[Molecuilder-devel] [SCM] MoleCuilder branch findBestMatching_HigherBondDegrees created. v1.4.5-40-g2df8f03
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The branch, findBestMatching_HigherBondDegrees has been created
at 2df8f03de678873fd4893bc695c15dfb2baed154 (commit)
- Log -----------------------------------------------------------------
commit 2df8f03de678873fd4893bc695c15dfb2baed154
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 5cd0c01d3293a635c1da2bd793518ba04738eb37
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 9fc27da9dcd012345967223df0baee8879080630
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 acec70e202f4044f8d42bd6097a7f709d5f11ca9
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 9625bbfd02bb7b5b8fa07ca95aa7306a244627e0
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 844b94b994c6208cfe9f9856a5e5121d642bb6b0
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 4dc743debf9491456934d97ad37a255ca61c484f
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 2a2d8503882c4119a3e4f2966620f69c3e625958
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 340547df85785010d86e6f18436e01ff8db8af16
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 846c853264acf8d4799925a3601755226a34aafc
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 1e8c867ef68a86fdbeb4a98c7efe70b3eeae91bb
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 09ec9b7e0a368ac5cab79be100d8779e70fdfbbe
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Sat Jul 12 13:55:44 2014 +0200
tempcommit: Extracted get() to extra module.
commit 3639b9875db838404cee01dfc0b2c5c48284aa74
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Mon Jul 14 22:14:36 2014 +0200
Added case 0 and 1 to SphericalPointDistribution.
commit d8167e1b6d304045dacb7222e37b5fcebb87616f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Mon Jul 14 22:14:26 2014 +0200
Added case 0 and 1 to saturateAtoms().
commit bf8c37e62015e75e80bc8e67b1045956987c5e47
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 3fbdfbe5c8eefa8f98578ee40e314821963b2a71
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 847a19cbecb25ff5e9fb700aefb5c17325fb2cd9
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 5b8d193a2b3b7a0700f232a00eabc3fa19b16cd7
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 9344a9969937b0960b1610c3d5d7df1c2a21de60
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 3ae3aa39aa73a6a83ec14400c3539d9839b0c5fe
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 e401aa70a6f25a1138e3493a693bd29a2b3a4ab7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Jun 5 19:16:26 2014 +0200
Implemented rotations via boost::quaternions.
commit 900ee80bf6467c1da9ad01b86ea1e7a7041eb131
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 27ba2c799724cd9a6121c4e8b2a1d0865ff7d1c7
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 2a72eff1a77ee435c7dcc9e2d236de076026990d
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 cd80c552438d2363d47e01ec873c599f8c757d6e
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 22e6dac35e2644bbd09aab89dee66ffdd76627a0
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 fbb16d7138ca586231e19511978bbc20fb9975aa
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 31e59fb2b9c500d57e762be5059c1cb7ac11f675
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu May 29 20:15:26 2014 +0200
Added unit tests for SphericalPointDistribution.
commit 465bc2529bae68c6028e31502ce9d336e3258808
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 5870b5b1e66a76563dc034aadaaa4d645c9e83be
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 f46c4387ed4849a2b2ae189e31827a153fa65106
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 7414e5cd0fca8a4cfe755a3eb9423ccb6305b9db
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 ecf5333632140eaeb22aace2f2d10ca995c42ccd
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 65ce6501b46bf096e98a8dc363380b58c7ded4f4
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 33ea47fd820fb196d78a4545693e1273162c671c
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 e99d4f93951ff55ad8224cfa179c4804b375aeab
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 6f7f656a890de97442f4f63e64f6f086cfb6b8d9
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 84ea50df3e76dd78b71cbe859592887c56f81818
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 efeb2665aeeeb24d3497611030d993afc6a686c2
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 8c4fc3cf00fdeddea494c6eb9a3d6c86cb750ea7
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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