[vtk-developers] vtkChemistry pushed for review

[David Lonie]

Hi list,

I've pushed the vtkChemistry branch to Gerrit. I've chunked the kit
into a total of 17 patches to make it a bit more manageable. Most
commits also contain several tests that check for regressions and
provide examples of intended usage. In a nutshell,

- e18a93a Added vtkElectronActor/vtkElectronMapper to vtkChemistry.
Classes that control rendering of electronic data (as vtkImageData)
using isosurface, contouring, and volume rendering methods

- e41ed36 Added vtkSimpleBondPerceiver to vtkChemistry.
Very simple algorithm that searches for bonds in a collection of
atomic positions. If two atoms are close enough (based on their atomic
radii), a single bond is added.

- b7dacdd Added vtkMoleculeAlgorithm to vtkChemistry
Abstract base class added for vtkSimpleBondPerceiver

- ae31fe0 Added vtkProgrammableElectronicData to vtkChemistry.
- 1fcfabe Added OpenQube support to vtkChemistry.
- 3f03c8e Added vtkAbstractElectronicData to vtkChemistry.
Storage and usage of electronic information. vtkAbstractElectronicData
defines an interface for interacting with a collection of vtkImageData
objects that represent molecular orbitals or electron density. The
vtkOpenQubeMoleculeSource reader is used to generate a molecule with
associated electronic data from a variety of common quantum mechanics
calculation outputs, using the OpenQube library. The
vtkProgrammableElectronicData is a simple subclass of
vtkAbstractElectronicData that uses Set/Get methods to manage its
content.

Note: OpenQube support relies on some patches that are currently
pending upstream. However, vtkChemistry will build without OpenQube
support if the libraries are not found.

- 85b0468 Added vtkMoleculeMapper to the Chemistry kit.
vtkMoleculeMapper provides common molecular geometry rendering styles
-- ball and stick, VDW spheres, liquorice stick, etc. It is rather
customizable to allow for user-defined appearances.

- 1be4846 Use a custom selection ID array with Glyph3DMapper/HardwareSelector.
Allows a specified vtkIdTypeArray to be used for the information
returned when performing selection on a scene that renders using
vtkGlyph3DMapper.

- efc0866 Added some polydata generators to the Chemisty kit.
These generate polydata that represent molecular geometry.
vtkMoleculeMapper is preferred, but these may prove useful for more
advanced usage.

- 143ed06 Added a CML molecule reader to the Chemistry kit.
Simple CML format reader. Currently supports reading molecular
geometry, and not much else.

- cc5a76d Added vtkPeriodicTable and associated classes to Chemistry kit.
Classes that provide elemental information, such as atomic number to
symbol conversions, etc. Uses the Blue Obelisk Data Repository.

- bc6bb00 Added VTK_INSTALL_SHARE_DIR to CMake.
This is where the Blue Obelisk Data Repo files are installed

- 2cf5105 Added a vtkSetVtkNewMacro to return ivars that are wrapped in vtkNew.
Does what it says :-)

- b0a2cc5 Added vtkMolecule, vtkAtom, and vtkBond to the vtkFiltering kit.
Molecular geometry data object. These are in vtkFiltering because of
changes in vtkDataObjectTypes.cxx.

- 67a43d9 Added a Chemistry kit layout.
- 582300a Fix typo in vtkRenderedAreaPicker.
Misc.

- 51367e2 Added some vector math functions to vtkVector.
Expand the capabilities of vtkVector. There have been a few other
threads on this list relating to this patch.

I'll be checking gerrit often if there are any concerns/comments on
the patches. It's been a lot of fun hacking on vtk this summer -- I'll
definitely continue working on vtkChemistry when I find time to.
Thanks to everyone who helped get this project going!

Cheers,

Dave