From: <mig...@us...> - 2006-05-06 20:15:27
|
Revision: 5072 Author: migueljmol Date: 2006-05-06 13:15:11 -0700 (Sat, 06 May 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=5072&view=rev Log Message: ----------- 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: -------------- trunk/Jmol/src/org/jmol/viewer/Atom.java trunk/Jmol/src/org/jmol/viewer/Bond.java trunk/Jmol/src/org/jmol/viewer/Dots.java trunk/Jmol/src/org/jmol/viewer/Frame.java trunk/Jmol/src/org/jmol/viewer/MeasuresRenderer.java trunk/Jmol/src/org/jmol/viewer/Monomer.java trunk/Jmol/src/org/jmol/viewer/NucleicMonomer.java trunk/Jmol/src/org/jmol/viewer/NucleicPolymer.java trunk/Jmol/src/org/jmol/viewer/Polyhedra.java trunk/Jmol/src/org/jmol/viewer/Polymer.java trunk/Jmol/src/org/jmol/viewer/SasNeighborFinder.java trunk/Jmol/src/org/jmol/viewer/Sasurface1.java trunk/Jmol/src/org/jmol/viewer/Sticks.java trunk/Jmol/src/org/jmol/viewer/VectorsRenderer.java Added Paths: ----------- trunk/Jmol/src/org/jmol/vecmath/ trunk/Jmol/src/org/jmol/vecmath/Point3fi.java Added: trunk/Jmol/src/org/jmol/vecmath/Point3fi.java =================================================================== --- trunk/Jmol/src/org/jmol/vecmath/Point3fi.java (rev 0) +++ trunk/Jmol/src/org/jmol/vecmath/Point3fi.java 2006-05-06 20:15:11 UTC (rev 5072) @@ -0,0 +1,33 @@ +/* $RCSfile$ + * $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: mi...@jm... + * + * 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: trunk/Jmol/src/org/jmol/viewer/Atom.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Atom.java 2006-05-06 14:13:33 UTC (rev 5071) +++ trunk/Jmol/src/org/jmol/viewer/Atom.java 2006-05-06 20:15:11 UTC (rev 5072) @@ -26,6 +26,7 @@ import org.jmol.g3d.Graphics3D; import org.jmol.bspt.Tuple; +import org.jmol.vecmath.Point3fi; import java.util.Hashtable; import java.util.BitSet; @@ -34,7 +35,7 @@ import javax.vecmath.Vector3f; import javax.vecmath.Point3i; -final class Atom implements Tuple { +final class Atom extends Point3fi implements Tuple { final static byte VISIBLE_FLAG = 0x01; final static byte VIBRATION_VECTOR_FLAG = 0x02; @@ -42,10 +43,6 @@ Group group; int atomIndex; - Point3f point3f; - int screenX; - int screenY; - int screenZ; short screenDiameter; short modelIndex; // we want this here for the BallsRenderer byte elementNumber; @@ -76,7 +73,7 @@ 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; @@ -368,9 +365,9 @@ 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; @@ -483,25 +480,25 @@ } 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() { @@ -536,12 +533,12 @@ // 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]; Atom atomOther = bond.atom1 != this ? bond.atom1 : bond.atom2; - float dist2 = point3f.distanceSquared(atomOther.point3f); + float dist2 = distanceSquared(atomOther); if (dist2 > dist2Longest) { bondLongest = bond; dist2Longest = dist2; @@ -815,15 +812,15 @@ 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': @@ -1052,9 +1049,9 @@ 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: trunk/Jmol/src/org/jmol/viewer/Bond.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Bond.java 2006-05-06 14:13:33 UTC (rev 5071) +++ trunk/Jmol/src/org/jmol/viewer/Bond.java 2006-05-06 20:15:11 UTC (rev 5072) @@ -157,12 +157,12 @@ 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: trunk/Jmol/src/org/jmol/viewer/Dots.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Dots.java 2006-05-06 14:13:33 UTC (rev 5071) +++ trunk/Jmol/src/org/jmol/viewer/Dots.java 2006-05-06 20:15:11 UTC (rev 5072) @@ -253,7 +253,7 @@ void setAtomI(int indexI) { this.indexI = indexI; atomI = frame.atoms[indexI]; - centerI = atomI.point3f; + centerI = atomI; radiusI = getAppropriateRadius(atomI); radiiIP2 = radiusI + radiusP; radiiIP2 *= radiiIP2; @@ -337,7 +337,7 @@ if (! bsSelected.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) { @@ -347,7 +347,7 @@ neighborPlusProbeRadii2 = Util.doubleLength(neighborPlusProbeRadii2); } neighbors[neighborCount] = neighbor; - neighborCenters[neighborCount] = neighbor.point3f; + neighborCenters[neighborCount] = neighbor; neighborIndices[neighborCount] = neighbor.atomIndex; float neighborPlusProbeRadii = neighborRadius + radiusP; neighborPlusProbeRadii2[neighborCount] = Modified: trunk/Jmol/src/org/jmol/viewer/Frame.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Frame.java 2006-05-06 14:13:33 UTC (rev 5071) +++ trunk/Jmol/src/org/jmol/viewer/Frame.java 2006-05-06 20:15:11 UTC (rev 5072) @@ -691,7 +691,7 @@ } Point3f getAtomPoint3f(int atomIndex) { - return atoms[atomIndex].point3f; + return atoms[atomIndex]; } int getBondCount() { @@ -861,7 +861,7 @@ 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); } @@ -922,7 +922,7 @@ 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) @@ -1535,12 +1535,12 @@ void convertEuclideanToFractional() { for (int i = atomCount; --i >= 0; ) - matrixEuclideanToFractional.transform(atoms[i].point3f); + matrixEuclideanToFractional.transform(atoms[i]); } void convertFractionalToEuclidean() { for (int i = atomCount; --i >= 0; ) - matrixFractionalToEuclidean.transform(atoms[i].point3f); + matrixFractionalToEuclidean.transform(atoms[i]); } Point3f findFractionalAdjustment() { @@ -1562,20 +1562,20 @@ void applyFractionalAdjustment(Point3f adjustment) { System.out.println("applyFractionalAdjustment(" + adjustment + ")"); for (int i = atomCount; --i >= 0; ) - atoms[i].point3f.sub(adjustment); + atoms[i].sub(adjustment); } void calcAtomsMinMax(Point3f pointMin, Point3f pointMax) { float minX, minY, minZ, maxX, maxY, maxZ; Point3f pointT; - pointT = atoms[0].point3f; + pointT = atoms[0]; minX = maxX = pointT.x; minY = maxY = pointT.y; minZ = maxZ = pointT.z; for (int i = atomCount; --i > 0; ) { // note that the 0 element was set above - pointT = atoms[i].point3f; + pointT = atoms[i]; float t; t = pointT.x; if (t < minX) { minX = t; } @@ -1670,7 +1670,7 @@ //////////////////////////////////////////////////////////////// float getDistance(int atomIndexA, int atomIndexB) { - return atoms[atomIndexA].point3f.distance(atoms[atomIndexB].point3f); + return atoms[atomIndexA].distance(atoms[atomIndexB]); } Vector3f vectorBA; @@ -1681,9 +1681,9 @@ 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); @@ -1693,10 +1693,10 @@ 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) { Modified: trunk/Jmol/src/org/jmol/viewer/MeasuresRenderer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/MeasuresRenderer.java 2006-05-06 14:13:33 UTC (rev 5071) +++ trunk/Jmol/src/org/jmol/viewer/MeasuresRenderer.java 2006-05-06 20:15:11 UTC (rev 5072) @@ -179,7 +179,7 @@ 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; @@ -188,7 +188,7 @@ 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: trunk/Jmol/src/org/jmol/viewer/Monomer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Monomer.java 2006-05-06 14:13:33 UTC (rev 5071) +++ trunk/Jmol/src/org/jmol/viewer/Monomer.java 2006-05-06 20:15:11 UTC (rev 5072) @@ -116,7 +116,7 @@ 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)]; } //////////////////////////////////////////////////////////////// @@ -131,8 +131,7 @@ } 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) { @@ -160,7 +159,7 @@ 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: trunk/Jmol/src/org/jmol/viewer/NucleicMonomer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/NucleicMonomer.java 2006-05-06 14:13:33 UTC (rev 5071) +++ trunk/Jmol/src/org/jmol/viewer/NucleicMonomer.java 2006-05-06 20:15:11 UTC (rev 5072) @@ -198,7 +198,7 @@ for (int i = 6; --i >= 0; ) { Atom atom = getAtomFromOffsetIndex(i + 3); atom.formalChargeAndFlags |= Atom.VISIBLE_FLAG; - ring6Points[i] = atom.point3f; + ring6Points[i] = atom; } } @@ -209,7 +209,7 @@ for (int i = 5; --i >= 0; ) { Atom atom = getAtomFromOffsetIndex(ring5OffsetIndexes[i]); atom.formalChargeAndFlags |= Atom.VISIBLE_FLAG; - ring5Points[i] = atom.point3f; + ring5Points[i] = atom; } return isPurine; } Modified: trunk/Jmol/src/org/jmol/viewer/NucleicPolymer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/NucleicPolymer.java 2006-05-06 14:13:33 UTC (rev 5071) +++ trunk/Jmol/src/org/jmol/viewer/NucleicPolymer.java 2006-05-06 20:15:11 UTC (rev 5072) @@ -63,7 +63,7 @@ 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: trunk/Jmol/src/org/jmol/viewer/Polyhedra.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Polyhedra.java 2006-05-06 14:13:33 UTC (rev 5071) +++ trunk/Jmol/src/org/jmol/viewer/Polyhedra.java 2006-05-06 20:15:11 UTC (rev 5072) @@ -363,9 +363,9 @@ Polyhedron validatePolyhedronNew(Atom centralAtom, int vertexCount, Atom[] otherAtoms) { int faceCount = 0; - Point3f centralAtomPoint = centralAtom.point3f; + Point3f centralAtomPoint = centralAtom; for (int i = vertexCount; --i >= 0;) { - centerVectors[i] = new Vector3f(otherAtoms[i].point3f); + centerVectors[i] = new Vector3f(otherAtoms[i]); centerVectors[i].sub(centralAtomPoint); } @@ -384,9 +384,9 @@ if (centerVectors[i].angle(centerVectors[k]) > centralAngleMax || centerVectors[j].angle(centerVectors[k]) > centralAngleMax) continue; - Point3f pointI = otherAtoms[i].point3f; - Point3f pointJ = otherAtoms[j].point3f; - Point3f pointK = otherAtoms[k].point3f; + Point3f pointI = otherAtoms[i]; + Point3f pointJ = otherAtoms[j]; + Point3f pointK = otherAtoms[k]; getNormalFromCenter(centralAtomPoint, pointI, pointJ, pointK, false, normalT); Modified: trunk/Jmol/src/org/jmol/viewer/Polymer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Polymer.java 2006-05-06 14:13:33 UTC (rev 5071) +++ trunk/Jmol/src/org/jmol/viewer/Polymer.java 2006-05-06 20:15:11 UTC (rev 5072) @@ -197,11 +197,11 @@ } 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: trunk/Jmol/src/org/jmol/viewer/SasNeighborFinder.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/SasNeighborFinder.java 2006-05-06 14:13:33 UTC (rev 5071) +++ trunk/Jmol/src/org/jmol/viewer/SasNeighborFinder.java 2006-05-06 20:15:11 UTC (rev 5072) @@ -85,7 +85,7 @@ System.out.println("setAtomI:" + indexI); this.indexI = indexI; atomI = atoms[indexI]; - centerI = atomI.point3f; + centerI = atomI; radiusI = atomI.getVanderwaalsRadiusFloat(); radiiIP = radiusI + radiusP; radiiIP2 = radiiIP * radiiIP; @@ -136,7 +136,7 @@ if (! bsSelected.get(neighbor.atomIndex)) continue; float neighborRadius = neighbor.getVanderwaalsRadiusFloat(); - if (centerI.distance(neighbor.point3f) > + if (centerI.distance(neighbor) > radiusI + radiusP + radiusP + neighborRadius) continue; if (neighborCount == neighborAtoms.length) { @@ -147,7 +147,7 @@ neighborPlusProbeRadii2 = Util.doubleLength(neighborPlusProbeRadii2); } neighborAtoms[neighborCount] = neighbor; - neighborCenters[neighborCount] = neighbor.point3f; + neighborCenters[neighborCount] = neighbor; neighborIndexes[neighborCount] = neighbor.atomIndex; float radii = neighborRadius + radiusP; neighborPlusProbeRadii[neighborCount] = radii; Modified: trunk/Jmol/src/org/jmol/viewer/Sasurface1.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Sasurface1.java 2006-05-06 14:13:33 UTC (rev 5071) +++ trunk/Jmol/src/org/jmol/viewer/Sasurface1.java 2006-05-06 20:15:11 UTC (rev 5072) @@ -518,8 +518,8 @@ } void calcVectors() { - Point3f centerA = frame.atoms[ixA].point3f; - Point3f centerB = frame.atoms[ixB].point3f; + Point3f centerA = frame.atoms[ixA]; + Point3f centerB = frame.atoms[ixB]; axisUnitVector.sub(centerB, centerA); axisUnitVector.normalize(); @@ -891,7 +891,7 @@ int ix = isEdgeA ? ixA : ixB; Atom atom = frame.atoms[ix]; calcZeroPoint(isEdgeA, zeroPointT); - gem.clipGeodesic(isEdgeA, atom.point3f, atom.getVanderwaalsRadiusFloat(), + gem.clipGeodesic(isEdgeA, atom, atom.getVanderwaalsRadiusFloat(), zeroPointT, axisUnitVector, convexVertexMaps[ix]); } @@ -919,12 +919,12 @@ void calcClippingPlaneCenterPoints(Point3f centerPointA, Point3f centerPointB) { calcZeroPoint(true, zeroPointT); - Point3f centerA = frame.atoms[ixA].point3f; + Point3f centerA = frame.atoms[ixA]; calcClippingPlaneCenter(centerA, axisUnitVector, zeroPointT, centerPointA); calcZeroPoint(false, zeroPointT); - Point3f centerB = frame.atoms[ixB].point3f; + Point3f centerB = frame.atoms[ixB]; calcClippingPlaneCenter(centerB, axisUnitVector, zeroPointT, centerPointB); } @@ -950,7 +950,7 @@ int ix = isEdgeA ? ixA : ixB; Atom atom = frame.atoms[ix]; float atomRadius = atom.getVanderwaalsRadiusFloat(); - Point3f atomCenter = atom.point3f; + Point3f atomCenter = atom; gem.reset(); calcZeroAndCenterPoints(isEdgeA, atomCenter, zeroPointT, centerPointT); boolean dump = false; Modified: trunk/Jmol/src/org/jmol/viewer/Sticks.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Sticks.java 2006-05-06 14:13:33 UTC (rev 5071) +++ trunk/Jmol/src/org/jmol/viewer/Sticks.java 2006-05-06 20:15:11 UTC (rev 5072) @@ -187,7 +187,7 @@ 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; @@ -201,7 +201,7 @@ 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; @@ -230,7 +230,7 @@ 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: trunk/Jmol/src/org/jmol/viewer/VectorsRenderer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/VectorsRenderer.java 2006-05-06 14:13:33 UTC (rev 5071) +++ trunk/Jmol/src/org/jmol/viewer/VectorsRenderer.java 2006-05-06 20:15:11 UTC (rev 5072) @@ -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. |
From: <ha...@us...> - 2006-09-14 06:10:49
|
