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Create IOChemistry module, refactor vtkMoleculeReaderBase

Angelos Angelopoulos requested to merge aangelos28/vtk:improve-moleculereader into master

IOChemistry Module

A new IOChemistry module is created that contains all chemistry-related readers for improved cohesion.

Refactored vtkMoleculeReaderBase

vtkMoleculeReaderBase is an old class that needed updating. There was also a bug where atom types were one less than they should be (for example, if you open a PDB file with ParaView you will see that atom types are wrong and rgb colors are incorrect). The class was changed to use the vtkPeriodicTable Blue Obelisk dataset instead of the previous hardcoded static arrays to reduce code duplication and improve accuracy.

  • Used smart pointers
  • Improved variable names
  • Improved documentation
  • Improved structure
  • Replaced static arrays with vtkPeriodicTable in vtkMoleculeReaderBase
  • Fixed atomType values being one less in vtkMoleculeReaderBase
  • Updated vtkProteinRibbonFilter according to the atomType changes
  • Added documentation to vtkMoleculeReaderBase::ReadMolecule(), MakeAtomType(), MakeBonds()
  • Rename vtkMoleculeReaderBase::MakeBonds() newPoints parameter to points for clarity
  • Changed "scanning" to "reading" in debug output

Moved Classes

  • vtkCMLMoleculeReader: From DomainsChemistry to IOChemistry
  • vtkGaussianCubeReader: From IOGeometry to IOChemistry
  • vtkGaussianCubeReader2: From IOGeometry to IOChemistry
  • vtkMoleculeReaderBase: From IOGeometry to IOChemistry
  • vtkPDBReader: From From IOGeometry to IOChemistry
  • vtkVASPAnimationReader: From DomainsChemistry to IOChemistry
  • vtkVASPTessellationReader: From DomainsChemistry to IOChemistry
  • vtkXYZMolReader: From IOGeometry to IOChemistry
  • vtkXYZMolReader2: From IOGeometry to IOChemistry
Edited by Angelos Angelopoulos

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