>OK, was thinking about this some more, and actually there's a good >programming reason for undoing that and going back to .point3f. The >reason is that then I can know and search for when I'm accessing that >important field. Yes?
For me, it was a good simplification to introduce Point3fi (and Miguel made several other modifications based on this one to simplify more). But, do as you wish, if you really want to revert this one, do it. IMHO, the simplification has more interests than drawbacks, but I am not developping much this time. Nico > >Bob > >Nicolas Vervelle wrote: > >> >> >> Bob Hanson wrote: >> >>> This is the one that really broke 10.9 for me. I'd like to have it >>> undone, please. Or else let me know when you have compiled and have >>> all the places fixed. Really, I don't care. I sort of like not having >>> to say atom.point3f, but if it means >>> >>> atom.point3f.set(atom1.point3f) >>> >>> no longer has a simple equivalent, then I vote to undo it. >>> >> atom.set(atom1) should work. >> >> Nico >> >>> Bob >>> >>> [EMAIL PROTECTED] wrote: >>> >>>> Revision: 5453 >>>> http://svn.sourceforge.net/jmol/?rev=5453&view=rev >>>> Author: nicove >>>> Date: 2006-08-30 13:30:56 -0700 (Wed, 30 Aug 2006) >>>> >>>> Log Message: >>>> ----------- >>>> Reapplying r5072: >>>> Introduced Point3fi class which includeds members for screen >>>> coordinates. Atom derives from Point3fi. >>>> At atom can now be treated like a Point3f, so there are a number of >>>> places >>>> in the code that can probably be simplified because we don't have to >>>> call a method to ask an atom for its Point3f. >>>> >>>> Modified Paths: >>>> -------------- >>>> branches/v10_9/Jmol/src/org/jmol/quantum/QuantumCalculation.java >>>> branches/v10_9/Jmol/src/org/jmol/viewer/Atom.java >>>> branches/v10_9/Jmol/src/org/jmol/viewer/Bond.java >>>> branches/v10_9/Jmol/src/org/jmol/viewer/Dipole.java >>>> branches/v10_9/Jmol/src/org/jmol/viewer/Dots.java >>>> branches/v10_9/Jmol/src/org/jmol/viewer/Frame.java >>>> branches/v10_9/Jmol/src/org/jmol/viewer/Isosurface.java >>>> branches/v10_9/Jmol/src/org/jmol/viewer/LcaoCartoon.java >>>> branches/v10_9/Jmol/src/org/jmol/viewer/MeasuresRenderer.java >>>> branches/v10_9/Jmol/src/org/jmol/viewer/ModelManager.java >>>> branches/v10_9/Jmol/src/org/jmol/viewer/Monomer.java >>>> branches/v10_9/Jmol/src/org/jmol/viewer/NucleicMonomer.java >>>> branches/v10_9/Jmol/src/org/jmol/viewer/NucleicPolymer.java >>>> branches/v10_9/Jmol/src/org/jmol/viewer/Polyhedra.java >>>> branches/v10_9/Jmol/src/org/jmol/viewer/Polymer.java >>>> branches/v10_9/Jmol/src/org/jmol/viewer/Sticks.java >>>> branches/v10_9/Jmol/src/org/jmol/viewer/VectorsRenderer.java >>>> >>>> Added Paths: >>>> ----------- >>>> branches/v10_9/Jmol/src/org/jmol/vecmath/ >>>> branches/v10_9/Jmol/src/org/jmol/vecmath/Point3fi.java >>>> >>>> Modified: >>>> branches/v10_9/Jmol/src/org/jmol/quantum/QuantumCalculation.java >>>> =================================================================== >>>> --- >>>> branches/v10_9/Jmol/src/org/jmol/quantum/QuantumCalculation.java >>>> 2006-08-30 19:41:22 UTC (rev 5452) >>>> +++ >>>> branches/v10_9/Jmol/src/org/jmol/quantum/QuantumCalculation.java >>>> 2006-08-30 20:30:56 UTC (rev 5453) >>>> @@ -223,7 +223,7 @@ >>>> for (int i = 0; i < atoms.length; i++) { >>>> if (atoms[i] == null) >>>> continue; >>>> - this.atomCoordBohr[i] = new Point3f(atoms[i].point3f); >>>> + this.atomCoordBohr[i] = new Point3f(atoms[i]); >>>> this.atomCoordBohr[i].scale(bohr_per_angstrom); >>>> } >>>> >>>> >>>> Added: branches/v10_9/Jmol/src/org/jmol/vecmath/Point3fi.java >>>> =================================================================== >>>> --- >>>> branches/v10_9/Jmol/src/org/jmol/vecmath/Point3fi.java >>>> >>>> (rev 0) >>>> +++ branches/v10_9/Jmol/src/org/jmol/vecmath/Point3fi.java >>>> 2006-08-30 20:30:56 UTC (rev 5453) >>>> @@ -0,0 +1,32 @@ >>>> +/* $RCSfile$ >>>> + * $Author: egonw $ >>>> + * $Date: 2005-11-10 10:52:44 -0500 (Thu, 10 Nov 2005) $ >>>> + * $Revision: 4255 $ >>>> + * >>>> + * Copyright (C) 2006 Miguel, Jmol Development, www.jmol.org >>>> + * >>>> + * Contact: [EMAIL PROTECTED] >>>> + * >>>> + * This