Menu
▾
▴
[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/viewer/datamodel ArrowLineShape.java,1.2,1.3 AtomShape.java,1.14,1.15 Axes.java,1.2,1.3 BondShape.java,1.9,1.10 BoundingBox.java,1.1,1.2 DotsRenderer.java,1.5,1.6 FrameRenderer.java,1.4,1.5 JmolFrame.java,1.13,1.14 JmolFrameBuilder.java,1.5,1.6 LineShape.java,1.1,1.2 MeasurementShape.java,1.6,1.7
|
From: Michael T H. <mic...@us...> - 2003-08-29 22:00:07
|
Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel
In directory sc8-pr-cvs1:/tmp/cvs-serv20647/src/org/openscience/jmol/viewer/datamodel
Modified Files:
ArrowLineShape.java AtomShape.java Axes.java BondShape.java
BoundingBox.java DotsRenderer.java FrameRenderer.java
JmolFrame.java JmolFrameBuilder.java LineShape.java
MeasurementShape.java
Log Message:
converted viewer to use floats instead of doubles
Index: ArrowLineShape.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/ArrowLineShape.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- ArrowLineShape.java 29 Aug 2003 19:06:52 -0000 1.2
+++ ArrowLineShape.java 29 Aug 2003 22:00:00 -0000 1.3
@@ -28,7 +28,7 @@
import org.openscience.jmol.viewer.JmolViewer;
import java.awt.Rectangle;
-import javax.vecmath.Point3d;
+import javax.vecmath.Point3f;
import javax.vecmath.Point3i;
public class ArrowLineShape extends LineShape {
@@ -42,7 +42,7 @@
final static int shaftDivisor = 5;
final static int finDivisor = 6;
- public ArrowLineShape(Point3d pointOrigin, Point3d pointVector) {
+ public ArrowLineShape(Point3f pointOrigin, Point3f pointVector) {
super(pointOrigin, pointVector);
headWidthAngstroms =
(float)pointOrigin.distance(this.pointEnd) / widthDivisor;
Index: AtomShape.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/AtomShape.java,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- AtomShape.java 29 Aug 2003 19:06:52 -0000 1.14
+++ AtomShape.java 29 Aug 2003 22:00:00 -0000 1.15
@@ -32,14 +32,14 @@
import java.awt.Rectangle;
-import javax.vecmath.Point3d;
+import javax.vecmath.Point3f;
import javax.vecmath.Point3i;
public class AtomShape implements Bspt.Tuple {
public Object clientAtom;
JmolFrame frame;
- Point3d point3d;
+ Point3f point3f;
int x, y, z;
byte atomicNumber;
byte styleAtom;
@@ -65,7 +65,7 @@
pprop = new ProteinProp(pdbRecord);
}
setStyleMarAtom(viewer.getStyleAtom(), viewer.getMarAtom());
- this.point3d = new Point3d(viewer.getAtomX(clientAtom),
+ this.point3f = new Point3f(viewer.getAtomX(clientAtom),
viewer.getAtomY(clientAtom),
viewer.getAtomZ(clientAtom));
this.strLabel = viewer.getLabelAtom(this, atomIndex);
@@ -247,7 +247,7 @@
}
public void transform(JmolViewer viewer) {
- Point3i screen = viewer.transformPoint(point3d);
+ Point3i screen = viewer.transformPoint(point3f);
x = screen.x;
y = screen.y;
z = screen.z;
@@ -266,26 +266,26 @@
return frame.viewer.getAtomTypeName(atomicNumber, clientAtom);
}
- public Point3d getPoint3d() {
- return point3d;
+ public Point3f getPoint3f() {
+ return point3f;
}
public float getAtomX() {
- return (float)point3d.x;
+ return (float)point3f.x;
}
public float getAtomY() {
- return (float)point3d.y;
+ return (float)point3f.y;
}
public float getAtomZ() {
- return (float)point3d.z;
+ return (float)point3f.z;
}
public float getDimensionValue(int dimension) {
return (float)(dimension == 0
- ? point3d.x
- : (dimension == 1 ? point3d.y : point3d.z));
+ ? point3f.x
+ : (dimension == 1 ? point3f.y : point3f.z));
}
public float getVanderwaalsRadius() {
