June 2014 - Molecuilder-devel

[SCM] MoleCuilder branch QtGUI_LogBox created. v1.4.5-10-g0ef9127
by git＠ins.uni-bonn.de 28 Jun '14

28 Jun '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, QtGUI_LogBox has been created at 0ef9127937748a00a4b5acfe70e56c991aed77b0 (commit) - Log ----------------------------------------------------------------- commit 0ef9127937748a00a4b5acfe70e56c991aed77b0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 19 23:30:53 2014 +0200 QtLogBox catches mousePressEvent and selects atom in log. - this should ease graphical debugging a lot. commit e0b5f07b569ad48c9e5c6ed53968f1e215c43d1b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 19 23:00:14 2014 +0200 Added QtLogBox to QtMainWindow, using QDebugStream to display log. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch QtGUI_LogBox deleted. v1.4.5-10-g8b1dc21
by git＠ins.uni-bonn.de 28 Jun '14

28 Jun '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, QtGUI_LogBox has been deleted was 8b1dc21bdb83b06fcbbce1b30347d51fe1acf7cc ----------------------------------------------------------------------- 8b1dc21bdb83b06fcbbce1b30347d51fe1acf7cc QtLogBox catches mousePressEvent and selects atom in log. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch StatusToAllActions created. v1.4.5-13-g26b4d62
by git＠ins.uni-bonn.de 27 Jun '14

27 Jun '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, StatusToAllActions has been created at 26b4d62081a948abd7e73ffa88b6aec3eb1e5234 (commit) - Log ----------------------------------------------------------------- commit 26b4d62081a948abd7e73ffa88b6aec3eb1e5234 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 19 15:56:27 2014 +0200 All Actions now give correct failure status via STATUS() macro. commit 0b6b770c3a01e40e913e85102527423a7acc09e0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 19 15:55:01 2014 +0200 ActionQueue gives caught failure of Action and success via pushStatus(). commit 378f2d5ba8914489acde58f6de2d54c2e0ae84ba Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 19 13:02:54 2014 +0200 Updated all UI's StatusIndicator classes to use ActionStatusList. - CommandLineStatusIndicator and TextStatusIndicator just print the message. - QtStatusBar has a QTimer that updates the status message in second intervals. commit 26b4eb453c6d8c6ccdb34e5b8a56f055e76a561b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 19 11:17:06 2014 +0200 Added observable ActionStatusList to ActionQueue. - this allows to fetch Status messages from Actions at a central place. - Action::pushStatus() as befriended proxy to ActionQueue::pushStatus() added. - equipped ActionStatusList with a thread lock to protect access. commit 3ded2b779a607bf609e8dbfd11734a0b924f6597 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 19 14:28:15 2014 +0200 FIX: TxMenu and CommandLineWindow lacked waitQueue() in the wait-for-key loop. - this has occured due to queueAction() introduction. - otherwise the UI is destroyed before even the first Action has started. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch StatusToAllActions deleted. v1.4.5-5-gffe4889
by git＠ins.uni-bonn.de 27 Jun '14

27 Jun '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, StatusToAllActions has been deleted was ffe48897f51117b06b84ecf4999b484bde338000 ----------------------------------------------------------------------- ffe48897f51117b06b84ecf4999b484bde338000 All Actions now give correct failure status via STATUS() macro. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Decrease_Testsuite_Runtime created. v1.4.5-8-g1b1fa57
by git＠ins.uni-bonn.de 27 Jun '14

27 Jun '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Decrease_Testsuite_Runtime has been created at 1b1fa5704cd7e88e0af6f128b9e17b69d9aac345 (commit) - Log ----------------------------------------------------------------- ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch QtGUI_LogBox created. v1.4.5-10-g8b1dc21
by git＠ins.uni-bonn.de 27 Jun '14

27 Jun '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, QtGUI_LogBox has been created at 8b1dc21bdb83b06fcbbce1b30347d51fe1acf7cc (commit) - Log ----------------------------------------------------------------- commit 8b1dc21bdb83b06fcbbce1b30347d51fe1acf7cc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 19 23:30:53 2014 +0200 QtLogBox catches mousePressEvent and selects atom in log. - this should ease graphical debugging a lot. commit f241b693a65b5785c350feeb2142a8a8e8b98e2f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 19 23:00:14 2014 +0200 Added QtLogBox to QtMainWindow, using QDebugStream to display log. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Fragmentation_Automation_wo_JobMarket created. v1.4.5-28-gef0dc6a
by git＠ins.uni-bonn.de 27 Jun '14

