/* * 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 java.awt.*; import java.util.*; import vtk.*; import org.simtk.geometry3d.*; import org.simtk.molecularstructure.*; import org.simtk.util.Selectable; /** * @author Christopher Bruns * * Draw a space-filling van der Waals sphere around each atom in the structure */ public class BackboneCurveCartoon extends MolecularCartoonClass { double baseRodRadius = 0.50; double ribbonThickness = 0.70; double studElevation = 0.50; double ribbonWidth = 1.5; /** * How many spline segments per residue */ static double splineFactor = 5.0; boolean drawSmoothSpline = true; boolean drawSmoothSpline2 = false; // Coloring vtkLookupTable lut = new vtkLookupTable(); static final int selectionColorIndex = 255; static final int highlightColorIndex = 254; static final int invisibleColorIndex = 253; static final Color selectionColor = new Color(80, 80, 255); static final Color highlightColor = new Color(250, 250, 50); private int baseColorIndex = 150; private Hashtable colorIndices = new Hashtable(); NucleotideStickCartoon baseRods; // NucleotideStickCaps baseCaps; BackboneSpheres studs; vtkAssembly assembly = new vtkAssembly(); public BackboneCurveCartoon() { this(0.50); } public BackboneCurveCartoon(double radius) { baseRodRadius = radius; lut.SetNumberOfTableValues(256); lut.SetRange(1.0, 60.0); lut.SetAlphaRange(1.0, 1.0); lut.SetValueRange(1.0, 1.0); lut.SetHueRange(0.0, 1.0); lut.SetSaturationRange(0.5, 0.5); lut.Build(); lut.SetTableValue(selectionColorIndex, selectionColor.getRed()/255.0, selectionColor.getGreen()/255.0, selectionColor.getBlue()/255.0, 1.0); lut.SetTableValue(highlightColorIndex, highlightColor.getRed()/255.0, highlightColor.getGreen()/255.0, highlightColor.getBlue()/255.0, 1.0); lut.SetTableValue(invisibleColorIndex, 0.0, 0.0, 0.0, 0.0); baseRods = new NucleotideStickCartoon(baseRodRadius); // baseCaps = new NucleotideStickCaps(baseRodRadius); studs = new BackboneSpheres(ribbonThickness/2.0 + studElevation); assembly.AddPart(baseRods.getActor()); // assembly.AddPart(baseCaps.getActor()); assembly.AddPart(studs.getActor()); } public void updateCoordinates() { // TODO } public void select(Selectable s) { baseRods.select(s); // baseCaps.select(s); studs.select(s); } public void unSelect(Selectable s) { baseRods.unSelect(s); // baseCaps.unSelect(s); studs.unSelect(s); } public void unSelect() { baseRods.unSelect(); // baseCaps.unSelect(); studs.unSelect(); } public void highlight(LocatedMolecule m) { baseRods.highlight(m); // baseCaps.highlight(m); studs.highlight(m); } public void hide(LocatedMolecule m) { baseRods.hide(m); // baseCaps.hide(m); studs.hide(m); } public void hide() { baseRods.hide(); // baseCaps.hide(m); studs.hide(); } public void show(LocatedMolecule m) { baseRods.show(m); // baseCaps.show(m); studs.show(m); } public void show() { baseRods.show(); // baseCaps.show(m); studs.show(); } public void clear() { baseRods.clear(); // baseCaps.clear(); studs.clear(); } public vtkAssembly getAssembly() {return assembly;} public void add(LocatedMolecule m) { baseRods.add(m); // baseCaps.show(m); studs.add(m); addMolecule(m); super.add(m); } public void addMolecule(LocatedMolecule molecule) { if (! (molecule instanceof BiopolymerClass)) return; BiopolymerClass biopolymer = (BiopolymerClass) molecule; vtkPoints linePoints = new vtkPoints(); vtkPoints lineNormals = new vtkPoints(); vtkFloatArray lineScalars = new vtkFloatArray(); for (Iterator