[Molecuilder-devel] [SCM] MoleCuilder branch Generalize_AddHydrogenSaturation created. v1.4.5-25-ge82bbb7

Wed Jun 18 10:34:59 CEST 2014

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The branch, Generalize_AddHydrogenSaturation has been created
        at  e82bbb7fc6750560a3c172437d0a90fb697ff754 (commit)

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commit e82bbb7fc6750560a3c172437d0a90fb697ff754
Author: Frederik Heber <heber at 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 at 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 at 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 at 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 at 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 at 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 at 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 at ins.uni-bonn.de>
Date:   Thu Jun 5 19:16:26 2014 +0200

    Implemented rotations via boost::quaternions.

commit 396a4f29629e0e1a03d37b5f96e60a909dd10d73
Author: Frederik Heber <heber at 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 at 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 at 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 at 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 at 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 at 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 at 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 at ins.uni-bonn.de>
Date:   Thu May 29 20:15:26 2014 +0200

    Added unit tests for SphericalPointDistribution.

commit 62dd72bf296faef924a8b99335755f0f4de4ea4e
Author: Frederik Heber <heber at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at ins.uni-bonn.de>
Date:   Fri Jun 13 13:22:14 2014 +0200

    FIX: VectorContent::Normalize() did not check for zero factor.

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