# # ChangeLog for src # # Generated by Trac 1.6 # Jun 2, 2025, 6:07:02 PM Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [8e4471] * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) Added "arbitrary" rotation for matchSphericalPointDistributionsTest_2(). Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [92bc5c] * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) Adding QuaternionTest for SphericalPointDistributionUnitTest, fixed ... Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [f9d85f] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) Implemented rotations via boost::quaternions. Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [8d38e6] * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (modified) Added more unit test functions up to N=8 to ... Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [946948] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) FIX: SphericalPointDistribution succeeds with unit test. - removed ... Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [7e81ca] * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) Added Logging to SphericalPointDistribution for debugging. Mon, 12 Sep 2016 14:03:15 GMT Frederik Heber [6cb1cd] * src/Actions/AtomAction/SaturateAction.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate_carbon.at (modified) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate_nitrogen.at (modified) Removing SphericalPointDistribution::getSimplePolygon() to allow for ... Mon, 12 Sep 2016 14:03:11 GMT Frederik Heber [0c42f2] * src/Actions/AtomAction/SaturateAction.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution_getPoints.cpp (modified) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate_carbon.at (modified) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate_nitrogen.at (modified) Extended SaturateAction to be able to deal with bonded atoms. - ... Sat, 10 Sep 2016 16:01:20 GMT Frederik Heber [64cafb2] * src/Actions/AtomAction/SaturateAction.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (added) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.hpp (added) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate_carbon.at (modified) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate_nitrogen.at (modified) Revert "Trimmed down SphericalPointDistribution to what is needed at ... Sat, 10 Sep 2016 16:01:20 GMT Frederik Heber [d32f60] * src/builder_init.cpp (modified) FIX: Corrected copyright year to current one. Sat, 10 Sep 2016 16:01:20 GMT Frederik Heber [1745b7] * src/Actions/BondAction/BondAddAction.cpp (modified) * src/Actions/BondAction/BondAddAction.def (modified) * tests/Python/AllActions/options.dat (modified) AddBondAction also sets a desired bond degree. Sat, 10 Sep 2016 16:01:20 GMT Frederik Heber [2312fc6] * src/Fragmentation/Exporters/SaturatedBond.cpp (modified) SaturateBond now uses default angle and Bond length with warning when ... Sat, 10 Sep 2016 16:01:20 GMT Frederik Heber [f723fa] * src/LinkedCell/LinkedCell_Model.cpp (modified) FIX: In debug we asserted possible deleteNode() in LinkedCell_model. ... Fri, 09 Sep 2016 17:23:11 GMT Frederik Heber [2ae247] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) FIX: Clearing FragmentationResultsContainer before adding results in ... Fri, 09 Sep 2016 17:23:11 GMT Frederik Heber [f83e26] * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) FIX: FragmentationResultContainer did not clear cycles on clear(). Fri, 09 Sep 2016 17:23:11 GMT Frederik Heber [d20335] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Removed parsing and saving of fragment results in analyse-fragment- ... Fri, 09 Sep 2016 17:10:10 GMT Frederik Heber [73a5f7] * doc/userguide/userguide.xml (modified) * src/Actions/FragmentationAction/ParseFragmentResultsAction.cpp (added) * src/Actions/FragmentationAction/ParseFragmentResultsAction.def (added) * src/Actions/FragmentationAction/ParseFragmentResultsAction.hpp (added) * src/Actions/FragmentationAction/SaveFragmentResultsAction.cpp (added) * src/Actions/FragmentationAction/SaveFragmentResultsAction.def (added) * src/Actions/FragmentationAction/SaveFragmentResultsAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/ParseSaveFragmentResults/post/results_empty.dat (added) * tests/regression/Fragmentation/ParseSaveFragmentResults/pre/create_results_dat.py (added) * tests/regression/Fragmentation/ParseSaveFragmentResults/pre/results.dat (added) * tests/regression/Fragmentation/ParseSaveFragmentResults/testsuite-fragmentation-parse-save-fragment-results.