27 Jun '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Fragmentation_Automation_wo_JobMarket has been created at ef0dc6aec0daf62326d90b941f9d8b2e0cd8abfb (commit) - Log ----------------------------------------------------------------- commit ef0dc6aec0daf62326d90b941f9d8b2e0cd8abfb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Apr 27 16:36:58 2014 +0200 Removed (very) old joiner and analyzer programs. - they are not needed anymore when FragmentationAutomation works also without JobMarket now. commit 21854c7e3d111962fab06041bc7dab5f959cccee Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Apr 23 13:57:20 2014 +0200 Using MPQCCommandFragmentController in FragmentationAutomationAction. - FragmentationAction does not lament missing JobMarket and output-types. commit b84db242bb23b3f493f94c9fd568ac2d27ea1d19 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Apr 23 13:57:57 2014 +0200 Added MPQCCommandFragmentController. - MPQCCommandFragmentController mimicks JobMarket's FragmentController or SpecificFragmentController, respectively, without relying on JobMarket. - modified FragmentJob to grant MPQCCommandFragmentController access to to setId(). In JobMarket access is granted to FragmentController which we do not inherit from here. commit 7f8c9ad6477b6f1c9412bc613327680267c2d70f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Apr 26 19:19:09 2014 +0200 FIX: Need to purge FragmentationResultContainer. - otherwise molecuilder stalls on quit. - requires JobMarket includes for pyMoleCuilder. commit 786d28e4533ffcfc1d63d95f08f65c92dd946946 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Apr 23 13:24:32 2014 +0200 Lib..FragmentationAutomation and lib..Jobs now also compiled without JobMarket. - FragmentationAutomationAction, MolecularDynamics.., and ParseFragmentJobs.. are also compiled, makes sense with upcoming MPQCCommandFragmentController. - must not compile SpecificFragmentController or MPQCFragmentController without JobMarket. - now requires libboost_iostreams. - this is due to MPQCCommandJob fiddling with streams to convert results. commit 2cc7faa758cecbb1c378dc72c67f25dfd7cbd323 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Apr 23 13:25:58 2014 +0200 LibJobMarket only compiled in if CONDJOBMARKET. commit 1dfe00d53becf9875c49a1c974659affcd083a2b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Apr 23 13:43:17 2014 +0200 Added inclusion switch on HAVE_JOBMARKET for files depending on JobMarket. - this is preparatory for using MPQCCommandJob without JobMarket. - this is possible with several basic files taken over from JobMarket project. - changes to ExportGraph_ToJobs, needs to export MPQCCommandJob when no HAVE_JOBMARKET is given. commit c3de511c88d74c7dd3ee27b035ff60e0ecf0b720 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Apr 23 13:19:14 2014 +0200 Added FragmentJob, ..Result, JobId, SystemCommandJob, and types from JobMarket. - taken over from version v1.1.4 with disclaimer adapted. - changed include paths to JobMarket -> Jobs/JobMarket. - these files are only used when no HAVE_JOBMARKET is defined. - SystemCommandJob had Info, causing extra Chronos entry. commit a498c1b15125817769fd9b27a366acd471b6b413 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Apr 22 18:11:59 2014 +0200 Extracted ResultContainer from ReceiveResultContainer. commit d4eaf11f136baa85a4bdfa982418399b22a44110 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Apr 22 17:59:51 2014 +0200 Renamed ResultContainer -> ReceivedResultContainer. - this belongs to SpecificFragmentController. - renamed _ResultContainer_impl -> _ReceiveResultContainer_impl. - FIX: also renamed inclusion guard. commit a42feea2484491fdb28f92c73043956e00a2d922 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Apr 24 23:56:03 2014 +0200 FIX: lib...FragmentationAutomation was linked in outside CONDJOBMARKET. commit 37ef6d9c81dd05d5433115e175bac28b62275986 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Mar 20 18:29:00 2014 +0100 Changed element class and periodentafel to have and use functions from ion. - If ionization is zero, fall back to other function. commit 31bd9c87bb06e45f77fe0e6e5b0d8ca6a9751ae7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Mar 20 18:28:44 2014 +0100 Added ion class, derived from element. commit 9b68fc02f36ed091c9bb88104aedd4c88c66f0dd Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Mar 5 23:12:01 2014 +0100 FitParticleChargesAction now averages over all fitted partial charges. - i.e. we iterate over all fragments and not just fit the first. commit 550f2a98ea5244ef1fc747f6debbc4635e941f7c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Mar 5 22:36:44 2014 +0100 Enhanced error messages in FitParticleChargesAction. commit e1fe7e9e5ab6e5acab3403d31d4139a02a1c1754 