Revision: 5538 http://svn.sourceforge.net/jmol/?rev=5538&view=rev Author: hansonr Date: 2006-09-13 23:10:39 -0700 (Wed, 13 Sep 2006) Log Message: ----------- any-color stereo Modified Paths: -------------- trunk/Jmol/src/org/jmol/g3d/Graphics3D.java trunk/Jmol/src/org/jmol/viewer/Eval.java trunk/Jmol/src/org/jmol/viewer/JmolConstants.java trunk/Jmol/src/org/jmol/viewer/Token.java trunk/Jmol/src/org/jmol/viewer/TransformManager.java trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/g3d/Graphics3D.java =================================================================== --- trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2006-09-13 21:49:56 UTC (rev 5537) +++ trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2006-09-14 06:10:39 UTC (rev 5538) @@ -582,17 +582,34 @@ anaglyphChannelBytes[i] = (byte)pbuf[i]; } - public void applyBlueOrGreenAnaglyph(boolean blueChannel) { - int shiftCount = blueChannel ? 0 : 8; - for (int i = pbuf.length; --i >= 0; ) - pbuf[i] = ((pbuf[i] & 0xFFFF0000) | - ((anaglyphChannelBytes[i] & 0x000000FF) << shiftCount)); + public void applyCustomAnaglyph(int[] stereoColors) { + int color1 = stereoColors[0]; + int color2 = stereoColors[1] & 0x00FFFFFF; + for (int i = pbuf.length; --i >= 0;) { + int a = anaglyphChannelBytes[i] & 0x000000FF; + a = (a | ((a | (a << 8)) << 8)) & color2; + pbuf[i] = (pbuf[i] & color1) | a; + } } + public void applyGreenAnaglyph() { + for (int i = pbuf.length; --i >= 0; ) { + int green = (anaglyphChannelBytes[i] & 0x000000FF) << 8; + pbuf[i] = (pbuf[i] & 0xFFFF0000) | green; + } + } + + public void applyBlueAnaglyph() { + for (int i = pbuf.length; --i >= 0; ) { + int blue = anaglyphChannelBytes[i] & 0x000000FF; + pbuf[i] = (pbuf[i] & 0xFFFF0000) | blue; + } + } + public void applyCyanAnaglyph() { for (int i = pbuf.length; --i >= 0; ) { - int blueAndGreen = anaglyphChannelBytes[i] & 0x000000FF; - int cyan = (blueAndGreen << 8) | blueAndGreen; + int blue = anaglyphChannelBytes[i] & 0x000000FF; + int cyan = (blue << 8) | blue; pbuf[i] = pbuf[i] & 0xFFFF0000 | cyan; } } Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-13 21:49:56 UTC (rev 5537) +++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-14 06:10:39 UTC (rev 5538) @@ -1609,6 +1609,8 @@ // see www.usm.maine.edu/~rhodes/0Help/StereoViewing.html float degrees = -5; boolean degreesSeen = false; + int[] colors = new int[2]; + int colorpt = 0; for (int i = 1; i < statementLength; ++i) { switch (statement[i].tok) { case Token.on: @@ -1617,6 +1619,13 @@ case Token.off: stereoMode = JmolConstants.STEREO_NONE; break; + case Token.colorRGB: + if (colorpt > 1) + badArgumentCount(); + if (!degreesSeen) + degrees = 3; + colors[colorpt++] = getArgbParam(i); + break; case Token.integer: case Token.decimal: degrees = floatParameter(i); @@ -1644,7 +1653,10 @@ } } viewer.setStereoDegrees(degrees); - viewer.setStereoMode(stereoMode); + if (colorpt == 2) + viewer.setStereoMode(colors); + else + viewer.setStereoMode(stereoMode); } void connect() throws ScriptException { Modified: trunk/Jmol/src/org/jmol/viewer/JmolConstants.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2006-09-13 21:49:56 UTC (rev 5537) +++ trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2006-09-14 06:10:39 UTC (rev 5538) @@ -2283,6 +2283,7 @@ public final static int STEREO_REDCYAN = 2; public final static int STEREO_REDBLUE = 3; public final static int STEREO_REDGREEN = 4; + public final static int STEREO_CUSTOM = 5; // all of these things are compile-time constants // if they are false then the compiler should take them away Modified: trunk/Jmol/src/org/jmol/viewer/Token.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Token.java 2006-09-13 21:49:56 UTC (rev 5537) +++ trunk/Jmol/src/org/jmol/viewer/Token.java 2006-09-14 06:10:39 UTC (rev 5538) @@ -85,7 +85,6 @@ // every predefined is also valid in an expression context final static int comparator = (1 << 17) | expression; final static int predefinedset = (1 << 18) | expression; - final static int colorparam = (1 << 19); final static int specialstring = (1 << 20); // echo, label // generally, the minus sign is used to denote atom ranges // this property is used for the few commands which allow negative integers @@ -99,8 +98,10 @@ // allows initial quote to indicate some parameters may not be strings // Bob Hanson 2006/04 final static int specialstring2 = (1 << 24); // echo, label - + final static int colorparam = (1 << 19); + + // These are unrelated final static int varArgCount = (1 << 4); final static int onDefault1 = (1 << 5) | 1; @@ -143,7 +144,7 @@ final static int slab = command | 33 | bool; final static int cpk = command | 35 | setparam | bool | negnums; final static int ssbond = command | 36 | setparam | bool; - final static int stereo = command | 38 | setspecial | bool | negnums; + final static int stereo = command | 38 | colorparam;// | setspecial | bool | negnums ; final static int strands = command | 39 | setparam | bool; final static int structure = command | 40; final static int trace = command | 41 | bool; Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2006-09-13 21:49:56 UTC (rev 5537) +++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2006-09-14 06:10:39 UTC (rev 5538) @@ -1534,8 +1534,15 @@ //////////////////////////////////////////////////////////////// int stereoMode; - + int[] stereoColors; + void setStereoMode(int[] twoColors) { + stereoMode = JmolConstants.STEREO_CUSTOM; + stereoColors = twoColors; + viewer.setGreyscaleRendering(true); + } + void setStereoMode(int stereoMode) { + stereoColors = null; this.stereoMode = stereoMode; viewer.setGreyscaleRendering(stereoMode >= JmolConstants.STEREO_REDCYAN); } Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2006-09-13 21:49:56 UTC (rev 5537) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2006-09-14 06:10:39 UTC (rev 5538) @@ -1882,6 +1882,7 @@ case JmolConstants.STEREO_REDCYAN: case JmolConstants.STEREO_REDBLUE: case JmolConstants.STEREO_REDGREEN: + case JmolConstants.STEREO_CUSTOM: setRectClip(null); g3d.beginRendering(rectClip.x, rectClip.y, rectClip.width, rectClip.height, transformManager.getStereoRotationMatrix(true), @@ -1896,11 +1897,19 @@ repaintManager.render(g3d, rectClip, modelManager.getFrame(), repaintManager.displayModelIndex); g3d.endRendering(); - if (stereoMode == JmolConstants.STEREO_REDCYAN) + switch (stereoMode) { + case JmolConstants.STEREO_REDCYAN: g3d.applyCyanAnaglyph(); - else - g3d - .applyBlueOrGreenAnaglyph(stereoMode == JmolConstants.STEREO_REDBLUE); + break; + case JmolConstants.STEREO_CUSTOM: + g3d.applyCustomAnaglyph(transformManager.stereoColors); + break; + case JmolConstants.STEREO_REDBLUE: + g3d.applyBlueAnaglyph(); + break; + default: + g3d.applyGreenAnaglyph(); + } Image img = g3d.getScreenImage(); try { g.drawImage(img, 0, 0, null); @@ -3233,6 +3242,11 @@ transformManager.setStereoMode(stereoMode); } + void setStereoMode(int[] twoColors) { + transformManager.setStereoMode(twoColors); + } + + int getStereoMode() { return transformManager.stereoMode; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2006-09-14 11:57:39
|
Revision: 5539 http://svn.sourceforge.net/jmol/?rev=5539&view=rev Author: hansonr Date: 2006-09-14 04:57:33 -0700 (Thu, 14 Sep 2006) Log Message: ----------- stereo, but... Modified Paths: -------------- trunk/Jmol/src/org/jmol/g3d/Graphics3D.java trunk/Jmol/src/org/jmol/viewer/Eval.java Modified: trunk/Jmol/src/org/jmol/g3d/Graphics3D.java =================================================================== --- trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2006-09-14 06:10:39 UTC (rev 5538) +++ trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2006-09-14 11:57:33 UTC (rev 5539) @@ -583,6 +583,7 @@ } public void applyCustomAnaglyph(int[] stereoColors) { + //best if complementary, but they do not have to be0 int color1 = stereoColors[0]; int color2 = stereoColors[1] & 0x00FFFFFF; for (int i = pbuf.length; --i >= 0;) { Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-14 06:10:39 UTC (rev 5538) +++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-14 11:57:33 UTC (rev 5539) @@ -1625,6 +1625,8 @@ if (!degreesSeen) degrees = 3; colors[colorpt++] = getArgbParam(i); + if (colorpt == 1) + colors[colorpt] = ~colors[0]; break; case Token.integer: case Token.decimal: @@ -1653,7 +1655,7 @@ } } viewer.setStereoDegrees(degrees); - if (colorpt == 2) + if (colorpt > 0) viewer.setStereoMode(colors); else viewer.setStereoMode(stereoMode); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2006-09-14 19:26:59
|
Revision: 5547 http://svn.sourceforge.net/jmol/?rev=5547&view=rev Author: nicove Date: 2006-09-14 12:26:49 -0700 (Thu, 14 Sep 2006) Log Message: ----------- Fixing Eclipse 3.2 warnings Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/CsfReader.java trunk/Jmol/src/org/jmol/viewer/CompoundDocument.java trunk/Jmol/src/org/jmol/viewer/Eval.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/CsfReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/CsfReader.java 2006-09-14 19:24:36 UTC (rev 5546) +++ trunk/Jmol/src/org/jmol/adapter/smarter/CsfReader.java 2006-09-14 19:26:49 UTC (rev 5547) @@ -332,7 +332,7 @@ int iatom = atomSetCollection.getFirstAtomSetAtomCount(); int xyzpt = 0; Atom[] atoms = atomSetCollection.atoms; - out: for (; (line = reader.readLine()) != null;) { + for (; (line = reader.readLine()) != null;) { if (line.startsWith("property_flags:")) break; String tokens[] = getTokens(line); Modified: trunk/Jmol/src/org/jmol/viewer/CompoundDocument.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/CompoundDocument.java 2006-09-14 19:24:36 UTC (rev 5546) +++ trunk/Jmol/src/org/jmol/viewer/CompoundDocument.java 2006-09-14 19:26:49 UTC (rev 5547) @@ -130,7 +130,7 @@ boolean isBigEndian = true; - private class CmpDocHeader { + class CmpDocHeader { //512 bytes //offset 0: @@ -204,7 +204,7 @@ } } - private class CmpDocDirectoryEntry { + class CmpDocDirectoryEntry { // 128 bytes //offset 0: byte[] unicodeName = new byte[64]; Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-14 19:24:36 UTC (rev 5546) +++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-14 19:26:49 UTC (rev 5547) @@ -1804,7 +1804,7 @@ if (statementLength > 5 || statementLength < 2) badArgumentCount(); int tok = statement[1].tok; - outer: switch (tok) { + switch (tok) { case Token.dollarsign: colorNamedObject(2); return; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2006-09-16 14:54:31
|
Revision: 5562 http://svn.sourceforge.net/jmol/?rev=5562&view=rev Author: hansonr Date: 2006-09-16 07:54:22 -0700 (Sat, 16 Sep 2006) Log Message: ----------- background model N Modified Paths: -------------- trunk/Jmol/src/org/jmol/api/JmolViewer.java trunk/Jmol/src/org/jmol/viewer/Dipole.java trunk/Jmol/src/org/jmol/viewer/Eval.java trunk/Jmol/src/org/jmol/viewer/Pmesh.java trunk/Jmol/src/org/jmol/viewer/RepaintManager.java trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/api/JmolViewer.java =================================================================== --- trunk/Jmol/src/org/jmol/api/JmolViewer.java 2006-09-16 14:53:18 UTC (rev 5561) +++ trunk/Jmol/src/org/jmol/api/JmolViewer.java 2006-09-16 14:54:22 UTC (rev 5562) @@ -133,7 +133,7 @@ abstract public boolean modelHasVibrationVectors(int atomSetIndex); abstract public int getModelCount(); - abstract public int getDisplayModelIndex(); + abstract public int getDisplayModelIndex(); // can return -2 - modelIndex if a background model is displayed abstract public int getAtomCount(); abstract public int getBondCount(); abstract public int getGroupCount(); Modified: trunk/Jmol/src/org/jmol/viewer/Dipole.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Dipole.java 2006-09-16 14:53:18 UTC (rev 5561) +++ trunk/Jmol/src/org/jmol/viewer/Dipole.java 2006-09-16 14:54:22 UTC (rev 5562) @@ -67,6 +67,8 @@ short colix, short mad, boolean visible) { this.viewer = viewer; this.modelIndex = viewer.getDisplayModelIndex(); + if (this.modelIndex < -1) + this.modelIndex = -2 - this.modelIndex; this.thisID = thisID; this.dipoleInfo = dipoleInfo; this.g3d = g3d; Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-16 14:53:18 UTC (rev 5561) +++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-16 14:54:22 UTC (rev 5562) @@ -2852,6 +2852,8 @@ } void conformation() throws ScriptException { + if (viewer.getDisplayModelIndex() <= -2) + evalError("\"conformation\" not allowed with background model displayed"); BitSet bsConformations; if (statementLength == 1) { bsConformations = viewer.setConformation(); @@ -3224,7 +3226,8 @@ } void frame(int offset, boolean useModelNumber) throws ScriptException { - useModelNumber = true; // for now -- as before -- remove to implement + useModelNumber = true; + // for now -- as before -- remove to implement // frame/model difference if (statementLength <= offset) badArgumentCount(); @@ -3543,6 +3546,11 @@ Logger.info("logging level set to " + ilevel); break; } + if (str.equalsIgnoreCase("backgroundModel")) { + int modelIndex = viewer.getModelNumberIndex(intParameter(2)); + viewer.setBackgroundModelIndex(modelIndex); + break; + } viewer.setBooleanProperty((String) statement[1].value, getSetBoolean()); break; case Token.background: Modified: trunk/Jmol/src/org/jmol/viewer/Pmesh.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Pmesh.java 2006-09-16 14:53:18 UTC (rev 5561) +++ trunk/Jmol/src/org/jmol/viewer/Pmesh.java 2006-09-16 14:54:22 UTC (rev 5562) @@ -166,11 +166,13 @@ int modelCount = viewer.getModelCount(); if (modelCount < 2) isFixed = true; - if (isFixed) { - currentMesh.modelIndex = -1; - } else { - currentMesh.modelIndex = viewer.getDisplayModelIndex(); + int modelIndex = -1; + if (!isFixed) { + modelIndex = viewer.getDisplayModelIndex(); + if (modelIndex < -1) + modelIndex = -2 - modelIndex; } + currentMesh.modelIndex = modelIndex; } Modified: trunk/Jmol/src/org/jmol/viewer/RepaintManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/RepaintManager.java 2006-09-16 14:53:18 UTC (rev 5561) +++ trunk/Jmol/src/org/jmol/viewer/RepaintManager.java 2006-09-16 14:54:22 UTC (rev 5562) @@ -43,7 +43,7 @@ } int displayModelIndex = 0; - boolean setDisplayModelIndex(int modelIndex) { + void setDisplayModelIndex(int modelIndex) { Frame frame = viewer.getFrame(); if (frame == null || modelIndex < 0 || @@ -51,21 +51,36 @@ displayModelIndex = -1; else displayModelIndex = modelIndex; + if (displayModelIndex == -1) + setBackgroundModelIndex(0); viewer.setTainted(true); viewer.setStatusFrameChanged(modelIndex); - getAnimationRangeVisible(); - return true; + setFrameRangeVisible(); } + int backgroundModelIndex = 0; + void setBackgroundModelIndex(int modelIndex) { + // no background unless only a SINGLE model is being displayed (for now) + Frame frame = viewer.getFrame(); + if (frame == null || modelIndex < 0 || modelIndex >= frame.getModelCount() || + displayModelIndex == -1) + modelIndex = 0; + backgroundModelIndex = modelIndex; + viewer.setTainted(true); + setFrameRangeVisible(); + } + private BitSet bsVisibleFrames = new BitSet(); BitSet getVisibleFramesBitSet() { return bsVisibleFrames; } - void getAnimationRangeVisible() { + private void setFrameRangeVisible() { bsVisibleFrames.clear(); if (displayModelIndex >= 0) { bsVisibleFrames.set(displayModelIndex); + if (backgroundModelIndex > 0) + bsVisibleFrames.set(backgroundModelIndex); return; } if (frameStep == 0) Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2006-09-16 14:53:18 UTC (rev 5561) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2006-09-16 14:54:22 UTC (rev 5562) @@ -1121,6 +1121,7 @@ setFrankOn(styleManager.frankOn); repaintManager.initializePointers(1); setDisplayModelIndex(0); + setBackgroundModelIndex(0); setTainted(true); popHoldRepaint(); setStatusFileLoaded(3, fullPathName, fileName, modelManager @@ -1367,7 +1368,10 @@ } void convertFractionalCoordinates(Point3f pt) { - modelManager.convertFractionalCoordinates(getDisplayModelIndex(), pt); + int modelIndex = getDisplayModelIndex(); + if (modelIndex < 0) + return; + modelManager.convertFractionalCoordinates(modelIndex, pt); } Point3f getCenter() { @@ -1785,14 +1789,25 @@ refresh(0, "Viewer:rewindAnimation()"); } - boolean setDisplayModelIndex(int modelIndex) { - return repaintManager.setDisplayModelIndex(modelIndex); + void setDisplayModelIndex(int modelIndex) { + repaintManager.setDisplayModelIndex(modelIndex); } public int getDisplayModelIndex() { - return repaintManager.displayModelIndex; + // modified to indicate if there is also a background model index + int modelIndex = repaintManager.displayModelIndex; + int backgroundIndex = getBackgroundModelIndex(); + return (backgroundIndex > 0 ? -2 - modelIndex : modelIndex); } + void setBackgroundModelIndex(int modelIndex) { + repaintManager.setBackgroundModelIndex(modelIndex); + } + + public int getBackgroundModelIndex() { + return repaintManager.backgroundModelIndex; + } + FrameRenderer getFrameRenderer() { return repaintManager.frameRenderer; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2006-09-18 03:07:37
