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ReadPDB

vtk-examples/Cxx/IO/ReadPDB

Description

This example reads Protein Data Bank files. The example expects a file in .pdb format for example src/Testing/Data/lys.pdb.

Other languages

See (CSharp)

Question

If you have a question about this example, please use the VTK Discourse Forum

Code

ReadPDB.cxx

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

#include <cmath>

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

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

  vtkNew<vtkPDBReader> pdb;
  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;
  vtkNew<vtkSphereSource> sphere;
  sphere->SetCenter(0, 0, 0);
  sphere->SetRadius(1);
  sphere->SetThetaResolution(static_cast<int>(resolution));
  sphere->SetPhiResolution(static_cast<int>(resolution));

  vtkNew<vtkGlyph3D> glyph;
  glyph->SetInputConnection(pdb->GetOutputPort());
  glyph->SetOrient(1);
  glyph->SetColorMode(1);
  // glyph->ScalingOn();
  glyph->SetScaleMode(2);
  glyph->SetScaleFactor(0.25);
  glyph->SetSourceConnection(sphere->GetOutputPort());

  vtkNew<vtkPolyDataMapper> atomMapper;
  atomMapper->SetInputConnection(glyph->GetOutputPort());
  atomMapper->UseLookupTableScalarRangeOff();
  atomMapper->ScalarVisibilityOn();
  atomMapper->SetScalarModeToDefault();

  vtkNew<vtkLODActor> atom;
  atom->SetMapper(atomMapper);
  atom->GetProperty()->SetRepresentationToSurface();
  atom->GetProperty()->SetInterpolationToGouraud();
  atom->GetProperty()->SetAmbient(0.1);
  atom->GetProperty()->SetDiffuse(0.7);
  atom->GetProperty()->SetSpecular(0.5);
  atom->GetProperty()->SetSpecularPower(80);
  atom->GetProperty()->SetSpecularColor(colors->GetColor3d("White").GetData());
  atom->SetNumberOfCloudPoints(30000);

  renderer->AddActor(atom);

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

  vtkNew<vtkPolyDataMapper> bondMapper;
  bondMapper->SetInputConnection(tube->GetOutputPort());
  bondMapper->UseLookupTableScalarRangeOff();
  bondMapper->ScalarVisibilityOff();
  bondMapper->SetScalarModeToDefault();

  vtkNew<vtkLODActor> bond;
  bond->SetMapper(bondMapper);
  bond->GetProperty()->SetRepresentationToSurface();
  bond->GetProperty()->SetInterpolationToGouraud();
  bond->GetProperty()->SetAmbient(0.1);
  bond->GetProperty()->SetDiffuse(0.7);
  bond->GetProperty()->SetSpecular(0.5);
  bond->GetProperty()->SetSpecularPower(80);
  bond->GetProperty()->SetSpecularColor(colors->GetColor3d("White").GetData());

  renderer->AddActor(bond);

  renderWindow->SetWindowName("ReadPDB");
  renderWindow->Render();
  interactor->Initialize();
  interactor->Start();

  return EXIT_SUCCESS;
}

CMakeLists.txt

cmake_minimum_required(VERSION 3.12 FATAL_ERROR)

project(ReadPDB)

find_package(VTK COMPONENTS 
)

if (NOT VTK_FOUND)
  message(FATAL_ERROR "ReadPDB: Unable to find the VTK build folder.")
endif()

# Prevent a "command line is too long" failure in Windows.
set(CMAKE_NINJA_FORCE_RESPONSE_FILE "ON" CACHE BOOL "Force Ninja to use response files.")
add_executable(ReadPDB MACOSX_BUNDLE ReadPDB.cxx )
  target_link_libraries(ReadPDB PRIVATE ${VTK_LIBRARIES}
)
# vtk_module_autoinit is needed
vtk_module_autoinit(
  TARGETS ReadPDB
  MODULES ${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

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