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Feb 27 21:15:41 2014 +0100 FunctionModel now uses list_of_arguments to split sequence of subsets of distances. - this fixes ambiguities with the set of distances: Imagine the distances within a water molecule as OH (A) and HH (B). We then may have a sequence of argument_t as AABAAB. And with the current implementation of CompoundPotential::splitUpArgumentsByModels() we would always choose the latter (and more complex) model. Hence, we make two calls to TriplePotential_Angle, instead of calls twice to PairPotential_Harmonic for A, one to PairPotential_Harmonic for B, and once to TriplePotential_Angle for AAB. - now, we new list looks like A,A,B,AAB where each tuple of distances can be uniquely associated with a specific potential. - changed signatures of EmpiricalPotential::operator(), ::derivative(), ::parameter_derivative(). This involved changing all of the current specific potentials and CompoundPotential. - TrainingData must discern between the InputVector_t (just all distances) and the FilteredInputVector_t (tuples of subsets of distances). - FunctionApproximation now has list_of_arguments_t as parameter to evaluate() and evaluate_derivative(). - DOCU: docu change in TrainingData. commit 16227a32089e461901d97290d3e2fb626919cf26 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Feb 27 22:44:28 2014 +0100 Removed FunctionModel::getSpecificExtractor() that is not needed anymore. - it was only used in FitPotentialAction generating WorstFragmentMap. - strangely required to change the order of some libraries (libMolecuilderFragmentation_Summation needed further down). commit f4496dfa7f4fdd324a537113b0d2419c2bc7496f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Feb 27 22:26:39 2014 +0100 Extracted associating each configuration with its L2 error into TrainingData. commit 4e009d7565cb91ce80fa628407fbf1936e23d12c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Feb 27 18:46:49 2014 +0100 Extracted function from PotentialFitPotentialAction::performCall(). - new function getNumbersFromElements(). - also added warning when take-best-of and set-threshold have both been used. commit 1ba8a154f0c3a28438bcfafdbb90182004c65f55 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Feb 27 20:07:56 2014 +0100 DOCU: Extended documentation on FunctionApproximation and potential fitting. commit 1b1fa5704cd7e88e0af6f128b9e17b69d9aac345 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 25 00:16:55 2014 +0200 TESTFIX: Reduced size of loaded file for regression test InvertMolecules to speed up. commit 89604a46c1db5a85643b922ce06b5f4b5f0c5345 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 25 00:14:38 2014 +0200 TESTFIX: Changed size of loaded file for unselection AllMolecules regression test. commit f678fc41737d988593634f12c8a2a6dbb76c282f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 25 00:06:02 2014 +0200 TESTFIX: Reduced box size in FillRegularGrid to speed up regression test. commit e4157b9b9699796a9b05157d81e33042b7670e3b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 25 00:02:45 2014 +0200 TESTFIX: Reduced box size in DipoleCorrelation-DiscreteAngle regression test to speed up. - the histogram files have not yet been changed. commit 6d3cb81a37b7c7089163a6bbf61f4c8e6874cc81 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 24 23:57:37 2014 +0200 TESTFIX: reduced dbond file size in regression test Molecules/BondFile. commit 2cc1cbe98dd0605266ded20ff583bfaf6b64fb77 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 24 23:29:38 2014 +0200 TESTFIX: FillSphericalSurface regression now with just 20 instead of 200 fill points. commit 1dbbebbd0643e4b6a024acbe95232cacda8a7a10 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 24 23:41:19 2014 +0200 TESTFIX: reduced required threshold for fit-potential regression tests to speed up. commit 0932c2cf081d696ef9cc91e7a5183c13064994e0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 26 09:41:59 2014 +0200 FIX: RandomNumberEngine_Encapsulation::clone() did not set the seed obtained from its prototype. - this caused all engines to always start with default seed of 1, irrespective of the set parameter. The engine is always cloned from prototypes in the factory that can be manipulated to change their parameters. Hence, clone needs to set the seed (the engine's only parameter). - EmpiricalPotentials now use RandomNumberGenerator to obtain random starting values. - TESTFIX: fit-potential regression tests now use fixed seed in order to always take the same amount of time (some test runs in debug mode take very long because of ill-chosen random values). ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch StatusToAllActions created. v1.4.5-5-gffe4889
by git＠ins.uni-bonn.de 19 Jun '14