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added parsing and saving of fragment results container state. - ... Fri, 09 Sep 2016 17:10:10 GMT Frederik Heber [ce0f63] * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) FIX: Clarified hint for FragmentationAutomationAction's resultfile. Fri, 09 Sep 2016 17:04:06 GMT Frederik Heber [e598f5] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) FIX: appendToHomologies() sorted force keysets which brough them out ... Fri, 09 Sep 2016 13:58:02 GMT Frederik Heber [4fa333] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Homology/AtomFragmentsMap.cpp (modified) * src/Fragmentation/Homology/AtomFragmentsMap.hpp (modified) FIX: AtomFragmentsMap::clear() did not clear fullkeysets. Fri, 09 Sep 2016 13:51:43 GMT Frederik Heber [61fc12] * src/Fragmentation/Fragmentation.cpp (modified) FIX: FragmentBOSSANOVA got full molecule as restricted keyset. - ... Fri, 09 Sep 2016 13:51:36 GMT Frederik Heber [34af97] * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (modified) * src/Fragmentation/unittests/KeySetsContainerUnitTest.hpp (modified) FIX: KeySetsContainer::insert(KeySetsContainer&) was not fully ... Fri, 09 Sep 2016 10:09:47 GMT Frederik Heber [9bdbc7] * src/UIElements/Views/Qt4/QtFragmentList.cpp (modified) * src/UIElements/Views/Qt4/QtFragmentList.hpp (modified) FIX: QtFragmentList controls access to clear() and refill() via mutex. Fri, 09 Sep 2016 10:09:47 GMT Frederik Heber [546f7d] * src/UIElements/Views/Qt4/QtFragmentList.cpp (modified) FIX: Selections in QtFragmentList works even under resorting. Fri, 09 Sep 2016 10:09:47 GMT Frederik Heber [d88397] * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) FIX: Skipping empty curves in QtHomologyList::refill(). - this does ... Fri, 09 Sep 2016 10:09:47 GMT Frederik Heber [4aed01] * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/QtFragmentList.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) * src/UIElements/Views/Qt4/QtNumericalItem.cpp (added) * src/UIElements/Views/Qt4/QtNumericalItem.hpp (added) FragmentList's and QtHomologyList's numerical columns are now ... Fri, 09 Sep 2016 10:09:47 GMT Frederik Heber [562b0a] * src/UIElements/Views/Qt4/QtFragmentList.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) FragmentList and HomologyList can be sorted by clicking column title. Fri, 09 Sep 2016 08:22:09 GMT Frederik Heber [d33f24] * src/Potentials/PotentialTrainer.cpp (modified) Added additional checks to training data sensibility of PotentialTrainer. Fri, 09 Sep 2016 08:22:09 GMT Frederik Heber [647148] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified) FIX: HomologyGraph's getNodeFromSet() and getEdgesFromSet ignored ... Fri, 09 Sep 2016 08:22:09 GMT Frederik Heber [27e6a7] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) Enhanced verbosity of printed homologous graphs. Fri, 09 Sep 2016 08:21:34 GMT Frederik Heber [ce70d25] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Added some asserts and checks in context of SaturatedFragment and ... Tue, 06 Sep 2016 14:36:46 GMT Frederik Heber [945797] * src/Potentials/PotentialTrainer.cpp (modified) * src/Potentials/PotentialTrainer.hpp (modified) FIX: PotentialTrainer::getFirstGraphwithSpecifiedElements() did not ... Tue, 06 Sep 2016 14:36:46 GMT Frederik Heber [29ce5f] * src/Potentials/PotentialTrainer.cpp (modified) PotentialTrainer checks whether compound potential contains ... Tue, 06 Sep 2016 14:36:46 GMT Frederik Heber [c6f2c5] * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (modified) FitCompoundPotentialAction checks whether potentials are registered yet. Tue, 06 Sep 2016 14:36:46 GMT Frederik Heber [0f5956] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * tests/Python/AllActions/options.dat (modified) Added "parse-state-files" option to fragment-molecule which is off by ... Tue, 06 Sep 2016 14:36:34 GMT Frederik Heber [d21933] * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtMainWindow.hpp (modified) * src/UIElements/Views/Qt4/QtLogBox.cpp (modified) * src/UIElements/Views/Qt4/QtLogBox.hpp (modified) Added second log