|
Revision: 5587 http://svn.sourceforge.net/jmol/?rev=5587&view=rev Author: hansonr Date: 2006-09-17 20:07:29 -0700 (Sun, 17 Sep 2006) Log Message: ----------- popup menu enhancements; label background pointer to atom Modified Paths: -------------- trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java trunk/Jmol/src/org/jmol/viewer/MouseManager.java trunk/Jmol/src/org/jmol/viewer/PickingManager.java trunk/Jmol/src/org/jmol/viewer/Text.java Modified: trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java =================================================================== --- trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java 2006-09-17 23:59:05 UTC (rev 5586) +++ trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java 2006-09-18 03:07:29 UTC (rev 5587) @@ -52,7 +52,7 @@ private static final String[][] structureContents = { { "popupMenu", "modelSetInfoMenu - selectMenu renderMenu labelMenu colorMenu - " + "zoomMenu spinMenu animateMenu - " + - "measurementsMenu crystalMenu optionsMenu - consoleMenu - " + + "measureMenu pickingMenu crystalMenu optionsMenu - consoleMenu - " + "aboutMenu" }, { "selectMenu", "selectAll selectNone - " + @@ -552,11 +552,30 @@ { "animfps30", "anim fps 30" }, { "animfps50", "anim fps 50" }, - { "measurementsMenu", "distanceNanometers distanceAngstroms distancePicometers" }, - { "distanceNanometers", "set measure nanometers" }, - { "distanceAngstroms", "set measure angstroms" }, - { "distancePicometers", "set measure picometers" }, + { "measureMenu", "measureOff measureDistance measureAngle measureTorsion measureDelete measureList distanceNanometers distanceAngstroms distancePicometers" }, + { "measureOff", "set pickingstyle MEASURE OFF; set picking OFF" }, + { "measureDistance", "set pickingstyle MEASURE; set picking MEASURE DISTANCE" }, + { "measureAngle", "set pickingstyle MEASURE; set picking MEASURE ANGLE" }, + { "measureTorsion", "set pickingstyle MEASURE; set picking MEASURE TORSION" }, + { "measureDelete", "measure delete" }, + { "measureList", "console;show measurements" }, + { "distanceNanometers", "select *; set measure nanometers" }, + { "distanceAngstroms", "select *; set measure angstroms" }, + { "distancePicometers", "select *; set measure picometers" }, + { "pickingMenu", "pickOff pickCenter pickLabel pickAtom pickChain pickElement pickGroup pickMolecule pickSite pickSpin" }, + { "pickOff" , "set picking off" }, + { "pickCenter" , "set picking center" }, +// { "pickDraw" , "set picking draw" }, + { "pickLabel" , "set picking label" }, + { "pickAtom" , "set picking atom" }, + { "pickChain" , "set picking chain" }, + { "pickElement" , "set picking element" }, + { "pickGroup" , "set picking group" }, + { "pickMolecule" , "set picking molecule" }, + { "pickSite" , "set picking site" }, + { "pickSpin" , "set picking spin" }, + { "crystalMenu", "axesMenu bbcageMenu uccageMenu" }, { "axesMenu", "axesOff axesDotted axesByPixelMenu axesByAngstromMenu colorAxesMenu" }, @@ -1079,11 +1098,31 @@ { "animfps30", "30" }, { "animfps50", "50" }, - { "measurementsMenu", GT._("Measurements") }, - { "distanceNanometers", GT._("Nanometers") }, - { "distanceAngstroms", GT._("Angstroms") }, - { "distancePicometers", GT._("Picometers") }, + { "measureMenu", GT._("Measurement") }, + { "measureOff", GT._("Double-Click starts all measurements") }, + { "measureDistance", GT._("Click for distance measurement") }, + { "measureAngle", GT._("Click for angle measurement") }, + { "measureTorsion", GT._("Click for torsion (dihedral) measurement") }, + { "measureDelete", GT._("Delete measurements") }, + { "measureList", GT._("List measurements") }, + { "distanceNanometers", GT._("Distance units nanometers") }, + { "distanceAngstroms", GT._("Distance units Angstroms") }, + { "distancePicometers", GT._("Distance units picometers") }, + { "pickingMenu", GT._("Set picking") }, + { "pickOff" , GT._("Off") }, + { "pickCenter" , GT._("Center") }, +// { "pickDraw" , GT._("moves arrows") }, + { "pickLabel" , GT._("Label") }, + { "pickAtom" , GT._("Select atom") }, + { "pickChain" , GT._("Select chain") }, + { "pickElement" , GT._("Select element") }, + { "pickGroup" , GT._("Select group") }, + { "pickMolecule" , GT._("Select molecule") }, + { "pickSite" , GT._("Select site") }, + { "pickSpin" , GT._("Spin") }, + + { "crystalMenu", GT._("Crystal") }, { "axesMenu", GT._("Axes") }, Modified: trunk/Jmol/src/org/jmol/viewer/MouseManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/MouseManager.java 2006-09-17 23:59:05 UTC (rev 5586) +++ trunk/Jmol/src/org/jmol/viewer/MouseManager.java 2006-09-18 03:07:29 UTC (rev 5587) @@ -48,6 +48,7 @@ boolean measurementMode = false; boolean drawMode = false; + boolean measuresEnabled = true; boolean hoverActive = false; boolean rubberbandSelectionMode = false; @@ -199,14 +200,23 @@ } void setMouseMode() { + drawMode = false; + measuresEnabled = true; switch (viewer.getPickingMode()) { case JmolConstants.PICKING_DRAW: drawMode = true; - exitMeasurementMode(); + // fall through... + //other cases here? + case JmolConstants.PICKING_LABEL: + case JmolConstants.PICKING_MEASURE_DISTANCE: + case JmolConstants.PICKING_MEASURE_ANGLE: + case JmolConstants.PICKING_MEASURE_TORSION: + measuresEnabled=false; break; default: - drawMode = false; + return; } + exitMeasurementMode(); } void mouseClicked(long time, int x, int y, int modifiers, int clickCount) { @@ -243,6 +253,7 @@ void mouseSingleClick(int x, int y, int modifiers, int nearestAtomIndex) { //viewer.setStatusUserAction("mouseSingleClick: " + modifiers); + setMouseMode(); if (logMouseEvents) Logger.debug("mouseSingleClick(" + x + "," + y + "," + modifiers + " nearestAtom=" + nearestAtomIndex); @@ -274,12 +285,13 @@ void mouseDoubleClick(int x, int y, int modifiers, int nearestAtomIndex) { //viewer.setStatusUserAction("mouseDoubleClick: " + modifiers); + setMouseMode(); switch (modifiers & BUTTON_MODIFIER_MASK) { case LEFT: if (measurementMode) { addToMeasurement(nearestAtomIndex, true); toggleMeasurement(); - } else if (!drawMode) { + } else if (!drawMode && measuresEnabled) { enterMeasurementMode(); addToMeasurement(nearestAtomIndex, true); } Modified: trunk/Jmol/src/org/jmol/viewer/PickingManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/PickingManager.java 2006-09-17 23:59:05 UTC (rev 5586) +++ trunk/Jmol/src/org/jmol/viewer/PickingManager.java 2006-09-18 03:07:29 UTC (rev 5587) @@ -175,8 +175,15 @@ void toggleMeasurement(int nAtoms) { countPlusIndexes[0] = nAtoms; - for (int i = 0; i < nAtoms; i++) - countPlusIndexes[i + 1] = queuedAtomIndexes[i]; + int iLast = -1; + int iThis; + for (int i = 0; i < nAtoms; i++) { + if (iLast == (iThis = queuedAtomIndexes[i])) { + queuedAtomCount = i; + return; + } + iLast = countPlusIndexes[i + 1] = iThis; + } viewer.toggleMeasurement(countPlusIndexes); } Modified: trunk/Jmol/src/org/jmol/viewer/Text.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Text.java 2006-09-17 23:59:05 UTC (rev 5586) +++ trunk/Jmol/src/org/jmol/viewer/Text.java 2006-09-18 03:07:29 UTC (rev 5587) @@ -363,6 +363,8 @@ // old static style -- quick, simple, no line breaks, odd alignment? + int x0 = x; + int y0 = y; int boxWidth = font3d.fontMetrics.stringWidth(strLabel) + 8; int boxHeight = ascent + descent + 8; int xBoxOffset, yBoxOffset; @@ -394,6 +396,7 @@ g3d.fillRect(bgcolix, x, y, z, zSlab, boxWidth, boxHeight); g3d.drawRect(colix, x + 1, y + 1, z - 1, zSlab, boxWidth - 2, boxHeight - 2); + g3d.drawLine(bgcolix, x0, y0, zSlab, x, y + boxHeight/2, zSlab); } g3d.drawString(strLabel, font3d, colix, x + 4, y + 4 + ascent, z - 1, zSlab); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2006-09-18 03:39:31
|
Revision: 5588 http://svn.sourceforge.net/jmol/?rev=5588&view=rev Author: hansonr Date: 2006-09-17 20:39:23 -0700 (Sun, 17 Sep 2006) Log Message: ----------- popup menu enhancements; fix for show selection halos on menu not loading Halo shape Modified Paths: -------------- trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java trunk/Jmol/src/org/jmol/viewer/Eval.java trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java =================================================================== --- trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java 2006-09-18 03:07:29 UTC (rev 5587) +++ trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java 2006-09-18 03:39:23 UTC (rev 5588) @@ -563,7 +563,8 @@ { "distanceAngstroms", "select *; set measure angstroms" }, { "distancePicometers", "select *; set measure picometers" }, - { "pickingMenu", "pickOff pickCenter pickLabel pickAtom pickChain pickElement pickGroup pickMolecule pickSite pickSpin" }, + { "pickingMenu", "pickOff pickCenter pickLabel pickAtom pickChain " + + "pickElement pickGroup pickMolecule pickSite pickSpin" }, { "pickOff" , "set picking off" }, { "pickCenter" , "set picking center" }, // { "pickDraw" , "set picking draw" }, @@ -576,6 +577,19 @@ { "pickSite" , "set picking site" }, { "pickSpin" , "set picking spin" }, + { "showMenu" , "showFile showIsosurface showMeasure showMo showModel " + + "showOrient showPDBHeader showSpacegroup showSymmetry extractMOL" }, + { "showFile", "show file"}, + { "showIsosurface", "show isosurface"}, + { "showMeasure", "show measure"}, + { "showMo", "show mo"}, + { "showModel", "show model"}, + { "showOrient", "show orientation"}, + { "showPDBHeader", "show PDBHeader"}, + { "showSpacegroup", "show spacegroup"}, + { "showSymmetry", "show symmetry"}, + { "extractMOL", "getproperty extractModel \"visible\" "}, + { "crystalMenu", "axesMenu bbcageMenu uccageMenu" }, { "axesMenu", "axesOff axesDotted axesByPixelMenu axesByAngstromMenu colorAxesMenu" }, @@ -658,7 +672,7 @@ { "rasmolColors", "set color rasmol" }, { "jmolColors", "set color jmol" }, - { "consoleMenu", "consoleOn consoleOff" }, + { "consoleMenu", "consoleOn consoleOff showMenu" }, { "consoleOn", "console" }, { "consoleOff", "console off" }, @@ -1121,8 +1135,19 @@ { "pickMolecule" , GT._("Select molecule") }, { "pickSite" , GT._("Select site") }, { "pickSpin" , GT._("Spin") }, + + { "showMenu" , GT._( "Show") }, + { "showFile", GT._("file")}, + { "showIsosurface", GT._( "isosurface")}, + { "showMeasure", GT._("measure")}, + { "showMo", GT._("molecular orbital")}, + { "showModel", GT._("model")}, + { "showOrient", GT._("orientation")}, + { "showPDBHeader", GT._("PDBHeader")}, + { "showSpacegroup", GT._("spacegroup")}, + { "showSymmetry", GT._("symmetry")}, + { "extractMOL", GT._("extract MOL data")}, - { "crystalMenu", GT._("Crystal") }, { "axesMenu", GT._("Axes") }, @@ -1195,7 +1220,7 @@ { "colorUccageHotPink", GT._("Hot Pink") }, { "optionsMenu", GT._("Options") }, - { "showSelectionsCheckbox", GT._("Show Selection Halos" ) }, + { "showSelectionsCheckbox", GT._("Show Selected Atoms" ) }, { "showHydrogensCheckbox", GT._("Show Hydrogens") }, { "showMeasurementsCheckbox", GT._("Show Measurements") }, { "perspectiveDepthCheckbox", GT._("Perspective Depth") }, Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-18 03:07:29 UTC (rev 5587) +++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-18 03:39:23 UTC (rev 5588) @@ -3637,7 +3637,6 @@ switch (statement[2].tok) { case Token.on: case Token.selected: - viewer.loadShape(JmolConstants.SHAPE_HALOS); showHalo = true; case Token.off: case Token.none: Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2006-09-18 03:07:29 UTC (rev 5587) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2006-09-18 03:39:23 UTC (rev 5588) @@ -2756,6 +2756,7 @@ } public void setSelectionHaloEnabled(boolean selectionHaloEnabled) { + loadShape(JmolConstants.SHAPE_HALOS); modelManager.setSelectionHaloEnabled(selectionHaloEnabled); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2006-09-18 20:54:27
|
