# ReadPDB

VTKExamples/CSharp/IO/ReadPDB

### Description

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

Here is a sample file.

A tutorial on how to setup a Windows Forms Application utilizing ActiViz.NET can be found here: Setup a Windows Forms Application to use ActiViz.NET

Other Languages

See (Cxx)

### Code

ReadPDB.cs

    using System;
    using System.Collections.Generic;
    using System.ComponentModel;
    using System.Windows.Forms;
    using System.Diagnostics;
    using System.IO;

    using Kitware.VTK;

    namespace ActiViz.Examples {
       public partial class Form1 : Form {
          public Form1() {
             InitializeComponent();
          }

          private void renderWindowControl1_Load(object sender, EventArgs e) {
             try {
                ReadPDB();
             }
             catch(Exception ex) {
                MessageBox.Show(ex.Message, "Exception", MessageBoxButtons.OK);
             }
          }

          private void ReadPDB() {
             // Path to vtk data must be set as an environment variable
             // VTK_DATA_ROOT = "C:\VTK\vtkdata-5.8.0"
             vtkTesting test = vtkTesting.New();
             string root = test.GetDataRoot();
             string filePath = System.IO.Path.Combine(root, @"Data\caffeine.pdb");

             vtkPDBReader pdb = vtkPDBReader.New();
             pdb.SetFileName(filePath);
             pdb.SetHBScale(1.0);
             pdb.SetBScale(1.0);
             pdb.Update();
             Debug.WriteLine("# of atoms is: " + pdb.GetNumberOfAtoms());
             // if molecule contains a lot of atoms, reduce the resolution of the sphere (represents an atom) for faster rendering
             int resolution = (int)Math.Floor(Math.Sqrt(300000.0 / pdb.GetNumberOfAtoms())); // 300000.0 is an empriric value
             if(resolution > 20)
                resolution = 20;
             else if(resolution < 4)
                resolution = 4;

             Debug.WriteLine("Resolution is: " + resolution);
             vtkSphereSource sphere = vtkSphereSource.New();
             sphere.SetCenter(0, 0, 0);
             sphere.SetRadius(1);
             sphere.SetThetaResolution(resolution);
             sphere.SetPhiResolution(resolution);

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

             vtkPolyDataMapper atomMapper = vtkPolyDataMapper.New();
             atomMapper.SetInputConnection(glyph.GetOutputPort());
             atomMapper.UseLookupTableScalarRangeOff();
             atomMapper.ScalarVisibilityOn();
             atomMapper.SetScalarModeToDefault();

             vtkLODActor atom = 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(1, 1, 1);
             atom.SetNumberOfCloudPoints(30000);

             vtkTubeFilter tube = vtkTubeFilter.New();
             tube.SetInputConnection(pdb.GetOutputPort());
             tube.SetNumberOfSides(resolution);
             tube.CappingOff();
             tube.SetRadius(0.2);
             // turn off variation of tube radius with scalar values
             tube.SetVaryRadius(0);
             tube.SetRadiusFactor(10);

             vtkPolyDataMapper bondMapper = vtkPolyDataMapper.New();
             bondMapper.SetInputConnection(tube.GetOutputPort());
             bondMapper.UseLookupTableScalarRangeOff();
             bondMapper.ScalarVisibilityOff();
             bondMapper.SetScalarModeToDefault();

             vtkLODActor bond = 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(1, 1, 1);
             bond.GetProperty().SetDiffuseColor(1.0000, 0.8941, 0.70981);

             // get a reference to the renderwindow of our renderWindowControl1
             vtkRenderWindow renderWindow = renderWindowControl1.RenderWindow;
             // renderer
             vtkRenderer renderer = renderWindow.GetRenderers().GetFirstRenderer();
             // set background color
             renderer.SetBackground(0.2, 0.3, 0.4);
             // add our actor to the renderer
             renderer.AddActor(atom);
             renderer.AddActor(bond);
          }
       }
    }