library is free software; you can redistribute it and/or >>>> + * modify it under the terms of the GNU Lesser General Public >>>> + * License as published by the Free Software Foundation; either >>>> + * version 2.1 of the License, or (at your option) any later version. >>>> + * >>>> + * This library is distributed in the hope that it will be useful, >>>> + * but WITHOUT ANY WARRANTY; without even the implied warranty of >>>> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU >>>> + * Lesser General Public License for more details. >>>> + * >>>> + * You should have received a copy of the GNU Lesser General Public >>>> + * License along with this library; if not, write to the Free >>>> Software >>>> + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA >>>> 02110-1301 USA. >>>> + */ >>>> + >>>> +package org.jmol.vecmath; >>>> +import javax.vecmath.Point3f; >>>> + >>>> +public class Point3fi extends Point3f { >>>> + public int screenX; >>>> + public int screenY; >>>> + public int screenZ; >>>> +} >>>> >>>> Modified: branches/v10_9/Jmol/src/org/jmol/viewer/Atom.java >>>> =================================================================== >>>> --- branches/v10_9/Jmol/src/org/jmol/viewer/Atom.java 2006-08-30 >>>> 19:41:22 UTC (rev 5452) >>>> +++ branches/v10_9/Jmol/src/org/jmol/viewer/Atom.java 2006-08-30 >>>> 20:30:56 UTC (rev 5453) >>>> @@ -26,6 +26,7 @@ >>>> package org.jmol.viewer; >>>> >>>> import org.jmol.util.Logger; >>>> +import org.jmol.vecmath.Point3fi; >>>> >>>> import org.jmol.g3d.Graphics3D; >>>> import org.jmol.bspt.Tuple; >>>> @@ -36,7 +37,7 @@ >>>> import javax.vecmath.Vector3f; >>>> import javax.vecmath.Point3i; >>>> >>>> -final public class Atom implements Tuple { >>>> +final public class Atom extends Point3fi implements Tuple { >>>> >>>> final static byte VIBRATION_VECTOR_FLAG = 0x02; >>>> final static byte IS_HETERO_FLAG = 0x04; >>>> @@ -44,10 +45,6 @@ >>>> Group group; >>>> int atomIndex; >>>> int atomSite; >>>> - public Point3f point3f; >>>> - int screenX; >>>> - int screenY; >>>> - int screenZ; >>>> short screenDiameter; >>>> short modelIndex; // we want this here for the BallsRenderer >>>> byte elementNumber; >>>> @@ -69,7 +66,7 @@ >>>> Atom(Point3f pt) { //just a point -- just enough to determine >>>> a position >>>> isSimple = true; >>>> - point3f = new Point3f(pt); >>>> + this.x = pt.x; this.y = pt.y; this.z = pt.z; >>>> //must be transformed later -- Polyhedra; >>>> formalChargeAndFlags = 0; >>>> madAtom = 0; >>>> @@ -98,8 +95,7 @@ >>>> this.colixAtom = viewer.getColixAtom(this); >>>> this.alternateLocationID = (byte)alternateLocationID; >>>> setMadAtom(viewer.getMadAtom()); >>>> - - this.point3f = new Point3f(x, y, z); >>>> + this.x = x; this.y = y; this.z = z; >>>> if (isHetero) >>>> formalChargeAndFlags |= IS_HETERO_FLAG; >>>> >>>> @@ -396,9 +392,9 @@ >>>> Vector3f[] vibrationVectors; >>>> if ((formalChargeAndFlags & VIBRATION_VECTOR_FLAG) == 0 || >>>> (vibrationVectors = group.chain.frame.vibrationVectors) == >>>> null) >>>> - screen = viewer.transformPoint(point3f); >>>> + screen = viewer.transformPoint(this); >>>> else - screen = viewer.transformPoint(point3f, >>>> vibrationVectors[atomIndex]); >>>> + screen = viewer.transformPoint(this, >>>> vibrationVectors[atomIndex]); >>>> screenX = screen.x; >>>> screenY = screen.y; >>>> screenZ = screen.z; >>>> @@ -548,25 +544,25 @@ >>>> } >>>> >>>> Point3f getPoint3f() { >>>> - return point3f; >>>> + return this; >>>> } >>>> >>>> float getAtomX() { >>>> - return point3f.x; >>>> + return x; >>>> } >>>> >>>> float getAtomY() { >>>> - return point3f.y; >>>> + return y; >>>> } >>>> >>>> float getAtomZ() { >>>> - return point3f.z; >>>> + return z; >>>> } >>>> >>>> public float getDimensionValue(int dimension) { >>>> return (dimension == 0 >>>> - ? point3f.x >>>> - : (dimension == 1 ? point3f.y : point3f.z)); >>>> + ? x >>>> + : (dimension == 1 ? y : z)); >>>> } >>>> >>>> short getVanderwaalsMar() { >>>> @@ -601,11 +597,11 @@ >>>> // established bonds >>>> // note that this algorithm works when maximum valence == 0 >>>> Bond getLongestBondToDiscard(Atom atomChallenger) { >>>> - float