19 Jun '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, StatusToAllActions has been created at ffe48897f51117b06b84ecf4999b484bde338000 (commit) - Log ----------------------------------------------------------------- commit ffe48897f51117b06b84ecf4999b484bde338000 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 19 15:56:27 2014 +0200 All Actions now give correct failure status via STATUS() macro. commit 0c97ae3c6e80a4bfb7335c17516e13768eeb2a9d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 19 15:55:01 2014 +0200 ActionQueue gives caught failure of Action and success via pushStatus(). commit b8cbb2ba3c8313dbb06da64b9e946e423926b9ec Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 19 13:02:54 2014 +0200 Updated all UI's StatusIndicator classes to use ActionStatusList. - CommandLineStatusIndicator and TextStatusIndicator just print the message. - QtStatusBar has a QTimer that updates the status message in second intervals. commit c37ef8c451875cf29fdbc5ccacb6824377f33fbb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 19 11:17:06 2014 +0200 Added observable ActionStatusList to ActionQueue. - this allows to fetch Status messages from Actions at a central place. - Action::pushStatus() as befriended proxy to ActionQueue::pushStatus() added. - equipped ActionStatusList with a thread lock to protect access. commit 2aa9ef3809506a1158331a345bf5475b6f87f77a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 19 14:28:15 2014 +0200 FIX: TxMenu and CommandLineWindow lacked waitQueue() in the wait-for-key loop. - this has occured due to queueAction() introduction. - otherwise the UI is destroyed before even the first Action has started. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Add_SaturateAtomsAction created. v1.4.5-30-g6de8af2
by git＠ins.uni-bonn.de 18 Jun '14

