rdkit/rdkit — pull request #106 by ptosco (2013-09-24 09:33:12+00:00)
Title: UFF corrections as per Marcus Martin suggestions

The only relevant changes to implement Marcus Martin corrections
(http://towhee.sourceforge.net/forcefields/uff.html)
to original Rappe' UFF equations are in Code/ForceField/UFF/AngleBend.cpp
and Code/ForceField/UFF/BondStretch.cpp; the changes in
Code/ForceField/UFF/TorsionAngle.cpp are purely cosmetic.

Tests modified according to the small differences in geometries
and energies following the implementation of those corrections:
- Code/ForceField/UFF/testUFFForceField.cpp,
- Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py,
- Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp,
- Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py,
- rdkit/Chem/Pharm3D/UnitTestEmbed.py

Coordinate files modified according to the small differences in
geometries following the implementation of those corrections:
- Code/GraphMol/DistGeomHelpers/test_data/initCoords.random.sdf