Revision: 5598 http://svn.sourceforge.net/jmol/?rev=5598&view=rev Author: nicove Date: 2006-09-18 13:54:02 -0700 (Mon, 18 Sep 2006) Log Message: ----------- Fix PickingManager text for translation Modified Paths: -------------- trunk/Jmol/src/org/jmol/translation/Jmol/Jmol.pot trunk/Jmol/src/org/jmol/translation/Jmol/ca.po trunk/Jmol/src/org/jmol/translation/Jmol/de.po trunk/Jmol/src/org/jmol/translation/Jmol/es.po trunk/Jmol/src/org/jmol/translation/Jmol/et.po trunk/Jmol/src/org/jmol/translation/Jmol/fr.po trunk/Jmol/src/org/jmol/translation/Jmol/nl.po trunk/Jmol/src/org/jmol/translation/Jmol/pt.po trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po trunk/Jmol/src/org/jmol/viewer/PickingManager.java Modified: trunk/Jmol/src/org/jmol/translation/Jmol/Jmol.pot =================================================================== --- trunk/Jmol/src/org/jmol/translation/Jmol/Jmol.pot 2006-09-18 18:36:17 UTC (rev 5597) +++ trunk/Jmol/src/org/jmol/translation/Jmol/Jmol.pot 2006-09-18 20:54:02 UTC (rev 5598) @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: PACKAGE VERSION\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-15 23:16+0200\n" +"POT-Creation-Date: 2006-09-18 22:49+0200\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n" "Language-Team: LANGUAGE <LL...@li...>\n" @@ -16,15 +16,15 @@ "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" -#: org/jmol/viewer/PickingManager.java:165 -msgid "pick " +#: org/jmol/viewer/PickingManager.java:167 +msgid "pick one more atoms in order to spin the model around an axis" msgstr "" -#: org/jmol/viewer/PickingManager.java:167 -msgid " atoms in order to spin the model around an axis" +#: org/jmol/viewer/PickingManager.java:168 +msgid "pick two atoms in order to spin the model around an axis" msgstr "" -#: org/jmol/viewer/PickingManager.java:214 +#: org/jmol/viewer/PickingManager.java:229 msgid "atoms selected" msgstr "" @@ -220,7 +220,7 @@ msgstr "" #: org/openscience/jmol/app/GuiMap.java:56 -#: org/openscience/jmol/app/ScriptWindow.java:82 +#: org/openscience/jmol/app/ScriptWindow.java:83 msgid "Close" msgstr "" @@ -565,7 +565,7 @@ msgstr "" #: org/openscience/jmol/app/GuiMap.java:157 -#: org/openscience/jmol/app/ScriptWindow.java:63 +#: org/openscience/jmol/app/ScriptWindow.java:64 msgid "Jmol Script Console" msgstr "" @@ -731,7 +731,7 @@ msgstr "" #: org/openscience/jmol/app/Jmol.java:476 -#: org/openscience/jmol/app/ScriptWindow.java:95 +#: org/openscience/jmol/app/ScriptWindow.java:96 msgid "Clear" msgstr "" @@ -747,19 +747,19 @@ msgid "Macros" msgstr "" -#: org/openscience/jmol/app/Jmol.java:1119 +#: org/openscience/jmol/app/Jmol.java:1120 msgid "Open URL" msgstr "" -#: org/openscience/jmol/app/Jmol.java:1120 +#: org/openscience/jmol/app/Jmol.java:1121 msgid "Enter URL of molecular model" msgstr "" -#: org/openscience/jmol/app/Jmol.java:1207 +#: org/openscience/jmol/app/Jmol.java:1208 msgid "IO Exception:" msgstr "" -#: org/openscience/jmol/app/Jmol.java:1379 +#: org/openscience/jmol/app/Jmol.java:1380 msgid "File not loaded" msgstr "" @@ -1064,15 +1064,15 @@ msgid "Open" msgstr "" -#: org/openscience/jmol/app/ScriptWindow.java:86 +#: org/openscience/jmol/app/ScriptWindow.java:87 msgid "Run" msgstr "" -#: org/openscience/jmol/app/ScriptWindow.java:90 +#: org/openscience/jmol/app/ScriptWindow.java:91 msgid "Halt" msgstr "" -#: org/openscience/jmol/app/ScriptWindow.java:99 +#: org/openscience/jmol/app/ScriptWindow.java:100 msgid "Help" msgstr "" Modified: trunk/Jmol/src/org/jmol/translation/Jmol/ca.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/Jmol/ca.po 2006-09-18 18:36:17 UTC (rev 5597) +++ trunk/Jmol/src/org/jmol/translation/Jmol/ca.po 2006-09-18 20:54:02 UTC (rev 5598) @@ -7,7 +7,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-15 23:16+0200\n" +"POT-Creation-Date: 2006-09-18 22:49+0200\n" "PO-Revision-Date: 2006-01-30 03:35+0100\n" "Last-Translator: Toni Hermoso Pulido <to...@so...>\n" "Language-Team: Catalan <jmo...@li...>\n" @@ -17,15 +17,15 @@ "X-Poedit-Language: Catalan\n" "X-Poedit-Country: ANDORRA\n" -#: org/jmol/viewer/PickingManager.java:165 -msgid "pick " +#: org/jmol/viewer/PickingManager.java:167 +msgid "pick one more atoms in order to spin the model around an axis" msgstr "" -#: org/jmol/viewer/PickingManager.java:167 -msgid " atoms in order to spin the model around an axis" +#: org/jmol/viewer/PickingManager.java:168 +msgid "pick two atoms in order to spin the model around an axis" msgstr "" -#: org/jmol/viewer/PickingManager.java:214 +#: org/jmol/viewer/PickingManager.java:229 #, fuzzy msgid "atoms selected" msgstr "conjunt d'àtoms" @@ -223,7 +223,7 @@ msgstr "Im&primeix..." #: org/openscience/jmol/app/GuiMap.java:56 -#: org/openscience/jmol/app/ScriptWindow.java:82 +#: org/openscience/jmol/app/ScriptWindow.java:83 msgid "Close" msgstr "Tanca" @@ -568,7 +568,7 @@ msgstr "Novetats" #: org/openscience/jmol/app/GuiMap.java:157 -#: org/openscience/jmol/app/ScriptWindow.java:63 +#: org/openscience/jmol/app/ScriptWindow.java:64 #, fuzzy msgid "Jmol Script Console" msgstr "Consola del Jmol" @@ -741,7 +741,7 @@ msgstr "Consola del Jmol" #: org/openscience/jmol/app/Jmol.java:476 -#: org/openscience/jmol/app/ScriptWindow.java:95 +#: org/openscience/jmol/app/ScriptWindow.java:96 msgid "Clear" msgstr "Neteja" @@ -757,19 +757,19 @@ msgid "Macros" msgstr "Macroinstruccions" -#: org/openscience/jmol/app/Jmol.java:1119 +#: org/openscience/jmol/app/Jmol.java:1120 msgid "Open URL" msgstr "Obre un URL" -#: org/openscience/jmol/app/Jmol.java:1120 +#: org/openscience/jmol/app/Jmol.java:1121 msgid "Enter URL of molecular model" msgstr "Introduïu l'URL d'un model molecular" -#: org/openscience/jmol/app/Jmol.java:1207 +#: org/openscience/jmol/app/Jmol.java:1208 msgid "IO Exception:" msgstr "S'ha produït una excepció IO:" -#: org/openscience/jmol/app/Jmol.java:1379 +#: org/openscience/jmol/app/Jmol.java:1380 msgid "File not loaded" msgstr "No s'ha carregat el fitxer" @@ -1076,15 +1076,15 @@ msgid "Open" msgstr "Obre" -#: org/openscience/jmol/app/ScriptWindow.java:86 +#: org/openscience/jmol/app/ScriptWindow.java:87 msgid "Run" msgstr "Executa" -#: org/openscience/jmol/app/ScriptWindow.java:90 +#: org/openscience/jmol/app/ScriptWindow.java:91 msgid "Halt" msgstr "Para" -#: org/openscience/jmol/app/ScriptWindow.java:99 +#: org/openscience/jmol/app/ScriptWindow.java:100 msgid "Help" msgstr "Ajuda" Modified: trunk/Jmol/src/org/jmol/translation/Jmol/de.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/Jmol/de.po 2006-09-18 18:36:17 UTC (rev 5597) +++ trunk/Jmol/src/org/jmol/translation/Jmol/de.po 2006-09-18 20:54:02 UTC (rev 5598) @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Jmol 10\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-15 23:16+0200\n" +"POT-Creation-Date: 2006-09-18 22:49+0200\n" "PO-Revision-Date: 2006-04-14 18:00+0100\n" "Last-Translator: Sebastian Lisken <sebastianlisken at users.sourceforge." "net>\n" @@ -18,15 +18,15 @@ "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" -#: org/jmol/viewer/PickingManager.java:165 -msgid "pick " +#: org/jmol/viewer/PickingManager.java:167 +msgid "pick one more atoms in order to spin the model around an axis" msgstr "" -#: org/jmol/viewer/PickingManager.java:167 -msgid " atoms in order to spin the model around an axis" +#: org/jmol/viewer/PickingManager.java:168 +msgid "pick two atoms in order to spin the model around an axis" msgstr "" -#: org/jmol/viewer/PickingManager.java:214 +#: org/jmol/viewer/PickingManager.java:229 #, fuzzy msgid "atoms selected" msgstr "Atome ausgewählt" @@ -224,7 +224,7 @@ msgstr "&Drucken..." #: org/openscience/jmol/app/GuiMap.java:56 -#: org/openscience/jmol/app/ScriptWindow.java:82 +#: org/openscience/jmol/app/ScriptWindow.java:83 msgid "Close" msgstr "Schließen" @@ -569,7 +569,7 @@ msgstr "Neuigkeiten" #: org/openscience/jmol/app/GuiMap.java:157 -#: org/openscience/jmol/app/ScriptWindow.java:63 +#: org/openscience/jmol/app/ScriptWindow.java:64 #, fuzzy msgid "Jmol Script Console" msgstr "Jmol-Konsole" @@ -740,7 +740,7 @@ msgstr "Jmol-Konsole" #: org/openscience/jmol/app/Jmol.java:476 -#: org/openscience/jmol/app/ScriptWindow.java:95 +#: org/openscience/jmol/app/ScriptWindow.java:96 msgid "Clear" msgstr "Leeren" @@ -756,19 +756,19 @@ msgid "Macros" msgstr "Makros" -#: org/openscience/jmol/app/Jmol.java:1119 +#: org/openscience/jmol/app/Jmol.java:1120 msgid "Open URL" msgstr "URL öffnen" -#: org/openscience/jmol/app/Jmol.java:1120 +#: org/openscience/jmol/app/Jmol.java:1121 msgid "Enter URL of molecular model" msgstr "URL eines Molekül-Modells eingeben" -#: org/openscience/jmol/app/Jmol.java:1207 +#: org/openscience/jmol/app/Jmol.java:1208 msgid "IO Exception:" msgstr "IO-Fehler:" -#: org/openscience/jmol/app/Jmol.java:1379 +#: org/openscience/jmol/app/Jmol.java:1380 msgid "File not loaded" msgstr "Datei wurde nicht geladen" @@ -1077,15 +1077,15 @@ msgid "Open" msgstr "Öffnen" -#: org/openscience/jmol/app/ScriptWindow.java:86 +#: org/openscience/jmol/app/ScriptWindow.java:87 msgid "Run" msgstr "Ausführen" -#: org/openscience/jmol/app/ScriptWindow.java:90 +#: org/openscience/jmol/app/ScriptWindow.java:91 msgid "Halt" msgstr "Stoppen" -#: org/openscience/jmol/app/ScriptWindow.java:99 +#: org/openscience/jmol/app/ScriptWindow.java:100 msgid "Help" msgstr "Hilfe" Modified: trunk/Jmol/src/org/jmol/translation/Jmol/es.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/Jmol/es.po 2006-09-18 18:36:17 UTC (rev 5597) +++ trunk/Jmol/src/org/jmol/translation/Jmol/es.po 2006-09-18 20:54:02 UTC (rev 5598) @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Jmol 10\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-15 23:16+0200\n" +"POT-Creation-Date: 2006-09-18 22:49+0200\n" "PO-Revision-Date: 2006-03-24 20:08+0100\n" "Last-Translator: Angel Herráez <ang...@ua...>\n" "Language-Team: Spanish <Jmo...@li...>\n" @@ -19,15 +19,17 @@ "X-Poedit-Country: SPAIN\n" "X-Poedit-SourceCharset: utf-8\n" -#: org/jmol/viewer/PickingManager.java:165 -msgid "pick " -msgstr "elige" - #: org/jmol/viewer/PickingManager.java:167 -msgid " atoms in order to spin the model around an axis" +#, fuzzy +msgid "pick one more atoms in order to spin the model around an axis" msgstr " átomos para que el modelo gire en torno a un eje" -#: org/jmol/viewer/PickingManager.java:214 +#: org/jmol/viewer/PickingManager.java:168 +#, fuzzy +msgid "pick two atoms in order to spin the model around an axis" +msgstr " átomos para que el modelo gire en torno a un eje" + +#: org/jmol/viewer/PickingManager.java:229 msgid "atoms selected" msgstr "átomos seleccionados" @@ -223,7 +225,7 @@ msgstr "&Imprimir..." #: org/openscience/jmol/app/GuiMap.java:56 -#: org/openscience/jmol/app/ScriptWindow.java:82 +#: org/openscience/jmol/app/ScriptWindow.java:83 msgid "Close" msgstr "Cerrar" @@ -568,7 +570,7 @@ msgstr "Novedades" #: org/openscience/jmol/app/GuiMap.java:157 -#: org/openscience/jmol/app/ScriptWindow.java:63 +#: org/openscience/jmol/app/ScriptWindow.java:64 #, fuzzy msgid "Jmol Script Console" msgstr "Consola de Jmol" @@ -737,7 +739,7 @@ msgstr "Consola de Jmol" #: org/openscience/jmol/app/Jmol.java:476 -#: org/openscience/jmol/app/ScriptWindow.java:95 +#: org/openscience/jmol/app/ScriptWindow.java:96 msgid "Clear" msgstr "Limpiar" @@ -753,19 +755,19 @@ msgid "Macros" msgstr "Macros" -#: org/openscience/jmol/app/Jmol.java:1119 +#: org/openscience/jmol/app/Jmol.java:1120 msgid "Open URL" msgstr "Abrir URL" -#: org/openscience/jmol/app/Jmol.java:1120 +#: org/openscience/jmol/app/Jmol.java:1121 msgid "Enter URL of molecular model" msgstr "Escribe la URL del modelo molecular" -#: org/openscience/jmol/app/Jmol.java:1207 +#: org/openscience/jmol/app/Jmol.java:1208 msgid "IO Exception:" msgstr "Error de entrada/salida:" -#: org/openscience/jmol/app/Jmol.java:1379 +#: org/openscience/jmol/app/Jmol.java:1380 msgid "File not loaded" msgstr "El archivo no se ha cargado" @@ -1075,15 +1077,15 @@ msgid "Open" msgstr "Abrir" -#: org/openscience/jmol/app/ScriptWindow.java:86 +#: org/openscience/jmol/app/ScriptWindow.java:87 msgid "Run" msgstr "Ejecutar" -#: org/openscience/jmol/app/ScriptWindow.java:90 +#: org/openscience/jmol/app/ScriptWindow.java:91 msgid "Halt" msgstr "Detener" -#: org/openscience/jmol/app/ScriptWindow.java:99 +#: org/openscience/jmol/app/ScriptWindow.java:100 msgid "Help" msgstr "Ayuda" @@ -1095,6 +1097,9 @@ msgid "What's New in Jmol" msgstr "Novedades en Jmol" +#~ msgid "pick " +#~ msgstr "elige" + #~ msgid "Rasmol Scripts" #~ msgstr "Guiones de Rasmol" Modified: trunk/Jmol/src/org/jmol/translation/Jmol/et.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/Jmol/et.po 2006-09-18 18:36:17 UTC (rev 5597) +++ trunk/Jmol/src/org/jmol/translation/Jmol/et.po 2006-09-18 20:54:02 UTC (rev 5598) @@ -6,7 +6,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-15 23:16+0200\n" +"POT-Creation-Date: 2006-09-18 22:49+0200\n" "PO-Revision-Date: 2006-03-17 20:19+0100\n" "Last-Translator: Ivo Sarak <iv...@ra...>\n" "Language-Team: Estonian <Jmo...@li...>\n" @@ -17,15 +17,15 @@ "X-Poedit-Country: Estonia\n" "X-Poedit-Basepath: ../../../..\n" -#: org/jmol/viewer/PickingManager.java:165 -msgid "pick " +#: org/jmol/viewer/PickingManager.java:167 +msgid "pick one more atoms in order to spin the model around an axis" msgstr "" -#: org/jmol/viewer/PickingManager.java:167 -msgid " atoms in order to spin the model around an axis" +#: org/jmol/viewer/PickingManager.java:168 +msgid "pick two atoms in order to spin the model around an axis" msgstr "" -#: org/jmol/viewer/PickingManager.java:214 +#: org/jmol/viewer/PickingManager.java:229 #, fuzzy msgid "atoms selected" msgstr "atom set" @@ -223,7 +223,7 @@ msgstr "&Prindi..." #: org/openscience/jmol/app/GuiMap.java:56 -#: org/openscience/jmol/app/ScriptWindow.java:82 +#: org/openscience/jmol/app/ScriptWindow.java:83 msgid "Close" msgstr "Sulge" @@ -568,7 +568,7 @@ msgstr "Mida on uut?" #: org/openscience/jmol/app/GuiMap.java:157 -#: org/openscience/jmol/app/ScriptWindow.java:63 +#: org/openscience/jmol/app/ScriptWindow.java:64 #, fuzzy msgid "Jmol Script Console" msgstr "Jmol konsool" @@ -737,7 +737,7 @@ msgstr "Jmol konsool" #: org/openscience/jmol/app/Jmol.java:476 -#: org/openscience/jmol/app/ScriptWindow.java:95 +#: org/openscience/jmol/app/ScriptWindow.java:96 msgid "Clear" msgstr "Puhasta" @@ -753,19 +753,19 @@ msgid "Macros" msgstr "Makrod" -#: org/openscience/jmol/app/Jmol.java:1119 +#: org/openscience/jmol/app/Jmol.java:1120 msgid "Open URL" msgstr "Ava URL" -#: org/openscience/jmol/app/Jmol.java:1120 +#: org/openscience/jmol/app/Jmol.java:1121 msgid "Enter URL of molecular model" msgstr "Sisesta molekulaarmudeli URL" -#: org/openscience/jmol/app/Jmol.java:1207 +#: org/openscience/jmol/app/Jmol.java:1208 msgid "IO Exception:" msgstr "IO eriolukord:" -#: org/openscience/jmol/app/Jmol.java:1379 +#: org/openscience/jmol/app/Jmol.java:1380 msgid "File not loaded" msgstr "Fail ei ole loetud" @@ -1071,15 +1071,15 @@ msgid "Open" msgstr "Ava" -#: org/openscience/jmol/app/ScriptWindow.java:86 +#: org/openscience/jmol/app/ScriptWindow.java:87 msgid "Run" msgstr "Käivita" -#: org/openscience/jmol/app/ScriptWindow.java:90 +#: org/openscience/jmol/app/ScriptWindow.java:91 msgid "Halt" msgstr "Seiska" -#: org/openscience/jmol/app/ScriptWindow.java:99 +#: org/openscience/jmol/app/ScriptWindow.java:100 msgid "Help" msgstr "Abi" Modified: trunk/Jmol/src/org/jmol/translation/Jmol/fr.