Index: Axes.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/Axes.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- Axes.java 26 Aug 2003 13:52:26 -0000 1.2
+++ Axes.java 29 Aug 2003 22:00:00 -0000 1.3
@@ -29,7 +29,7 @@
import java.awt.Font;
import java.awt.FontMetrics;
-import javax.vecmath.Point3d;
+import javax.vecmath.Point3f;
import javax.vecmath.Point3i;
public class Axes {
@@ -40,14 +40,14 @@
AxisShape[] axisShapes;
Shape[] allShapes;
- final Point3d pointOrigin = new Point3d();
- Point3d[] unitAxisPoints = {
- new Point3d( 1, 0, 0),
- new Point3d( 0, 1, 0),
- new Point3d( 0, 0, 1),
- new Point3d(-1, 0, 0),
- new Point3d( 0,-1, 0),
- new Point3d( 0, 0,-1)
+ final Point3f pointOrigin = new Point3f();
+ Point3f[] unitAxisPoints = {
+ new Point3f( 1, 0, 0),
+ new Point3f( 0, 1, 0),
+ new Point3f( 0, 0, 1),
+ new Point3f(-1, 0, 0),
+ new Point3f( 0,-1, 0),
+ new Point3f( 0, 0,-1)
};
String[] axisLabels = { "+X", "+Y", "+Z",
@@ -64,7 +64,7 @@
axisShapes = new AxisShape[6];
for (int i = 0; i < 6; ++i)
allShapes[i+1] = axisShapes[i] =
- new AxisShape(new Point3d(unitAxisPoints[i]), axisLabels[i]);
+ new AxisShape(new Point3f(unitAxisPoints[i]), axisLabels[i]);
}
public Shape[] getShapes() {
@@ -75,9 +75,9 @@
if (modeAxes == JmolViewer.AXES_NONE)
return;
pointOrigin.set(viewer.getBoundingBoxCenter());
- Point3d corner = viewer.getBoundingBoxCorner();
+ Point3f corner = viewer.getBoundingBoxCorner();
for (int i = 0; i < 6; ++i) {
- Point3d axisPoint = axisShapes[i].getPoint();
+ Point3f axisPoint = axisShapes[i].getPoint();
axisPoint.set(unitAxisPoints[i]);
if (modeAxes == JmolViewer.AXES_BBOX) {
// we have just set the axisPoint to be a unit on a single axis
@@ -114,14 +114,14 @@
}
class AxisShape extends Shape {
- Point3d pointAxisEnd;
+ Point3f pointAxisEnd;
String label;
- AxisShape(Point3d pointAxisEnd, String label) {
+ AxisShape(Point3f pointAxisEnd, String label) {
this.pointAxisEnd = pointAxisEnd;
this.label = label;
}
- Point3d getPoint() {
+ Point3f getPoint() {
return pointAxisEnd;
}
Index: BondShape.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/BondShape.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- BondShape.java 29 Aug 2003 19:06:52 -0000 1.9
+++ BondShape.java 29 Aug 2003 22:00:00 -0000 1.10
@@ -31,9 +31,6 @@
import java.awt.Rectangle;
-import javax.vecmath.Point3d;
-import javax.vecmath.Point3i;
-
public class BondShape {
public final static byte COVALENT = 3;
Index: BoundingBox.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/BoundingBox.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- BoundingBox.java 16 Aug 2003 14:50:44 -0000 1.1
+++ BoundingBox.java 29 Aug 2003 22:00:00 -0000 1.2
@@ -29,27 +29,27 @@
import java.awt.Font;
import java.awt.FontMetrics;
-import javax.vecmath.Point3d;
+import javax.vecmath.Point3f;
import javax.vecmath.Point3i;
public class BoundingBox {
JmolViewer viewer;
- Point3d pointOrigin;
- Point3d pointCorner;
+ Point3f pointOrigin;
+ Point3f pointCorner;
BboxShape[] bboxShapes;
- Point3d[] unitBboxPoints = {
- new Point3d( 1, 1, 1),
- new Point3d( 1, 1,-1),
- new Point3d( 1,-1, 1),
- new Point3d( 1,-1,-1),
- new Point3d(-1, 1, 1),
- new Point3d(-1, 1,-1),
- new Point3d(-1,-1, 1),
- new Point3d(-1,-1,-1),
+ Point3f[] unitBboxPoints = {
+ new Point3f( 1, 1, 1),
+ new Point3f( 1, 1,-1),
+ new Point3f( 1,-1, 1),
+ new Point3f( 1,-1,-1),
+ new Point3f(-1, 1, 1),
+ new Point3f(-1, 1,-1),
+ new Point3f(-1,-1, 1),
+ new Point3f(-1,-1,-1),
};
public BoundingBox(JmolViewer viewer) {
@@ -58,7 +58,7 @@
