/* * 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 Apr 26, 2005 * */ package org.simtk.moleculargraphics.cartoon; import vtk.*; import java.awt.*; import java.util.*; import org.simtk.geometry3d.*; import org.simtk.molecularstructure.*; import org.simtk.molecularstructure.atom.*; /** * @author Christopher Bruns * * Draw a simple colored line joining each pair of bonded atoms. * Plus a cross at each non-bonded atom */ public class WireFrameCartoon extends GlyphCartoon { // Key: glyph index number value: atoms at the other end of a bond Hashtable otherAtomIndices = new Hashtable(); static double crossSize = 1.0; static vtkLineSource lineSource; static { lineSource = new vtkLineSource(); lineSource.SetPoint1(-0.5, 0.0, 0.0); lineSource.SetPoint2(0.5, 0.0, 0.0); } public WireFrameCartoon() { super(); // Use lines as the glyph primitive setGlyphSource(lineSource.GetOutput()); // lineGlyph.SetSource(sphereSource.GetOutput()); scaleByNormal(); // Do not adjust size colorByScalar(); // Take color from glyph scalar glyphActor.GetProperty().SetLineWidth(2.0); } 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; for (Iterator i = residue.getAtomIterator(); i.hasNext(); ) { Atom atom = (Atom) i.next(); addAtom(atom, currentObjects); } } else if (molecule instanceof Biopolymer) { Biopolymer biopolymer = (Biopolymer) molecule; for (Iterator iterResidue = biopolymer.residues().iterator(); iterResidue.hasNext(); ) { addMolecule((Residue) iterResidue.next(), currentObjects); } } else for (Iterator i1 = molecule.getAtomIterator(); i1.hasNext(); ) { Atom atom = (Atom) i1.next(); addAtom(atom, currentObjects); } } void addAtom(Atom atom, Vector parentObjects) { if (atom == null) return; // Don't add things that have already been added if (glyphColors.containsKey(atom)) 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(atom); Vector3D c = atom.getCoordinates(); int colorScalar = (int) (atom.getMass()); Color col = atom.getDefaultColor(); lut.SetTableValue(colorScalar, col.getRed()/255.0, col.getGreen()/255.0, col.getBlue()/255.0, 1.0); // For unbonded atoms, put a cross at atom position if (atom.getBonds().size() == 0) { createSingleAtomGlyph(atom, currentObjects, colorScalar); } // For bonded atoms, draw a line for each bond else for (Iterator i2 = atom.getBonds().iterator(); i2.hasNext(); ) { Atom atom2 = (Atom) i2.next(); createBondGlyph(atom, atom2, currentObjects, colorScalar); } } public void show(Molecule molecule) { addMolecule(molecule, null); glyphColors.show(molecule); } /** Change graphics primitives only for those objects that have moved * * @param molecule */ public void updateCoordinates(Molecule molecule) { // Each bond glyph depends on two atoms, asymmetrically boolean modified = false; for (Iterator i = molecule.getAtomIterator(); i.hasNext(); ) { Atom atom = (Atom) i.next(); if (glyphColors.containsKey(atom)) { Vector glyphs = (Vector) glyphColors.objectGlyphs.get(atom); // TODO encapsulate this for (Iterator g = glyphs.iterator();g.hasNext();) { GlyphPosition pos = (GlyphPosition) g.next(); if (atom.getBonds().size() < 1) { // Single atom glyph, only need to change center pos.setPosition(atom.getCoordinates()); modified = true; } else { int glyphIndex = pos.arrayIndex; if (otherAtomIndices.containsKey(new Integer(glyphIndex))) { Atom atom2 = (Atom) otherAtomIndices.get(new Integer(glyphIndex)); DoubleVector3D normal = getBondNormal(atom, atom2); DoubleVector3D middle = getBondMiddle(atom, atom2); pos.setPosition(middle); pos.setNormal(normal); // Even if the other atom is not in the modified molecule, it should be redrawn anyway if (! molecule.containsAtom(atom2)) { normal = getBondNormal(atom2, atom); middle = getBondMiddle(atom2, atom); // TODO find glyph at the other side of the bond } modified = true; } } } } } if (modified) { linePoints.Modified(); lineNormals.Modified(); } else { System.out.println("No modification"); } } private DoubleVector3D getBondNormal(Atom a1, Atom a2) { Vector3D c = a1.getCoordinates(); MathVector midpoint = c.plus(a2.getCoordinates()).scale(0.5); // middle of bond MathVector b = c.plus(midpoint).scale(0.5); // middle of half-bond MathVector n = midpoint.minus(c); // direction/length vector return new DoubleVector3D(n); } private DoubleVector3D getBondMiddle(Atom a1, Atom a2) { Vector3D c = a1.getCoordinates(); MathVector midpoint = c.plus(a2.getCoordinates()).scale(0.5); // middle of bond MathVector b = c.plus(midpoint).scale(0.5); // middle of half-bond return new DoubleVector3D(b); } private void createBondGlyph(Atom atom, Atom atom2, Vector currentObjects, int colorScalar) { DoubleVector3D b = getBondMiddle(atom, atom2); DoubleVector3D n = getBondNormal(atom, atom2); linePoints.InsertNextPoint(b.getX(), b.getY(), b.getZ()); lineNormals.InsertNextTuple3(n.getX(), n.getY(), n.getZ()); int glyphIndex = lineScalars.GetNumberOfTuples(); glyphColors.add(currentObjects, lineData, glyphIndex, colorScalar); otherAtomIndices.put(new Integer(glyphIndex), atom2); lineScalars.InsertNextValue(colorScalar); } private void createSingleAtomGlyph(Atom atom, Vector currentObjects, int colorScalar) { Vector3D c = atom.getCoordinates(); // X linePoints.InsertNextPoint(c.getX(), c.getY(), c.getZ()); lineNormals.InsertNextTuple3(crossSize, 0.0, 0.0); glyphColors.add(currentObjects, lineData, lineScalars.GetNumberOfTuples(), colorScalar); lineScalars.InsertNextValue(colorScalar); // Y linePoints.InsertNextPoint(c.getX(), c.getY(), c.getZ()); lineNormals.InsertNextTuple3(0.0, crossSize, 0.0); glyphColors.add(currentObjects, lineData, lineScalars.GetNumberOfTuples(), colorScalar); lineScalars.InsertNextValue(colorScalar); // Z linePoints.InsertNextPoint(c.getX(), c.getY(), c.getZ()); lineNormals.InsertNextTuple3(0.0, 0.0, crossSize); glyphColors.add(currentObjects, lineData, lineScalars.GetNumberOfTuples(), colorScalar); lineScalars.InsertNextValue(colorScalar); } }