[Molecuilder-devel] [SCM] MoleCuilder branch findBestMatching_HigherBondDegrees created. v1.4.6-37-g8437328
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commit 84373283aed9dfacd2c29f96607356331923b332
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Sat Jul 12 21:07:44 2014 +0200
recurseMatching() now takes connections into account.
- matchSphericalPointDistribution() replaced by getRemainingPoints() as that
describes what it does. match...() sounds symmetrical which the function
is no longer as connection is associated with former _newpolygon.
- SphericalPointDistribution now has internal points and adjacency,
initialized by initSelf().
- findBestMatching() and getRemainingPoints() are no longer static functions.
- all unit tests are working again, including the .._multiple() that tests
for joint points due to bond degree greater than 1.
- the huge case switch in SaturatedFragment::saturateAtom() now resides in
initSelf().
commit ccccd2c961ffe80db854a7902cacbcf26c44ff73
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Sat Jul 12 18:19:46 2014 +0200
Removed all IsZero() checking and special cases for the triangle idea.
commit f3234b14f3c6731657a1772d6798b8dc48d5ed02
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Sat Jul 12 13:57:54 2014 +0200
Added getConnections() to SphericalPointDistribution.
- we use tesselation in order to extract the connection information between
nearest neighboring points from the BoundaryLines of the tesselation. The
triangles are ideal as they assure that no point lies within a triangle,
hence all these points may be safely combined.
- functions reside in extra module as with get().
- added extensive unit tests.
commit 299a7418d1a00dade644adc26d036813970664b7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Sat Jul 12 13:56:14 2014 +0200
Added new convenience library libMolecuilderTesselation.
- we need this for getting the connection information between the nearest
neighboring points on the sphere.
commit 9bb93c279b1a6f5c62bd8e6b0ac9c67ffd7aa462
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Jul 10 00:08:37 2014 +0200
Added calculation of center of minimum distance by bisection.
- this will give us a unique a definite point independent of the (rotational)
position of the point set on the unit sphere.
commit 79c70688bd13a002a24660be2c7eccc92bd5fcdb
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Wed Jul 9 23:14:53 2014 +0200
Refactoring SphericalPointDistribution to combine point list and subset of indices.
- added struct PolygonWithIndices.
commit 455400b95d97c90534c16a21a700e019cf50dc68
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Mon Jul 14 22:05:51 2014 +0200
FIX: Determining angle with respect to oldCenter and not projecting anymore.
commit 30e64c99c35980d249eb3de86f93b718245dba44
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Jul 3 19:17:04 2014 +0200
SphericalPointDistribution is now working with bond degree weights.
- L1THRESHOLD in recurseMatching() moved over to class body.
- increased verbosity level of ...Matching() functions by one, added note on
eventually chosen matching and why.
- we assert that bestL2 is not too large.
- FIX: calculateErrorOfMatching() did not use absolute value of gap for L1
error.
commit 34521176aca2aeaecb4a822b1c372f38fd1978cf
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Mon Jun 30 11:35:42 2014 +0200
recurseMatching() now works on IndexTupleList_t.
- also rewrote calculatePairwiseDistances() and calculateErrorOfMatching().
commit e81c43f2e7435c5688ea6faeda1bfcd437c76469
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Sun Jun 29 23:20:49 2014 +0200
Extracted joinPoints() function to make it accessible to tests.
- added unit test.
- moved some function definitions around and added documentation.
commit 09be85056bb9145bf23af92fc25cc64ef4ccfa3f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Sun Jun 29 20:02:32 2014 +0200
Extended SphericalPointDistribution::Polygon_t to WeightedPolygon_t.
- contains additionally the weights from the already present points.
- in order to deal sensibly with present bonds of higher degree (>1) that shift
neighboring occupied orbitals even further away, we additionally pass on the
bond degree. This indicates how many points of the N points have to be
accumulated for this on present bond.
commit 739623e1eccbc0e0214d2ee07d09962b2b74d38b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Jun 12 09:23:12 2014 +0200
Using the idea of three points giving a triangle to find rotation axis.
