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 (Cxx)

Code¶

ReadCML.java

import vtk.vtkActor;
import vtk.vtkNamedColors;
import vtk.vtkNativeLibrary;
import vtk.vtkRenderWindow;
import vtk.vtkRenderWindowInteractor;
import vtk.vtkRenderer;
import vtk.vtkCMLMoleculeReader;
import vtk.vtkMoleculeMapper;

public class ReadCML 
{
  // -----------------------------------------------------------------
  // Load VTK library and print which library was not properly loaded
  static 
  {
    if (!vtkNativeLibrary.LoadAllNativeLibraries()) 
    {
      for (vtkNativeLibrary lib : vtkNativeLibrary.values()) 
      {
        if (!lib.IsLoaded()) 
        {
          System.out.println(lib.GetLibraryName() + " not loaded");
        }
      }
    }
    vtkNativeLibrary.DisableOutputWindow(null);
  }
  // -----------------------------------------------------------------


  public static void main(String args[]) 
  {
    //parse command line arguments
    if (args.length != 1) 
    {
      System.err.println("Usage: java -classpath ... Filename(.cml) e.g porphyrin.cml");
      return;
    }
    String inputFilename = args[0];

    vtkNamedColors colors = new vtkNamedColors();

    //Renderer Background Color
    double Bgcolor[] = new double[4];

    colors.GetColor("Silver", Bgcolor);

    vtkCMLMoleculeReader cmlSource = new vtkCMLMoleculeReader();

    cmlSource.SetFileName(inputFilename);

    vtkMoleculeMapper molmapper = new vtkMoleculeMapper();
    molmapper.SetInputConnection(cmlSource.GetOutputPort());

    molmapper.UseBallAndStickSettings();

    vtkActor actor = new vtkActor();
    actor.SetMapper(molmapper);
    actor.GetProperty().SetDiffuse(.7);
    actor.GetProperty().SetSpecular(.5);
    actor.GetProperty().SetSpecularPower(20.0);

    // Create the renderer, render window and interactor.
    vtkRenderer ren = new vtkRenderer();
    vtkRenderWindow renWin = new vtkRenderWindow();
    renWin.AddRenderer(ren);
    vtkRenderWindowInteractor iren = new vtkRenderWindowInteractor();
    iren.SetRenderWindow(renWin);

    // Visualise
    ren.AddActor(actor);
    ren.SetBackground(Bgcolor);

    renWin.SetSize(300, 300);
    renWin.SetMultiSamples(0);
    renWin.Render();

    iren.Initialize();
    iren.Start();
  }
}