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/Jmol/fr.po 2006-09-18 18:36:17 UTC (rev 5597) +++ trunk/Jmol/src/org/jmol/translation/Jmol/fr.po 2006-09-18 20:54:02 UTC (rev 5598) @@ -7,7 +7,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-15 23:16+0200\n" +"POT-Creation-Date: 2006-09-18 22:49+0200\n" "PO-Revision-Date: 2006-02-19 17:18+0100\n" "Last-Translator: Nicolas Vervelle <ni...@us...>\n" "Language-Team: French <Jmo...@li...>\n" @@ -18,15 +18,15 @@ "X-Poedit-Country: France\n" "X-Poedit-Basepath: ../../../..\n" -#: org/jmol/viewer/PickingManager.java:165 -msgid "pick " +#: org/jmol/viewer/PickingManager.java:167 +msgid "pick one more atoms in order to spin the model around an axis" msgstr "" -#: org/jmol/viewer/PickingManager.java:167 -msgid " atoms in order to spin the model around an axis" +#: org/jmol/viewer/PickingManager.java:168 +msgid "pick two atoms in order to spin the model around an axis" msgstr "" -#: org/jmol/viewer/PickingManager.java:214 +#: org/jmol/viewer/PickingManager.java:229 #, fuzzy msgid "atoms selected" msgstr "groupe d'atomes" @@ -223,7 +223,7 @@ msgstr "Im&primer..." #: org/openscience/jmol/app/GuiMap.java:56 -#: org/openscience/jmol/app/ScriptWindow.java:82 +#: org/openscience/jmol/app/ScriptWindow.java:83 msgid "Close" msgstr "Fermer" @@ -568,7 +568,7 @@ msgstr "Les Nouveautés" #: org/openscience/jmol/app/GuiMap.java:157 -#: org/openscience/jmol/app/ScriptWindow.java:63 +#: org/openscience/jmol/app/ScriptWindow.java:64 #, fuzzy msgid "Jmol Script Console" msgstr "Console Jmol" @@ -739,7 +739,7 @@ msgstr "Console Jmol" #: org/openscience/jmol/app/Jmol.java:476 -#: org/openscience/jmol/app/ScriptWindow.java:95 +#: org/openscience/jmol/app/ScriptWindow.java:96 msgid "Clear" msgstr "Effacer" @@ -755,19 +755,19 @@ msgid "Macros" msgstr "Macros" -#: org/openscience/jmol/app/Jmol.java:1119 +#: org/openscience/jmol/app/Jmol.java:1120 msgid "Open URL" msgstr "Ouvrir une URL" -#: org/openscience/jmol/app/Jmol.java:1120 +#: org/openscience/jmol/app/Jmol.java:1121 msgid "Enter URL of molecular model" msgstr "Saisissez l'URL d'un modèle moléculaire" -#: org/openscience/jmol/app/Jmol.java:1207 +#: org/openscience/jmol/app/Jmol.java:1208 msgid "IO Exception:" msgstr "Exception E/S!" -#: org/openscience/jmol/app/Jmol.java:1379 +#: org/openscience/jmol/app/Jmol.java:1380 msgid "File not loaded" msgstr "Fichier non chargé" @@ -1077,15 +1077,15 @@ msgid "Open" msgstr "Ouvrir" -#: org/openscience/jmol/app/ScriptWindow.java:86 +#: org/openscience/jmol/app/ScriptWindow.java:87 msgid "Run" msgstr "Exécuter" -#: org/openscience/jmol/app/ScriptWindow.java:90 +#: org/openscience/jmol/app/ScriptWindow.java:91 msgid "Halt" msgstr "Arrêter" -#: org/openscience/jmol/app/ScriptWindow.java:99 +#: org/openscience/jmol/app/ScriptWindow.java:100 msgid "Help" msgstr "?" Modified: trunk/Jmol/src/org/jmol/translation/Jmol/nl.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/Jmol/nl.po 2006-09-18 18:36:17 UTC (rev 5597) +++ trunk/Jmol/src/org/jmol/translation/Jmol/nl.po 2006-09-18 20:54:02 UTC (rev 5598) @@ -7,7 +7,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-15 23:16+0200\n" +"POT-Creation-Date: 2006-09-18 22:49+0200\n" "PO-Revision-Date: 2006-04-09 11:48+0100\n" "Last-Translator: Egon Willighagen <eg...@jm...>\n" "Language-Team: Dutch <jmo...@li...>\n" @@ -17,15 +17,15 @@ "X-Poedit-Language: Dutch\n" "X-Poedit-Country: The Netherlands\n" -#: org/jmol/viewer/PickingManager.java:165 -msgid "pick " +#: org/jmol/viewer/PickingManager.java:167 +msgid "pick one more atoms in order to spin the model around an axis" msgstr "" -#: org/jmol/viewer/PickingManager.java:167 -msgid " atoms in order to spin the model around an axis" +#: org/jmol/viewer/PickingManager.java:168 +msgid "pick two atoms in order to spin the model around an axis" msgstr "" -#: org/jmol/viewer/PickingManager.java:214 +#: org/jmol/viewer/PickingManager.java:229 #, fuzzy msgid "atoms selected" msgstr "atoomset" @@ -223,7 +223,7 @@ msgstr "&Printen..." #: org/openscience/jmol/app/GuiMap.java:56 -#: org/openscience/jmol/app/ScriptWindow.java:82 +#: org/openscience/jmol/app/ScriptWindow.java:83 msgid "Close" msgstr "Sluiten" @@ -568,7 +568,7 @@ msgstr "Wat is Nieuw" #: org/openscience/jmol/app/GuiMap.java:157 -#: org/openscience/jmol/app/ScriptWindow.java:63 +#: org/openscience/jmol/app/ScriptWindow.java:64 #, fuzzy msgid "Jmol Script Console" msgstr "Jmol Console" @@ -737,7 +737,7 @@ msgstr "Jmol Console" #: org/openscience/jmol/app/Jmol.java:476 -#: org/openscience/jmol/app/ScriptWindow.java:95 +#: org/openscience/jmol/app/ScriptWindow.java:96 msgid "Clear" msgstr "Wissen" @@ -753,19 +753,19 @@ msgid "Macros" msgstr "Macro's" -#: org/openscience/jmol/app/Jmol.java:1119 +#: org/openscience/jmol/app/Jmol.java:1120 msgid "Open URL" msgstr "Open URL" -#: org/openscience/jmol/app/Jmol.java:1120 +#: org/openscience/jmol/app/Jmol.java:1121 msgid "Enter URL of molecular model" msgstr "Geef URL van molecuulmodel" -#: org/openscience/jmol/app/Jmol.java:1207 +#: org/openscience/jmol/app/Jmol.java:1208 msgid "IO Exception:" msgstr "IO-fout:" -#: org/openscience/jmol/app/Jmol.java:1379 +#: org/openscience/jmol/app/Jmol.java:1380 msgid "File not loaded" msgstr "Bestand niet geladen" @@ -1072,15 +1072,15 @@ msgid "Open" msgstr "Open" -#: org/openscience/jmol/app/ScriptWindow.java:86 +#: org/openscience/jmol/app/ScriptWindow.java:87 msgid "Run" msgstr "Starten" -#: org/openscience/jmol/app/ScriptWindow.java:90 +#: org/openscience/jmol/app/ScriptWindow.java:91 msgid "Halt" msgstr "Stoppen" -#: org/openscience/jmol/app/ScriptWindow.java:99 +#: org/openscience/jmol/app/ScriptWindow.java:100 msgid "Help" msgstr "Help" Modified: trunk/Jmol/src/org/jmol/translation/Jmol/pt.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/Jmol/pt.po 2006-09-18 18:36:17 UTC (rev 5597) +++ trunk/Jmol/src/org/jmol/translation/Jmol/pt.po 2006-09-18 20:54:02 UTC (rev 5598) @@ -6,7 +6,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-15 23:16+0200\n" +"POT-Creation-Date: 2006-09-18 22:49+0200\n" "PO-Revision-Date: 2005-12-20 07:33-0000\n" "Last-Translator: Metro <por...@gm...>\n" "Language-Team: Portugal@Folding <Jmo...@li...>\n" @@ -17,15 +17,15 @@ "X-Poedit-Country: Portugal\n" "X-Poedit-Basepath: ../../../..\n" -#: org/jmol/viewer/PickingManager.java:165 -msgid "pick " +#: org/jmol/viewer/PickingManager.java:167 +msgid "pick one more atoms in order to spin the model around an axis" msgstr "" -#: org/jmol/viewer/PickingManager.java:167 -msgid " atoms in order to spin the model around an axis" +#: org/jmol/viewer/PickingManager.java:168 +msgid "pick two atoms in order to spin the model around an axis" msgstr "" -#: org/jmol/viewer/PickingManager.java:214 +#: org/jmol/viewer/PickingManager.java:229 #, fuzzy msgid "atoms selected" msgstr "Grupo de átomos" @@ -223,7 +223,7 @@ msgstr "&Print..." #: org/openscience/jmol/app/GuiMap.java:56 -#: org/openscience/jmol/app/ScriptWindow.java:82 +#: org/openscience/jmol/app/ScriptWindow.java:83 msgid "Close" msgstr "Fechar" @@ -568,7 +568,7 @@ msgstr "O que há de novo" #: org/openscience/jmol/app/GuiMap.java:157 -#: org/openscience/jmol/app/ScriptWindow.java:63 +#: org/openscience/jmol/app/ScriptWindow.java:64 #, fuzzy msgid "Jmol Script Console" msgstr "Consola Jmol" @@ -737,7 +737,7 @@ msgstr "Consola Jmol" #: org/openscience/jmol/app/Jmol.java:476 -#: org/openscience/jmol/app/ScriptWindow.java:95 +#: org/openscience/jmol/app/ScriptWindow.java:96 msgid "Clear" msgstr "Limpar" @@ -753,19 +753,19 @@ msgid "Macros" msgstr "Macros" -#: org/openscience/jmol/app/Jmol.java:1119 +#: org/openscience/jmol/app/Jmol.java:1120 msgid "Open URL" msgstr "Abrir URL" -#: org/openscience/jmol/app/Jmol.java:1120 +#: org/openscience/jmol/app/Jmol.java:1121 msgid "Enter URL of molecular model" msgstr "Escrever URL de um modelo molecular" -#: org/openscience/jmol/app/Jmol.java:1207 +#: org/openscience/jmol/app/Jmol.java:1208 msgid "IO Exception:" msgstr "Excepção IO:" -#: org/openscience/jmol/app/Jmol.java:1379 +#: org/openscience/jmol/app/Jmol.java:1380 msgid "File not loaded" msgstr "Ficheiro não carregado" @@ -1073,15 +1073,15 @@ msgid "Open" msgstr "Abrir" -#: org/openscience/jmol/app/ScriptWindow.java:86 +#: org/openscience/jmol/app/ScriptWindow.java:87 msgid "Run" msgstr "Executar" -#: org/openscience/jmol/app/ScriptWindow.java:90 +#: org/openscience/jmol/app/ScriptWindow.java:91 msgid "Halt" msgstr "Parar" -#: org/openscience/jmol/app/ScriptWindow.java:99 +#: org/openscience/jmol/app/ScriptWindow.java:100 msgid "Help" msgstr "Ajuda" Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot 2006-09-18 18:36:17 UTC (rev 5597) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot 2006-09-18 20:54:02 UTC (rev 5598) @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: PACKAGE VERSION\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 20:08+0200\n" +"POT-Creation-Date: 2006-09-18 22:49+0200\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n" "Language-Team: LANGUAGE <LL...@li...>\n" @@ -1060,12 +1060,12 @@ msgid "Translations" msgstr "" -#: org/jmol/viewer/PickingManager.java:166 -msgid "pick " +#: org/jmol/viewer/PickingManager.java:167 +msgid "pick one more atoms in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:168 -msgid " atoms in order to spin the model around an axis" +msgid "pick two atoms in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:229 Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po 2006-09-18 18:36:17 UTC (rev 5597) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po 2006-09-18 20:54:02 UTC (rev 5598) @@ -6,7 +6,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 20:08+0200\n" +"POT-Creation-Date: 2006-09-18 22:49+0200\n" "PO-Revision-Date: 2006-01-30 03:37+0100\n" "Last-Translator: Toni Hermoso Pulido <to...@so...>\n" "Language-Team: Catalan <Jmo...@li...>\n" @@ -1078,12 +1078,12 @@ msgid "Translations" msgstr "Traduccions" -#: org/jmol/viewer/PickingManager.java:166 -msgid "pick " +#: org/jmol/viewer/PickingManager.java:167 +msgid "pick one more atoms in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:168 -msgid " atoms in order to spin the model around an axis" +msgid "pick two atoms in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:229 Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po 2006-09-18 18:36:17 UTC (rev 5597) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po 2006-09-18 20:54:02 UTC (rev 5598) @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: JmolApplet 10\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 20:08+0200\n" +"POT-Creation-Date: 2006-09-18 22:49+0200\n" "PO-Revision-Date: 2006-04-14 18:00+0100\n" "Last-Translator: Sebastian Lisken <sebastianlisken at users.sourceforge." "net>\n" @@ -1078,12 +1078,12 @@ msgid "Translations" msgstr "Übersetzungen" -#: org/jmol/viewer/PickingManager.java:166 -msgid "pick " +#: org/jmol/viewer/PickingManager.java:167 +msgid "pick one more atoms in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:168 -msgid " atoms in order to spin the model around an axis" +msgid "pick two atoms in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:229 Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po 2006-09-18 18:36:17 UTC (rev 5597) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po 2006-09-18 20:54:02 UTC (rev 5598) @@ -2,7 +2,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 20:08+0200\n" +"POT-Creation-Date: 2006-09-18 22:49+0200\n" "PO-Revision-Date: 2006-04-14 17:48+0100\n" "Last-Translator: Angel Herráez <ang...@ua...>\n" "Language-Team: Spanish <Jmo...@li...>\n" @@ -1077,12 +1077,14 @@ msgid "Translations" msgstr "Traducciones" -#: org/jmol/viewer/PickingManager.java:166 -msgid "pick " -msgstr "elige" +#: org/jmol/viewer/PickingManager.java:167 +#, fuzzy +msgid "pick one more atoms in order to spin the model around an axis" +msgstr " átomos para que el modelo gire en torno a un eje" #: org/jmol/viewer/PickingManager.java:168 -msgid " atoms in order to spin the model around an axis" +#, fuzzy +msgid "pick two atoms in order to spin the model around an axis" msgstr " átomos para que el modelo gire en torno a un eje" #: org/jmol/viewer/PickingManager.java:229 @@ -1093,6 +1095,9 @@ msgid "Jmol executing script ..." msgstr "Jmol ejecutando un guión..." +#~ msgid "pick " +#~ msgstr "elige" + #~ msgid "Nanometers" #~ msgstr "Nanómetros" Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po 2006-09-18 18:36:17 UTC (rev 5597) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po 2006-09-18 20:54:02 UTC (rev 5598) @@ -6,7 +6,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 20:08+0200\n" +"POT-Creation-Date: 2006-09-18 22:49+0200\n" "PO-Revision-Date: 2006-03-17 20:19+0100\n" "Last-Translator: Ivo Sarak <iv...@ra...>\n" "Language-Team: Estonian <Jmo...@li...>\n" @@ -1079,12 +1079,12 @@ msgid "Translations" msgstr "Tõlked" -#: org/jmol/viewer/PickingManager.java:166 -msgid "pick " +#: org/jmol/viewer/PickingManager.java:167 +msgid "pick one more atoms in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:168 -msgid " atoms in order to spin the model around an axis" +msgid "pick two atoms in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:229 Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po 2006-09-18 18:36:17 UTC (rev 5597) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po 2006-09-18 20:54:02 UTC (rev 5598) @@ -7,7 +7,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 20:08+0200\n" +"POT-Creation-Date: 2006-09-18 22:49+0200\n" "PO-Revision-Date: 2006-04-14 18:11+0100\n" "Last-Translator: Nicolas Vervelle <ni...@us...>\n" "Language-Team: French <Jmo...@li...