bboxShapes = new BboxShape[8];
for (int i = 0; i < 8; ++i)
bboxShapes[i] =
- new BboxShape(new Point3d(unitBboxPoints[i]), i);
+ new BboxShape(new Point3f(unitBboxPoints[i]), i);
}
public Shape[] getBboxShapes() {
@@ -66,10 +66,10 @@
}
public void recalc() {
- Point3d pointOrigin = viewer.getBoundingBoxCenter();
- Point3d pointCorner = viewer.getBoundingBoxCorner();
+ Point3f pointOrigin = viewer.getBoundingBoxCenter();
+ Point3f pointCorner = viewer.getBoundingBoxCorner();
for (int i = 0; i < 8; ++i) {
- Point3d pointBbox = bboxShapes[i].getPoint();
+ Point3f pointBbox = bboxShapes[i].getPoint();
pointBbox.set(unitBboxPoints[i]);
pointBbox.x *= pointCorner.x;
pointBbox.y *= pointCorner.y;
@@ -79,15 +79,15 @@
}
class BboxShape extends Shape {
- Point3d point;
+ Point3f point;
int myIndex;
- BboxShape(Point3d point, int myIndex) {
+ BboxShape(Point3f point, int myIndex) {
this.point = point;
this.myIndex = myIndex;
}
- Point3d getPoint() {
+ Point3f getPoint() {
return point;
}
Index: DotsRenderer.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/DotsRenderer.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- DotsRenderer.java 29 Aug 2003 19:06:52 -0000 1.5
+++ DotsRenderer.java 29 Aug 2003 22:00:00 -0000 1.6
@@ -32,8 +32,8 @@
import java.awt.Rectangle;
import java.util.Hashtable;
-import javax.vecmath.Vector3d;
-import javax.vecmath.Point3d;
+import javax.vecmath.Vector3f;
+import javax.vecmath.Point3f;
import javax.vecmath.Point3i;
public class DotsRenderer {
@@ -84,7 +84,7 @@
// I have no idea what this number should be
int neighborCount;
AtomShape[] neighbors = new AtomShape[16];
- Point3d[] neighborCenters = new Point3d[16];
+ Point3f[] neighborCenters = new Point3f[16];
float[] neighborRadii2 = new float[16];
void getNeighbors(AtomShape atom, float vdwRadius, float probeRadius) {
@@ -99,7 +99,7 @@
AtomShape[] neighborsNew = new AtomShape[2 * neighborCount];
System.arraycopy(neighbors, 0, neighborsNew, 0, neighborCount);
neighbors = neighborsNew;
- Point3d[] centersNew = new Point3d[2 * neighborCount];
+ Point3f[] centersNew = new Point3f[2 * neighborCount];
System.arraycopy(neighborCenters, 0, centersNew, 0, neighborCount);
neighborCenters = centersNew;
float[] radiiNew = new float[2 * neighborCount];
@@ -107,7 +107,7 @@
neighborRadii2 = radiiNew;
}
neighbors[neighborCount] = neighbor;
- neighborCenters[neighborCount] = neighbor.point3d;
+ neighborCenters[neighborCount] = neighbor.point3f;
float effectiveRadius = (neighbor.getVanderwaalsRadius() +
probeRadius);
neighborRadii2[neighborCount] = effectiveRadius * effectiveRadius;
@@ -119,19 +119,19 @@
System.out.println("myVdwRadius=" + myVdwRadius +
" maxVdwRadius=" + maxVdwRadius +
" distMax=" + (myVdwRadius + maxVdwRadius));
- Point3d me = atom.getPoint3d();
+ Point3f me = atom.getPoint3f();
for (int i = 0; i < neighborCount; ++i) {
System.out.println(" dist=" +
- me.distance(neighbors[i].getPoint3d()));
+ me.distance(neighbors[i].getPoint3f()));
}
*/
}
int[] bitmap;
- Point3d pointT = new Point3d();
+ Point3f pointT = new Point3f();
- void calcBits(Point3d myCenter, float vdwRadius, float probeRadius) {
- Vector3d[] vertices = icosohedron.vertices;
+ void calcBits(Point3f myCenter, float vdwRadius, float probeRadius) {
+ Vector3f[] vertices = icosohedron.vertices;
int dotCount = vertices.length;
setAllBits(bitmap, dotCount);
if (neighborCount == 0)
@@ -157,7 +157,7 @@
float vdwRadius = atom.getVanderwaalsRadius();
float probeRadius = viewer.getSolventProbeRadius();