view for stderr. Tue, 06 Sep 2016 14:36:34 GMT Frederik Heber [3d61c7] * configure.ac (modified) * src/UIElements/Views/Qt4/QtLogBox.cpp (modified) Added configure enable-switch for qtgui's capturing of stdout. Tue, 06 Sep 2016 14:36:17 GMT Frederik Heber [0249ce] * src/World.cpp (modified) FIX: Pop..Action need to check whether stack is actually non-empty. ... Wed, 18 May 2016 22:03:03 GMT Frederik Heber [ed8a68] * src/Parser/Makefile.am (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/TremoloParser_ElementKeys.cpp (deleted) * src/Parser/TremoloParser_ElementKeys.hpp (deleted) * src/Parser/unittests/Makefile.am (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserTremolo_ElementKeysUnitTest.cpp (deleted) * src/Parser/unittests/ParserTremolo_ElementKeysUnitTest.hpp (deleted) Removed TremoloParser's ElementKeys, superceded by ParticleRegistry. Wed, 18 May 2016 22:03:03 GMT Frederik Heber [30e5dc] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (deleted) * src/Actions/ParserAction/ParseTremoloPotentialsAction.def (deleted) * src/Actions/ParserAction/ParseTremoloPotentialsAction.hpp (deleted) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials.at (deleted) * tests/regression/Parser/testsuite-parser.at (modified) Removed ParseTremoloPotentialsAction. - TESTFIX: removed regression ... Wed, 18 May 2016 22:03:03 GMT Frederik Heber [740f9f] * src/Parser/TremoloParser.cpp (modified) TremoloParser::readAtomDataLine() uses ParticleRegistry and ... Wed, 18 May 2016 22:03:03 GMT Frederik Heber [045228] * src/Parser/TremoloParser_ElementKeys.cpp (modified) * src/Parser/unittests/ParserTremolo_ElementKeysUnitTest.cpp (modified) TremoloParser's ElementKeys now registers types also with ... Wed, 18 May 2016 22:03:03 GMT Frederik Heber [d7bb964] * src/Actions/PotentialAction/ParseParticleParametersAction.cpp (modified) * tests/regression/Potential/SaveParseParticleParameters/pre/harmonic.particles (modified) * tests/regression/Potential/SaveParseParticleParameters/testsuite-potential-save-parse-particle-parameters.at (modified) ParseParticleParametersAction now uses TremoloPotentialFileParser. ... Wed, 18 May 2016 22:03:03 GMT Frederik Heber [d96482] * src/Potentials/Makefile.am (modified) * src/Potentials/RegistrySerializer.hpp (modified) * src/Potentials/RegistrySerializer_Particle.cpp (added) * tests/regression/Potential/FitPartialCharges/testsuite-potential-fit-partial-charges.at (modified) * tests/regression/Potential/SaveParseParticleParameters/testsuite-potential-save-parse-particle-parameters.at (modified) Added specialization of RegistrySerializer for Particle. - this ... Wed, 18 May 2016 22:03:03 GMT Frederik Heber [a44d70] * src/Potentials/Makefile.am (modified) * src/Potentials/TremoloPotentialFileParser.cpp (added) * src/Potentials/TremoloPotentialFileParser.hpp (added) Placed all TREMOLO Potential parsing into distinct structure. Wed, 18 May 2016 22:03:03 GMT Frederik Heber [afb7c0] * src/Potentials/Makefile.am (modified) * src/Potentials/TremoloPotentialTypes.cpp (added) * src/Potentials/TremoloPotentialTypes.hpp (added) Added TremoloPotentialTypes that contains map on tremolo potential ... Wed, 18 May 2016 22:03:03 GMT Frederik Heber [0550b6] * src/Potentials/RegistryDeserializer_impl.hpp (modified) RegistryDeserializer stops on curly brackets. - these indicate ... Wed, 18 May 2016 22:03:03 GMT Frederik Heber [35d171] * src/Potentials/Particles/Particle.cpp (modified) FIX: Particle lower-cases all but first letter of element name in ... Wed, 18 May 2016 22:03:03 GMT Frederik Heber [4795cd] * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) Extracted writeEntry() in TremoloParser::saveLine(). Wed, 18 May 2016 22:03:00 GMT Frederik Heber [797a40] * src/Parser/PdbParser.cpp (modified) PdbParser sets and save Atom's ParticleName. Wed, 18 May 2016 22:02:57 GMT Frederik Heber [f20b4b] * src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) FitPartialChargesAction sets atom's particlename after fitting. Wed, 18 May 2016 22:02:57 GMT Frederik Heber [4f42c9] * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) VMGFragmentController uses atom's particlename to get associated ... Wed, 18 May 2016 22:02:57 GMT Frederik Heber [843590] * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_atominfo.hpp (modified) Adding