dist2Longest = >>>> point3f.distanceSquared(atomChallenger.point3f); >>>> + float dist2Longest = distanceSquared(atomChallenger); >>>> Bond bondLongest = null; >>>> for (int i = bonds.length; --i >= 0; ) { >>>> Bond bond = bonds[i]; >>>> - float dist2 = >>>> point3f.distanceSquared(bond.getOtherAtom(this).point3f); >>>> + float dist2 = distanceSquared(bond.getOtherAtom(this)); >>>> if (dist2 > dist2Longest) { >>>> bondLongest = bond; >>>> dist2Longest = dist2; >>>> @@ -966,15 +962,15 @@ >>>> strT = JmolConstants.elementSymbols[elementNumber]; >>>> break; >>>> case 'x': >>>> - floatT = point3f.x; >>>> + floatT = x; >>>> floatIsSet = true; >>>> break; >>>> case 'y': >>>> - floatT = point3f.y; >>>> + floatT = y; >>>> floatIsSet = true; >>>> break; >>>> case 'z': >>>> - floatT = point3f.z; >>>> + floatT = z; >>>> floatIsSet = true; >>>> break; >>>> case 'X': >>>> @@ -1110,9 +1106,9 @@ >>>> Point3f pt = getFractionalCoord(); >>>> new Point3f(); >>>> try { >>>> - >>>> group.chain.frame.cellInfo[modelIndex].matrixEuclideanToFractional.transform(point3f,pt); >>>> >>>> >>>> + >>>> group.chain.frame.cellInfo[modelIndex].matrixEuclideanToFractional.transform(this,pt); >>>> >>>> >>>> } catch (Exception e) { >>>> - pt = point3f; >>>> + pt = this; >>>> } >>>> return (ch == 'X' ? pt.x : ch == 'Y' ? pt.y : pt.z); >>>> } >>>> @@ -1120,9 +1116,9 @@ >>>> Point3f getFractionalCoord() { >>>> Point3f pt = new Point3f(); >>>> try { >>>> - >>>> group.chain.frame.cellInfo[modelIndex].matrixEuclideanToFractional.transform(point3f,pt); >>>> >>>> >>>> + >>>> group.chain.frame.cellInfo[modelIndex].matrixEuclideanToFractional.transform(this,pt); >>>> >>>> >>>> } catch (Exception e) { >>>> - pt = point3f; >>>> + pt = this; >>>> } >>>> return pt; >>>> } >>>> @@ -1148,7 +1144,7 @@ >>>> } >>>> >>>> String getInfoXYZ() { >>>> - return getIdentity() + " " + point3f; >>>> + return getIdentity() + " " + x + " " + y + " " + z; >>>> } >>>> >>>> String getIdentity() { >>>> @@ -1270,9 +1266,9 @@ >>>> Hashtable getPublicProperties() { >>>> Hashtable ht = new Hashtable(); >>>> ht.put("element", getElementSymbol()); >>>> - ht.put("x", new Double(point3f.x)); >>>> - ht.put("y", new Double(point3f.y)); >>>> - ht.put("z", new Double(point3f.z)); >>>> + ht.put("x", new Double(x)); >>>> + ht.put("y", new Double(y)); >>>> + ht.put("z", new Double(z)); >>>> ht.put("atomIndex", new Integer(atomIndex)); >>>> ht.put("modelIndex", new Integer(modelIndex)); >>>> ht.put("argb", new Integer(getArgb())); >>>> >>>> Modified: branches/v10_9/Jmol/src/org/jmol/viewer/Bond.java >>>> =================================================================== >>>> --- branches/v10_9/Jmol/src/org/jmol/viewer/Bond.java 2006-08-30 >>>> 19:41:22 UTC (rev 5452) >>>> +++ branches/v10_9/Jmol/src/org/jmol/viewer/Bond.java 2006-08-30 >>>> 20:30:56 UTC (rev 5453) >>>> @@ -183,12 +183,12 @@ >>>> ht.put("order", getOrderName()); >>>> ht.put("radius", new Double(getRadius())); >>>> ht.put("modelIndex", new Integer(atom1.modelIndex)); >>>> - ht.put("xA", new Double(atom1.point3f.x)); >>>> - ht.put("yA", new Double(atom1.point3f.y)); >>>> - ht.put("zA", new Double(atom1.point3f.z)); >>>> - ht.put("xB", new Double(atom2.point3f.x)); >>>> - ht.put("yB", new Double(atom2.point3f.y)); >>>> - ht.put("zB", new Double(atom2.point3f.z)); >>>> + ht.put("xA", new Double(atom1.x)); >>>> + ht.put("yA", new Double(atom1.y)); >>>> + ht.put("zA", new Double(atom1.z)); >>>> + ht.put("xB", new Double(atom2.x)); >>>> + ht.put("yB", new Double(atom2.y)); >>>> + ht.put("zB", new Double(atom2.z)); >>>> return ht; >>>> } >>>> } >>>> >>>> Modified: branches/v10_9/Jmol/src/org/jmol/viewer/Dipole.java >>>> =================================================================== >>>> --- branches/v10_9/Jmol/src/org/jmol/viewer/Dipole.java >>>> 2006-08-30 19:41:22 UTC (rev 5452) >>>> +++ branches/v10_9/Jmol/src/org/jmol/viewer/Dipole.java >>>> 2006-08-30 20:30:56 UTC (rev 5453) >>>> @@ -148,7 +148,7 @@ >>>> void set(Atom atom1, Atom atom2, float value) { >>>> //also from frame >>>> set(value); >>>> - set(atom1.point3f, atom2.point3f); >>>> + set(atom1, atom2); >>>> offsetSide = Dipoles.DEFAULT_OFFSETSIDE; >>>> mad = Dipoles.DEFAULT_MAD; >>>> atoms[0] = atom1; >>>> @@ -157,9 +157,9 @@ >>>> } >>>> >>>> void centerDipole() { >>>> - float f = atoms[0].point3f.distance(atoms[1].point3f) / (2 * >>>> dipoleValue) >>>> + float f = atoms[0].distance(atoms[1]) / (2 * dipoleValue) >>>> - 0.5f; >>>> - origin.scaleAdd(f, vector, atoms[0].point3f); >>>> + origin.scaleAdd(f, vector, atoms[0]); >>>> center = new Point3f(); >>>> center.scaleAdd(0.5f, vector, origin); >>>> bond = atoms[0].getBond(atoms[1]); >>>> >>>> Modified: branches/v10_9/Jmol/src/org/jmol/viewer/Dots.java >>>> =================================================================== >>>> --- branches/v10_9/Jmol/src/org/jmol/viewer/Dots.java 2006-08-30 >>>> 19:41:22 UTC (rev 5452) >>>> +++ branches/v10_9/Jmol/src/org/jmol/viewer/Dots.java 2006-08-30 >>>> 20:30:56 UTC (rev 5453) >>>> @@ -356,7 +356,7 @@ >>>> void setAtomI(int indexI) { >>>> this.indexI = indexI; >>>> atomI = frame.atoms[indexI]; >>>> - centerI = atomI.point3f; >>>> + centerI = atomI; >>>> radiusI = getAppropriateRadius(atomI); >>>> radiiIP2 = radiusI + radiusP; >>>> radiiIP2 *= radiiIP2; >>>> @@ -536,7 +536,7 @@ >>>> if (onlySelectedDots && !bsOn.get(neighbor.atomIndex)) >>>> continue; >>>> float neighborRadius = getAppropriateRadius(neighbor); >>>> - if (centerI.distance(neighbor.point3f) > >>>> + if (centerI.distance(neighbor) > >>>> radiusI + radiusP + radiusP + neighborRadius) >>>> continue; >>>> if (neighborCount == neighbors.length) { >>>> @@ -547,7 +547,7 @@ >>>> neighborRadii2 = Util.doubleLength(neighborRadii2); >>>> } >>>> neighbors[neighborCount] = neighbor; >>>> - neighborCenters[neighborCount] = neighbor.point3f; >>>> + neighborCenters[neighborCount] = neighbor; >>>> neighborIndices[neighborCount] = neighbor.atomIndex; >>>> float neighborPlusProbeRadii = neighborRadius + radiusP; >>>> neighborPlusProbeRadii2[neighborCount] = >>>> >>>> Modified: branches/v10_9/Jmol/src/org/jmol/viewer/Frame.java >>>> =================================================================== >>>> --- branches/v10_9/Jmol/src/org/jmol/viewer/Frame.java 2006-08-30 >>>> 19:41:22 UTC (rev 5452) >>>> +++ branches/v10_9/Jmol/src/org/jmol/viewer/Frame.java 2006-08-30 >>>> 20:30:56 UTC (rev 5453) >>>> @@ -883,7 +883,7 @@ >>>> } >>>> >>>> Point3f getAtomPoint3f(int atomIndex) { >>>> - return atoms[atomIndex].point3f; >>>> + return atoms[atomIndex]; >>>> } >>>> >>>> int getBondCount() { >>>> @@ -1061,7 +1061,7 @@ >>>> Point3f average = this.averageAtomPoint; >>>> average.set(0, 0, 0); >>>> for (int i = atomCount; --i >= 0;) >>>> - average.add(atoms[i].point3f); >>>> + average.add(atoms[i]); >>>> average.scale(1f / atomCount); >>>> } >>>> >>>> @@ -1093,7 +1093,7 @@ >>>> float maxRadius = 0; >>>> for (int i = atomCount; --i >= 0;) { >>>> Atom atom = atoms[i]; >>>> - float distAtom = center.distance(atom.point3f); >>>> + float distAtom = center.distance(atom); >>>> float radiusVdw = atom.getVanderwaalsRadiusFloat(); >>>> float outerVdw = distAtom + radiusVdw; >>>> if (outerVdw > maxRadius) >>>> @@ -1700,17 +1700,17 @@ >>>> int modelIndex = atoms[i].modelIndex; >>>> if (!cellInfo[modelIndex].coordinatesAreFractional) >>>> continue; >>>> - cellInfo[modelIndex].transform(atoms[i].point3f); >>>> + cellInfo[modelIndex].transform(atoms[i]); >>>> } >>>> } >>>> } >>>> >>>> void calcAtomsMinMax(Point3f pointMin, Point3f pointMax) { >>>> - pointMin.set(atoms[0].point3f); >>>> - pointMax.set(atoms[0].point3f); >>>> + pointMin.set(atoms[0]); >>>> + pointMax.set(atoms[0]); >>>> for (int i = atomCount; --i > 0;) { >>>> // note that the 0 element was set above >>>> - checkMinMax(atoms[i].point3f, pointMin, pointMax); >>>> + checkMinMax(atoms[i], pointMin, pointMax); >>>> } >>>> } >>>> >>>> @@ -1751,7 +1751,7 @@ >>>> return ptCenter; >>>> for (int i = atomCount; --i >= 0;) { >>>> if (bs.get(i)) >>>> - ptCenter.add(atoms[i].point3f); >>>> + ptCenter.add(atoms[i]); >>>> } >>>> ptCenter.scale(1.0f / nPoints); >>>> return ptCenter; >>>> @@ -2223,7 +2223,7 @@ >>>> } >>>> >>>> float getDistance(int atomIndexA, int atomIndexB) { >>>> - return >>>> atoms[atomIndexA].point3f.distance(atoms[atomIndexB].point3f); >>>> + return