getNeighbors(atom, vdwRadius, probeRadius);
- calcBits(atom.getPoint3d(), vdwRadius, probeRadius);
+ calcBits(atom.getPoint3f(), vdwRadius, probeRadius);
int indexLast;
for (indexLast = bitmap.length;
--indexLast >= 0 && bitmap[indexLast] == 0; )
@@ -203,8 +203,8 @@
class Icosohedron {
- Vector3d[] vertices;
- Vector3d[] verticesTransformed;
+ Vector3f[] vertices;
+ Vector3f[] verticesTransformed;
// byte[] intensitiesTransformed;
int screenCoordinateCount;
int[] screenCoordinates;
@@ -212,23 +212,23 @@
short[] faceIndices;
Icosohedron() {
- vertices = new Vector3d[12];
- vertices[0] = new Vector3d(0, 0, halfRoot5);
+ vertices = new Vector3f[12];
+ vertices[0] = new Vector3f(0, 0, halfRoot5);
for (int i = 0; i < 5; ++i) {
- vertices[i+1] = new Vector3d(Math.cos(i * oneFifth),
- Math.sin(i * oneFifth),
- 0.5);
- vertices[i+6] = new Vector3d(Math.cos(i * oneFifth + oneTenth),
- Math.sin(i * oneFifth + oneTenth),
- -0.5);
+ vertices[i+1] = new Vector3f((float)Math.cos(i * oneFifth),
+ (float)Math.sin(i * oneFifth),
+ 0.5f);
+ vertices[i+6] = new Vector3f((float)Math.cos(i * oneFifth + oneTenth),
+ (float)Math.sin(i * oneFifth + oneTenth),
+ -0.5f);
}
- vertices[11] = new Vector3d(0, 0, -halfRoot5);
+ vertices[11] = new Vector3f(0, 0, -halfRoot5);
for (int i = 12; --i >= 0; )
vertices[i].normalize();
faceIndices = faceIndicesInitial;
- verticesTransformed = new Vector3d[12];
+ verticesTransformed = new Vector3f[12];
for (int i = 12; --i >= 0; )
- verticesTransformed[i] = new Vector3d();
+ verticesTransformed[i] = new Vector3f();
screenCoordinates = new int[3 * 12];
// intensities = new byte[12];
// intensitiesTransformed = new byte[12];
@@ -236,7 +236,7 @@
void transform() {
for (int i = vertices.length; --i >= 0; ) {
- Vector3d t = verticesTransformed[i];
+ Vector3f t = verticesTransformed[i];
viewer.transformVector(vertices[i], t);
// intensitiesTransformed[i] =
// Shade3D.calcIntensity((float)t.x, (float)t.y, (float)t.z);
@@ -270,7 +270,7 @@
if (! getBit(visibilityMap, iDot))
continue;
// intensities[iintensities++] = intensitiesTransformed[iDot];
- Vector3d vertex = verticesTransformed[iDot];
+ Vector3f vertex = verticesTransformed[iDot];
screenCoordinates[icoordinates++] = x
+ (int)((scaledRadius*vertex.x) + (vertex.x < 0 ? -0.5 : 0.5));
screenCoordinates[icoordinates++] = y
@@ -291,12 +291,12 @@
int nFaceIndicesOld = faceIndicesOld.length;
int nEdgesOld = nVerticesOld + nFaceIndicesOld/3 - 2;
int nVerticesNew = nVerticesOld + nEdgesOld;
- Vector3d[] verticesNew = new Vector3d[nVerticesNew];
+ Vector3f[] verticesNew = new Vector3f[nVerticesNew];
System.arraycopy(vertices, 0, verticesNew, 0, nVerticesOld);
vertices = verticesNew;
- verticesTransformed = new Vector3d[nVerticesNew];
+ verticesTransformed = new Vector3f[nVerticesNew];
for (int i = nVerticesNew; --i >= 0; )
- verticesTransformed[i] = new Vector3d();
+ verticesTransformed[i] = new Vector3f();
screenCoordinates = new int[3 * nVerticesNew];
// intensitiesTransformed = new byte[nVerticesNew];
// intensities
@@ -353,9 +353,9 @@
Short iv = (Short)htVertex.get(hashKey);
if (iv != null)
return iv.shortValue();
- Vector3d vertexNew = new Vector3d(vertices[i1]);
+ Vector3f vertexNew = new Vector3f(vertices[i1]);
vertexNew.add(vertices[i2]);
- vertexNew.scale(0.5);
+ vertexNew.scale(0.5f);
vertexNew.normalize();
htVertex.put(hashKey, new Short(iVertexNew));
vertices[iVertexNew] = vertexNew;
