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[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/render AtomShape.java,1.70,1.71 BondShape.java,1.3,1.4 JmolFrame.java,1.8,1.9
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From: Michael T H. <mic...@us...> - 2003-08-13 20:28:34
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Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/render
In directory sc8-pr-cvs1:/tmp/cvs-serv26640/src/org/openscience/jmol/render
Modified Files:
AtomShape.java BondShape.java JmolFrame.java
Log Message:
eliminated sort, tweaked transforms, worked on JmolFrame
Index: AtomShape.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/render/AtomShape.java,v
retrieving revision 1.70
retrieving revision 1.71
diff -u -r1.70 -r1.71
--- AtomShape.java 12 Aug 2003 18:18:10 -0000 1.70
+++ AtomShape.java 13 Aug 2003 16:39:46 -0000 1.71
@@ -35,7 +35,7 @@
import javax.vecmath.Point3d;
import javax.vecmath.Point3i;
-public class AtomShape extends Shape {
+public class AtomShape extends Shape implements Bspt.Tuple {
public JmolFrame frame;
public short atomIndex = -1;
@@ -53,27 +53,21 @@
public String strLabel;
- public AtomShape(JmolFrame frame, Object clientAtom) {
+ public AtomShape(JmolFrame frame, int atomIndex, Object clientAtom) {
DisplayControl control = frame.control;
this.frame = frame;
+ this.atomIndex = (short)atomIndex;
this.clientAtom = clientAtom;
this.atomicNumber = (byte) control.getAtomicNumber(clientAtom);
this.colixAtom = control.getColixAtom(atomicNumber, clientAtom);
- this.strLabel = control.getLabelAtom(atomicNumber, clientAtom, 0);
+ this.strLabel = control.getLabelAtom(atomicNumber, clientAtom, atomIndex);
this.colixDots = 0;
this.marDots = 0;
setStyleMarAtom(control.getStyleAtom(), control.getMarAtom());
this.point3d = control.getPoint3d(clientAtom);
}
- // FIXME need to pass in the atomIndex to the AtomShape constructor
- public void setAtomIndex(int atomIndex) {
- this.atomIndex = (short)atomIndex;
- }
-
public int getAtomIndex() {
- if (atomIndex == -1)
- throw new IndexOutOfBoundsException();
return atomIndex;
}
@@ -88,13 +82,14 @@
return false;
}
- public void bondMutually(AtomShape atomShapeOther, int order) {
+ public BondShape bondMutually(AtomShape atomShapeOther, int order) {
if (isBonded(atomShapeOther))
- return;
+ return null;
BondShape bondShape = new BondShape(this, atomShapeOther, order,
frame.control);
addBond(bondShape);
atomShapeOther.addBond(bondShape);
+ return bondShape;
}
private void addBond(BondShape bondShape) {
@@ -260,9 +255,8 @@
public void render(Graphics25D g25d, DisplayControl control) {
if (atomicNumber == 1 && !control.getShowHydrogens())
return;
- if (control.getShowBonds())
- renderBonds(control);
- if (control.getShowAtoms() && isClipVisible(control.atomRenderer.clip))
+ renderBonds(control);
+ if (isClipVisible(control.atomRenderer.clip))
control.atomRenderer.render(this);
if (strLabel != null)
control.labelRenderer.render(this);
@@ -379,8 +373,18 @@
return point3d.z;
}
+ public double getDimensionValue(int dimension) {
+ return (dimension == 0
+ ? point3d.x
+ : (dimension == 1 ? point3d.y : point3d.z));
