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
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Question
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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); } } }