Index: FrameRenderer.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/FrameRenderer.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- FrameRenderer.java 29 Aug 2003 15:52:16 -0000 1.4
+++ FrameRenderer.java 29 Aug 2003 22:00:00 -0000 1.5
@@ -28,7 +28,6 @@
import org.openscience.jmol.viewer.JmolViewer;
import org.openscience.jmol.viewer.protein.ProteinProp;
import org.openscience.jmol.viewer.g3d.Graphics3D;
-import javax.vecmath.Point3d;
import java.util.Hashtable;
import java.util.BitSet;
import java.awt.Rectangle;
Index: JmolFrame.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/JmolFrame.java,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- JmolFrame.java 29 Aug 2003 19:06:52 -0000 1.13
+++ JmolFrame.java 29 Aug 2003 22:00:00 -0000 1.14
@@ -28,7 +28,7 @@
import org.openscience.jmol.viewer.JmolViewer;
import org.openscience.jmol.viewer.protein.ProteinProp;
import org.openscience.jmol.viewer.g3d.Graphics3D;
-import javax.vecmath.Point3d;
+import javax.vecmath.Point3f;
import java.util.Hashtable;
import java.util.BitSet;
import java.awt.Rectangle;
@@ -196,9 +196,9 @@
dotsConvexCount = iLast + 1;
}
- Point3d centerBoundingBox;
- Point3d cornerBoundingBox;
- Point3d centerRotation;
+ Point3f centerBoundingBox;
+ Point3f cornerBoundingBox;
+ Point3f centerRotation;
float radiusBoundingBox;
float radiusRotation;
@@ -207,17 +207,17 @@
return radiusBoundingBox;
}
- public Point3d getBoundingBoxCenter() {
+ public Point3f getBoundingBoxCenter() {
findBounds();
return centerBoundingBox;
}
- public Point3d getBoundingBoxCorner() {
+ public Point3f getBoundingBoxCorner() {
findBounds();
return cornerBoundingBox;
}
- public Point3d getRotationCenter() {
+ public Point3f getRotationCenter() {
findBounds();
return centerRotation;
}
@@ -227,7 +227,7 @@
return radiusRotation;
}
- public void setRotationCenter(Point3d newCenterOfRotation) {
+ public void setRotationCenter(Point3f newCenterOfRotation) {
if (newCenterOfRotation != null) {
centerRotation = newCenterOfRotation;
radiusRotation = calcRadius(centerRotation);
@@ -256,44 +256,44 @@
// Note that this is not really the geometric center of the molecule
// ... for this we would need to do a Minimal Enclosing Sphere calculation
float minX, minY, minZ, maxX, maxY, maxZ;
- Point3d point;
+ Point3f point;
if (crystalCellLineCount == 0) { // non-crystal, so find extremes of atoms
- point = atomShapes[0].getPoint3d();
- minX = maxX = (float)point.x;
- minY = maxY = (float)point.y;
- minZ = maxZ = (float)point.z;
+ point = atomShapes[0].getPoint3f();
+ minX = maxX = point.x;
+ minY = maxY = point.y;
+ minZ = maxZ = point.z;
for (int i = atomShapeCount; --i > 0; ) {
// note that the 0 element was set above
- point = atomShapes[i].getPoint3d();
+ point = atomShapes[i].getPoint3f();
float t;
- t = (float)point.x;
+ t = point.x;
if (t < minX) { minX = t; }
else if (t > maxX) { maxX = t; }
- t = (float)point.y;
+ t = point.y;
if (t < minY) { minY = t; }
else if (t > maxY) { maxY = t; }
- t = (float)point.z;
+ t = point.z;
if (t < minZ) { minZ = t; }
else if (t > maxZ) { maxZ = t; }
}
} else { // a crystal cell, so use center of crystal cell box
point = crystalCellLines[0].getPoint1();
- minX = maxX = (float)point.x;
- minY = maxY = (float)point.y;
- minZ = maxZ = (float)point.z;
+ minX = maxX = point.x;
+ minY = maxY = point.y;
+ minZ = maxZ = point.z;
for (int i = crystalCellLineCount; --i >= 0; ) {
point = crystalCellLines[i].getPoint1();
int j = 0;
do {
float t;
- t = (float)point.x;
+ t = point.x;
if (t < minX) { minX = t; }
else if (t > maxX) { maxX = t; }