+ }
+
public double getVanderwaalsRadius() {
return frame.control.getVanderwaalsRadius(atomicNumber, clientAtom);
+ }
+
+ public double getCovalentRadius() {
+ return getVanderwaalsRadius();
}
public ProteinProp getProteinProp() {
Index: BondShape.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/render/BondShape.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- BondShape.java 11 Aug 2003 23:35:57 -0000 1.3
+++ BondShape.java 13 Aug 2003 16:39:46 -0000 1.4
@@ -85,6 +85,11 @@
return (order & BACKBONE) != 0;
}
+ public void delete() {
+ atomShape1.deleteBond(this);
+ atomShape2.deleteBond(this);
+ }
+
public void setStyle(byte style) {
this.style = style;
}
Index: JmolFrame.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/render/JmolFrame.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- JmolFrame.java 12 Aug 2003 14:38:43 -0000 1.8
+++ JmolFrame.java 13 Aug 2003 16:39:46 -0000 1.9
@@ -24,9 +24,8 @@
*/
package org.openscience.jmol.render;
+
import org.openscience.jmol.DisplayControl;
-import org.openscience.jmol.UseJavaSort;
-import org.openscience.jmol.applet.NonJavaSort;
import org.openscience.jmol.g25d.Graphics25D;
import javax.vecmath.Point3d;
import java.util.Hashtable;
@@ -38,26 +37,40 @@
public DisplayControl control;
Shape[] shapes;
- public JmolFrame(DisplayControl control) {
+ final static int growthIncrement = 128;
+ int atomShapeCount = 0;
+ AtomShape[] atomShapes;
+ int bondShapeCount = 0;
+ BondShape[] bondShapes;
+
+ public JmolFrame(DisplayControl control, int atomCount) {
this.control = control;
+ atomShapes = new AtomShape[atomCount];
+ bondShapes = new BondShape[atomCount * 2];
}
- int atomShapeCount = 0;
- final static int growthIncrement = 128;
- int iaMax = growthIncrement;
- AtomShape[] atomShapes = new AtomShape[growthIncrement];
+ public JmolFrame(DisplayControl control) {
+ this(control, growthIncrement);
+ }
+
+ public void finalize() {
+ htAtomMap = null;
+ }
- public void addAtomShape(AtomShape atomShape) {
- if (atomShapeCount == iaMax) {
- AtomShape[] newAtomShapes = new AtomShape[iaMax + growthIncrement];
- System.arraycopy(atomShapes, 0, newAtomShapes, 0, iaMax);
+ public AtomShape addAtom(Object clientAtom) {
+ if (atomShapeCount == atomShapes.length) {
+ AtomShape[] newAtomShapes =
+ new AtomShape[atomShapes.length + growthIncrement];
+ System.arraycopy(atomShapes, 0, newAtomShapes, 0, atomShapes.length);
atomShapes = newAtomShapes;
- iaMax += growthIncrement;
}
- atomShape.setAtomIndex(atomShapeCount);
+ AtomShape atomShape = new AtomShape(this, atomShapeCount, clientAtom);
atomShapes[atomShapeCount++] = atomShape;
if (htAtomMap != null)
- htAtomMap.put(atomShape.clientAtom, atomShape);
+ htAtomMap.put(clientAtom, atomShape);
+ if (bspt != null)
+ bspt.addTuple(atomShape);
+ return atomShape;
}
public int getAtomCount() {
@@ -80,6 +93,18 @@
}
}
+ private void addBondShape(BondShape bondShape) {
+ if (bondShape == null)
+ return;
+ if (bondShapeCount == bondShapes.length) {
+ BondShape[] newBondShapes =
+ new BondShape[bondShapes.length + growthIncrement];
+ System.arraycopy(bondShapes, 0, newBondShapes, 0, bondShapes.length);
+ bondShapes = newBondShapes;
