Reduce error tolerance for MMFF charges

This reduces the error tolerance for partial charges in
the MMFF validation test.

Change-Id: I5228311267d2a1e176a557b73651d9620431fc59
Mark VBO as dirty when vertex colors change

This fixes a bug in which the GraphicsVertexBuffer class was
not marking its VBO as dirty when the vertex colors were changed
with the setColors() method.

Change-Id: I49a18b3c89654088672afe61eef076c76d770e1a
Add ElectrostaticPotential color mode to GraphicsMolecularSurfaceItem

This adds support for coloring molecular surfaces by electrostatic
potential. For now, the colors for the electrostatic potential ranges
are hard coded but this will be made configurable in the future.

Change-Id: I4bd1e51fc2d5914e147287a039c59827064e8e8c
Add electrostatic potential coloring to surface-viewer demo

This adds support for the new ElectrostaticPotential surface
coloring option to the surface-viewer demo application.

Change-Id: I475d57e92ff94de422ef015659ad7cad195719d8
Merge topic 'reduce-mmff-error-tolerance' into master

c18d993f Reduce error tolerance for MMFF charges
Merge topic 'electrostatic-potential-surface' into master

60a16abe Add electrostatic potential coloring to surface-viewer demo
b9c45774 Add ElectrostaticPotential color mode to GraphicsMolecularSurfaceItem
2bd8ad3b Mark VBO as dirty when vertex colors change
Fix misspellings

This fixes a few misspellings in variables and comments.

Change-Id: I654ed4b8c840f828f05dde149571f09612bbf084
Add boost::graph_traits specialization for Molecule

This adds a specialization of the boost::graph_traits template
for the Molecule class. This allows for chemkit::Molecule's to
be used with the algorithms from the Boost graph library.

Change-Id: I1f2db378397f5572506e6ce0c20bc521edd81239
Merge topic 'fix-misspellings' into master

85557be5 Fix misspellings
Rename 'mlogp' descriptor to 'moriguchi-logp'

This renames the 'mlogp' descriptor to 'moriguchi-logp'. The
name for the descriptor is being changed to differentiate it
from the soon to be added 'mannhold-logp' descriptor.

Change-Id: I7ecf7ad45338db049c4fa9e629302244b8c6cf99
Add 'mannhold-logp' descriptor

This adds a new molecular descriptor named 'mannhold-logp'
which predicts the logP of a molecule using a simple atom
count based method.

Change-Id: I304a2d6ad875db80f895286aa0cb3e9f6329d4bb
Fix bug when calculating index of OOP-bending parameters

This fixes a minor bug when calculating the index for the
out of plane bending parameters in the MMFF force field.

Thanks to Robert Hanson for spotting this bug.

Change-Id: I9fac4fdf355fa3ea80381ee43c363c0da6e7f1da
Add atomic polarizability descriptors

This adds a new plugin named 'apol' which implements two
molecular descriptors based on the atomic polarizabilities
of the atoms in the molecule.

Change-Id: Idad493081343fe9faca8c833a5ec6867499f329c
Merge topic 'molecule-graph-traits' into master

3c8206ff Add boost::graph_traits specialization for Molecule
Use the add_test() function with NAME and COMMAND

This changes the call to add_test() to use the new version
with NAME and COMMAND arguments. This fixes issues where the
tests could not be found and thus were not being run.

Change-Id: Iea2152fce50023c0a4ad025a878d2a147018048a
Merge topic 'fix-mmff-oop-bending-paramters' into master

b980b22f Fix bug when calculating index of OOP-bending parameters
Add CHEMKIT_OS_* variables to top-level CMakeLists.txt

This moves the CHEMKIT_OS_* CMake variables to the top-level
CMakeLists.txt file so that they can be used by the tests
directories as well as the source directories.

Change-Id: I6c94ce23102839d4eaa763717dd88a92d3f5fefa
Only enable plugins.Xtc test when the xtc plugin is enabled

This fixes a bug in which the plugins.Xtc test was being built
and run even when the xtc plugin was not. The xtc plugin and its
test require that the platform to support XDR and thus it is only
enabled on UNIX systems (excluding Mac OSX).

Change-Id: I1b3abfd0d22de5c4e5c4755312f8a9bfe9c3e90e
Merge topic 'add-test-with-name-command' into master

9fb7966d Use the add_test() function with NAME and COMMAND
Merge topic 'disable-xtc-test-on-mac' into master

4239c2ce Only enable plugins.Xtc test when the xtc plugin is enabled
b595a736 Add CHEMKIT_OS_* variables to top-level CMakeLists.txt