/* * 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 7, 2005 * */ package org.simtk.moleculargraphics.cartoon; import org.simtk.geometry3d.*; import org.simtk.molecularstructure.*; import org.simtk.molecularstructure.nucleicacid.*; import java.awt.Color; import java.util.*; import vtk.*; /** * * @author Christopher Bruns * * These shapes do not work for vtkGlyph3D because they are too asymmetric * and their orientations cannot be fully specified. Sucks. */ public class DuplexResidueWedge extends TensorGlyphCartoon { double wedgeThickness = 2.0; double wedgeRadius = 8.0; private int baseColorIndex = 150; private Hashtable colorIndices = new Hashtable(); public DuplexResidueWedge() { this(8.0); } public DuplexResidueWedge(double r) { super(); wedgeRadius = r; // Make a cylinder vtkCylinderSource cylinderSource = new vtkCylinderSource(); cylinderSource.SetResolution(15); cylinderSource.SetRadius(wedgeRadius); cylinderSource.SetHeight(wedgeThickness); cylinderSource.SetCapping(1); // 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.SetTransform(cylinderTransform); // Cut the cylinder in half // Set the plane to use in cutting the cylinder in half vtkPlane clipPlane = new vtkPlane(); clipPlane.SetNormal(0.0, 1.0, 0.0); clipPlane.SetOrigin(0.0, 0.0, 0.0); vtkClipPolyData clipper = new vtkClipPolyData(); clipper.SetInput(cylinderFilter.GetOutput()); clipper.SetClipFunction(clipPlane); clipper.GenerateClipScalarsOn(); clipper.GenerateClippedOutputOn(); // clipper.SetValue(0.5); // causes plane to be placed a bit wrong // Close up place where clip was vtkCutter cutEdges = new vtkCutter(); cutEdges.SetInput(cylinderFilter.GetOutput()); cutEdges.SetCutFunction(clipPlane); cutEdges.GenerateCutScalarsOn(); cutEdges.SetValue(0, 0.5); vtkStripper cutStrips = new vtkStripper(); cutStrips.SetInput(cutEdges.GetOutput()); cutStrips.Update(); vtkPolyData cutPoly = new vtkPolyData(); cutPoly.SetPoints(cutStrips.GetOutput().GetPoints()); cutPoly.SetPolys(cutStrips.GetOutput().GetLines()); // Triangle filter is robust enough to ignore the duplicate point at // the beginning and end of the polygons and triangulate them. vtkTriangleFilter cutTriangles = new vtkTriangleFilter(); cutTriangles.SetInput(cutPoly); vtkAppendPolyData appendFilter = new vtkAppendPolyData(); appendFilter.AddInput(clipper.GetClippedOutput()); appendFilter.AddInput(cutTriangles.GetOutput()); // Resmooth the surface shading after the append filter chunked it vtkPolyDataNormals dataNormals = new vtkPolyDataNormals(); dataNormals.SetFeatureAngle(80.0); // Angles smaller than this are smoothed dataNormals.SetInput(appendFilter.GetOutput()); // Use lines as the glyph primitive setGlyphSource(dataNormals.GetOutput()); // lineGlyph.SetSource(sphereSource.GetOutput()); scaleNone(); // Do not adjust size colorByScalar(); // Take color from glyph scalar // orientByNormal(); // not supported for tensorGlyph glyphActor.GetProperty().BackfaceCullingOff(); } public void show(Molecule molecule) { addMolecule(molecule); } void addMolecule(Molecule molecule) { if (! (molecule instanceof NucleicAcid)) return; NucleicAcid nucleicAcid = (NucleicAcid) molecule; Vector duplexen = nucleicAcid.identifyHairpins(); for (Iterator iterDuplex = duplexen.iterator(); iterDuplex.hasNext(); ) { Duplex duplex = (Duplex) iterDuplex.next(); Cylinder duplexCylinder = DuplexCylinderCartoon.doubleHelixCylinder(duplex); Vector3D duplexDirection = new DoubleVector3D( duplexCylinder.getHead().minus(duplexCylinder.getTail()).unit() ); Line3D duplexAxis = new Line3D(duplexDirection, duplexCylinder.getTail()); for (Iterator iterBasePair = duplex.basePairs().iterator(); iterBasePair.hasNext(); ) { BasePair basePair = (BasePair) iterBasePair.next(); // Nucleotide residue = (Nucleotide) iterResidue.next(); Nucleotide residue1 = basePair.getResidue1(); Nucleotide residue2 = basePair.getResidue2(); // Put residue position on cylinder axis Vector3D baseCentroid1 = residue1.get(Nucleotide.baseGroup).getCenterOfMass(); Vector3D baseCentroid2 = residue2.get(Nucleotide.baseGroup).getCenterOfMass(); Vector3D baseCentroid = new DoubleVector3D( baseCentroid1.plus(baseCentroid2).scale(0.5) ); Vector3D helixCenter = duplexAxis.getClosestPoint(baseCentroid); // Put residue normal perpendicular to helix axis, along base-pair direction Vector3D backbonePosition1 = residue1.getBackbonePosition(); Vector3D backbonePosition2 = residue2.getBackbonePosition(); Vector3D residueDirection = new DoubleVector3D( backbonePosition2.minus(backbonePosition1) ); Vector3D thirdDirection = new DoubleVector3D( duplexDirection.cross(residueDirection).unit() ); // Make it all neatly orthogonal residueDirection = thirdDirection.cross(duplexDirection); Residue residues[] = {residue1, residue2}; for (int i = 0; i < 2; i++) { Residue residue = residues[i]; Vector currentObjects = new Vector(); // assign molecular object on which to index this wedge currentObjects.add(molecule); currentObjects.add(duplex); 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(); linePoints.InsertNextPoint(helixCenter.getX(), helixCenter.getY(), helixCenter.getZ()); lineNormals.InsertNextTuple3(residueDirection.getX(), residueDirection.getY(), residueDirection.getZ()); // Tensors for full orientation // Vector3D otherDirection = duplexDirection.cross(residueDirection).unit(); tensors.InsertNextTuple9(duplexDirection.getX(),duplexDirection.getY(),duplexDirection.getZ(), residueDirection.getX(),residueDirection.getY(),residueDirection.getZ(), thirdDirection.getX(),thirdDirection.getY(),thirdDirection.getZ()); // TODO glyphColors.add(currentObjects, lineData, lineScalars.GetNumberOfTuples(), colorScalar); lineScalars.InsertNextValue(colorScalar); // Reverse the orientation for the other residue residueDirection.selfScale(-1.0); duplexDirection.selfScale(-1.0); } } } } }