atoms[atomIndexA].distance(atoms[atomIndexB]); >>>> } >>>> >>>> Vector3f vectorBA; >>>> @@ -2234,9 +2234,9 @@ >>>> vectorBA = new Vector3f(); >>>> vectorBC = new Vector3f(); >>>> } >>>> - Point3f pointA = atoms[atomIndexA].point3f; >>>> - Point3f pointB = atoms[atomIndexB].point3f; >>>> - Point3f pointC = atoms[atomIndexC].point3f; >>>> + Point3f pointA = atoms[atomIndexA]; >>>> + Point3f pointB = atoms[atomIndexB]; >>>> + Point3f pointC = atoms[atomIndexC]; >>>> vectorBA.sub(pointA, pointB); >>>> vectorBC.sub(pointC, pointB); >>>> float angle = vectorBA.angle(vectorBC); >>>> @@ -2246,8 +2246,8 @@ >>>> >>>> float getTorsion(int atomIndexA, int atomIndexB, int atomIndexC, >>>> int atomIndexD) { >>>> - return computeTorsion(atoms[atomIndexA].point3f, >>>> atoms[atomIndexB].point3f, >>>> - atoms[atomIndexC].point3f, atoms[atomIndexD].point3f); >>>> + return computeTorsion(atoms[atomIndexA], atoms[atomIndexB], >>>> + atoms[atomIndexC], atoms[atomIndexD]); >>>> } >>>> >>>> static float toDegrees(float angleRadians) { >>>> @@ -2489,14 +2489,14 @@ >>>> Point3f getAveragePosition(int atomIndex1, int atomIndex2) { >>>> Atom atom1 = atoms[atomIndex1]; >>>> Atom atom2 = atoms[atomIndex2]; >>>> - return new Point3f((atom1.point3f.x + atom2.point3f.x) / 2, >>>> - (atom1.point3f.y + atom2.point3f.y) / 2, >>>> - (atom1.point3f.z + atom2.point3f.z) / 2); >>>> + return new Point3f((atom1.x + atom2.x) / 2, >>>> + (atom1.y + atom2.y) / 2, >>>> + (atom1.z + atom2.z) / 2); >>>> } >>>> >>>> Vector3f getAtomVector(int atomIndex1, int atomIndex2) { >>>> - Vector3f V = new Vector3f(atoms[atomIndex1].point3f); >>>> - V.sub(atoms[atomIndex2].point3f); >>>> + Vector3f V = new Vector3f(atoms[atomIndex1]); >>>> + V.sub(atoms[atomIndex2]); >>>> return V; >>>> } >>>> >>>> @@ -2525,7 +2525,7 @@ >>>> float c2 = partialCharges[atom2.atomIndex]; >>>> if (c1 != c2) { >>>> Dipole dipole = dipoles.findDipole(atom1, atom2, true); >>>> - float value = (c1 - c2) / 2f * >>>> atom1.point3f.distance(atom2.point3f) >>>> + float value = (c1 - c2) / 2f * atom1.distance(atom2) >>>> / E_ANG_PER_DEBYE; >>>> if (value < 0) { >>>> dipole.set(atom2, atom1, -value); >>>> @@ -2725,17 +2725,17 @@ >>>> void setAtomCoord(int atomIndex, float x, float y, float z) { >>>> if (atomIndex < 0 || atomIndex >= atomCount) >>>> return; >>>> - atoms[atomIndex].point3f.x = x; >>>> - atoms[atomIndex].point3f.y = y; >>>> - atoms[atomIndex].point3f.z = z; >>>> + atoms[atomIndex].x = x; >>>> + atoms[atomIndex].y = y; >>>> + atoms[atomIndex].z = z; >>>> } >>>> >>>> void setAtomCoordRelative(int atomIndex, float x, float y, float z) { >>>> if (atomIndex < 0 || atomIndex >= atomCount) >>>> return; >>>> - atoms[atomIndex].point3f.x += x; >>>> - atoms[atomIndex].point3f.y += y; >>>> - atoms[atomIndex].point3f.z += z; >>>> + atoms[atomIndex].x += x; >>>> + atoms[atomIndex].y += y; >>>> + atoms[atomIndex].z += z; >>>> } >>>> >>>> String hybridization; >>>> @@ -2763,7 +2763,7 @@ >>>> if (atom.bonds[i].isCovalent()) { >>>> ++nBonds; >>>> atom1 = atom.bonds[i].getOtherAtom(atom); >>>> - n.sub(atom.point3f, atom1.point3f); >>>> + n.sub(atom, atom1); >>>> n.normalize(); >>>> z.add(n); >>>> switch (nBonds) { >>>> @@ -2956,15 +2956,15 @@ >>>> case 1: >>>> viewer.getPrincipalAxes(i, z, x, "sp3a", false); >>>> pt = new Point3f(z); >>>> - pt.scaleAdd(1.1f, atom.point3f); >>>> + pt.scaleAdd(1.1f, atom); >>>> hAtoms[n++] = pt; >>>> viewer.getPrincipalAxes(i, z, x, "sp3b", false); >>>> pt = new Point3f(z); >>>> - pt.scaleAdd(1.1f, atom.point3f); >>>> + pt.scaleAdd(1.1f, atom); >>>> hAtoms[n++] = pt; >>>> viewer.getPrincipalAxes(i, z, x, "sp3c", false); >>>> pt = new Point3f(z); >>>> - pt.scaleAdd(1.1f, atom.point3f); >>>> + pt.scaleAdd(1.1f, atom); >>>> hAtoms[n++] = pt; >>>> break; >>>> case 2: >>>> @@ -2972,18 +2972,18 @@ >>>> && hybridization != "sp") { >>>> viewer.getPrincipalAxes(i, z, x, "lpa", false); >>>> pt = new Point3f(z); >>>> - pt.scaleAdd(1.1f, atom.point3f); >>>> + pt.scaleAdd(1.1f, atom); >>>> hAtoms[n++] = pt; >>>> viewer.getPrincipalAxes(i, z, x, "lpb", false); >>>> pt = new