- we calculate the center of either triangle and rotate the center of the
ideal point distribution to match the one from the given points.
- next we have the triangles normals as axis, take the first matching point
and rotate align it.
- we have to deal with a lot of special cases: What if only zero, one, or
two points are given ...
- in general we assume that the triangle lies relatively flat on the sphere's
surface but what if the origin is in the triangle plane or even the
calculated center is at the origin ...
commit 0221dd96e476cd906da483767c0720be67aa2efa
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 459cb215c5aaff35348da26627f899d062c1bab0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Jun 24 18:39:55 2014 +0200
tempcommit: Removed skipping of scripts in tests/Fragmentation again.
commit 019956cbdd1f29b2e25d6fbebd00d9ee089c883f
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.
- TESTFIX: removed QuaternionTest from SphericalPointDistributionTest.
commit 6e6ac8887bcd442e8f99f5617bccb5cb993b45d9
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 58074bd81bc53778839be4e389dfca6e6a08fd41
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).
- removed XFAIL from FragmentMolecule and StoreSaturatedFragment regression
tests.
commit d887b9a8e45b626ce32175d07592cc0a2c84e05e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Jun 5 19:16:26 2014 +0200
Implemented rotations via boost::quaternions.
commit 0f99c00acc8e10b6a3fdc43633148d8f96c156d7
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.
- marked unit test as XFAIL.
commit 2e2ab4c0c5db85d7d08340d6a9757b60dc8d2fa8
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.
- TESTS: Removed XFAIL from FragmentMolecule cycles regression test.
commit 9a970729e39cd12d20109261c377a9875f9b8d7b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Mon Jun 2 16:51:33 2014 +0200
FIX: SphericalPointDistribution succeeds with unit test.
- removed XFAIL from FragmentationAutomation regression tests.
commit 30cd476821124282d0339ca217f42b31781a4a2e
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 8be52eb93e07efad5c321af8f08069a6eb6e34b6
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 43cef5bdab8a49793e3bf2ab01a351923606c17f
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.
- TESTS: temporarily skipping all Fragmentation regression tests,
FragmentationAutomation regression tests marked as XFAIL.
commit fce8c1345985e3a228b3386a565613e2b279b057
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu May 29 20:15:26 2014 +0200
Added unit tests for SphericalPointDistribution.
commit 1078546931ea95529f87659dbd77106c65322055
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.
- TEST: dimethyl_bromomalonate marked as XFAIL.
commit 5e493c056cc54287b7bf9b6271f93fe8dc2ff945
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 b1f0cd777ea2c2da39e74352ad4ef59f3f95c8fc
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 d1a9684753cced0c8a32d168f5d719269ee83636
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 29dc30eb0a9af60e3d5d95705c3dc27681e79ec1
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 82627213ad32b651ea7dd756756f310db41361bc
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 9ab2fb34a97f30798bf58a15dabc522338530163
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 ca38704916242f977db4bf7c96bb0adea7dd0593
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 030ede0ba59a8d3ccca23d71162da9db37656473
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Jul 10 19:06:56 2014 +0200
Vector::Is...() functions extended for numeric threshold.
- if none given we use LINALG_MYEPSILON(), otherwise given to function.
- this allows for rounding-sensible IsEqualTo() checking and more.
commit 73fa9ef7159349c386272c868091c9cbd2df9ffa
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Jul 3 19:13:39 2014 +0200
FIX: Plane's cstor did not check for linear dependence in a numerical stable way.
- we check with NormSquared() and we use Projection() instead of Angle() to
check whether vectors are linear dependent.
commit 0fa470da645ae2613038cd51107035cf812961a2
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.
commit 54705ccefd926c54e18d97c6ac2433c15a322695
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Mon Jun 23 20:00:48 2014 +0200
FIX: CodePatterns_LIBS was introduced in AM_LDFLAGS and not in LIBS.
- this might have caused problems with libtool not correctly noting down this
lib as a dependency.
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