[Molecuilder-devel] [SCM] MoleCuilder branch Generalize_AddHydrogenSaturation created. v1.4.5-11-g43efd11

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The branch, Generalize_AddHydrogenSaturation has been created
        at  43efd11e0dd5155fd4722c6a8367d617440a17dd (commit)

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commit 43efd11e0dd5155fd4722c6a8367d617440a17dd
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 d4bb11a516848e3baf622aa3706957ac05062c8c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu May 29 20:15:26 2014 +0200

    Added unit tests for SphericalPointDistribution.

commit eb4169ba8d4e50baf4599ba431fde66d07504407
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.

commit 17064a47bf26ea24e411a57a6cc6501acf7e9eaa
Author: Frederik Heber <heber at 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 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 1f2e289d601710d30b08eaf9a1615936ed07d4d2
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 837f8b93e5f635c301942a7face0aa6929c8b501
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 42fdcdd773c43c0f2c86b88cd1d5aba7dc88eec6
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 896d6b6f16e9e0c6c2c0c6a592258bfd63c91e70
Author: Frederik Heber <heber at 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 at 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 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.

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