- t = (float)point.y;
+ t = point.y;
if (t < minY) { minY = t; }
else if (t > maxY) { maxY = t; }
- t = (float)point.z;
+ t = point.z;
if (t < minZ) { minZ = t; }
else if (t > maxZ) { maxZ = t; }
point = crystalCellLines[i].getPoint2();
@@ -301,19 +301,19 @@
}
}
- centerBoundingBox = new Point3d((minX + maxX) / 2,
+ centerBoundingBox = new Point3f((minX + maxX) / 2,
(minY + maxY) / 2,
(minZ + maxZ) / 2);
- cornerBoundingBox = new Point3d(maxX, maxY, maxZ);
+ cornerBoundingBox = new Point3f(maxX, maxY, maxZ);
cornerBoundingBox.sub(centerBoundingBox);
}
- private float calcRadius(Point3d center) {
- float radius = 0.0f;
+ private float calcRadius(Point3f center) {
+ float radius = 0;
for (int i = atomShapeCount; --i >= 0; ) {
AtomShape atomShape = atomShapes[i];
- Point3d posAtom = atomShape.getPoint3d();
- float distAtom = (float)center.distance(posAtom);
+ Point3f posAtom = atomShape.getPoint3f();
+ float distAtom = center.distance(posAtom);
float radiusVdw = atomShape.getVanderwaalsRadius();
float distVdw = distAtom + radiusVdw;
@@ -335,20 +335,20 @@
for (int i = lineShapeCount; --i >= 0; ) {
LineShape ls = lineShapes[i];
float distLineEnd;
- distLineEnd = (float)center.distance(ls.getPoint1());
+ distLineEnd = center.distance(ls.getPoint1());
if (distLineEnd > radius)
radius = distLineEnd;
- distLineEnd = (float)center.distance(ls.getPoint2());
+ distLineEnd = center.distance(ls.getPoint2());
if (distLineEnd > radius)
radius = distLineEnd;
}
for (int i = crystalCellLineCount; --i >= 0; ) {
LineShape ls = crystalCellLines[i];
float distLineEnd;
- distLineEnd = (float)center.distance(ls.getPoint1());
+ distLineEnd = center.distance(ls.getPoint1());
if (distLineEnd > radius)
radius = distLineEnd;
- distLineEnd = (float)center.distance(ls.getPoint2());
+ distLineEnd = center.distance(ls.getPoint2());
if (distLineEnd > radius)
radius = distLineEnd;
}
@@ -582,7 +582,7 @@
return withinAtomIterator;
}
- public AtomShapeIterator getWithinIterator(Point3d point, float radius) {
+ public AtomShapeIterator getWithinIterator(Point3f point, float radius) {
pointWrapper.setPoint(point);
withinPointIterator.initialize(pointWrapper, radius);
return withinPointIterator;
@@ -611,16 +611,16 @@
}
class PointWrapper implements Bspt.Tuple {
- Point3d point;
+ Point3f point;
- void setPoint(Point3d point) {
+ void setPoint(Point3f point) {
this.point.set(point);
}
public float getDimensionValue(int dim) {
return (dim == 0
- ? (float)point.x
- : (dim == 1 ? (float)point.y : (float)point.z));
+ ? point.x
+ : (dim == 1 ? point.y : point.z));
}
}
Index: JmolFrameBuilder.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/JmolFrameBuilder.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- JmolFrameBuilder.java 29 Aug 2003 18:29:02 -0000 1.5
+++ JmolFrameBuilder.java 29 Aug 2003 22:00:00 -0000 1.6
@@ -26,7 +26,7 @@
import org.openscience.jmol.viewer.JmolViewer;
import org.openscience.jmol.viewer.JmolModelAdapter;
-import javax.vecmath.Point3d;
+import javax.vecmath.Point3f;
public class JmolFrameBuilder {
@@ -83,10 +83,10 @@
if (iterVector != null)
while (iterVector.hasNext()) {
iterVector.moveNext();
- Point3d point1 = new Point3d(iterVector.getPoint1X(),
+ Point3f point1 = new Point3f(iterVector.getPoint1X(),
iterVector.getPoint1Y(),
iterVector.getPoint1Z());
- Point3d point2 = new Point3d(iterVector.getPoint2X(),
+ Point3f point2 = new Point3f(iterVector.getPoint2X(),
iterVector.getPoint2Y(),
iterVector.getPoint2Z());
frame.addLineShape(new ArrowLineShape(point1, point2));