18 Jun '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Add_SaturateAtomsAction has been created at 6de8af2811afb747a88e9e9fd96f40baa71e43b8 (commit) - Log ----------------------------------------------------------------- commit 6de8af2811afb747a88e9e9fd96f40baa71e43b8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 2 17:19:56 2014 +0200 tempcommit: Marking some fragmentation expression tests again as working. Merge with ... commit 19c651b9af7c202503d99b98b3675c5f3222f0c9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 17 18:21:10 2014 +0200 Added regression test for saturate-atoms. commit ea9e2ae818f63c3302be23d3d23431aabd4dbc0b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 16 15:33:42 2014 +0200 Added SaturateAtomsAction. - also added undo/redo. commit 7972fc8a8e9d36e4002e1cb2fb7d7e7d5b7eec84 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 16 15:27:44 2014 +0200 Added (fake) RealHydrogenPool which just creates hydrogens in the real world. - this is used to saturate molecules. commit f6b19b2294ee5be2a857d754f673912eb1d355b5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 17 18:48:23 2014 +0200 FIX: Allowing AtomicInfo only atoms not associated to molecules. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Generalize_AddHydrogenSaturation created. v1.4.5-25-ge82bbb7
by git＠ins.uni-bonn.de 18 Jun '14

18 Jun '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Generalize_AddHydrogenSaturation has been created at e82bbb7fc6750560a3c172437d0a90fb697ff754 (commit) - Log ----------------------------------------------------------------- commit e82bbb7fc6750560a3c172437d0a90fb697ff754 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jun 13 13:23:12 2014 +0200 Triangle case is now done properly. - when both centers are at origin, we still need to rotate the planes to match (i.e. the normals), and afterwards we need to rotate around self for proper orientation. commit efce7f3f66e3af0a52fc92be312bf0315c834a1b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 12 09:31:24 2014 +0200 Extracted construction of axis and angle for various cases when Centers are zero. commit ea5c03bbef19dfba90a28d91dfcdbd7f7813f36f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 12 09:23:12 2014 +0200 Checking whether oldCenter or newCenter are zero. commit f6893998dee1bf416a2ed569175c7d03fb6c9948 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:58:13 2014 +0200 Extended SphericalPointDistributionUnitTest to two and three matching points for all functions. commit 54ff0d95eaa0f809efb59cf977eded5d672bcf63 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:42:39 2014 +0200 Dropped quaternion rotation for simple arbitrary rotation axis and angle. - with newCenter, oldCenter and the cross product we have all we need: a rotation axis and an angle. We don't need to burden ourselves with those stupid, absolutely not working quaternions. - removeMatchingPoints() now works on an array. - Orientation rotation was wrong way round, added check. commit a2d87350c03eb34255e021f57b32e9ec5c8daedf Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:18:40 2014 +0200 Added "arbitrary" rotation for matchSphericalPointDistributionsTest_2(). commit ff1c4fb9313a3358a329c3503007b5c7825d84b6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:17:10 2014 +0200 Adding QuaternionTest for SphericalPointDistributionUnitTest, fixed tests. - just first two components get flipped when first point is at (0,1,0). commit 0b487f1e7f727e3abfea911f5a7bd0460264e0f4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 5 19:16:26 2014 +0200 Implemented rotations via boost::quaternions. commit 396a4f29629e0e1a03d37b5f96e60a909dd10d73 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 4 13:23:31 2014 +0200 Added more unit test functions up to N=8 to SphericalPointDistributionUnitTest. commit 11596ef740378ffd386f73685a1e50030953da58 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 4 13:22:49 2014 +0200 Fixes to SaturatedFragment::saturateFragment(). - properly setting up the number of points and the "old" polygon. - properly filling in the hydrogen atoms at the calculated places. - We have the number of remaining bonds plus the rest. The rest is the valence minus the number of remaining bonds each weighted with its degree. This gives the right number of places to put hydrogens and fill up the valence. commit 53fe6b8da6effb00a4fef8532be78a8ea8689f6f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 2 16:51:33 2014 +0200 FIX: SphericalPointDistribution succeeds with unit test. commit 649e71000a4f93c39b1f44da065b0d756ee3ccc1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 30 15:06:25 2014 +0200 Added Logging to SphericalPointDistribution for debugging. commit fd145b143baf0809c887f315ed87d19bd71e86dd Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 30 15:28:15 2014 +0200 Shifted all SphericalPointDistribution::get() specializations into .cpp file. commit d10943d6bc8a0570ecbde78c9e51ef5ba77b4e9e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 30 15:31:15 2014 +0200 Moved all code from header of SphericalPointDistribution into cpp module. commit af1507fdfb335793560935f81e69b579d7b2734c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 20:15:49 2014 +0200 SphericalPointDistribution now has full functionality. - we look for a best matching between present points and desired ideal configuration, we rotate for alignment and fill all remaining vacant points with hydrogens. commit e3ec3ebe6974d353fa28242fac3ccb2eb31ff303 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 20:15:26 2014 +0200 Added unit tests for SphericalPointDistribution. commit 62dd72bf296faef924a8b99335755f0f4de4ea4e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 13:29:27 2014 +0200 Reimplemented SaturatedFragment::saturateAtom() and added ::setHydrogenReplacement(). - this is now based on an ideal distribution of electrons around an atom via the VSPER model which we match as closely as possible with the still bound neighboring atoms and fill all remaining vacant spots with hydrogens. - SaturatedFragment sets father simply to the _given_ atom. commit 88594a83dd008a4e9b24fe9205b31a5d2d16401c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 13:29:03 2014 +0200 Added matchSphericalPointDistributions() to SphericalPointDistribution. - so far we do nothing. commit 3bb01abf67e45acb5f6ac85d9e3fcdd7c7073ed0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 13:11:39 2014 +0200 Added SphericalPointDistribution for points on spherical surface according to VSEPR. - this is taken from CreateVspeShape.py from Christian Neuen. commit 986f5e23193a68329511333c166a510ff6b8a10f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 12:00:26 2014 +0200 Added SaturateFragment()::saturateAtom() replacing all cut bonds at once. - so far, we have just outsourced the loop over each cut bond into this function. commit 6648f3c1974848221ed96a0e17ac5cb62652c109 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 12:30:49 2014 +0200 FIX: BondedParticleInfo::BondList is now a typedef. - removed the define. commit d60061a9fe7ef8590109e544d78fb26fb15b2a00 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 11:55:28 2014 +0200 Refactored SaturatedFragment::saturate() using list of cut bonds. - this is preparatory for replacing AddHydrogenReplacementAtom(). commit c7dcd239943c0de6620cbc833cf560a83e8e80dd Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 26 21:53:59 2013 +0200 SaturatedFragment::AddHydrogenReplacementAtom() uses degree 1 if other is missing. commit 956212d1f419a9d21ccf6d2457cc6f2f779f9338 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 26 21:49:32 2013 +0200 Removed molecule::AddHydrogenReplacement() and BreadthFirstSearchAdd. - this capability has been transfered to SaturatedFragment, and BFSAdd has not been used for a long, long time. commit a479674d71b29968105191c460bfa6bda4d492b4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jun 13 13:22:14 2014 +0200 FIX: VectorContent::Normalize() did not check for zero factor. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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