Point3f(z); >>>> - pt.scaleAdd(1.1f, atom.point3f); >>>> + pt.scaleAdd(1.1f, atom); >>>> hAtoms[n++] = pt; >>>> } >>>> break; >>>> case 3: >>>> if (viewer.getPrincipalAxes(i, z, x, "sp3", true)) { >>>> pt = new Point3f(z); >>>> - pt.scaleAdd(1.1f, atom.point3f); >>>> + pt.scaleAdd(1.1f, atom); >>>> hAtoms[n++] = pt; >>>> } >>>> default: >>>> >>>> Modified: branches/v10_9/Jmol/src/org/jmol/viewer/Isosurface.java >>>> =================================================================== >>>> --- branches/v10_9/Jmol/src/org/jmol/viewer/Isosurface.java >>>> 2006-08-30 19:41:22 UTC (rev 5452) >>>> +++ branches/v10_9/Jmol/src/org/jmol/viewer/Isosurface.java >>>> 2006-08-30 20:30:56 UTC (rev 5453) >>>> @@ -3948,7 +3948,7 @@ >>>> Atom atom = atoms[i]; >>>> if (atom.modelIndex != modelIndex) >>>> continue; >>>> - Point3f pt = new Point3f(atom.point3f); >>>> + Point3f pt = new Point3f(atom); >>>> if (nSelected == 0 || bsSelected.get(i)) { >>>> float rA = atom.getVanderwaalsRadiusFloat() + >>>> qm_marginAngstroms; >>>> if (pt.x - rA < xyzMin.x) >>>> @@ -3994,7 +3994,7 @@ >>>> Atom atom = atoms[i]; >>>> if (atom.modelIndex != modelIndex) >>>> continue; >>>> - pt.set(atom.point3f); >>>> + pt.set(atom); >>>> pt.scale(1 / ANGSTROMS_PER_BOHR); >>>> jvxlFileHeader += atom.elementNumber + " " + >>>> atom.elementNumber + ".0 " >>>> + pt.x + " " + pt.y + " " + pt.z + "\n"; >>>> @@ -4097,7 +4097,7 @@ >>>> if (!atomSet.get(i)) >>>> continue; >>>> atomNo[iAtom] = atoms[i].elementNumber; >>>> - solvent_ptAtom[iAtom] = atoms[i].point3f; >>>> + solvent_ptAtom[iAtom] = atoms[i]; >>>> solvent_atomRadius[iAtom++] = >>>> atoms[i].getVanderwaalsRadiusFloat() >>>> + solventExtendedAtomRadius; >>>> } >>>> @@ -4152,7 +4152,7 @@ >>>> for (int i = 0; i < nAtoms; i++) { >>>> if (atomSet.get(i)) >>>> continue; >>>> - pt = atoms[i].point3f; >>>> + pt = atoms[i]; >>>> float rA = atoms[i].getVanderwaalsRadiusFloat() >>>> + solventExtendedAtomRadius; >>>> if (pt.x + rA > xyzMin.x && pt.x - rA < xyzMax.x && pt.y + rA >>>> > xyzMin.y >>>> @@ -4177,7 +4177,7 @@ >>>> for (int i = firstSet; i <= lastSet; i++) { >>>> if (!bsNearby.get(i)) >>>> continue; >>>> - solvent_ptAtom[iAtom] = atoms[i].point3f; >>>> + solvent_ptAtom[iAtom] = atoms[i]; >>>> solvent_atomRadius[iAtom++] = >>>> atoms[i].getVanderwaalsRadiusFloat() >>>> + solventExtendedAtomRadius; >>>> } >>>> >>>> Modified: branches/v10_9/Jmol/src/org/jmol/viewer/LcaoCartoon.java >>>> =================================================================== >>>> --- branches/v10_9/Jmol/src/org/jmol/viewer/LcaoCartoon.java >>>> 2006-08-30 19:41:22 UTC (rev 5452) >>>> +++ branches/v10_9/Jmol/src/org/jmol/viewer/LcaoCartoon.java >>>> 2006-08-30 20:30:56 UTC (rev 5453) >>>> @@ -155,7 +155,7 @@ >>>> } >>>> super.setProperty("lcaoType",type,null); >>>> Vector3f[] axes = { new Vector3f(), new Vector3f(), >>>> - new Vector3f(frame.atoms[iAtom].point3f)}; >>>> + new Vector3f(frame.atoms[iAtom])}; >>>> if (viewer.getPrincipalAxes(iAtom, axes[0], axes[1], type, true)) >>>> super.setProperty("lcaoCartoon",axes,null); >>>> } >>>> >>>> Modified: branches/v10_9/Jmol/src/org/jmol/viewer/MeasuresRenderer.java >>>> =================================================================== >>>> --- branches/v10_9/Jmol/src/org/jmol/viewer/MeasuresRenderer.java >>>> 2006-08-30 19:41:22 UTC (rev 5452) >>>> +++ branches/v10_9/Jmol/src/org/jmol/viewer/MeasuresRenderer.java >>>> 2006-08-30 20:30:56 UTC (rev 5453) >>>> @@ -164,7 +164,7 @@ >>>> matrixT.set(aaT); >>>> pointT.set(measurement.pointArc); >>>> matrixT.transform(pointT); >>>> - pointT.add(atomB.point3f); >>>> + pointT.add(atomB); >>>> Point3i screenArc = viewer.transformPoint(pointT); >>>> int zArc = screenArc.z - zOffset; >>>> if (zArc < 0) zArc = 0; >>>> @@ -173,7 +173,7 @@ >>>> pointT.set(measurement.pointArc); >>>> pointT.scale(1.1f); >>>> matrixT.transform(pointT); >>>> - pointT.add(atomB.point3f); >>>> + pointT.add(atomB); >>>> Point3i screenLabel = viewer.transformPoint(pointT); >>>> int zLabel = screenLabel.z - zOffset; >>>> paintMeasurementString(screenLabel.x, screenLabel.y, zLabel, >>>> >>>> Modified: branches/v10_9/Jmol/src/org/jmol/viewer/ModelManager.java >>>> =================================================================== >>>> --- branches/v10_9/Jmol/src/org/jmol/viewer/ModelManager.java >>>> 2006-08-30 19:41:22 UTC (rev 5452) >>>> +++ branches/v10_9/Jmol/src/org/jmol/viewer/ModelManager.java >>>> 2006-08-30 20:30:56 UTC (rev 5453) >>>> @@ -652,7 +652,7 @@ >>>> } >>>> >>>> float getBondLength(int i) { >>>> - return getBondAtom1(i).point3f.distance(getBondAtom2(i).point3f); >>>> + return getBondAtom1(i).distance(getBondAtom2(i)); >>>> } >>>> Atom getBondAtom1(int i) { >>>> >>>> Modified: branches/v10_9/Jmol/src/org/jmol/viewer/Monomer.java >>>> =================================================================== >>>> --- branches/v10_9/Jmol/src/org/jmol/viewer/Monomer.java >>>> 2006-08-30 19:41:22 UTC (rev 5452) >>>> +++ branches/v10_9/Jmol/src/org/jmol/viewer/Monomer.java >>>> 2006-08-30 20:30:56 UTC (rev 5453) >>>> @@ -129,7 +129,7 @@ >>>> final Point3f getAtomPointFromOffset(byte offset) { >>>> if (offset == -1) >>>> return null; >>>> - return chain.frame.atoms[firstAtomIndex + (offset & >>>> 0xFF)].point3f; >>>> + return chain.frame.atoms[firstAtomIndex + (offset & 0xFF)]; >>>> } >>>> >>>> //////////////////////////////////////////////////////////////// >>>> @@ -144,8 +144,7 @@ >>>> } >>>> >>>> final Point3f getAtomPointFromOffsetIndex(int offsetIndex) { >>>> - Atom atom = getAtomFromOffsetIndex(offsetIndex); >>>> - return atom == null ? null : atom.point3f; >>>> + return getAtomFromOffsetIndex(offsetIndex); >>>> } >>>> >>>> final Atom getSpecialAtom(byte[] interestingIDs, byte >>>> specialAtomID) { >>>> @@ -173,7 +172,7 @@ >>>> int offset = offsets[i] & 0xFF; >>>> if (offset == 255) >>>> return null; >>>> - return chain.frame.atoms[firstAtomIndex + offset].point3f; >>>> + return chain.frame.atoms[firstAtomIndex + offset]; >>>> } >>>> } >>>> return null; >>>> >>>> Modified: branches/v10_9/Jmol/src/org/jmol/viewer/NucleicMonomer.java >>>> =================================================================== >>>> --- branches/v10_9/Jmol/src/org/jmol/viewer/NucleicMonomer.java >>>> 2006-08-30 19:41:22 UTC (rev 5452) >>>> +++ branches/v10_9/Jmol/src/org/jmol/viewer/NucleicMonomer.java >>>> 2006-08-30 20:30:56 UTC (rev 5453) >>>> @@ -191,7 +191,7 @@ >>>> void getBaseRing6Points(Point3f[] ring6Points) { >>>> for (int i = 6; --i >= 0; ) { >>>> Atom atom = getAtomFromOffsetIndex(i + 3); >>>> - ring6Points[i] = atom.point3f; >>>> + ring6Points[i] = atom; >>>> } >>>> } >>>> >>>> @@ -201,7 +201,7 @@ >>>> if (isPurine) >>>> for (int i = 5; --i >= 0; ) { >>>> Atom atom = getAtomFromOffsetIndex(ring5OffsetIndexes[i]); >>>> - ring5Points[i] = atom.point3f; >>>> + ring5Points[i] = atom; >>>> } >>>> return isPurine; >>>> } >>>> >>>> Modified: branches/v10_9/Jmol/src/org/jmol/viewer/NucleicPolymer.java >>>> =================================================================== >>>> --- branches/v10_9/Jmol/src/org/jmol/viewer/NucleicPolymer.java >>>> 2006-08-30 19:41:22 UTC (rev 5452) >>>> +++ branches/v10_9/Jmol/src/org/jmol/viewer/NucleicPolymer.java >>>> 2006-08-30 20:30:56 UTC (rev 5453) >>>> @@ -64,7 +64,7 @@ >>>> if (! otherNucleotide.isPyrimidine()) >>>> continue; >>>> Atom otherN3 = otherNucleotide.getN3(); >>>> - float dist2 = myN1.point3f.distanceSquared(otherN3.point3f); >>>> + float dist2 = myN1.distanceSquared(otherN3); >>>> if (dist2 < minDist2) { >>>> bestNucleotide = otherNucleotide; >>>> bestN3 = otherN3; >>>> >>>> Modified: branches/v10_9/Jmol/src/org/jmol/viewer/Polyhedra.java >>>> =================================================================== >>>> --- branches/v10_9/Jmol/src/org/jmol/viewer/Polyhedra.java >>>> 2006-08-30 19:41:22 UTC (rev 5452) >>>> +++ branches/v10_9/Jmol/src/org/jmol/viewer/Polyhedra.java >>>> 2006-08-30 20:30:56 UTC (rev 5453) >>>> @@ -301,10 +301,10 @@ >>>> float dAverage = 0; >>>> >>>> Point3f[] points = new Point3f[MAX_VERTICES * 3]; >>>> - points[ptCenter] = centralAtom.point3f; >>>> + points[ptCenter] = centralAtom; >>>> otherAtoms[ptCenter] = centralAtom; >>>> for (int i = 0; i < ptCenter; i++) { >>>> - points[i] = otherAtoms[i].point3f; >>>> + points[i] = otherAtoms[i]; >>>> dAverage += points[ptCenter].distance(points[i]); >>>> } >>>> dAverage = dAverage / ptCenter; >>>> >>>> Modified: branches/v10_9/Jmol/src/org/jmol/viewer/Polymer.java >>>> =================================================================== >>>> --- branches/v10_9/Jmol/src/org/jmol/viewer/Polymer.java >>>> 2006-08-30 19:41:22 UTC (rev 5452) >>>> +++ branches/v10_9/Jmol/src/org/jmol/viewer/Polymer.java >>>> 2006-08-30 20:30:56 UTC (rev 5453) >>>> @@ -194,11 +194,11 @@ >>>> } >>>> >>>> final Point3f getInitiatorPoint() { >>>> - return monomers[0].getInitiatorAtom().point3f; >>>> + return monomers[0].getInitiatorAtom(); >>>> } >>>> >>>> final Point3f getTerminatorPoint() { >>>> - return monomers[monomerCount - 1].getTerminatorAtom().point3f; >>>> + return monomers[monomerCount - 1].getTerminatorAtom(); >>>> } >>>> >>>> final Atom getLeadAtom(int monomerIndex) { >>>> >>>> Modified: branches/v10_9/Jmol/src/org/jmol/viewer/Sticks.java >>>> =================================================================== >>>> --- branches/v10_9/Jmol/src/org/jmol/viewer/Sticks.java >>>> 2006-08-30 19:41:22 UTC (rev 5452) >>>> +++ branches/v10_9/Jmol/src/org/jmol/viewer/Sticks.java >>>> 2006-08-30 20:30:56 UTC (rev 5453) >>>> @@ -189,7 +189,7 @@ >>>> if (! bsA.get(iA)) >>>> continue; >>>> Atom atomA = atoms[iA]; >>>> - Point3f pointA = atomA.point3f; >>>> + Point3f pointA = atomA; >>>> for (int iB = atomCount; --iB >= 0; ) { >>>> if (iB == iA) >>>> continue; >>>> @@ -206,7 +206,7 @@ >>>> continue; >>>> if (CREATE_ONLY == connectOperation && bondAB != null) >>>> continue; >>>> - float distanceSquared = pointA.distanceSquared(atomB.point3f); >>>> + float distanceSquared = pointA.distanceSquared(atomB); >>>> if (distanceSquared < minDistanceSquared || >>>> distanceSquared > maxDistanceSquared) >>>> continue; >>>> @@ -235,7 +235,7 @@ >>>> if (bsA.get(atom1.atomIndex) && bsB.get(atom2.atomIndex) || >>>> bsA.get(atom2.atomIndex) && bsB.get(atom1.atomIndex)) { >>>> if (bond.atom1.isBonded(bond.atom2)) { >>>> - float distanceSquared = >>>> atom1.point3f.distanceSquared(atom2.point3f); >>>> + float distanceSquared = atom1.distanceSquared(atom2); >>>> if (distanceSquared >= minDistanceSquared && >>>> distanceSquared <= maxDistanceSquared) >>>> if (order == NULL_BOND_ORDER || >>>> >>>> Modified: branches/v10_9/Jmol/src/org/jmol/viewer/VectorsRenderer.java >>>> =================================================================== >>>> --- branches/v10_9/Jmol/src/org/jmol/viewer/VectorsRenderer.java >>>> 2006-08-30 19:41:22 UTC (rev 5452) >>>> +++ branches/v10_9/Jmol/src/org/jmol/viewer/VectorsRenderer.java >>>> 2006-08-30 20:30:56 UTC (rev 5453) >>>> @@ -87,14 +87,14 @@ >>>> >>>> // to have the vectors move when vibration is turned on >>>> float vectorScale = viewer.getVectorScale(); >>>> - pointVectorEnd.scaleAdd(vectorScale, vibrationVector, >>>> atom.point3f); >>>> + pointVectorEnd.scaleAdd(vectorScale, vibrationVector, atom); >>>> viewer.transformPoint(pointVectorEnd, vibrationVector, >>>> screenVectorEnd); >>>> diameter = (mad <= 20) >>>> ? mad >>>> : viewer.scaleToScreen(screenVectorEnd.z, mad); >>>> pointArrowHead.scaleAdd(vectorScale * arrowHeadBase, >>>> - vibrationVector, atom.point3f); >>>> + vibrationVector, atom); >>>> viewer.transformPoint(pointArrowHead, vibrationVector, >>>> screenArrowHead); >>>> headWidthPixels = diameter * 3 / 2; >>>> >>>> >>>> This was sent by the SourceForge.net collaborative development >>>> platform, the world's largest Open Source development site. >>>> >>>> ------------------------------------------------------------------------- >>>> >>>> Using Tomcat but need to do more? Need to support web services, >>>> security? >>>> Get stuff done quickly with pre-integrated technology to make your >>>> job easier >>>> Download IBM WebSphere Application Server v.1.0.1 based on Apache >>>> Geronimo >>>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >>>> >>>> _______________________________________________ >>>> Jmol-commits mailing list >>>> [email protected] >>>> https://lists.sourceforge.net/lists/listinfo/jmol-commits >>>> >>>> >>> >>> >>> >>> > > ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