@@ -99,10 +99,10 @@
if (iterCell != null)
for (int i = 0; iterCell.hasNext(); ++i) {
iterCell.moveNext();
- Point3d point1 = new Point3d(iterCell.getPoint1X(),
+ Point3f point1 = new Point3f(iterCell.getPoint1X(),
iterCell.getPoint1Y(),
iterCell.getPoint1Z());
- Point3d point2 = new Point3d(iterCell.getPoint2X(),
+ Point3f point2 = new Point3f(iterCell.getPoint2X(),
iterCell.getPoint2Y(),
iterCell.getPoint2Z());
LineShape line;
Index: LineShape.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/LineShape.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- LineShape.java 16 Aug 2003 14:50:44 -0000 1.1
+++ LineShape.java 29 Aug 2003 22:00:00 -0000 1.2
@@ -28,28 +28,28 @@
import org.openscience.jmol.viewer.g3d.Graphics3D;
import java.awt.Rectangle;
-import javax.vecmath.Point3d;
+import javax.vecmath.Point3f;
import javax.vecmath.Point3i;
public class LineShape extends Shape {
- Point3d pointOrigin;
- Point3d pointEnd;
+ Point3f pointOrigin;
+ Point3f pointEnd;
int xEnd, yEnd, zEnd;
public LineShape() {
}
- public LineShape(Point3d pointOrigin, Point3d pointEnd) {
+ public LineShape(Point3f pointOrigin, Point3f pointEnd) {
this.pointOrigin = pointOrigin;
this.pointEnd = pointEnd;
}
- public Point3d getPoint1() {
+ public Point3f getPoint1() {
return pointOrigin;
}
- public Point3d getPoint2() {
+ public Point3f getPoint2() {
return pointEnd;
}
Index: MeasurementShape.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/MeasurementShape.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- MeasurementShape.java 20 Aug 2003 15:55:50 -0000 1.6
+++ MeasurementShape.java 29 Aug 2003 22:00:00 -0000 1.7
@@ -28,8 +28,8 @@
import org.openscience.jmol.viewer.JmolViewer;
import org.openscience.jmol.viewer.g3d.Graphics3D;
-import javax.vecmath.Point3d;
-import javax.vecmath.Vector3d;
+import javax.vecmath.Point3f;
+import javax.vecmath.Vector3f;
//import freeware.PrintfFormat;
import java.awt.Font;
@@ -42,10 +42,10 @@
public String strMeasurement;
public MeasurementShape(JmolViewer viewer, int count, int[] atomIndices) {
- Point3d point1 = viewer.getPoint3d(atomIndices[0]);
- Point3d point2 = viewer.getPoint3d(atomIndices[1]);
- Point3d point3 = null;
- Point3d point4 = null;
+ Point3f point1 = viewer.getPoint3f(atomIndices[0]);
+ Point3f point2 = viewer.getPoint3f(atomIndices[1]);
+ Point3f point3 = null;
+ Point3f point4 = null;
switch (count) {
case 2:
strMeasurement = formatDistance(point1.distance(point2));;
@@ -54,33 +54,33 @@
pointEnd = point2;
break;
case 3:
- point3 = viewer.getPoint3d(atomIndices[2]);
- Vector3d vector12 = new Vector3d(point1);
+ point3 = viewer.getPoint3f(atomIndices[2]);
+ Vector3f vector12 = new Vector3f(point1);
vector12.sub(point2);
- Vector3d vector32 = new Vector3d(point3);
+ Vector3f vector32 = new Vector3f(point3);
vector32.sub(point2);
- double angle = toDegrees(vector12.angle(vector32));
+ float angle = toDegrees(vector12.angle(vector32));
strMeasurement = formatAngle(angle);
- pointOrigin = new Point3d(point1);
+ pointOrigin = new Point3f(point1);
pointOrigin.scaleAdd(3, point2);
- pointOrigin.scale(.25);
- pointEnd = new Point3d(point3);
+ pointOrigin.scale(0.25f);
+ pointEnd = new Point3f(point3);
pointEnd.scaleAdd(3, point2);
- pointEnd.scale(.25);
+ pointEnd.scale(0.25f);
break;
case 4:
- point3 = viewer.getPoint3d(atomIndices[2]);
- point4 = viewer.getPoint3d(atomIndices[3]);
- double dihedral = computeDihedral(point1, point2, point3, point4);
+ point3 = viewer.getPoint3f(atomIndices[2]);
