index 16424cd..b934b4a 100644
---- a/source/TEST/ParameterSection_test.C
-+++ b/source/TEST/ParameterSection_test.C
-@@ -55,7 +55,7 @@ CHECK(ParameterSection::extractSection(Parameters& parameters, const String& sec
-   bool result;
- 	CAPTURE_OUTPUT_LEVEL(2000)
- 		result = ps.extractSection(param, "Section1");
--	COMPARE_OUTPUT("ParameterSection::extractSection: error reading section Section1 of file "BALL_TEST_DATA_PATH(ParameterSection_test.ini)":\nWrong number of fields in the format line: 0. FORMAT:\n")
-+	COMPARE_OUTPUT("ParameterSection::extractSection: error reading section Section1 of file " BALL_TEST_DATA_PATH(ParameterSection_test.ini)":\nWrong number of fields in the format line: 0. FORMAT:\n")
- 	TEST_EQUAL(result, false)
- 	TEST_EQUAL(ps.getSectionName(), "Section1")
- 
diff --git a/sci-chemistry/ball/files/ball-1.4.1-libsvm.patch b/sci-chemistry/ball/files/ball-1.4.1-libsvm.patch
deleted file mode 100644
index c85506d72733..000000000000
--- a/sci-chemistry/ball/files/ball-1.4.1-libsvm.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-From 60a5f677587046b3e2077872c21b005bad549b85 Mon Sep 17 00:00:00 2001
-Message-Id: <60a5f677587046b3e2077872c21b005bad549b85.1332678065.git.jlec@gentoo.org>
-From: Justin Lecher <jlec@gentoo.org>
-Date: Sun, 25 Mar 2012 14:15:16 +0200
-Subject: [PATCH 1/2] Correct deprecated usage of svm_destroy_model to
- svm_free_and_destroy_model
-
----
- source/QSAR/libsvmModel.C |    2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-diff --git a/source/QSAR/libsvmModel.C b/source/QSAR/libsvmModel.C
-index 58ce4dc..1f24e15 100644
---- a/source/QSAR/libsvmModel.C
-+++ b/source/QSAR/libsvmModel.C
-@@ -81,7 +81,7 @@ void LibsvmModel::train()
- 		
- 		//free(prob);
- 		//free(prob->y); free(prob->x);
--		svm_destroy_model((::svm_model*)svm_train_result_);
-+		svm_free_and_destroy_model((::svm_model**)svm_train_result_);
- 	}
- }
- 
diff --git a/sci-chemistry/ball/files/ball-1.4.1-pthread.patch b/sci-chemistry/ball/files/ball-1.4.1-pthread.patch
deleted file mode 100644
index 5ca9699dc7bd..000000000000
--- a/sci-chemistry/ball/files/ball-1.4.1-pthread.patch
+++ /dev/null
@@ -1,19 +0,0 @@
- CMakeLists.txt |    5 +++++
- 1 files changed, 5 insertions(+), 0 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index a68497f..264f321 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -426,6 +426,11 @@ LIST(APPEND BALL_DEP_LIBRARIES
- 	${PYTHON_LIBRARIES}
- )
- 
-+
-+IF(UNIX)
-+	LIST(APPEND BALL_DEP_LIBRARIES "pthread")
-+ENDIF()
-+
- IF(TBB_FOUND)
- 	LIST(APPEND BALL_DEP_LIBRARIES ${TBB_LIBRARIES})
- ENDIF()
diff --git a/sci-chemistry/ball/files/ball-1.4.1-python.patch b/sci-chemistry/ball/files/ball-1.4.1-python.patch
deleted file mode 100644
index f7a235a3bd78..000000000000
--- a/sci-chemistry/ball/files/ball-1.4.1-python.patch
+++ /dev/null
@@ -1,82 +0,0 @@
- source/PYTHON/EXTENSIONS/BALL/file.sip             |    2 +-
- source/PYTHON/EXTENSIONS/BALL/periodicBoundary.sip |    4 ++--
- source/PYTHON/EXTENSIONS/VIEW/mainControl.sip      |    2 +-
- source/PYTHON/pyInterpreter.C                      |    9 +++++----
- 4 files changed, 9 insertions(+), 8 deletions(-)
-
-diff --git a/source/PYTHON/EXTENSIONS/BALL/file.sip b/source/PYTHON/EXTENSIONS/BALL/file.sip
-index e29170a..6ec6dc4 100644
---- a/source/PYTHON/EXTENSIONS/BALL/file.sip
-+++ b/source/PYTHON/EXTENSIONS/BALL/file.sip
-@@ -70,7 +70,7 @@ class File
-   // std::fstream& getFileStream();
-   bool copyTo(const String&);
-   bool moveTo(const String&);
--  bool remove() const;
-+  bool remove();
-   bool renameTo(const String&);
-   bool truncate(int) const;
-   bool operator == (const File& /file/) const;
-diff --git a/source/PYTHON/EXTENSIONS/BALL/periodicBoundary.sip b/source/PYTHON/EXTENSIONS/BALL/periodicBoundary.sip
-index 2b79778..46daade 100644
---- a/source/PYTHON/EXTENSIONS/BALL/periodicBoundary.sip
-+++ b/source/PYTHON/EXTENSIONS/BALL/periodicBoundary.sip
-@@ -22,8 +22,8 @@ using namespace BALL;
-   void disable();
-   SimpleBox3 getBox() const;
-   void setBox(const SimpleBox3&);
--  int addSolvent(const String&) const;
--  int removeSolvent() const;
-+  int addSolvent(const String& /In/);
-+  int removeSolvent();
-   bool isEnabled() const;
-   void updateMolecules();
-   Options* options;
-diff --git a/source/PYTHON/EXTENSIONS/VIEW/mainControl.sip b/source/PYTHON/EXTENSIONS/VIEW/mainControl.sip
-index 0a6c319..61d4596 100644
---- a/source/PYTHON/EXTENSIONS/VIEW/mainControl.sip
-+++ b/source/PYTHON/EXTENSIONS/VIEW/mainControl.sip
-@@ -139,7 +139,7 @@ class MainControl
- 	virtual void openFile(const String&) throw();
- 	void saveBALLViewProjectFile(const String&);
- 	void loadBALLViewProjectFile(const String&) throw();
--	void quickSave() const;
-+	void quickSave();
- 	void quickLoad();
- 	void processEvents(Size);
- };
-diff --git a/source/PYTHON/pyInterpreter.C b/source/PYTHON/pyInterpreter.C
-index 155a09f..7a12c33 100644
---- a/source/PYTHON/pyInterpreter.C
-+++ b/source/PYTHON/pyInterpreter.C
-@@ -4,9 +4,9 @@
- // $Id: ball-1.4.1-python.patch,v 1.1 2012/03/25 14:13:39 jlec Exp $
- //
- 
--#include <Python.h>
--
- #include <BALL/PYTHON/pyInterpreter.h>
-+#include <Python.h>
-+
- #include <BALL/PYTHON/BALLPythonConfig.h>
- 
- #include <BALL/FORMAT/lineBasedFile.h>
-@@ -34,7 +34,6 @@ namespace BALL
- 		PyObject* result = PyRun_String(const_cast<char*>(str.c_str()), mode, context_, context_);
- 		if (PyErr_Occurred())
- 		{
--			PyErr_Print();
- 			PyObject* type;
- 			PyObject* value;
- 			PyObject* range;
-@@ -50,7 +49,9 @@ namespace BALL
- 			{	
- 				error_message_ += " (error message could not be parsed)";
- 			}
--			
-+
-+			PyErr_Print();
-+
- 			error_message_ += "\n";
- 
- 			return 0;