>\n" @@ -1083,12 +1083,12 @@ msgid "Translations" msgstr "Traductions" -#: org/jmol/viewer/PickingManager.java:166 -msgid "pick " +#: org/jmol/viewer/PickingManager.java:167 +msgid "pick one more atoms in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:168 -msgid " atoms in order to spin the model around an axis" +msgid "pick two atoms in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:229 Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po 2006-09-18 18:36:17 UTC (rev 5597) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po 2006-09-18 20:54:02 UTC (rev 5598) @@ -7,7 +7,7 @@ msgstr "" "Project-Id-Version: nl\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 20:08+0200\n" +"POT-Creation-Date: 2006-09-18 22:49+0200\n" "PO-Revision-Date: 2006-09-18 20:32+0100\n" "Last-Translator: Egon Willighagen <eg...@jm...>\n" "Language-Team: Nederlands <kde...@kd...>\n" @@ -30,7 +30,8 @@ msgstr "" "Jmol Applet versie {0} {1}.\n" " \n" -"Onderdeel van het OpenScience project. Zie http://www.jmol.org voor meer informatie." +"Onderdeel van het OpenScience project. Zie http://www.jmol.org voor meer " +"informatie." #: org/jmol/applet/Jmol.java:712 msgid "File Error:" @@ -1066,12 +1067,14 @@ msgid "Translations" msgstr "Translaties" -#: org/jmol/viewer/PickingManager.java:166 -msgid "pick " -msgstr "selecteer" +#: org/jmol/viewer/PickingManager.java:167 +#, fuzzy +msgid "pick one more atoms in order to spin the model around an axis" +msgstr "atomen in volgorde om het model rond een as te laten spinnen" #: org/jmol/viewer/PickingManager.java:168 -msgid " atoms in order to spin the model around an axis" +#, fuzzy +msgid "pick two atoms in order to spin the model around an axis" msgstr "atomen in volgorde om het model rond een as te laten spinnen" #: org/jmol/viewer/PickingManager.java:229 @@ -1082,28 +1085,39 @@ msgid "Jmol executing script ..." msgstr "Jmol voert script uit ..." +#~ msgid "pick " +#~ msgstr "selecteer" + #~ msgid "Nanometers" #~ msgstr "Nanometers" + #~ msgid "Angstroms" #~ msgstr "Angstroms" + #~ msgid "Picometers" #~ msgstr "Picometers" + #~ msgid "Open" #~ msgstr "Openen" + #~ msgid "Close" #~ msgstr "Sluiten" + #~ msgid "Jmol Molecular Visualization http://www.jmol.org" #~ msgstr "Jmol Moleculaire Visualisatie http://www.jmol.org" + #~ msgid "Jmol script completed" #~ msgstr "Jmol script is klaar" + #~ msgid "Name hidden" #~ msgstr "Naam verborgen" + #~ msgid "Wireframe Rotation" #~ msgstr "Draadmodelrotatie" + #~ msgid "" #~ "Jmol Applet. Part of the OpenScience project. See http://www.jmol.org " #~ "for more information" #~ msgstr "" #~ "Jmol Applet. Onderdeel van het OpenScience project. Zie http://www.jmol." #~ "org voor meer informatie." - Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po 2006-09-18 18:36:17 UTC (rev 5597) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po 2006-09-18 20:54:02 UTC (rev 5598) @@ -6,7 +6,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 20:08+0200\n" +"POT-Creation-Date: 2006-09-18 22:49+0200\n" "PO-Revision-Date: 2005-12-20 07:44-0000\n" "Last-Translator: Metro <por...@gm...>\n" "Language-Team: Portugal@Folding <Jmo...@li...>\n" @@ -1078,12 +1078,12 @@ msgid "Translations" msgstr "" -#: org/jmol/viewer/PickingManager.java:166 -msgid "pick " +#: org/jmol/viewer/PickingManager.java:167 +msgid "pick one more atoms in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:168 -msgid " atoms in order to spin the model around an axis" +msgid "pick two atoms in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:229 Modified: trunk/Jmol/src/org/jmol/viewer/PickingManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/PickingManager.java 2006-09-18 18:36:17 UTC (rev 5597) +++ trunk/Jmol/src/org/jmol/viewer/PickingManager.java 2006-09-18 20:54:02 UTC (rev 5598) @@ -163,9 +163,9 @@ queueAtom(atomIndex); if (queuedAtomCount < 2) { viewer.setSpinOn(false); - viewer.scriptStatus(GT._("pick " - + (queuedAtomCount == 1 ? "one more" : "two ") - + " atoms in order to spin the model around an axis")); + viewer.scriptStatus(queuedAtomCount == 1 ? + GT._("pick one more atoms in order to spin the model around an axis") : + GT._("pick two atoms in order to spin the model around an axis")); break; } viewer This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2006-09-18 21:26:48
|
Revision: 5600 http://svn.sourceforge.net/jmol/?rev=5600&view=rev Author: nicove Date: 2006-09-18 14:26:27 -0700 (Mon, 18 Sep 2006) Log Message: ----------- Orthograph Modified Paths: -------------- trunk/Jmol/src/org/jmol/translation/Jmol/Jmol.pot trunk/Jmol/src/org/jmol/translation/Jmol/ca.po trunk/Jmol/src/org/jmol/translation/Jmol/de.po trunk/Jmol/src/org/jmol/translation/Jmol/es.po trunk/Jmol/src/org/jmol/translation/Jmol/et.po trunk/Jmol/src/org/jmol/translation/Jmol/fr.po trunk/Jmol/src/org/jmol/translation/Jmol/nl.po trunk/Jmol/src/org/jmol/translation/Jmol/pt.po trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po trunk/Jmol/src/org/jmol/viewer/PickingManager.java Modified: trunk/Jmol/src/org/jmol/translation/Jmol/Jmol.pot =================================================================== --- trunk/Jmol/src/org/jmol/translation/Jmol/Jmol.pot 2006-09-18 21:13:38 UTC (rev 5599) +++ trunk/Jmol/src/org/jmol/translation/Jmol/Jmol.pot 2006-09-18 21:26:27 UTC (rev 5600) @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: PACKAGE VERSION\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 22:49+0200\n" +"POT-Creation-Date: 2006-09-18 23:24+0200\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n" "Language-Team: LANGUAGE <LL...@li...>\n" @@ -17,7 +17,7 @@ "Content-Transfer-Encoding: 8bit\n" #: org/jmol/viewer/PickingManager.java:167 -msgid "pick one more atoms in order to spin the model around an axis" +msgid "pick one more atom in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:168 Modified: trunk/Jmol/src/org/jmol/translation/Jmol/ca.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/Jmol/ca.po 2006-09-18 21:13:38 UTC (rev 5599) +++ trunk/Jmol/src/org/jmol/translation/Jmol/ca.po 2006-09-18 21:26:27 UTC (rev 5600) @@ -7,7 +7,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 22:49+0200\n" +"POT-Creation-Date: 2006-09-18 23:24+0200\n" "PO-Revision-Date: 2006-01-30 03:35+0100\n" "Last-Translator: Toni Hermoso Pulido <to...@so...>\n" "Language-Team: Catalan <jmo...@li...>\n" @@ -18,7 +18,7 @@ "X-Poedit-Country: ANDORRA\n" #: org/jmol/viewer/PickingManager.java:167 -msgid "pick one more atoms in order to spin the model around an axis" +msgid "pick one more atom in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:168 Modified: trunk/Jmol/src/org/jmol/translation/Jmol/de.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/Jmol/de.po 2006-09-18 21:13:38 UTC (rev 5599) +++ trunk/Jmol/src/org/jmol/translation/Jmol/de.po 2006-09-18 21:26:27 UTC (rev 5600) @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Jmol 10\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 22:49+0200\n" +"POT-Creation-Date: 2006-09-18 23:24+0200\n" "PO-Revision-Date: 2006-04-14 18:00+0100\n" "Last-Translator: Sebastian Lisken <sebastianlisken at users.sourceforge." "net>\n" @@ -19,7 +19,7 @@ "Content-Transfer-Encoding: 8bit\n" #: org/jmol/viewer/PickingManager.java:167 -msgid "pick one more atoms in order to spin the model around an axis" +msgid "pick one more atom in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:168 Modified: trunk/Jmol/src/org/jmol/translation/Jmol/es.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/Jmol/es.po 2006-09-18 21:13:38 UTC (rev 5599) +++ trunk/Jmol/src/org/jmol/translation/Jmol/es.po 2006-09-18 21:26:27 UTC (rev 5600) @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Jmol 10\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 22:49+0200\n" +"POT-Creation-Date: 2006-09-18 23:24+0200\n" "PO-Revision-Date: 2006-03-24 20:08+0100\n" "Last-Translator: Angel Herráez <ang...@ua...>\n" "Language-Team: Spanish <Jmo...@li...>\n" @@ -21,7 +21,7 @@ #: org/jmol/viewer/PickingManager.java:167 #, fuzzy -msgid "pick one more atoms in order to spin the model around an axis" +msgid "pick one more atom in order to spin the model around an axis" msgstr " átomos para que el modelo gire en torno a un eje" #: org/jmol/viewer/PickingManager.java:168 Modified: trunk/Jmol/src/org/jmol/translation/Jmol/et.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/Jmol/et.po 2006-09-18 21:13:38 UTC (rev 5599) +++ trunk/Jmol/src/org/jmol/translation/Jmol/et.po 2006-09-18 21:26:27 UTC (rev 5600) @@ -6,7 +6,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 22:49+0200\n" +"POT-Creation-Date: 2006-09-18 23:24+0200\n" "PO-Revision-Date: 2006-03-17 20:19+0100\n" "Last-Translator: Ivo Sarak <iv...@ra...>\n" "Language-Team: Estonian <Jmo...@li...>\n" @@ -18,7 +18,7 @@ "X-Poedit-Basepath: ../../../..\n" #: org/jmol/viewer/PickingManager.java:167 -msgid "pick one more atoms in order to spin the model around an axis" +msgid "pick one more atom in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:168 Modified: trunk/Jmol/src/org/jmol/translation/Jmol/fr.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/Jmol/fr.po 2006-09-18 21:13:38 UTC (rev 5599) +++ trunk/Jmol/src/org/jmol/translation/Jmol/fr.po 2006-09-18 21:26:27 UTC (rev 5600) @@ -7,7 +7,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 22:49+0200\n" +"POT-Creation-Date: 2006-09-18 23:24+0200\n" "PO-Revision-Date: 2006-02-19 17:18+0100\n" "Last-Translator: Nicolas Vervelle <ni...@us...>\n" "Language-Team: French <Jmo...@li...>\n" @@ -19,7 +19,7 @@ "X-Poedit-Basepath: ../../../..\n" #: org/jmol/viewer/PickingManager.java:167 -msgid "pick one more atoms in order to spin the model around an axis" +msgid "pick one more atom in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:168 Modified: trunk/Jmol/src/org/jmol/translation/Jmol/nl.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/Jmol/nl.po 2006-09-18 21:13:38 UTC (rev 5599) +++ trunk/Jmol/src/org/jmol/translation/Jmol/nl.po 2006-09-18 21:26:27 UTC (rev 5600) @@ -7,7 +7,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 22:49+0200\n" +"POT-Creation-Date: 2006-09-18 23:24+0200\n" "PO-Revision-Date: 2006-04-09 11:48+0100\n" "Last-Translator: Egon Willighagen <eg...@jm...>\n" "Language-Team: Dutch <jmo...@li...>\n" @@ -18,7 +18,7 @@ "X-Poedit-Country: The Netherlands\n" #: org/jmol/viewer/PickingManager.java:167 -msgid "pick one more atoms in order to spin the model around an axis" +msgid "pick one more atom in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:168 Modified: trunk/Jmol/src/org/jmol/translation/Jmol/pt.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/Jmol/pt.po 2006-09-18 21:13:38 UTC (rev 5599) +++ trunk/Jmol/src/org/jmol/translation/Jmol/pt.po 2006-09-18 21:26:27 UTC (rev 5600) @@ -6,7 +6,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 22:49+0200\n" +"POT-Creation-Date: 2006-09-18 23:24+0200\n" "PO-Revision-Date: 2005-12-20 07:33-0000\n" "Last-Translator: Metro <por...@gm...>\n" "Language-Team: Portugal@Folding <Jmo...@li...>\n" @@ -18,7 +18,7 @@ "X-Poedit-Basepath: ../../../..\n" #: org/jmol/viewer/PickingManager.java:167 -msgid "pick one more atoms in order to spin the model around an axis" +msgid "pick one more atom in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:168 Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot 2006-09-18 21:13:38 UTC (rev 5599) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot 2006-09-18 21:26:27 UTC (rev 5600) @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: PACKAGE VERSION\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 22:49+0200\n" +"POT-Creation-Date: 2006-09-18 23:25+0200\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n" "Language-Team: LANGUAGE <LL...@li...>\n" @@ -1061,7 +1061,7 @@ msgstr "" #: org/jmol/viewer/PickingManager.java:167 -msgid "pick one more atoms in order to spin the model around an axis" +msgid "pick one more atom in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:168 Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po 2006-09-18 21:13:38 UTC (rev 5599) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po 2006-09-18 21:26:27 UTC (rev 5600) @@ -6,7 +6,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 22:49+0200\n" +"POT-Creation-Date: 2006-09-18 23:25+0200\n" "PO-Revision-Date: 2006-01-30 03:37+0100\n" "Last-Translator: Toni Hermoso Pulido <to...@so...>\n" "Language-Team: Catalan <Jmo...@li...>\n" @@ -1079,7 +1079,7 @@ msgstr "Traduccions" #: org/jmol/viewer/PickingManager.java:167 -msgid "pick one more atoms in order to spin the model around an axis" +msgid "pick one more atom in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:168 Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po 2006-09-18 21:13:38 UTC (rev 5599) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po 2006-09-18 21:26:27 UTC (rev 5600) @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: JmolApplet 10\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 22:49+0200\n" +"POT-Creation-Date: 2006-09-18 23:25+0200\n" "PO-Revision-Date: 2006-04-14 18:00+0100\n" "Last-Translator: Sebastian Lisken <sebastianlisken at users.sourceforge." "net>\n" @@ -1079,7 +1079,7 @@ msgstr "Übersetzungen" #: org/jmol/viewer/PickingManager.java:167 -msgid "pick one more atoms in order to spin the model around an axis" +msgid "pick one more atom in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:168 Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po 2006-09-18 21:13:38 UTC (rev 5599) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po 2006-09-18 21:26:27 UTC (rev 5600) @@ -2,7 +2,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 22:49+0200\n" +"POT-Creation-Date: 2006-09-18 23:25+0200\n" "PO-Revision-Date: 2006-04-14 17:48+0100\n" "Last-Translator: Angel Herráez <ang...@ua...>\n" "Language-Team: Spanish <Jmo...@li...>\n" @@ -1079,7 +1079,7 @@ #: org/jmol/viewer/PickingManager.java:167 #, fuzzy -msgid "pick one more atoms in order to spin the model around an axis" +msgid "pick one more atom in order to spin the model around an axis" msgstr " átomos para que el modelo gire en torno a un eje" #: org/jmol/viewer/PickingManager.java:168 Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po 2006-09-18 21:13:38 UTC (rev 5599) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po 2006-09-18 21:26:27 UTC (rev 5600) @@ -6,7 +6,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 22:49+0200\n" +"POT-Creation-Date: 2006-09-18 23:25+0200\n" "PO-Revision-Date: 2006-03-17 20:19+0100\n" "Last-Translator: Ivo Sarak <iv...