+ point4 = viewer.getPoint3f(atomIndices[3]);
+ float dihedral = computeDihedral(point1, point2, point3, point4);
strMeasurement = formatAngle(dihedral);
- pointOrigin = new Point3d(point1);
+ pointOrigin = new Point3f(point1);
pointOrigin.add(point2);
- pointOrigin.scale(0.5);
- pointEnd = new Point3d(point3);
+ pointOrigin.scale(0.5f);
+ pointEnd = new Point3f(point3);
pointEnd.add(point4);
- pointEnd.scale(0.5);
+ pointEnd.scale(0.5f);
break;
default:
System.out.println("Invalid count to measurement shape:" + count);
@@ -107,14 +107,14 @@
private static PrintfFormat dihedralFormat = new PrintfFormat("%0.1f\u00b0");
*/
- String formatDistance(double dist) {
- dist = (int)(dist * 1000 + .5);
+ String formatDistance(float dist) {
+ dist = (int)(dist * 1000 + 0.5f);
dist /= 1000;
return "" + dist + '\u00C5';
}
- String formatAngle(double angle) {
- angle = (int)(angle * 10 + (angle >= 0 ? 0.5 : -0.5));
+ String formatAngle(float angle) {
+ angle = (int)(angle * 10 + (angle >= 0 ? 0.5f : -0.5f));
angle /= 10;
return "" + angle + '\u00B0';
}
@@ -158,52 +158,52 @@
atomIndices[3] == this.atomIndices[0]));
}
- public double computeDihedral(Point3d p1, Point3d p2,
- Point3d p3, Point3d p4) {
+ public float computeDihedral(Point3f p1, Point3f p2,
+ Point3f p3, Point3f p4) {
- double ijx = p1.x - p2.x;
- double ijy = p1.y - p2.y;
- double ijz = p1.z - p2.z;
-
- double kjx = p3.x - p2.x;
- double kjy = p3.y - p2.y;
- double kjz = p3.z - p2.z;
-
- double klx = p3.x - p4.x;
- double kly = p3.y - p4.y;
- double klz = p3.z - p4.z;
-
- double ax = ijy * kjz - ijz * kjy;
- double ay = ijz * kjx - ijx * kjz;
- double az = ijx * kjy - ijy * kjx;
- double cx = kjy * klz - kjz * kly;
- double cy = kjz * klx - kjx * klz;
- double cz = kjx * kly - kjy * klx;
-
- double ai2 = 1.0 / (ax * ax + ay * ay + az * az);
- double ci2 = 1.0 / (cx * cx + cy * cy + cz * cz);
-
- double ai = Math.sqrt(ai2);
- double ci = Math.sqrt(ci2);
- double denom = ai * ci;
- double cross = ax * cx + ay * cy + az * cz;
- double cosang = cross * denom;
- if (cosang > 1.0) {
- cosang = 1.0;
+ float ijx = p1.x - p2.x;
+ float ijy = p1.y - p2.y;
+ float ijz = p1.z - p2.z;
+
+ float kjx = p3.x - p2.x;
+ float kjy = p3.y - p2.y;
+ float kjz = p3.z - p2.z;
+
+ float klx = p3.x - p4.x;
+ float kly = p3.y - p4.y;
+ float klz = p3.z - p4.z;
+
+ float ax = ijy * kjz - ijz * kjy;
+ float ay = ijz * kjx - ijx * kjz;
+ float az = ijx * kjy - ijy * kjx;
+ float cx = kjy * klz - kjz * kly;
+ float cy = kjz * klx - kjx * klz;
+ float cz = kjx * kly - kjy * klx;
+
+ float ai2 = 1f / (ax * ax + ay * ay + az * az);
+ float ci2 = 1f / (cx * cx + cy * cy + cz * cz);
+
+ float ai = (float)Math.sqrt(ai2);
+ float ci = (float)Math.sqrt(ci2);
+ float denom = ai * ci;
+ float cross = ax * cx + ay * cy + az * cz;
+ float cosang = cross * denom;
+ if (cosang > 1) {
+ cosang = 1;
}
- if (cosang < -1.0) {
- cosang = -1.0;
+ if (cosang < -1) {
+ cosang = -1;
}
- double dihedral = toDegrees(Math.acos(cosang));
- double dot = ijx*cx + ijy*cy + ijz*cz;
- double absDot = Math.abs(dot);
+ float dihedral = toDegrees((float)Math.acos(cosang));
+ float dot = ijx*cx + ijy*cy + ijz*cz;
+ float absDot = (float)Math.abs(dot);
dihedral = (dot/absDot > 0) ? dihedral : -dihedral;
return dihedral;
}
- public static double toDegrees(double angrad) {
- return angrad * 180.0 / Math.PI;
+ public static float toDegrees(float angrad) {
+ return angrad * 180 / (float)Math.PI;
}
public String toString() {
|