# ReadPDB

VTKExamples/Cxx/IO/ReadPDB

### Description

This example reads Protein Data Bank files. The example expects a file in .pdb format.

Here is a sample file.

### Code

ReadPDB.cxx

    #include <vtkSmartPointer.h>
    #include <vtkPDBReader.h>

    #include <cmath>
    #include <vtkGlyph3D.h>
    #include <vtkLODActor.h>
    #include <vtkPolyDataMapper.h>
    #include <vtkProperty.h>
    #include <vtkRenderWindow.h>
    #include <vtkRenderWindowInteractor.h>
    #include <vtkRenderer.h>
    #include <vtkSphereSource.h>
    #include <vtkTubeFilter.h>
    #include <vtkNamedColors.h>

    int main (int argc, char *argv[])
    {
      if (argc < 2)
      {
        std::cerr << "Usage: " << argv[0] << " Filename(.pdb)" << std::endl;
        return EXIT_FAILURE;
      }
      vtkSmartPointer<vtkNamedColors> colors =
        vtkSmartPointer<vtkNamedColors>::New();

      vtkSmartPointer<vtkRenderer> renderer =
        vtkSmartPointer<vtkRenderer>::New();
      renderer->SetBackground(colors->GetColor3d("SlateGray").GetData());
      vtkSmartPointer<vtkRenderWindow> renderWindow =
        vtkSmartPointer<vtkRenderWindow>::New();
      renderWindow->AddRenderer(renderer);
      renderWindow->SetSize(640, 480);
      vtkSmartPointer<vtkRenderWindowInteractor> interactor =
        vtkSmartPointer<vtkRenderWindowInteractor>::New();
      interactor->SetRenderWindow(renderWindow);

      vtkSmartPointer<vtkPDBReader> pdb =
        vtkSmartPointer<vtkPDBReader>::New();
      pdb->SetFileName(argv[1]);
      pdb->SetHBScale(1.0);
      pdb->SetBScale(1.0);
      pdb->Update();
      std::cout <<"# of atoms is: " << pdb->GetNumberOfAtoms() << std::endl;

      double resolution = std::sqrt(300000.0 / pdb->GetNumberOfAtoms());
      if (resolution > 20)
      {
        resolution = 20;
      }
      if (resolution < 4)
      {
        resolution = 4;
      }
      std::cout <<"Resolution is: " << resolution << std::endl;
      vtkSmartPointer<vtkSphereSource> sphere =
        vtkSmartPointer<vtkSphereSource>::New();
      sphere->SetCenter(0, 0, 0);
      sphere->SetRadius(1);
      sphere->SetThetaResolution(static_cast<int>(resolution));
      sphere->SetPhiResolution(static_cast<int>(resolution));

      vtkSmartPointer<vtkGlyph3D> glyph =
        vtkSmartPointer<vtkGlyph3D>::New();
      glyph->SetInputConnection(pdb->GetOutputPort());
      glyph->SetOrient(1);
      glyph->SetColorMode(1);
      // glyph->ScalingOn();
      glyph->SetScaleMode(2);
      glyph->SetScaleFactor(.25);
      glyph->SetSourceConnection(sphere->GetOutputPort());

      vtkSmartPointer<vtkPolyDataMapper> atomMapper =
        vtkSmartPointer<vtkPolyDataMapper>::New();
      atomMapper->SetInputConnection(glyph->GetOutputPort());
      atomMapper->UseLookupTableScalarRangeOff();
      atomMapper->ScalarVisibilityOn();
      atomMapper->SetScalarModeToDefault();

      vtkSmartPointer<vtkLODActor> atom =
        vtkSmartPointer<vtkLODActor>::New();
      atom->SetMapper(atomMapper);
      atom->GetProperty()->SetRepresentationToSurface();
      atom->GetProperty()->SetInterpolationToGouraud();
      atom->GetProperty()->SetAmbient(0.15);
      atom->GetProperty()->SetDiffuse(0.85);
      atom->GetProperty()->SetSpecular(0.1);
      atom->GetProperty()->SetSpecularPower(30);
      atom->GetProperty()->SetSpecularColor(colors->GetColor3d("White").GetData());
      atom->SetNumberOfCloudPoints(30000);

      renderer->AddActor(atom);

      vtkSmartPointer<vtkTubeFilter> tube =
        vtkSmartPointer<vtkTubeFilter>::New();
      tube->SetInputConnection(pdb->GetOutputPort());
      tube->SetNumberOfSides(static_cast<int>(resolution));
      tube->CappingOff();
      tube->SetRadius(0.2);
      tube->SetVaryRadius(0);
      tube->SetRadiusFactor(10);

      vtkSmartPointer<vtkPolyDataMapper> bondMapper =
        vtkSmartPointer<vtkPolyDataMapper>::New();
      bondMapper->SetInputConnection(tube->GetOutputPort());
      bondMapper->UseLookupTableScalarRangeOff();
      bondMapper->ScalarVisibilityOff();
      bondMapper->SetScalarModeToDefault();

      vtkSmartPointer<vtkLODActor> bond =
        vtkSmartPointer<vtkLODActor>::New();
      bond->SetMapper(bondMapper);
      bond->GetProperty()->SetRepresentationToSurface();
      bond->GetProperty()->SetInterpolationToGouraud();
      bond->GetProperty()->SetAmbient(0.15);
      bond->GetProperty()->SetDiffuse(0.85);
      bond->GetProperty()->SetSpecular(0.1);
      bond->GetProperty()->SetSpecularPower(30);
      bond->GetProperty()->SetSpecularColor(colors->GetColor3d("White").GetData());

      renderer->AddActor(bond);

      interactor->Initialize();
      interactor->Start();

      return EXIT_SUCCESS;
    }

### CMakeLists.txt

    cmake_minimum_required(VERSION 2.8)

    PROJECT(ReadPDB)

    find_package(VTK REQUIRED)
    include(${VTK_USE_FILE})

    add_executable(ReadPDB MACOSX_BUNDLE ReadPDB.cxx )

    target_link_libraries(ReadPDB ${VTK_LIBRARIES})

### Download and Build ReadPDB

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

    cd ReadPDB/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:

    ./ReadPDB

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