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 43efd11e0dd5155fd4722c6a8367d617440a17dd (commit) - Log ----------------------------------------------------------------- commit 43efd11e0dd5155fd4722c6a8367d617440a17dd Author: Frederik Heber <heber@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 d4bb11a516848e3baf622aa3706957ac05062c8c Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu May 29 20:15:26 2014 +0200 Added unit tests for SphericalPointDistribution. commit eb4169ba8d4e50baf4599ba431fde66d07504407 Author: Frederik Heber <heber@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. commit 17064a47bf26ea24e411a57a6cc6501acf7e9eaa Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu May 29 13:29:03 2014 +0200 tempcommit: Added matchSphericalPointDistributions() to SphericalPointDistribution. - so far we do nothing. commit 5714141b8597e64fc23e1440a9cf5132cf99ed60 Author: Frederik Heber <heber@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 1f2e289d601710d30b08eaf9a1615936ed07d4d2 Author: Frederik Heber <heber@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 837f8b93e5f635c301942a7face0aa6929c8b501 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu May 29 12:30:49 2014 +0200 FIX: BondedParticleInfo::BondList is now a typedef. - removed the define. commit 42fdcdd773c43c0f2c86b88cd1d5aba7dc88eec6 Author: Frederik Heber <heber@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 896d6b6f16e9e0c6c2c0c6a592258bfd63c91e70 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Aug 27 00:07:18 2013 +0200 tempcommit: Allow S-O bonds to be saturated. - we don't have double bond info nor angle info. So this is just a test fix. commit 37af8fd1d5e372c7bd6478d7f759de871494aa40 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Mon Aug 26 21:53:59 2013 +0200 SaturatedFragment::AddHydrogenReplacementAtom() uses degree 1 if other is missing. commit 4474a555cbe0407e720b396332a9d441fc833013 Author: Frederik Heber <heber@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. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder