* Fixes atom documentation
* Fixes#1461
This is a complicated one. Basically URANGE_CHECK when
used on unsigned integers has a problem when the size of
the range it’s checking is 0. The standard operations is
to check
URANGE(num, size-1)
Which (for unsigned integers) obviously rolls over.
This fixes all usage cases to be
URANGE(num+1, size)
And fixes the bugs found. (addBond and the mmff tests)
* Fixes#1461 - Updates URANGE_CHECK to be 0<=x<hi
- fixed a bug in Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp
which caused misassignment of atom types in CYGUAN01 upon shuffling
the order of atoms in the validation SDF files
- added checks for acos and asin function parameters to be within
a (-1, 1) range
to the current value) (C++/Python)
- added absolute/relative AngleConstraints (C++/Python)
- added absolute/relative TorsionConstraints (C++/Python)
- added PositionConstraints (C++/Python)
- exposed fixedPoints from Python
- added relevant C++/Python tests
- removed a number of redundant "this->" in member functions
- moved some getGrad() code into Utils::calcAngleBendGrad and
Utils::calcTorsionGrad to avoid repeating the same code
for constraints
4-membered rings containing sp2 atoms. The hack consists in
altering on-the-fly the theta0 equilibrium angle, depending on
ring size and collocation of the two edges of the angle (i.e.,
both edges inside the ring or one inside and one outside)
- Added a relevant test in
Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp
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
