[Molecuilder-devel] [SCM] MoleCuilder branch findBestMatching_HigherBondDegrees created. v1.4.6-37-g32cfaab
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commit 32cfaab88f63a122cc5885985b96503048d92a05
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 7c73042ce3ecfd0229d9ffc11a0d6b519f339f9c
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 6750c12cb19911e7bb5d746995ab74bc6da56e48
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 36d6d262176326d6bca5d9fa3e6c1ffbc32d218a
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 0582456e28195231839168d506923f51e3734958
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 2b523bd65dcce9bf7c6cc1737860fafd93b58184
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 f9596827dae2cf9bcb2b4edb5638f646bf96754f
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 c3ec1bbeddeaf487adf754a72062e8057ad715cc
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 42651d59cf8359611afa940937b329dd955e0588
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 8327a81827f6c3b48a510b008c3ad6864116d9b3
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 abab6cc2c35cf1f86014477bfcbfe31ceb2d5816
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 ea30df3279ae1c1dd3b8b5a691e756830c4cbf69
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 4eb8662e9ea6e43fdb6e875574c2e8c4fe9cd157
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 07df22983d48abb8c008a57c72374069f08af7c4
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Jun 24 18:39:55 2014 +0200
tempcommit: All scripts in tests/Fragmentation added again.
commit d8c1bad2c68f0c8174def8f6fde0bdbec8e4140b
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 3eec68b7518abae29e0938025a6e94dce32d69fe
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 37b6ab4eb7884a58087a297211e2792e8c4e20ff
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 3e675ef05b13282c13d5f66303055b61955515b1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Jun 5 19:16:26 2014 +0200
Implemented rotations via boost::quaternions.
commit f22a9f3f5a25efd7fdea746b77e7477637465e7f
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 2f9510330f2000749bd70de7a77efef928cff83c
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.
- marked again all tests/Fragmentation scripts as XFAIL.
commit 5ee335e69787dd65e7fe1dd2d2e8a1f59867f62a
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 tests/Fragmentation scripts again.
commit b805acbb7248f6ff6d0a99b6510098b8d92bbadc
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 9420d52eda268e085ea3c30226ac7c25c33bdbba
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 d663b8dbe908b90a550d679a1c1981af0df0e269
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.
- temporarily removed all tests/Fragmentation tests.
commit fff44a135d0a59ea42e78f3efc8b080438425a13
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu May 29 20:15:26 2014 +0200
Added unit tests for SphericalPointDistribution.
commit 2bba27e7f7f57c25ca0b57d3615f8ebe482597e8
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 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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