+ }
+ bondShapes[bondShapeCount++] = bondShape;
+ }
+
public void bondAtomShapes(Object clientAtom1, Object clientAtom2,
int order) {
if (htAtomMap == null)
@@ -90,7 +115,7 @@
AtomShape atomShape2 = (AtomShape)htAtomMap.get(clientAtom2);
if (atomShape2 == null)
return;
- atomShape1.bondMutually(atomShape2, order);
+ addBondShape(atomShape1.bondMutually(atomShape2, order));
}
public void bondAtomShapes(AtomShape atomShape1, Object clientAtom2,
@@ -100,12 +125,12 @@
AtomShape atomShape2 = (AtomShape)htAtomMap.get(clientAtom2);
if (atomShape2 == null)
return;
- atomShape1.bondMutually(atomShape2, order);
+ addBondShape(atomShape1.bondMutually(atomShape2, order));
}
public void bondAtomShapes(AtomShape atomShape1, AtomShape atomShape2,
int order) {
- atomShape1.bondMutually(atomShape2, order);
+ addBondShape(atomShape1.bondMutually(atomShape2, order));
}
private Point3d centerBoundingBox;
@@ -317,46 +342,21 @@
System.arraycopy(bboxShapes, 0, shapes, i, bboxShapeCount);
i += bboxShapeCount;
}
-
- /*
- if (frame instanceof CrystalFrame) {
- CrystalFrame crystalFrame = (CrystalFrame) frame;
- double[][] rprimd = crystalFrame.getRprimd();
-
- // The three primitives vectors with arrows
- for (int i = 0; i < 3; i++) {
- VectorShape vector = new VectorShape(zeroPoint,
- new Point3d(rprimd[i][0], rprimd[i][1], rprimd[i][2]), false,
- true);
- shapesVector.addElement(vector);
- }
-
- // The full primitive cell
- if (true) {
- // Depends on the settings...TODO
- Vector boxEdges = crystalFrame.getBoxEdges();
- for (int i = 0; i < boxEdges.size(); i = i + 2) {
- LineShape line =
- new LineShape((Point3d) boxEdges.elementAt(i),
- (Point3d) boxEdges.elementAt(i + 1));
- shapesVector.addElement(line);
- }
- }
- }
- */
}
control.calcViewTransformMatrix();
- for (int i = 0; i < shapes.length; ++i) {
+
+ for (int i = 0; i < shapes.length; ++i)
shapes[i].transform(control);
- }
+ /*
if (control.jvm12orGreater) {
UseJavaSort.sortShapes(shapes);
} else {
NonJavaSort.sortShapes(shapes);
}
-
+ */
+
for (int i = shapes.length; --i >= 0 ; )
shapes[i].render(g25d, control);
}
@@ -367,7 +367,8 @@
public void addLineShape(LineShape shape) {
if (lineShapes == null || lineShapeCount == lineShapes.length) {
- LineShape[] newShapes = new LineShape[lineShapeCount + lineGrowthIncrement];
+ LineShape[] newShapes =
+ new LineShape[lineShapeCount + lineGrowthIncrement];
if (lineShapes != null)
System.arraycopy(lineShapes, 0, newShapes, 0, lineShapeCount);
lineShapes = newShapes;
@@ -381,9 +382,11 @@
public void addCrystalCellLine(LineShape line) {
if (crystalCellLines == null ||
crystalCellLineCount == crystalCellLines.length) {
- LineShape[] newShapes = new LineShape[crystalCellLineCount + lineGrowthIncrement];
+ LineShape[] newShapes =
+ new LineShape[crystalCellLineCount + lineGrowthIncrement];
if (crystalCellLines != null)
- System.arraycopy(crystalCellLines, 0, newShapes, 0, crystalCellLineCount);
+ System.arraycopy(crystalCellLines, 0, newShapes, 0,
+ crystalCellLineCount);
crystalCellLines = newShapes;
}
crystalCellLines[crystalCellLineCount++] = line;
@@ -551,4 +554,118 @@
}
}
+ private Bspt bspt;
+ // the maximumCovalentRadius seen in this molecule;