@ra...>\n" "Language-Team: Estonian <Jmo...@li...>\n" @@ -1080,7 +1080,7 @@ msgstr "Tõlked" #: org/jmol/viewer/PickingManager.java:167 -msgid "pick one more atoms in order to spin the model around an axis" +msgid "pick one more atom in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:168 Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po 2006-09-18 21:13:38 UTC (rev 5599) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po 2006-09-18 21:26:27 UTC (rev 5600) @@ -7,7 +7,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 22:49+0200\n" +"POT-Creation-Date: 2006-09-18 23:25+0200\n" "PO-Revision-Date: 2006-04-14 18:11+0100\n" "Last-Translator: Nicolas Vervelle <ni...@us...>\n" "Language-Team: French <Jmo...@li...>\n" @@ -1084,7 +1084,7 @@ msgstr "Traductions" #: org/jmol/viewer/PickingManager.java:167 -msgid "pick one more atoms in order to spin the model around an axis" +msgid "pick one more atom in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:168 Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po 2006-09-18 21:13:38 UTC (rev 5599) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po 2006-09-18 21:26:27 UTC (rev 5600) @@ -7,7 +7,7 @@ msgstr "" "Project-Id-Version: nl\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 22:49+0200\n" +"POT-Creation-Date: 2006-09-18 23:25+0200\n" "PO-Revision-Date: 2006-09-18 20:32+0100\n" "Last-Translator: Egon Willighagen <eg...@jm...>\n" "Language-Team: Nederlands <kde...@kd...>\n" @@ -1069,7 +1069,7 @@ #: org/jmol/viewer/PickingManager.java:167 #, fuzzy -msgid "pick one more atoms in order to spin the model around an axis" +msgid "pick one more atom in order to spin the model around an axis" msgstr "atomen in volgorde om het model rond een as te laten spinnen" #: org/jmol/viewer/PickingManager.java:168 Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po 2006-09-18 21:13:38 UTC (rev 5599) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po 2006-09-18 21:26:27 UTC (rev 5600) @@ -6,7 +6,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-18 22:49+0200\n" +"POT-Creation-Date: 2006-09-18 23:25+0200\n" "PO-Revision-Date: 2005-12-20 07:44-0000\n" "Last-Translator: Metro <por...@gm...>\n" "Language-Team: Portugal@Folding <Jmo...@li...>\n" @@ -1079,7 +1079,7 @@ msgstr "" #: org/jmol/viewer/PickingManager.java:167 -msgid "pick one more atoms in order to spin the model around an axis" +msgid "pick one more atom in order to spin the model around an axis" msgstr "" #: org/jmol/viewer/PickingManager.java:168 Modified: trunk/Jmol/src/org/jmol/viewer/PickingManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/PickingManager.java 2006-09-18 21:13:38 UTC (rev 5599) +++ trunk/Jmol/src/org/jmol/viewer/PickingManager.java 2006-09-18 21:26:27 UTC (rev 5600) @@ -164,7 +164,7 @@ if (queuedAtomCount < 2) { viewer.setSpinOn(false); viewer.scriptStatus(queuedAtomCount == 1 ? - GT._("pick one more atoms in order to spin the model around an axis") : + GT._("pick one more atom in order to spin the model around an axis") : GT._("pick two atoms in order to spin the model around an axis")); break; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2006-09-20 15:41:35
|
Revision: 5619 http://svn.sourceforge.net/jmol/?rev=5619&view=rev Author: hansonr Date: 2006-09-20 08:41:14 -0700 (Wed, 20 Sep 2006) Log Message: ----------- deuterium/tritium isotope support Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java trunk/Jmol/src/org/jmol/adapter/smarter/CubeReader.java trunk/Jmol/src/org/jmol/api/JmolAdapter.java trunk/Jmol/src/org/jmol/g3d/Graphics3D.java trunk/Jmol/src/org/jmol/popup/JmolPopup.java trunk/Jmol/src/org/jmol/viewer/Atom.java trunk/Jmol/src/org/jmol/viewer/Balls.java trunk/Jmol/src/org/jmol/viewer/Bond.java trunk/Jmol/src/org/jmol/viewer/ColorManager.java trunk/Jmol/src/org/jmol/viewer/Eval.java trunk/Jmol/src/org/jmol/viewer/Frame.java trunk/Jmol/src/org/jmol/viewer/FrameExportJmolAdapter.java trunk/Jmol/src/org/jmol/viewer/Isosurface.java trunk/Jmol/src/org/jmol/viewer/JmolConstants.java trunk/Jmol/src/org/jmol/viewer/ModelManager.java trunk/Jmol/src/org/jmol/viewer/Token.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java 2006-09-20 08:53:04 UTC (rev 5618) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java 2006-09-20 15:41:14 UTC (rev 5619) @@ -32,7 +32,7 @@ BitSet bsSymmetry; int atomSite; String elementSymbol; - byte elementNumber = -1; + short elementNumber = -1; String atomName; int formalCharge = Integer.MIN_VALUE; {set(Float.NaN, Float.NaN, Float.NaN);} @@ -131,7 +131,8 @@ 1 << ('r' - 'a') | 1 << ('s' - 'a') | 1 << ('u' - 'a'), - // Db Dy + // D Db Dy + 1 << 31 | 1 << ('b' - 'a') | 1 << ('y' - 'a'), // Er Es Eu @@ -216,7 +217,8 @@ 1 << ('m' - 'a') | 1 << ('n' - 'a') | 1 << ('r' - 'a'), - // Ta Tb Tc Te Th Ti Tl Tm + // T Ta Tb Tc Te Th Ti Tl Tm + 1 << 31 | 1 << ('a' - 'a') | 1 << ('b' - 'a') | 1 << ('c' - 'a') | Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2006-09-20 08:53:04 UTC (rev 5618) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2006-09-20 15:41:14 UTC (rev 5619) @@ -319,10 +319,7 @@ } static String getElementSymbol(int elementNumber) { - if (elementNumber < 0 - || elementNumber >= JmolConstants.elementSymbols.length) - elementNumber = 0; - return JmolConstants.elementSymbols[elementNumber]; + return JmolConstants.elementSymbolFromNumber(elementNumber); } void fillDataBlock(BufferedReader reader, String[][] data) throws Exception { Modified: trunk/Jmol/src/org/jmol/adapter/smarter/CubeReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/CubeReader.java 2006-09-20 08:53:04 UTC (rev 5618) +++ trunk/Jmol/src/org/jmol/adapter/smarter/CubeReader.java 2006-09-20 15:41:14 UTC (rev 5619) @@ -130,7 +130,7 @@ for (int i = 0; i < atomCount; ++i) { line = reader.readLine(); Atom atom = atomSetCollection.addNewAtom(); - atom.elementNumber = (byte)parseInt(line); + atom.elementNumber = (short)parseInt(line); //allowing atomicAndIsotope for JVXL format atom.partialCharge = parseFloat(line, ichNextParse); atom.x = parseFloat(line, ichNextParse) * ANGSTROMS_PER_BOHR; atom.y = parseFloat(line, ichNextParse) * ANGSTROMS_PER_BOHR; Modified: trunk/Jmol/src/org/jmol/api/JmolAdapter.java =================================================================== --- trunk/Jmol/src/org/jmol/api/JmolAdapter.java 2006-09-20 08:53:04 UTC (rev 5618) +++ trunk/Jmol/src/org/jmol/api/JmolAdapter.java 2006-09-20 15:41:14 UTC (rev 5619) @@ -393,7 +393,7 @@ public BitSet getAtomSymmetry() { return null; } public int getAtomSite() { return Integer.MIN_VALUE; } abstract public Object getUniqueID(); - public int getElementNumber() { return -1; } + public int getElementNumber() { return -1; } // may be atomicNumber + isotopeNumber*256 public String getElementSymbol() { return null; } public String getAtomName() { return null; } public int getFormalCharge() { return 0; } Modified: trunk/Jmol/src/org/jmol/g3d/Graphics3D.java =================================================================== --- trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2006-09-20 08:53:04 UTC (rev 5618) +++ trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2006-09-20 15:41:14 UTC (rev 5619) @@ -1535,6 +1535,7 @@ * changable colixes * give me a short ID and a color, and I will give you a colix * later, you can reassign the color if you want + * Used only for colorManager coloring of elements ****************************************************************/ short[] changableColixMap = new short[16]; Modified: trunk/Jmol/src/org/jmol/popup/JmolPopup.java =================================================================== --- trunk/Jmol/src/org/jmol/popup/JmolPopup.java 2006-09-20 08:53:04 UTC (rev 5618) +++ trunk/Jmol/src/org/jmol/popup/JmolPopup.java 2006-09-20 15:41:14 UTC (rev 5619) @@ -77,10 +77,11 @@ if (elementsComputedMenu == null || elementsPresentBitSet == null) return; removeAll(elementsComputedMenu); - for (int i = 0; i < JmolConstants.elementNames.length; ++i) { + for (int i = 0; i < JmolConstants.elementNumberMax; ++i) { + //no isotopes here for now if (elementsPresentBitSet.get(i)) { - String elementName = JmolConstants.elementNames[i]; - String elementSymbol = JmolConstants.elementSymbols[i]; + String elementName = JmolConstants.elementNameFromNumber(i); + String elementSymbol = JmolConstants.elementSymbolFromNumber(i); String entryName = elementSymbol + " - " + elementName; String script = "select " + elementName; addMenuItem(elementsComputedMenu, entryName, script); Modified: trunk/Jmol/src/org/jmol/viewer/Atom.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Atom.java 2006-09-20 08:53:04 UTC (rev 5618) +++ trunk/Jmol/src/org/jmol/viewer/Atom.java 2006-09-20 15:41:14 UTC (rev 5619) @@ -48,7 +48,7 @@ int atomSite; short screenDiameter; short modelIndex; // we want this here for the BallsRenderer - byte elementNumber; + private short atomicAndIsotopeNumber; byte formalChargeAndFlags; byte alternateLocationID; short madAtom; @@ -79,7 +79,7 @@ int atomIndex, BitSet atomSymmetry, int atomSite, - byte elementNumber, + short atomicAndIsotopeNumber, String atomName, int formalCharge, float partialCharge, int occupancy, @@ -93,7 +93,7 @@ this.atomSymmetry = atomSymmetry; this.atomSite = atomSite; this.atomIndex = atomIndex; - this.elementNumber = elementNumber; + this.atomicAndIsotopeNumber = atomicAndIsotopeNumber; this.formalChargeAndFlags = (byte)(formalCharge << 3); this.colixAtom = viewer.getColixAtom(this); this.alternateLocationID = (byte)alternateLocationID; @@ -345,7 +345,7 @@ int n = 0; for (int i = bonds.length; --i >= 0; ) if ((bonds[i].order & JmolConstants.BOND_COVALENT_MASK) != 0 - && bonds[i].getOtherAtom(this).elementNumber == 1) + && (bonds[i].getOtherAtom(this).getElementNumber()) == 1) ++n; return n; } @@ -409,12 +409,16 @@ screenDiameter = viewer.scaleToScreen(screenZ, madAtom); } - byte getElementNumber() { - return elementNumber; + short getElementNumber() { + return (short) (atomicAndIsotopeNumber % 256); } + + short getAtomicAndIsotopeNumber() { + return atomicAndIsotopeNumber; + } String getElementSymbol() { - return JmolConstants.elementSymbols[elementNumber]; + return JmolConstants.elementSymbolFromNumber(atomicAndIsotopeNumber); } String getAtomNameOrNull() { @@ -426,8 +430,7 @@ String getAtomName() { String atomName = getAtomNameOrNull(); - return (atomName != null - ? atomName : JmolConstants.elementSymbols[elementNumber]); + return (atomName != null ? atomName : getElementSymbol()); } String getPdbAtomName4() { @@ -574,15 +577,15 @@ } short getVanderwaalsMar() { - return JmolConstants.vanderwaalsMars[elementNumber]; + return JmolConstants.vanderwaalsMars[atomicAndIsotopeNumber % 256]; } float getVanderwaalsRadiusFloat() { - return JmolConstants.vanderwaalsMars[elementNumber] / 1000f; + return JmolConstants.vanderwaalsMars[atomicAndIsotopeNumber % 256] / 1000f; } short getBondingMar() { - return JmolConstants.getBondingMar(elementNumber, + return JmolConstants.getBondingMar(atomicAndIsotopeNumber % 256, formalChargeAndFlags >> 3); } @@ -990,7 +993,7 @@ strT = getAtomName(); break; case 'e': - strT = JmolConstants.elementSymbols[elementNumber]; + strT = JmolConstants.elementSymbolFromNumber(atomicAndIsotopeNumber); break; case 'x': floatT = x; Modified: trunk/Jmol/src/org/jmol/viewer/Balls.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Balls.java 2006-09-20 08:53:04 UTC (rev 5618) +++ trunk/Jmol/src/org/jmol/viewer/Balls.java 2006-09-20 15:41:14 UTC (rev 5619) @@ -85,7 +85,7 @@ ~JmolConstants.ATOM_IN_MODEL & ~myVisibilityFlag); if (atom.madAtom == JmolConstants.MAR_DELETED - || ! showHydrogens && atom.elementNumber == 1) + || ! showHydrogens && atom.getElementNumber() == 1) continue; if (! isOneFrame && bs.get(atom.modelIndex) || atom.modelIndex == displayModelIndex) { Modified: trunk/Jmol/src/org/jmol/viewer/Bond.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Bond.java 2006-09-20 08:53:04 UTC (rev 5618) +++ trunk/Jmol/src/org/jmol/viewer/Bond.java 2006-09-20 15:41:14 UTC (rev 5619) @@ -46,7 +46,7 @@ throw new NullPointerException(); this.atom1 = atom1; this.atom2 = atom2; - if (atom1.elementNumber == 16 && atom2.elementNumber == 16) + if (atom1.getElementNumber() == 16 && atom2.getElementNumber() == 16) order |= JmolConstants.BOND_SULFUR_MASK; if (order == JmolConstants.BOND_AROMATIC_MASK) order = JmolConstants.BOND_AROMATIC; Modified: trunk/Jmol/src/org/jmol/viewer/ColorManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/ColorManager.java 2006-09-20 08:53:04 UTC (rev 5618) +++ trunk/Jmol/src/org/jmol/viewer/ColorManager.java 2006-09-20 15:41:14 UTC (rev 5619) @@ -32,11 +32,15 @@ Viewer viewer; Graphics3D g3d; int[] argbsCpk; + int[] altArgbsCpk; ColorManager(Viewer viewer, Graphics3D g3d) { this.viewer = viewer; this.g3d = g3d; argbsCpk = JmolConstants.argbsCpk; + altArgbsCpk = new int[JmolConstants.altArgbsCpk.length]; + for (int i = JmolConstants.altArgbsCpk.length; --i >= 0; ) + altArgbsCpk[i] = JmolConstants.altArgbsCpk[i]; } void setDefaultColors(String colorScheme) { @@ -64,12 +68,17 @@ } for (int i = JmolConstants.argbsCpk.length; --i >= 0; ) g3d.changeColixArgb((short)i, argbsCpk[i]); + for (int i = JmolConstants.altArgbsCpk.length; --i >= 0; ) + g3d.changeColixArgb((short)(JmolConstants.elementNumberMax + i), altArgbsCpk[i]); } void copyArgbsCpk() { argbsCpk = new int[JmolConstants.argbsCpk.length]; for (int i = JmolConstants.argbsCpk.length; --i >= 0; ) argbsCpk[i] = JmolConstants.argbsCpk[i]; + altArgbsCpk = new int[JmolConstants.altArgbsCpk.length]; + for (int i = JmolConstants.altArgbsCpk.length; --i >= 0; ) + altArgbsCpk[i] = JmolConstants.altArgbsCpk[i]; } @@ -123,8 +132,12 @@ if ("cpk" == palette) { // Note that CPK colors can be changed based upon user preference // therefore, a changable colix is allocated in this case - short id = atom.getElementNumber(); - return g3d.getChangableColix(id, argbsCpk[id]); + short id = atom.getAtomicAndIsotopeNumber(); + if (id < 256) + return g3d.getChangableColix(id, argbsCpk[id]); + id = (short) JmolConstants.altElementIndexFromNumber(id); + return