i = biopolymer.getResidueIterator(); i.hasNext();) { PDBResidue residue = (PDBResidue) i.next(); Vector3D backbonePosition = residue.getBackbonePosition(); Vector3D sideChainPosition = residue.getSideChainPosition(); 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 ( (backbonePosition != null) && (sideChainPosition != null) ) { linePoints.InsertNextPoint(backbonePosition.getX(), backbonePosition.getY(), backbonePosition.getZ()); Vector3DClass normal = new Vector3DClass( sideChainPosition.minus(backbonePosition).unit() ); lineNormals.InsertNextPoint(normal.getX(), normal.getY(), normal.getZ()); lineScalars.InsertNextValue(colorScalar); } } vtkPoints backbonePoints = linePoints; vtkPoints backboneNormals = lineNormals; int numberOfInputPoints = linePoints.GetNumberOfPoints(); if (numberOfInputPoints < 1) return; int numberOfOutputPoints = numberOfInputPoints; if (drawSmoothSpline) { // Replace linePoints and lineNormals with smoothed // oversampled versions of themselves, by means of splines // TODO - put scalar data in too numberOfOutputPoints = (int)(numberOfInputPoints * splineFactor); // Set up one spline for each dimension vtkCardinalSpline splineX = new vtkCardinalSpline(); vtkCardinalSpline splineY = new vtkCardinalSpline(); vtkCardinalSpline splineZ = new vtkCardinalSpline(); // Another set of splines for the normal vectors vtkCardinalSpline normalSplineX = new vtkCardinalSpline(); vtkCardinalSpline normalSplineY = new vtkCardinalSpline(); vtkCardinalSpline normalSplineZ = new vtkCardinalSpline(); for (int i = 0; i < linePoints.GetNumberOfPoints(); i++) { splineX.AddPoint(i, linePoints.GetPoint(i)[0]); splineY.AddPoint(i, linePoints.GetPoint(i)[1]); splineZ.AddPoint(i, linePoints.GetPoint(i)[2]); normalSplineX.AddPoint(i, lineNormals.GetPoint(i)[0]); normalSplineY.AddPoint(i, lineNormals.GetPoint(i)[1]); normalSplineZ.AddPoint(i, lineNormals.GetPoint(i)[2]); } vtkPoints splinePoints = new vtkPoints(); vtkPoints splineNormals = new vtkPoints(); for (int i = 0; i < numberOfOutputPoints; i++) { double t = (numberOfInputPoints - 1.0)/(numberOfOutputPoints - 1.0) * i; splinePoints.InsertPoint(i, splineX.Evaluate(t), splineY.Evaluate(t), splineZ.Evaluate(t) ); Vector3DClass normal = new Vector3DClass( (new Vector3DClass( normalSplineX.Evaluate(t), normalSplineY.Evaluate(t), normalSplineZ.Evaluate(t))).unit() ); splineNormals.InsertPoint(i, normal.getX(), normal.getY(), normal.getZ() ); } linePoints = splinePoints; lineNormals = splineNormals; } vtkActor lineActor = new vtkActor(); // tube vtkCellArray lineCells = new vtkCellArray(); lineCells.InsertNextCell(numberOfOutputPoints); for (int i = 0; i < numberOfOutputPoints; i ++) lineCells.InsertCellPoint(i); vtkPolyData tubeData = new vtkPolyData(); tubeData.SetPoints(linePoints); tubeData.SetLines(lineCells); // Incorporate the lineNormals tubeData.GetPointData().SetNormals(lineNormals.GetData()); // TODO - expand scalars for spline representation // TODO - how to make this color the items? // tubeData.GetPointData().SetScalars(lineScalars); // causes crash // Shift each point backwards along normal, // so that extruded ribbon is centered on backbone position vtkPoints shiftedLinePoints = new vtkPoints(); for (int i = 0; i < linePoints.GetNumberOfPoints(); i++) { double[] point, normal; point = linePoints.GetPoint(i); normal = lineNormals.GetPoint(i); double[] shiftedPoint = { point[0] - normal[0] * 0.5 * ribbonThickness, point[1] - normal[1] * 