ProteinRibbons

VTKExamples/Cxx/Visualization/ProteinRibbons


Description

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

Here is a sample file.

Other Languages

See (Java)

Question

If you have a simple question about this example contact us at VTKExamplesProject If your question is more complex and may require extended discussion, please use the VTK Discourse Forum

Code

ProteinRibbons.cxx

#include <vtkProteinRibbonFilter.h>

#include <vtkActor.h>
#include <vtkCamera.h>
#include <vtkPolyDataMapper.h>
#include <vtkNew.h>
#include <vtkProperty.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkRenderWindow.h>
#include <vtkRenderer.h>
#include <vtkPDBReader.h>
#include <vtkInteractorStyleSwitch.h>

#include <vtkNamedColors.h>

int main(int argc, char *argv[])
{
  if (argc < 2)
  {
    std::cout << "Usage: " << argv[0] << " file.pdb" << std::endl;
    return EXIT_FAILURE;                                                                                
  }
  std::string fileName(argv[1]);

  // read protein from pdb
  vtkNew<vtkPDBReader> reader;
  reader->SetFileName(fileName.c_str());

  // setup ribbon filter
  vtkNew<vtkProteinRibbonFilter> ribbonFilter;
  ribbonFilter->SetInputConnection(reader->GetOutputPort());

  // setup poly data mapper
  vtkNew<vtkPolyDataMapper> polyDataMapper;
  polyDataMapper->SetInputConnection(ribbonFilter->GetOutputPort());

  // setup actor
  vtkNew<vtkActor> actor;
  actor->SetMapper(polyDataMapper);
  actor->GetProperty()->SetDiffuse(.7);
  actor->GetProperty()->SetSpecular(.5);
  actor->GetProperty()->SetSpecularPower(80.0);

  // setup render window
  vtkNew<vtkRenderer> renderer;
  vtkNew<vtkRenderWindow> renderWindow;
  renderWindow->AddRenderer(renderer);
  vtkNew<vtkRenderWindowInteractor> interactor;
  interactor->SetRenderWindow(renderWindow);
  vtkInteractorStyleSwitch* style =
    dynamic_cast<vtkInteractorStyleSwitch*>(interactor->GetInteractorStyle());
  style->SetCurrentStyleToTrackballCamera();

  vtkNew<vtkNamedColors> colors;
  renderer->AddActor(actor);
  renderer->SetBackground(colors->GetColor3d("Silver").GetData());
  renderWindow->SetSize(640, 480);

  renderer->ResetCamera();
  renderer->GetActiveCamera()->Zoom(1.5);
  renderer->ResetCameraClippingRange();
  renderWindow->Render();

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

  return EXIT_SUCCESS;
}

CMakeLists.txt

cmake_minimum_required(VERSION 3.3 FATAL_ERROR)

project(ProteinRibbons)

find_package(VTK COMPONENTS 
  vtkCommonColor
  vtkCommonCore
  vtkDomainsChemistry
  vtkDomainsChemistryOpenGL2
  vtkIOGeometry
  vtkInteractionStyle
  vtkRenderingContextOpenGL2
  vtkRenderingCore
  vtkRenderingFreeType
  vtkRenderingGL2PSOpenGL2
  vtkRenderingOpenGL2 QUIET)
if (NOT VTK_FOUND)
  message("Skipping ProteinRibbons: ${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(ProteinRibbons MACOSX_BUNDLE ProteinRibbons.cxx )
  target_link_libraries(ProteinRibbons PRIVATE ${VTK_LIBRARIES})
else ()
  # include all components
  add_executable(ProteinRibbons MACOSX_BUNDLE ProteinRibbons.cxx )
  target_link_libraries(ProteinRibbons PRIVATE ${VTK_LIBRARIES})
  # vtk_module_autoinit is needed
  vtk_module_autoinit(
    TARGETS ProteinRibbons
    MODULES ${VTK_LIBRARIES}
    )
endif () 

Download and Build ProteinRibbons

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

cd ProteinRibbons/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:

./ProteinRibbons

WINDOWS USERS

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