/* * Copyright (c) 2005, Stanford University. All rights reserved. * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions * are met: * - Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the distribution. * - Neither the name of the Stanford University nor the names of its * contributors may be used to endorse or promote products derived * from this software without specific prior written permission. * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS * FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE * COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, * BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE * POSSIBILITY OF SUCH DAMAGE. */ /* * Created on Jul 6, 2005 * */ package org.simtk.moleculargraphics.cartoon; import java.awt.Color; import java.util.*; import org.simtk.geometry3d.*; import org.simtk.molecularstructure.*; import vtk.*; public class BackboneStick extends GlyphCartoon { double sphereFudge = 1.05; // spheres aren't quit flush with cylinder for some reason int stickResolution = 5; double stickLength = 2.0; double stickRadius = 1.50; private int baseColorIndex = 150; private Hashtable colorIndices = new Hashtable(); public BackboneStick() { this(1.50); } public BackboneStick(double r) { super(); stickRadius = r; initialize(); } public BackboneStick(double r, int res) { super(); stickRadius = r; stickResolution = res; initialize(); } private void initialize() { // Make a cylinder to use as the basis of all bonds vtkCylinderSource cylinderSource = new vtkCylinderSource(); cylinderSource.SetResolution(stickResolution); cylinderSource.SetRadius(stickRadius); cylinderSource.SetHeight(stickLength); cylinderSource.SetCapping(0); // Cap the ends of the cylinder with spheres vtkSphereSource sphereSource1 = new vtkSphereSource(); sphereSource1.SetRadius(stickRadius * sphereFudge); sphereSource1.SetPhiResolution(6); sphereSource1.SetThetaResolution(stickResolution); // Rotate the spheres so it lines up just right with the cylinder vtkTransform sphere1Transform = new vtkTransform(); sphere1Transform.Identity(); sphere1Transform.Translate(0.0, -stickLength/2.0, 0.0); sphere1Transform.RotateX(90); vtkTransformPolyDataFilter sphere1Filter = new vtkTransformPolyDataFilter(); sphere1Filter.SetInput(sphereSource1.GetOutput()); sphere1Filter.SetTransform(sphere1Transform); vtkSphereSource sphereSource2 = new vtkSphereSource(); sphereSource2.SetRadius(stickRadius * sphereFudge); sphereSource2.SetPhiResolution(6); sphereSource2.SetThetaResolution(stickResolution); // Rotate the spheres so it lines up just right with the cylinder vtkTransform sphere2Transform = new vtkTransform(); sphere2Transform.Identity(); sphere2Transform.Translate(0.0, stickLength/2.0, 0.0); sphere2Transform.RotateX(90); vtkTransformPolyDataFilter sphere2Filter = new vtkTransformPolyDataFilter(); sphere2Filter.SetInput(sphereSource2.GetOutput()); sphere2Filter.SetTransform(sphere2Transform); vtkAppendPolyData append = new vtkAppendPolyData(); append.AddInput(cylinderSource.GetOutput()); append.AddInput(sphere1Filter.GetOutput()); append.AddInput(sphere2Filter.GetOutput()); // Rotate the cylinder so that the cylinder axis goes along the normals during glyphing vtkTransform cylinderTransform = new vtkTransform(); cylinderTransform.Identity(); cylinderTransform.RotateZ(90); vtkTransformPolyDataFilter cylinderFilter = new vtkTransformPolyDataFilter(); // cylinderFilter.SetInput(cylinderSource.GetOutput()); cylinderFilter.SetInput(append.GetOutput()); cylinderFilter.SetTransform(cylinderTransform); // Use lines as the glyph primitive setGlyphSource(cylinderFilter.GetOutput()); // lineGlyph.SetSource(sphereSource.GetOutput()); scaleNone(); // Do not adjust size colorByScalar(); // Take color from glyph scalar orientByNormal(); glyphActor.GetProperty().BackfaceCullingOn(); } public void show(Molecule molecule) { addMolecule(molecule, null); glyphColors.show(molecule); } void addMolecule(Molecule molecule, Vector parentObjects) { if (molecule == null) return; // Don't add things that have already been added if (glyphColors.containsKey(molecule)) return; // Collect molecular objects on which to index the glyphs Vector currentObjects = new Vector(); if (parentObjects != null) { for (int i = 0; i < parentObjects.size(); i++) currentObjects.add(parentObjects.get(i)); } currentObjects.add(molecule); // If it's a biopolymer, index the glyphs by residue if (molecule instanceof Residue) { Residue residue = (Residue) molecule; currentObjects.remove(currentObjects.size() - 1); addResidue(residue, currentObjects); } else if (molecule instanceof Biopolymer) { Biopolymer biopolymer = (Biopolymer) molecule; for (Iterator iterResidue = biopolymer.residues().iterator(); iterResidue.hasNext(); ) { addMolecule((Residue) iterResidue.next(), currentObjects); } } } void addResidue(Residue residue, Vector parentObjects) { if (residue == null) return; // Don't add things that have already been added if (glyphColors.containsKey(residue)) return; Vector3D backbonePosition = residue.getBackbonePosition(); if (backbonePosition == null) return; Vector3D nextPosition = null; if (residue.getNextResidue() != null) nextPosition = residue.getNextResidue().getBackbonePosition(); Vector3D previousPosition = null; if (residue.getPreviousResidue() != null) previousPosition = residue.getPreviousResidue().getBackbonePosition(); // Collect molecular objects on which to index the glyphs Vector currentObjects = new Vector(); if (parentObjects != null) { for (int i = 0; i < parentObjects.size(); i++) currentObjects.add(parentObjects.get(i)); } currentObjects.add(residue); Color color = residue.getDefaultColor(); if (! (colorIndices.containsKey(color))) { colorIndices.put(color, new Integer(baseColorIndex)); lut.SetTableValue(baseColorIndex, color.getRed()/255.0, color.getGreen()/255.0, color.getBlue()/255.0, 1.0); baseColorIndex ++; } int colorScalar = ((Integer) colorIndices.get(color)).intValue(); if (previousPosition != null) { // Point midway between two residues DoubleVector3D midPosition = new DoubleVector3D( backbonePosition.plus(previousPosition).scale(0.5) ); // Direction of this half bond // To make the two half-bonds line up flush, choose a deterministic direction between the two atoms if (residue.getResidueNumber() > residue.getPreviousResidue().getResidueNumber()) tileSticks(backbonePosition, midPosition, currentObjects, colorScalar); else tileSticks(midPosition, backbonePosition, currentObjects, colorScalar); } if (nextPosition != null) { // Point midway between two residues DoubleVector3D midPosition = new DoubleVector3D( backbonePosition.plus(nextPosition).scale(0.5) ); // Direction of this half bond // To make the two half-bonds line up flush, choose a deterministic direction between the two atoms if (residue.getResidueNumber() > residue.getNextResidue().getResidueNumber()) tileSticks(backbonePosition, midPosition, currentObjects, colorScalar); else tileSticks(midPosition, backbonePosition, currentObjects, colorScalar); } } private void tileSticks(Vector3D segmentStart, Vector3D segmentEnd, Vector currentObjects, int colorScalar) { DoubleVector3D segmentDirection = new DoubleVector3D( segmentEnd.minus(segmentStart) ); // Use sticks to tile path from atom center, c, to bond midpoint int numberOfSticks = (int) Math.ceil(segmentDirection.length() / stickLength); // Scale to unit length. NOTE - effect of this on calculations above and below segmentDirection = new DoubleVector3D( segmentDirection.unit() ); DoubleVector3D startStickCenter = new DoubleVector3D( segmentStart.plus(segmentDirection.scale(stickLength * 0.5)) ); DoubleVector3D endStickCenter = new DoubleVector3D( segmentEnd.minus(segmentDirection.scale(stickLength * 0.5)) ); DoubleVector3D stickCenterVector = new DoubleVector3D( endStickCenter.minus(startStickCenter) ); for (int s = 0; s < numberOfSticks; s++) { double alpha = 0.0; if (numberOfSticks > 1) alpha = s / (numberOfSticks - 1.0); DoubleVector3D stickCenter = new DoubleVector3D( startStickCenter.plus(stickCenterVector.scale(alpha)) ); linePoints.InsertNextPoint(stickCenter.getX(), stickCenter.getY(), stickCenter.getZ()); lineNormals.InsertNextTuple3(segmentDirection.getX(), segmentDirection.getY(), segmentDirection.getZ()); glyphColors.add(currentObjects, lineData, lineScalars.GetNumberOfTuples(), colorScalar); lineScalars.InsertNextValue(colorScalar); } } }