0.5 * ribbonThickness, point[2] - normal[2] * 0.5 * ribbonThickness }; shiftedLinePoints.InsertNextPoint(shiftedPoint); } tubeData.SetPoints(shiftedLinePoints); vtkRibbonFilter lineRibbon = new vtkRibbonFilter(); lineRibbon.SetWidth(ribbonWidth); lineRibbon.SetAngle(0); if (drawSmoothSpline2) { // TODO try to use vtkSplineFilter // causes crash vtkSplineFilter splineFilter = new vtkSplineFilter(); splineFilter.SetInput(tubeData); splineFilter.SetMaximumNumberOfSubdivisions((int)(splineFactor + 0.9)); lineRibbon.SetInput(splineFilter.GetOutput()); } else { lineRibbon.SetInput(tubeData); } vtkLinearExtrusionFilter ribbonThicknessFilter = new vtkLinearExtrusionFilter(); ribbonThicknessFilter.SetCapping(1); ribbonThicknessFilter.SetExtrusionTypeToNormalExtrusion(); ribbonThicknessFilter.SetScaleFactor(ribbonThickness); ribbonThicknessFilter.SetInput(lineRibbon.GetOutput()); // The polygons on the newly extruded edges are not smoothly shaded vtkPolyDataNormals dataNormals = new vtkPolyDataNormals(); dataNormals.SetFeatureAngle(80.0); // Angles smaller than this are smoothed dataNormals.SetInput(ribbonThicknessFilter.GetOutput()); vtkPolyDataMapper tubeMapper = new vtkPolyDataMapper(); // tubeMapper.SetInput(ribbonThicknessFilter.GetOutput()); // ribbon tubeMapper.SetInput(dataNormals.GetOutput()); // ribbon lineActor.SetMapper(tubeMapper); lineActor.AddPosition(0.0, 0.0, 0.0); assembly.AddPart(lineActor); } // static boolean drawWireFrame = false; // static boolean drawSmoothSpline = true; // static boolean drawFlatRibbon = true; // static double ribbonWidth = 1.5; // static double ribbonThickness = 0.7; // static double tubeThickness = 0.8; // // /** // * How many spline segments per residue // */ // static double splineFactor = 5.0; // // /** // * Update graphical primitives to reflect a change in atomic positions // * // */ // public void updateCoordinates() { // // TODO // } // // public vtkProp highlight(Residue residue, Color color) { // return null; // TODO // } // // public vtkAssembly represent(Molecule molecule) { // return represent(molecule, 1.00, null, 1.00); // } // public vtkAssembly represent(Molecule molecule, double scaleFactor, Color clr, double opacity) { // if (! (molecule instanceof Biopolymer)) return null; // Biopolymer biopolymer = (Biopolymer) molecule; // // vtkPoints linePoints = new vtkPoints(); // vtkPoints lineNormals = new vtkPoints(); // for (Iterator i = biopolymer.residues().iterator(); i.hasNext();) { // Residue residue = (Residue) i.next(); // BaseVector3D backbonePosition = residue.getBackbonePosition(); // BaseVector3D sideChainPosition = residue.getSideChainPosition(); // if ( (backbonePosition != null) && (sideChainPosition != null) ) { // linePoints.InsertNextPoint(backbonePosition.getX(), backbonePosition.getY(), backbonePosition.getZ()); // Vector3D normal = sideChainPosition.minus(backbonePosition).unit(); // lineNormals.InsertNextPoint(normal.getX(), normal.getY(), normal.getZ()); // } // } // // vtkPoints backbonePoints = linePoints; // vtkPoints backboneNormals = lineNormals; // // int numberOfInputPoints = linePoints.GetNumberOfPoints(); // if (numberOfInputPoints < 1) return null; // // int numberOfOutputPoints = numberOfInputPoints; // // if (drawSmoothSpline) { // // Replace linePoints and lineNormals with smoothed // // oversampled versions of themselves, by means of splines // // numberOfOutputPoints = (int)(numberOfInputPoints * splineFactor); // // // Set up one spline for each dimension // vtkCardinalSpline splineX = new vtkCardinalSpline(); // vtkCardinalSpline splineY = new vtkCardinalSpline(); // vtkCardinalSpline splineZ = new vtkCardinalSpline(); // // // Another set of splines for the normal vectors // vtkCardinalSpline normalSplineX = new vtkCardinalSpline(); // vtkCardinalSpline normalSplineY = new vtkCardinalSpline(); // vtkCardinalSpline normalSplineZ = new vtkCardinalSpline(); // // for (int i = 0; i < linePoints.GetNumberOfPoints(); i++) { // splineX.AddPoint(i, linePoints.GetPoint(i)[0]); // splineY.AddPoint(i, linePoints.GetPoint(i)[1]); // splineZ.AddPoint(i, linePoints.GetPoint(i)[2]); // // normalSplineX.AddPoint(i, lineNormals.GetPoint(i)[0]); // normalSplineY.AddPoint(i, lineNormals.GetPoint(i)[1]); // normalSplineZ.AddPoint(i, lineNormals.GetPoint(i)[2]); // } // // vtkPoints splinePoints = new vtkPoints(); // vtkPoints splineNormals = new vtkPoints(); // for (int i = 0; i < numberOfOutputPoints; i++) { // double t = (numberOfInputPoints - 1.0)/(numberOfOutputPoints - 1.0) * i; // splinePoints.InsertPoint(i, // splineX.Evaluate(t), // splineY.Evaluate(t), // splineZ.Evaluate(t) // ); // // Vector3D normal = (new Vector3D( // normalSplineX.Evaluate(t), // normalSplineY.Evaluate(t), // normalSplineZ.Evaluate(t))).unit(); // splineNormals.InsertPoint(i, // normal.getX(), // normal.getY(), // normal.getZ() // ); // } // // linePoints = splinePoints; // lineNormals = splineNormals; // } // // vtkActor lineActor = new vtkActor(); // tube // // if (drawWireFrame) { // vtkPolyLine backboneLine = new vtkPolyLine(); // backboneLine.GetPointIds().SetNumberOfIds(numberOfOutputPoints); // for (int i = 0; i < linePoints.GetNumberOfPoints(); i++) { // backboneLine.GetPointIds().SetId(i, i); // } // // // Wireframe // vtkUnstructuredGrid lineGrid = new vtkUnstructuredGrid(); // lineGrid.Allocate(1, 1); // lineGrid.InsertNextCell(backboneLine.GetCellType(), backboneLine.GetPointIds()); // // lineGrid.SetPoints(linePoints); // // vtkDataSetMapper lineMapper = new vtkDataSetMapper(); // lineMapper.SetInput(lineGrid); // // lineActor.SetMapper(lineMapper); // wireframe // } // // else { // Tube or ribbon // vtkCellArray lineCells = new vtkCellArray(); // lineCells.InsertNextCell(numberOfOutputPoints); // for (int i = 0; i < numberOfOutputPoints; i ++) // lineCells.InsertCellPoint(i); // // vtkPolyData tubeData = new vtkPolyData(); // tubeData.SetPoints(linePoints); // tubeData.SetLines(lineCells); // // // Incorporate the lineNormals // tubeData.GetPointData().SetNormals(lineNormals.GetData()); // // vtkPolyDataMapper tubeMapper = new vtkPolyDataMapper(); // // if (drawFlatRibbon) { // Ribbon not Tube // // Shift each point backwards along normal, // // so that extruded ribbon is centered on backbone position // vtkPoints shiftedLinePoints = new vtkPoints(); // for (int i = 0; i < linePoints.GetNumberOfPoints(); i++) { // double[] point, normal; // point = linePoints.GetPoint(i); // normal = lineNormals.GetPoint(i); // double[] shiftedPoint = { // point[0] - normal[0] * 0.5 * ribbonThickness, // point[1] - normal[1] * 0.5 * ribbonThickness, // point[2] - normal[2] * 0.5 * ribbonThickness // }; // shiftedLinePoints.InsertNextPoint(shiftedPoint); // } // tubeData.SetPoints(shiftedLinePoints); // // vtkRibbonFilter lineRibbon = new vtkRibbonFilter(); // lineRibbon.SetInput(tubeData); // lineRibbon.SetWidth(ribbonWidth); // lineRibbon.SetAngle(0); // // vtkLinearExtrusionFilter ribbonThicknessFilter = new vtkLinearExtrusionFilter(); // ribbonThicknessFilter.SetCapping(1); // ribbonThicknessFilter.SetExtrusionTypeToNormalExtrusion(); // ribbonThicknessFilter.SetScaleFactor(ribbonThickness); // ribbonThicknessFilter.SetInput(lineRibbon.GetOutput()); // // // The polygons on the newly extruded edges are not smoothly shaded // vtkPolyDataNormals dataNormals = new vtkPolyDataNormals(); // dataNormals.SetFeatureAngle(80.0); // Angles smaller than this are smoothed // dataNormals.SetInput(ribbonThicknessFilter.GetOutput()); // // // tubeMapper.SetInput(ribbonThicknessFilter.GetOutput()); // ribbon // tubeMapper.SetInput(dataNormals.GetOutput()); // ribbon // } // else { // Tube not ribbon // vtkTubeFilter lineTube = new vtkTubeFilter(); // lineTube.SetInput(tubeData); // lineTube.SetRadius(tubeThickness); // lineTube.SetNumberOfSides(5); // tubeMapper.SetInput(lineTube.GetOutput()); // tube // } // // lineActor.SetMapper(tubeMapper); // } // // lineActor.AddPosition(0.0, 0.0, 0.0); // // // Shiny black ribbon // // lineActor.GetProperty().SetColor(0.0,0.0,0.0); // // lineActor.GetProperty().SetSpecular(1.0); // // lineActor.GetProperty().SetSpecularColor(1.0,1.0,1.0); // // lineActor.GetProperty().SetSpecularPower(100); // // vtkAssembly assembly = new vtkAssembly(); // assembly.AddPart(lineActor); // // // // Spheres at Backbone residue positions // vtkSphereSource sphere = new vtkSphereSource(); // sphere.SetThetaResolution(6); // sphere.SetPhiResolution(6); // sphere.SetRadius(ribbonThickness + 0.2); // // vtkPolyData backbonePointData = new vtkPolyData(); // backbonePointData.SetPoints(backbonePoints); // // vtkGlyph3D spheres = new vtkGlyph3D(); // spheres.SetInput(backbonePointData); // spheres.SetSource(sphere.GetOutput()); // // vtkPolyDataMapper spheresMapper = new vtkPolyDataMapper(); // spheresMapper.SetInput(spheres.GetOutput()); // // vtkActor spheresActor = new vtkActor(); // spheresActor.SetMapper(spheresMapper); // spheresActor.GetProperty().SetOpacity(opacity); // spheresActor.GetProperty().BackfaceCullingOn(); // // assembly.AddPart(spheresActor); // // // // One rod per base // vtkCylinderSource rod = new vtkCylinderSource(); // rod.SetHeight(baseRodLength); // rod.SetCapping(1); // rod.SetRadius(baseRodRadius); // rod.SetResolution(5); // // // 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(rod.GetOutput()); // cylinderFilter.SetTransform(cylinderTransform); // // vtkPoints rodMidpoints = new vtkPoints(); // for (int i = 0; i < numberOfInputPoints; i++) { // double[] point = backbonePoints.GetPoint(i); // double[] normal = backboneNormals.GetPoint(i); // double[] midPoint = { // point[0] + normal[0] * 0.5 * baseRodLength, // point[1] + normal[1] * 0.5 * baseRodLength, // point[2] + normal[2] * 0.5 * baseRodLength // }; // rodMidpoints.InsertNextPoint(midPoint); // } // // vtkPolyData rodData = new vtkPolyData(); // rodData.SetPoints(rodMidpoints); // rodData.GetPointData().SetNormals(backboneNormals.GetData()); // // vtkGlyph3D rods = new vtkGlyph3D(); // rods.SetInput(rodData); // rods.SetSource(cylinderFilter.GetOutput()); // rods.SetVectorModeToUseNormal(); // // vtkPolyDataMapper rodsMapper = new vtkPolyDataMapper(); // rodsMapper.SetInput(rods.GetOutput()); // // vtkActor rodsActor = new vtkActor(); // rodsActor.SetMapper(rodsMapper); // // assembly.AddPart(rodsActor); // // return assembly; // } }