particlename member variable to Atom(Info). Wed, 18 May 2016 22:02:54 GMT Frederik Heber [f33ef9] * src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) FitPartialChargesAction checks whether AtomFragments has been loaded. Wed, 18 May 2016 22:02:54 GMT Frederik Heber [8eafd6] * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) * src/Potentials/PartialNucleiChargeFitter.cpp (modified) Fixed typo in PartialNucleiChargeFitter. Wed, 18 May 2016 22:02:54 GMT Frederik Heber [c4aeda] * src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) FitPartialChargesAction associates each atom with its particle as in ... Wed, 18 May 2016 22:02:54 GMT Frederik Heber [ed0f88] * src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) Using unique graph set as key to particle name in ... Wed, 18 May 2016 22:02:54 GMT Frederik Heber [91f907] * src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) FitPartialChargesAction only makes unique particles. - i.e. we give ... Wed, 18 May 2016 22:02:53 GMT Frederik Heber [c1ec8e] * src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) Split FitPartialChargesAction's extensive performCall() into ... Wed, 18 May 2016 22:02:53 GMT Frederik Heber [01120c] * src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) FitPartialChargesAction properly treats hydrogens now. Wed, 18 May 2016 22:02:53 GMT Frederik Heber [d8ed62] * doc/userguide/userguide.xml (modified) * src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) * src/Actions/PotentialAction/FitPartialChargesAction.def (modified) * tests/regression/Potential/FitPartialCharges/testsuite-potential-fit-partial-charges.at (modified) Rewrote FitPartialChargesAction to fit charges to currently selected ... Wed, 18 May 2016 22:02:07 GMT Frederik Heber [d9dbef] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToAtomFragments.cpp (added) * src/Fragmentation/Exporters/ExportGraph_ToAtomFragments.hpp (added) * src/Fragmentation/Makefile.am (modified) Added another ExportGraph for obtaining AtomFragmentsMap's ... Wed, 18 May 2016 22:02:07 GMT Frederik Heber [70aeed] * src/Fragmentation/Homology/AtomFragmentsMap.cpp (modified) * src/Fragmentation/Homology/AtomFragmentsMap.hpp (modified) Added additional "force" keysets to AtomFragmentsMap. Wed, 18 May 2016 22:02:07 GMT Frederik Heber [d410e25] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Interfragmenter.cpp (modified) * src/Fragmentation/Interfragmenter.hpp (modified) Interfragmenter now access singleton AtomFragmentsMap. - i.e. we do ... Wed, 18 May 2016 22:02:06 GMT Frederik Heber [3004d2] * doc/userguide/userguide.xml (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) FragmentationAction clears and inserts fragments into AtomFragments. Wed, 18 May 2016 22:02:06 GMT Frederik Heber [2fd88d1] * src/Fragmentation/Homology/AtomFragmentsMap.cpp (modified) * src/Fragmentation/Homology/AtomFragmentsMap.hpp (modified) * src/Fragmentation/Interfragmenter.cpp (modified) AtomFragmentsMap now may return partial map on a vector of atoms with ... Wed, 18 May 2016 22:02:06 GMT Frederik Heber [78202b] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/ParseAtomFragmentsAction.cpp (added) * src/Actions/PotentialAction/ParseAtomFragmentsAction.def (added) * src/Actions/PotentialAction/ParseAtomFragmentsAction.hpp (added) * src/Actions/PotentialAction/SaveAtomFragmentsAction.cpp (added) * src/Actions/PotentialAction/SaveAtomFragmentsAction.def (added) * src/Actions/PotentialAction/SaveAtomFragmentsAction.hpp (added) * src/Fragmentation/Homology/AtomFragmentsMap.hpp (modified) * src/Fragmentation/KeySet.hpp (modified) * tests/Python/AllActions/options.dat (modified) Adding potential action to parse and save atom fragment associations. ... Wed, 18 May 2016 22:02:06 GMT Frederik Heber [16d67a] * src/Fragmentation/Homology/AtomFragmentsMap.cpp (modified) * src/Fragmentation/Homology/AtomFragmentsMap.hpp (modified) AtomFragmentsMap is now serializable. Wed, 18 May 2016 22:02:06 GMT Frederik Heber [d713ce] * src/Fragmentation/Homology/AtomFragmentsMap.cpp (moved) * src/Fragmentation/Homology/AtomFragmentsMap.hpp (moved) * src/Fragmentation/Interfragmenter.cpp (modified) * src/Fragmentation/Interfragmenter.hpp (modified) * src/Fragmentation/Makefile.am (modified) AtomFragmentsMap is now a Singleton and part