# # ChangeLog for src/Fragmentation/Homology # # Generated by Trac 1.4.4 # Mar 23, 2025, 8:19:02 AM Wed, 13 Feb 2013 16:38:23 GMT Frederik Heber <heber@…> [312c0d] * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (added) FIX: HomologyContainerUnitTest does not require libMolecuilderUI ... Sun, 16 Dec 2012 19:47:28 GMT Frederik Heber <heber@…> [fe0355] * src/Fragmentation/Homology/HomologyGraph_getFromKeysetStub.cpp (moved) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) Split HomologyGraph_getFromKeyset module off from ... Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber <heber@…> [28e203] * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp (modified) FIX: nodes_t and edges_t in HomologyGraph must be a map. - there ... Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber <heber@…> [d058e6] * src/Fragmentation/Homology/HomologyContainer.hpp (modified) Exposed const begin,end of container in HomologyContainer to allow ... Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber <heber@…> [372c912] * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified) * src/Fragmentation/Homology/unittests/stubs/HomologyGraph_getFromKeysetStub.cpp (modified) Extended HomologyGraph to also be constructable from IndexSet ... Thu, 13 Dec 2012 10:12:51 GMT Frederik Heber <heber@…> [79ac03] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/AdaptivityMap.hpp (modified) * src/Fragmentation/AtomMask.hpp (added) * src/Fragmentation/Exporters/ExportGraph.cpp (added) * src/Fragmentation/Exporters/ExportGraph.hpp (added) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (added) * src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp (added) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (added) * src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp (added) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/Graph.hpp (modified) * src/Fragmentation/Homology/FragmentEdge.cpp (added) * src/Fragmentation/Homology/FragmentEdge.hpp (added) * src/Fragmentation/Homology/FragmentNode.cpp (added) * src/Fragmentation/Homology/FragmentNode.hpp (added) * src/Fragmentation/Homology/HomologyContainer.cpp (added) * src/Fragmentation/Homology/HomologyContainer.hpp (added) * src/Fragmentation/Homology/HomologyGraph.cpp (added) * src/Fragmentation/Homology/HomologyGraph.hpp (added) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (added) * src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/FragmentNodeUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/FragmentNodeUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/Makefile.am (added) * src/Fragmentation/Homology/unittests/stubs/HomologyGraph_getFromKeysetStub.cpp (added) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/Mask.hpp (added) * src/Fragmentation/MoleculeMask.hpp (added) * src/Fragmentation/SortIndex.cpp (added) * src/Fragmentation/SortIndex.hpp (added) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/fragmentation_helpers.hpp (modified) * src/Graph/AdjacencyList.cpp (added) * src/Graph/AdjacencyList.hpp (added) * src/Graph/CheckAgainstAdjacencyFile.cpp (deleted) * src/Graph/CheckAgainstAdjacencyFile.hpp (deleted) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.hpp (modified) * src/Graph/ListOfLocalAtoms.hpp (added) * src/Graph/Makefile.am (modified) * src/Graph/unittests/AdjacencyListUnitTest.cpp (added) * src/Graph/unittests/AdjacencyListUnitTest.hpp (added) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (deleted) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.hpp (deleted) * src/Graph/unittests/Makefile.am (modified) * src/MoleculeLeafClass.cpp (modified) * src/MoleculeLeafClass.hpp (modified) * src/MoleculeListClass.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/Makefile.am (modified) * tests/CodeChecks/testsuite-header-dist.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order1.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order2.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order3.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order4.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order1.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order2.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order3.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order4.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order1.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order2.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order3.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order4.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order5.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order6.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order1.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order2.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order3.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order4.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order5.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order6.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order1.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order2.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order3.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order4.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order5.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order6.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order1.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order2.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order3.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order4.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order5.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order6.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order1.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order2.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order3.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order4.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order5.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order6.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order1.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order2.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order3.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order4.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order5.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order6.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order1.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order2.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order3.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order4.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order5.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order6.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order1.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order2.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order3.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order4.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order5.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order6.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order1.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order2.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order3.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order4.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order5.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order6.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order1.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order2.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order3.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order4.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order5.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order6.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order1.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order2.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order3.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order4.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order5.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order6.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order1.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order2.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order3.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order4.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order5.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order6.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order1.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order2.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order3.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order4.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order5.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order6.at (modified) * tests/regression/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at (modified) * tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified) * tests/regression/Molecules/SaveAdjacency/post/test.adj (modified) Merge branch 'Fragmentation_Homology' into Candidate_v1.3.7 ... Thu, 13 Dec 2012 09:32:50 GMT Frederik Heber <heber@…> [12a24c] * src/Fragmentation/Homology/HomologyContainer.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.hpp (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) Added serialization to HomologyContainer and completed ... Thu, 13 Dec 2012 09:32:50 GMT Frederik Heber <heber@…> [67db80] * src/Fragmentation/Homology/FragmentEdge.cpp (modified) * src/Fragmentation/Homology/FragmentEdge.hpp (modified) * src/Fragmentation/Homology/FragmentNode.cpp (modified) * src/Fragmentation/Homology/FragmentNode.hpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified) * src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.hpp (modified) * src/Fragmentation/Homology/unittests/FragmentNodeUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/FragmentNodeUnitTest.hpp (modified) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.hpp (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) Added serialization capabilities to FragmentEdge, FragmentNode, and ... Mon, 03 Dec 2012 09:50:02 GMT Frederik Heber <heber@…> [e15ffe] * src/Fragmentation/Homology/HomologyContainer.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) Added HomologyContainer::operator<<(). Mon, 03 Dec 2012 09:50:02 GMT Frederik Heber <heber@…> [54a561] * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) Added output operator to HomologyGraph. Mon, 03 Dec 2012 09:50:02 GMT Frederik Heber <heber@…> [77b350] * src/Fragmentation/Homology/HomologyContainer.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (added) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/stubs/HomologyGraph_getFromKeysetStub.cpp (added) * src/Fragmentation/Makefile.am (modified) HomologyGraph may now be created from a given KeySet referring to ... Mon, 03 Dec 2012 09:50:02 GMT Frederik Heber <heber@…> [7b6b21f] * src/Fragmentation/Homology/HomologyGraph.cpp (added) * src/Fragmentation/Homology/HomologyGraph.hpp (added) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Makefile.am (modified) Added HomologyGraph that contains combined information on edges and ... Mon, 03 Dec 2012 09:50:01 GMT Frederik Heber <heber@…> [8387e0] * src/Fragmentation/Homology/FragmentEdge.cpp (added) * src/Fragmentation/Homology/FragmentEdge.hpp (added) * src/Fragmentation/Homology/FragmentNode.cpp (added) * src/Fragmentation/Homology/FragmentNode.hpp (added) * src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/FragmentNodeUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/FragmentNodeUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Makefile.am (modified) Added FragmentNode and FragmentEdge to contain all information for ... Mon, 03 Dec 2012 09:50:01 GMT Frederik Heber <heber@…> [4694df] * src/Fragmentation/Homology/HomologyContainer.cpp (added) * src/Fragmentation/Homology/HomologyContainer.hpp (added) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/Makefile.am (added) * src/Fragmentation/Makefile.am (modified) * src/unittests/Makefile.am (modified) Added class HomologyContainer and unit test. - is basically a ...