+ private double maxCovalentRadius = 0.0;
+
+ private Bspt getBspt() {
+ if (bspt == null) {
+ bspt = new Bspt(3);
+ for (int i = atomShapeCount; --i >= 0; ) {
+ AtomShape atom = atomShapes[i];
+ double covalentRadius = atom.getCovalentRadius();
+ if (covalentRadius > maxCovalentRadius)
+ maxCovalentRadius = covalentRadius;
+ bspt.addTuple(atom);
+ }
+ }
+ return bspt;
+ }
+
+ private void clearBspt() {
+ bspt = null;
+ }
+
+ public AtomShapeIterator getWithinIterator(AtomShape atomCenter,
+ double distance) {
+ return new WithinAtomShapeIterator(atomCenter, distance);
+ }
+
+ class WithinAtomShapeIterator implements AtomShapeIterator {
+
+ Bspt.EnumerateSphere enum;
+
+ WithinAtomShapeIterator(AtomShape atomCenter, double distance) {
+ enum = getBspt().enumSphere(atomCenter, distance);
+ }
+
+ public boolean hasNext() {
+ return enum.hasMoreElements();
+ }
+
+ public AtomShape next() {
+ return (AtomShape)enum.nextElement();
+ }
+ }
+
+ final static boolean showRebondTimes = true;
+
+ private double bondTolerance;
+ private double minBondDistance;
+ private double minBondDistance2;
+
+ public void rebond() {
+ deleteCovalentBonds();
+ long timeBegin, timeEnd;
+ if (showRebondTimes)
+ timeBegin = System.currentTimeMillis();
+ bondTolerance = control.getBondTolerance();
+ minBondDistance = control.getMinBondDistance();
+ minBondDistance2 = minBondDistance*minBondDistance;
+ Bspt bspt = getBspt();
+ for (int i = atomShapeCount; --i >= 0; ) {
+ AtomShape atom = atomShapes[i];
+ double myCovalentRadius = atom.getCovalentRadius();
+ double searchRadius =
+ myCovalentRadius + maxCovalentRadius + bondTolerance;
+ for (Bspt.EnumerateSphere e = bspt.enumHemiSphere(atom, searchRadius);
+ e.hasMoreElements(); ) {
+ AtomShape atomNear = (AtomShape)e.nextElement();
+ if (atomNear != atom) {
+ int order = getBondOrder(atom, myCovalentRadius,
+ atomNear, atomNear.getCovalentRadius(),
+ e.foundDistance2());
+ if (order > 0)
+ atom.bondMutually(atomNear, order);
+ }
+ }
+ if (showRebondTimes) {
+ timeEnd = System.currentTimeMillis();
+ System.out.println("maxCovalentRadius=" + maxCovalentRadius);
+ System.out.println("Time to autoBond=" + (timeEnd - timeBegin));
+ }
+ }
+ }
+
+ private int getBondOrder(AtomShape atomA, double covalentRadiusA,
+ AtomShape atomB, double covalentRadiusB,
+ double distance2) {
+ // System.out.println(" radiusA=" + covalentRadiusA +
+ // " radiusB=" + covalentRadiusB +
+ // " distance2=" + distance2 +
+ // " tolerance=" + bondTolerance);
+ double maxAcceptable = covalentRadiusA + covalentRadiusB + bondTolerance;
+ double maxAcceptable2 = maxAcceptable * maxAcceptable;
+ if (distance2 < minBondDistance2)
+ return 0;
+ if (distance2 <= maxAcceptable2)
+ return 1;
+ return 0;
+ }
+
+ private void deleteCovalentBonds() {
+ int indexNoncovalent = 0;
+ for (int i = 0; i < bondShapeCount; ++i) {
+ BondShape bond = bondShapes[i];
+ if (! bond.isCovalent()) {
+ if (i != indexNoncovalent) {
+ bondShapes[indexNoncovalent++] = bond;
+ bondShapes[i] = null;
+ }
+ } else {
+ bond.delete();
+ bondShapes[i] = null;
+ }
+ }
+ }
}
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