ReadCML

Description¶

This example uses vtkCMLMoleculeReader to read a Chemistry Markup Language file. CML has been developed by Peter Murray-Rust and Henry Rzepa since 1995. It is the de facto XML for chemistry, accepted by publishers and with more than 1 million lines of Open Source code supporting it.

Info

This example uses the file porphyrin.cml. A description of the molecule Porphyrin is described here.

Other Languages

See (Java)

Code¶

ReadCML.cxx

#include <vtkNew.h>
#include <vtkCMLMoleculeReader.h>

#include <vtkActor.h>
#include <vtkProperty.h>
#include <vtkCamera.h>
#include <vtkMolecule.h>
#include <vtkMoleculeMapper.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkRenderWindow.h>
#include <vtkRenderer.h>

#include <vtkNamedColors.h>

int main(int argc, char *argv[])
{
  std::string fname(argv[1]);
  vtkNew<vtkCMLMoleculeReader> cmlSource;

  cmlSource->SetFileName(fname.c_str());

  vtkNew<vtkMoleculeMapper> molmapper;
  molmapper->SetInputConnection(cmlSource->GetOutputPort());

  molmapper->UseBallAndStickSettings();

  vtkNew<vtkNamedColors> colors;

  vtkNew<vtkActor> actor;
  actor->SetMapper(molmapper);
  actor->GetProperty()->SetDiffuse(.7);
  actor->GetProperty()->SetSpecular(.5);
  actor->GetProperty()->SetSpecularPower(20.0);

  vtkNew<vtkRenderer> ren;
  vtkNew<vtkRenderWindow> renderWindow;
  renderWindow->AddRenderer(ren);
  vtkNew<vtkRenderWindowInteractor> iren;
  iren->SetRenderWindow(renderWindow);

  ren->AddActor(actor);

  ren->SetBackground(0.0,0.0,0.0);
  renderWindow->SetSize(640, 480);
  renderWindow->Render();
  ren->GetActiveCamera()->Zoom(2.0);
  ren->SetBackground(colors->GetColor3d("Silver").GetData());

  // Finally render the scene
  renderWindow->SetMultiSamples(0);
  renderWindow->GetInteractor()->Initialize();
  renderWindow->GetInteractor()->Start();

  return EXIT_SUCCESS;
}

CMakeLists.txt¶

cmake_minimum_required(VERSION 3.3 FATAL_ERROR)

project(ReadCML)

find_package(VTK COMPONENTS 
  vtkCommonColor
  vtkCommonCore
  vtkCommonDataModel
  vtkDomainsChemistry
  vtkDomainsChemistryOpenGL2
  vtkInteractionStyle
  vtkRenderingContextOpenGL2
  vtkRenderingCore
  vtkRenderingFreeType
  vtkRenderingGL2PSOpenGL2
  vtkRenderingOpenGL2 QUIET)
if (NOT VTK_FOUND)
  message("Skipping ReadCML: ${VTK_NOT_FOUND_MESSAGE}")
  return ()
endif()
message (STATUS "VTK_VERSION: ${VTK_VERSION}")
if (VTK_VERSION VERSION_LESS "8.90.0")
  # old system
  include(${VTK_USE_FILE})
  add_executable(ReadCML MACOSX_BUNDLE ReadCML.cxx )
  target_link_libraries(ReadCML PRIVATE ${VTK_LIBRARIES})
else ()
  # include all components
  add_executable(ReadCML MACOSX_BUNDLE ReadCML.cxx )
  target_link_libraries(ReadCML PRIVATE ${VTK_LIBRARIES})
  # vtk_module_autoinit is needed
  vtk_module_autoinit(
    TARGETS ReadCML
    MODULES ${VTK_LIBRARIES}
    )
endif ()

Download and Build ReadCML¶

Click here to download ReadCML and its CMakeLists.txt file. Once the tarball ReadCML.tar has been downloaded and extracted,

cd ReadCML/build

If VTK is installed:

cmake ..

If VTK is not installed but compiled on your system, you will need to specify the path to your VTK build:

cmake -DVTK_DIR:PATH=/home/me/vtk_build ..

Build the project:

make

and run it:

./ReadCML

WINDOWS USERS

Be sure to add the VTK bin directory to your path. This will resolve the VTK dll's at run time.