of Homology code. Wed, 18 May 2016 22:02:06 GMT Frederik Heber [bd6e5c] * src/Fragmentation/AtomFragmentsMap.cpp (modified) * src/Fragmentation/AtomFragmentsMap.hpp (modified) * src/Fragmentation/Interfragmenter.cpp (modified) * src/Fragmentation/Interfragmenter.hpp (modified) Prepared AtomFragmentsMap to work in ids, not instances. - no more ... Wed, 18 May 2016 22:02:06 GMT Frederik Heber [d45ed9] * src/Fragmentation/AtomFragmentsMap.cpp (added) * src/Fragmentation/AtomFragmentsMap.hpp (added) * src/Fragmentation/Interfragmenter.cpp (modified) * src/Fragmentation/Interfragmenter.hpp (modified) * src/Fragmentation/Makefile.am (modified) Abstracted atom -> fragment association out of Interfragmenter. Wed, 18 May 2016 22:02:06 GMT Frederik Heber [b0bc13] * src/Fragmentation/Homology/HomologyGraph.hpp (modified) FIX: HomologyGraph has explicit cstors for KeySet and IndexSet. - ... Wed, 18 May 2016 21:56:59 GMT Frederik Heber [7debff] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) VMGData additionally stores absolute residual. - we check for ... Wed, 18 May 2016 21:55:42 GMT Frederik Heber [f0dea0] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) FragmentationAutomationAction checks FragmentResults for non-zero ... Wed, 18 May 2016 21:55:40 GMT Frederik Heber [9ff818] * src/Fragmentation/Summation/Containers/MPQCData.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) MPQCJob and VMGJob contain reached and desired accuracy. - both set ... Sat, 07 May 2016 07:05:19 GMT Frederik Heber [a9099d] * src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) * src/Actions/PotentialAction/FitPartialChargesAction.def (modified) * src/Potentials/Particles/Particle.cpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Potential/FitPartialCharges/post/water.particles (modified) FitPartialChargesAction enforces net charge neutrality on default ... Sat, 07 May 2016 07:05:19 GMT Frederik Heber [666e9e] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * tests/Python/AllActions/options.dat (modified) VMGFragmentController and FragmentationAutomationAction accept ... Sat, 07 May 2016 07:05:19 GMT Frederik Heber [0ba27c9] * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp (modified) FragmentationLongRangeResults now takes additional implicit charge ... Sat, 07 May 2016 07:05:19 GMT Frederik Heber [276e2f] * src/Actions/PotentialAction/ParseHomologiesAction.cpp (modified) ParseHomologiesAction prints parsed homologies on larger verbosity ... Sat, 07 May 2016 07:03:56 GMT Frederik Heber [708ec1] * src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) * src/Actions/PotentialAction/FitPartialChargesAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Potential/FitPartialCharges/post/water.particles (added) * tests/regression/Potential/FitPartialCharges/testsuite-potential-fit-partial-charges.at (modified) Modified FitPartialChargesAction to register fitted particles with ... Sat, 07 May 2016 07:03:56 GMT Frederik Heber [2082637] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) * src/Actions/PotentialAction/ParseParticleParametersAction.cpp (added) * src/Actions/PotentialAction/ParseParticleParametersAction.def (added) * src/Actions/PotentialAction/ParseParticleParametersAction.hpp (added) * src/Actions/PotentialAction/SaveParticleParametersAction.cpp (added) * src/Actions/PotentialAction/SaveParticleParametersAction.def (added) * src/Actions/PotentialAction/SaveParticleParametersAction.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Potential/SaveParseParticleParameters/pre/harmonic.particles (added) * tests/regression/Potential/SaveParseParticleParameters/testsuite-potential-save-parse-particle-parameters.at (added) * tests/regression/Potential/testsuite-potential.at (modified) Added Parse- and SaveParticleParametersAction to parse/save ... Sat, 07 May 2016 07:03:56 GMT Frederik Heber [fde8e7] * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/ParsePotentialsAction.cpp (modified) * src/Actions/PotentialAction/SavePotentialsAction.cpp (modified) * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialDeserializer.cpp (deleted) * src/Potentials/PotentialDeserializer.hpp (deleted) * src/Potentials/PotentialSerializer.cpp (deleted) * src/Potentials/PotentialSerializer.hpp (deleted) * src/Potentials/PotentialTrainer.cpp (modified) * src/Potentials/RegistryDeserializer.hpp (added) * src/Potentials/RegistryDeserializer_impl.hpp (added) * src/Potentials/RegistrySerializer.hpp (added) * src/Potentials/RegistrySerializer_impl.hpp (added) Refactored PotentialSerializer and -Deserializer into more general ... Sat, 07 May 2016 07:03:56 GMT Frederik Heber [f6abb1] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialDeserializer.cpp (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/PotentialFactory.hpp (modified) * src/Potentials/StreamFactory_EmpiricalPotential.cpp (added) * src/Potentials/StreamFactory_EmpiricalPotential.hpp (added) PotentialFactory now also complies to templated StreamFactory. - ... Sat, 07 May 2016 07:03:56 GMT Frederik Heber [086e30] * src/Potentials/Makefile.am (modified) * src/Potentials/Particles/Particle.cpp (modified) * src/Potentials/Particles/Particle.hpp (modified) * src/Potentials/Particles/ParticleFactory.cpp (added) * src/Potentials/Particles/ParticleFactory.hpp (added) * src/Potentials/Particles/StreamFactory_Particle.cpp (added) * src/Potentials/Particles/StreamFactory_Particle.hpp (added) * src/Potentials/StreamFactory.hpp (added) Added ParticleFactory and general StreamFactory. - StreamFactory ... Sat, 07 May 2016 07:03:56 GMT Frederik Heber [fdfc52] * src/Actions/PotentialAction/ParsePotentialsAction.cpp (modified) * src/Potentials/Exceptions.hpp (modified) * src/Potentials/Particles/Particle.cpp (modified) * src/Potentials/SerializablePotential.cpp (modified) * src/Potentials/unittests/SerializablePotentialUnitTest.cpp (modified) Renamed all SerializablePotential..Exceptions to ... Sat, 07 May 2016 07:03:56 GMT Frederik Heber [fd5440] * src/Potentials/Particles/Particle.cpp (modified) * src/Potentials/Particles/Particle.hpp (modified) FIX: Particle's member variables are now public and fixes to stream ... Mon, 25 Apr 2016 07:06:12 GMT Frederik Heber [9d1a78] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) FIX: GLWorldScene used iterator also in NDEBUG, connect still outside ... Mon, 25 Apr 2016 07:06:12 GMT Frederik Heber [abb115] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.cpp (modified) FIX: QtMoleculeListView::rowsSelected() checks for illegal id from ... Mon, 25 Apr 2016 07:06:12 GMT Frederik Heber [097da7] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (modified) FIX: QtMoleculeList has flag to tell when nameChanged came from ... Mon, 25 Apr 2016 07:06:11 GMT Frederik Heber [006f6a] * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) QtObservedInstanceBoard::get..ToIndex() now serve -1 as illegal id ... Mon, 25 Apr 2016 07:06:11 GMT Frederik Heber [ffa69c] * src/Parser/PdbParser.cpp (modified) FIX: PdbParser scanned through all present atoms once per ATOM line. ... Mon, 25 Apr 2016 07:06:10 GMT Frederik Heber [30b134] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) FIX: GLWorldScene::removeBond() needs to check whether molecule ... Mon, 25 Apr 2016 07:06:10 GMT Frederik Heber [67c4ea] * src/molecule.hpp (modified) FIX: molecule returned BondCount twice as large. Mon, 25 Apr 2016 07:06:10 GMT Frederik Heber [0bddd1e] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) Made GLWorldScene::resetParent() safe for multiple threads. Mon, 25 Apr 2016 07:05:31 GMT Frederik Heber [ea7926] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) Split ObservedValueIndexLookup such that it is protected under atom ... Mon, 25 Apr 2016 07:05:31 GMT Frederik Heber [1eba7c] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) Protecting access to atom and bond functions in GLWorldScene with ... Mon, 25 Apr 2016 07:05:31 GMT Frederik Heber [efeeb7] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) GLWorldScene now holds onto atoms and bonds until ..Removed() signal ... Mon, 25 Apr 2016 07:05:31 GMT Frederik Heber [649f59] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) GLWorldScene removes stored observed values only after both parent is ... Mon, 25 Apr 2016 07:05:31 GMT Frederik Heber [136842] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) GLWorldScene needs to store observed values to ensure duration of ... Mon, 25 Apr 2016 07:02:56 GMT Frederik Heber [d16a06] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) FIX: GLMoleculeObject_atom did not use QtObservedAtom for selected.