g3d.getChangableColix( + (short) (JmolConstants.elementNumberMax + id), altArgbsCpk[id]); } if ("partialcharge" == palette) { // This code assumes that the range of partial charges is [-1, 1]. @@ -214,8 +227,8 @@ } else if ("insertion" == palette) { frame = viewer.getFrame(); //very inefficient! - index = quantize(frame.getInsertionCodeIndexInModel(atom.modelIndex, - atom.getInsertionCode()), 0, frame + index = quantize(frame.getInsertionCodeIndexInModel(atom.modelIndex, atom + .getInsertionCode()), 0, frame .getInsertionCountInModel(atom.modelIndex), JmolConstants.argbsRoygbScale.length); argb = JmolConstants.argbsRoygbScale[index]; @@ -354,16 +367,25 @@ flushCaches(); } - void setElementArgb(int elementNumber, int argb) { + void setElementArgb(int id, int argb) { if (argb == 0) { if (argbsCpk == JmolConstants.argbsCpk) return; - argb = JmolConstants.argbsCpk[elementNumber]; + if (id < 256) + argb = JmolConstants.argbsCpk[id]; + else + argb = JmolConstants.altArgbsCpk[JmolConstants.altElementIndexFromNumber(id)]; } else argb |= 0xFF000000; if (argbsCpk == JmolConstants.argbsCpk) copyArgbsCpk(); - argbsCpk[elementNumber] = argb; - g3d.changeColixArgb((short)elementNumber, argb); + if (id < 256) { + argbsCpk[id] = argb; + g3d.changeColixArgb((short)id, argb); + return; + } + id = JmolConstants.altElementIndexFromNumber(id); + altArgbsCpk[JmolConstants.altElementIndexFromNumber(id)] = argb; + g3d.changeColixArgb((short) (JmolConstants.elementNumberMax + id), argb); } } Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-20 08:53:04 UTC (rev 5618) +++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-20 15:41:14 UTC (rev 5619) @@ -315,33 +315,17 @@ predefine(JmolConstants.predefinedSets[iPredef]); // Now, define all the elements as predefined sets // hydrogen is handled specially, so don't define it - for (int i = JmolConstants.elementNames.length; --i > 1;) { - String definition = "@" + JmolConstants.elementNames[i] + " _e=" + i; + for (int i = JmolConstants.elementNumberMax; --i > 1;) { + String definition = "@" + JmolConstants.elementNameFromNumber(i)+ " _e=" + i; predefine(definition); } - for (int j = JmolConstants.alternateElementNumbers.length; --j >= 0;) { - String definition = "@" + JmolConstants.alternateElementNames[j] + " _e=" - + JmolConstants.alternateElementNumbers[j]; + for (int i = JmolConstants.altElementMax; --i >= 0;) { + String definition = "@" + JmolConstants.altElementNameFromIndex(i) + " _e=" + + JmolConstants.altElementNumberFromIndex(i); predefine(definition); } } - void predefineElements() { - // the name 'hydrogen' handled specially - for (int i = JmolConstants.elementNames.length; --i > 1;) { - String definition = "@" + JmolConstants.elementNames[i] + " _e=" + i; - if (!compiler.compile("#element", definition, true)) { - Logger.error("element definition error:" + definition); - continue; - } - Token[][] aatoken = compiler.getAatokenCompiled(); - Token[] statement = aatoken[0]; - // int tok = statement[1].tok; - String variable = (String) statement[1].value; - variables.put(variable, statement); - } - } - void predefine(String script) { if (compiler.compile("#predefine", script, true)) { Token[][] aatoken = compiler.getAatokenCompiled(); @@ -1003,9 +987,11 @@ propertyValue = atom.getAtomNumber(); break; case Token.elemno: - case Token.element: propertyValue = atom.getElementNumber(); break; + case Token.element: + propertyValue = atom.getAtomicAndIsotopeNumber(); + break; case Token.site: propertyValue = atom.getAtomSite(); break; @@ -1884,15 +1870,15 @@ viewer.setSelectionArgb(argb); return; } - for (int i = JmolConstants.elementNames.length; --i >= 0;) { - if (str.equalsIgnoreCase(JmolConstants.elementNames[i])) { + for (int i = JmolConstants.elementNumberMax; --i >= 0;) { + if (str.equalsIgnoreCase(JmolConstants.elementNameFromNumber(i))) { viewer.setElementArgb(i, getArgbParam(2)); return; } } - for (int i = JmolConstants.alternateElementNames.length; --i >= 0;) { - if (str.equalsIgnoreCase(JmolConstants.alternateElementNames[i])) { - viewer.setElementArgb(JmolConstants.alternateElementNumbers[i], + for (int i = JmolConstants.altElementMax; --i >= 0;) { + if (str.equalsIgnoreCase(JmolConstants.altElementNameFromIndex(i))) { + viewer.setElementArgb(JmolConstants.altElementNumberFromIndex(i), getArgbParam(2)); return; } Modified: trunk/Jmol/src/org/jmol/viewer/Frame.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Frame.java 2006-09-20 08:53:04 UTC (rev 5618) +++ trunk/Jmol/src/org/jmol/viewer/Frame.java 2006-09-20 15:41:14 UTC (rev 5619) @@ -116,7 +116,10 @@ int indexInModel; int nAtoms; int nElements; - int[] elementCounts = new int[120]; + int[] elementCounts = new int[JmolConstants.elementNumberMax]; + int[] altElementCounts = new int[JmolConstants.altElementMax]; + int elementNumberMax; + int altElementMax; String mf; BitSet atomList; @@ -137,43 +140,53 @@ this.moleculeIndex = moleculeIndex; this.modelIndex = modelIndex; this.indexInModel = indexInModel; - nAtoms = getElementAndAtomCount(atomList, elementCounts, atomCount); - nElements = countElements(elementCounts, JmolConstants.elementNumberMax); - mf = getMolecularFormula(elementCounts, JmolConstants.elementNumberMax); + getElementAndAtomCount(atomList); + mf = getMolecularFormula(); Logger.info("new Molecule (" + mf + ") " + (indexInModel + 1) + "/" + (modelIndex + 1)); } - int getElementAndAtomCount(BitSet atomList, int[] elementCounts, int atomMax) { - int nAtoms = 0; - for (int i = 0; i < atomMax; i++) + void getElementAndAtomCount(BitSet atomList) { + for (int i = 0; i < atomCount; i++) if (atomList.get(i)) { nAtoms++; - elementCounts[atoms[i].elementNumber]++; + int n = atoms[i].getAtomicAndIsotopeNumber(); + if (n < 256) { + elementCounts[n]++; + if (elementCounts[n] == 1) + nElements++; + elementNumberMax = Math.max(elementNumberMax, n); + } else { + n = JmolConstants.altElementIndexFromNumber(n); + altElementCounts[n]++; + if (altElementCounts[n] == 1) + nElements++; + altElementMax = Math.max(altElementMax, n); + } } - return nAtoms; } - int countElements(int[] elementCounts, int eMax) { - int count = 0; - for (int i = 1; i < eMax; i++) - if (elementCounts[i] > 0) - count++; - return count; - } - - String getMolecularFormula(int[] elementCounts, int eMax) { + String getMolecularFormula() { String mf = ""; String sep = ""; int nX; - for (int i = 1; i < eMax; i++) { + for (int i = 1; i < elementNumberMax; i++) { nX = elementCounts[i]; if (nX != 0) { - mf += sep + JmolConstants.elementSymbols[i] + " " + nX; + mf += sep + JmolConstants.elementSymbolFromNumber(i) + " " + nX; sep = " "; } } + for (int i = 1; i < altElementMax; i++) { + nX = altElementCounts[i]; + if (nX != 0) { + mf += sep + + JmolConstants.elementSymbolFromNumber(JmolConstants + .altElementNumberFromIndex(i)) + " " + nX; + sep = " "; + } + } return mf; } @@ -252,20 +265,21 @@ for (JmolAdapter.AtomIterator iterAtom = adapter .getAtomIterator(clientFile); iterAtom.hasNext();) { - byte elementNumber = (byte) iterAtom.getElementNumber(); + short elementNumber = (short) iterAtom.getElementNumber(); if (elementNumber <= 0) elementNumber = JmolConstants.elementNumberFromSymbol(iterAtom .getElementSymbol()); char alternateLocation = iterAtom.getAlternateLocationID(); - addAtom(iterAtom.getAtomSetIndex(), iterAtom.getAtomSymmetry(), iterAtom.getAtomSite(), iterAtom - .getUniqueID(), elementNumber, iterAtom.getAtomName(), iterAtom - .getFormalCharge(), iterAtom.getPartialCharge(), iterAtom - .getOccupancy(), iterAtom.getBfactor(), iterAtom.getX(), iterAtom - .getY(), iterAtom.getZ(), iterAtom.getIsHetero(), iterAtom - .getAtomSerial(), iterAtom.getChainID(), iterAtom.getGroup3(), - iterAtom.getSequenceNumber(), iterAtom.getInsertionCode(), iterAtom - .getVectorX(), iterAtom.getVectorY(), iterAtom.getVectorZ(), - alternateLocation, iterAtom.getClientAtomReference()); + addAtom(iterAtom.getAtomSetIndex(), iterAtom.getAtomSymmetry(), iterAtom + .getAtomSite(), iterAtom.getUniqueID(), elementNumber, iterAtom + .getAtomName(), iterAtom.getFormalCharge(), iterAtom + .getPartialCharge(), iterAtom.getOccupancy(), iterAtom.getBfactor(), + iterAtom.getX(), iterAtom.getY(), iterAtom.getZ(), iterAtom + .getIsHetero(), iterAtom.getAtomSerial(), iterAtom.getChainID(), + iterAtom.getGroup3(), iterAtom.getSequenceNumber(), iterAtom + .getInsertionCode(), iterAtom.getVectorX(), + iterAtom.getVectorY(), iterAtom.getVectorZ(), alternateLocation, + iterAtom.getClientAtomReference()); } fileHasHbonds = false; @@ -369,10 +383,11 @@ htAtomMap.clear(); } - void addAtom(int modelIndex, BitSet atomSymmetry, int atomSite, Object atomUid, byte atomicNumber, - String atomName, int formalCharge, float partialCharge, - int occupancy, float bfactor, float x, float y, float z, - boolean isHetero, int atomSerial, char chainID, String group3, + void addAtom(int modelIndex, BitSet atomSymmetry, int atomSite, + Object atomUid, short atomicAndIsotopeNumber, String atomName, + int formalCharge, float partialCharge, int occupancy, + float bfactor, float x, float y, float z, boolean isHetero, + int atomSerial, char chainID, String group3, int groupSequenceNumber, char groupInsertionCode, float vectorX, float vectorY, float vectorZ, char alternateLocationID, Object clientAtomReference) { @@ -396,10 +411,11 @@ if (atomCount == atoms.length) growAtomArrays(); - Atom atom = new Atom(viewer, this, currentModelIndex, atomCount, atomSymmetry, - atomSite, atomicNumber, atomName, formalCharge, partialCharge, occupancy, - bfactor, x, y, z, isHetero, atomSerial, chainID, group3, vectorX, vectorY, - vectorZ, alternateLocationID, clientAtomReference); + Atom atom = new Atom(viewer, this, currentModelIndex, atomCount, + atomSymmetry, atomSite, atomicAndIsotopeNumber, atomName, formalCharge, + partialCharge, occupancy, bfactor, x, y, z, isHetero, atomSerial, + chainID, group3, vectorX, vectorY, vectorZ, alternateLocationID, + clientAtomReference); atoms[atomCount] = atom; ++atomCount; htAtomMap.put(atomUid, atom); @@ -1540,7 +1556,7 @@ timeBegin = System.currentTimeMillis(); for (int i = atomCount; --i >= 0;) { Atom atom = atoms[i]; - int elementNumber = atom.elementNumber; + int elementNumber = atom.getElementNumber(); if (elementNumber != 7 && elementNumber != 8) continue; //float searchRadius = hbondMax; @@ -1548,7 +1564,7 @@ iter.initializeHemisphere(atom, hbondMax); while (iter.hasMoreElements()) { Atom atomNear = (Atom) iter.nextElement(); - int elementNumberNear = atomNear.elementNumber; + int elementNumberNear = atomNear.getElementNumber(); if (elementNumberNear != 7 && elementNumberNear != 8) continue; if (atomNear == atom) @@ -2046,9 +2062,10 @@ BitSet getVisibleElementBitSet(int atomIndex) { // only from user picking BitSet bs = getVisibleSet(); - int n = atoms[atomIndex].elementNumber; + int n = atoms[atomIndex].getElementNumber(); for (int i = 0; i < atomCount; i++) - if (bs.get(i) && (atoms[i].elementNumber != n || atoms[i].madAtom == 0)) + if (bs.get(i) + && (atoms[i].getElementNumber() != n || atoms[i].madAtom == 0)) bs.clear(i); return bs; } @@ -2075,7 +2092,7 @@ void findElementsPresent() { elementsPresent = new BitSet(); for (int i = atomCount; --i >= 0;) - elementsPresent.set(atoms[i].elementNumber); + elementsPresent.set(atoms[i].getElementNumber()); } BitSet getElementsPresentBitSet() { @@ -2902,7 +2919,7 @@ Point3f pt; // just not doing aldehydes here -- all A-X-B bent == sp3 for now for (int i = 0; i < atomCount; i++) - if (atomSet.get(i) && atoms[i].elementNumber == 6) { + if (atomSet.get(i) && atoms[i].getElementNumber() == 6) { Atom atom = atoms[i]; int nBonds = (atom.getCovalentHydrogenCount() > 0 ? 0 : atom .getCovalentBondCount()); @@ -2917,7 +2934,7 @@ Point3f[] hAtoms = new Point3f[n]; n = 0; for (int i = 0; i < atomCount; i++) - if (atomSet.get(i) && atoms[i].elementNumber == 6) { + if (atomSet.get(i) && atoms[i].getElementNumber() == 6) { Atom atom = atoms[i]; int nBonds = (atom.getCovalentHydrogenCount() > 0 ? 0 : atom .getCovalentBondCount()); Modified: trunk/Jmol/src/org/jmol/viewer/FrameExportJmolAdapter.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/FrameExportJmolAdapter.java 2006-09-20 08:53:04 UTC (rev 5618) +++ trunk/Jmol/src/org/jmol/viewer/FrameExportJmolAdapter.java 2006-09-20 15:41:14 UTC (rev 5619) @@ -71,7 +71,7 @@ return true; } public Object getUniqueID() { return new Integer(iatom); } - public int getElementNumber() { return atom.elementNumber; } + public int getElementNumber() { return atom.getElementNumber(); }//no isotope here public String getElementSymbol() { return atom.getElementSymbol(); } public int getFormalCharge() { return atom.getFormalCharge(); } public float getPartialCharge() { return atom.getPartialCharge(); } Modified: trunk/Jmol/src/org/jmol/viewer/Isosurface.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Isosurface.java 2006-09-20 08:53:04 UTC (rev 5618) +++ trunk/Jmol/src/org/jmol/viewer/Isosurface.java 2006-09-20 15:41:14 UTC (rev 5619) @@ -4004,8 +4004,9 @@ continue; pt.set(atom); pt.scale(1 / ANGSTROMS_PER_BOHR); - jvxlFileHeader += atom.elementNumber + " " + atom.elementNumber + ".0 " - + pt.x + " " + pt.y + " " + pt.z + "\n"; + jvxlFileHeader += atom.getAtomicAndIsotopeNumber() + " " + + atom.getAtomicAndIsotopeNumber() + ".0 " + pt.x + " " + pt.y + " " + + pt.z + "\n"; } atomCount = -Integer.MAX_VALUE; negativeAtomCount = false; @@ -4105,7 +4106,7 @@ for (int i = firstSet; i <= lastSet; i++) { if (!atomSet.get(i)) continue; - atomNo[iAtom] = atoms[i].elementNumber; + atomNo[iAtom] = atoms[i].getElementNumber(); solvent_ptAtom[iAtom] = atoms[i]; solvent_atomRadius[iAtom++] = atoms[i].getVanderwaalsRadiusFloat() + solventExtendedAtomRadius; Modified: trunk/Jmol/src/org/jmol/viewer/JmolConstants.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2006-09-20 08:53:04 UTC (rev 5618) +++ trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2006-09-20 15:41:14 UTC (rev 5619) @@ -203,7 +203,7 @@ * The default elementSymbols. Presumably the only entry which may cause * confusion is element 0, whose symbol we have defined as "Xx". */ - public final static String[] elementSymbols = { + private final static String[] elementSymbols = { "Xx", // 0 "H", // 1 "He", // 2 @@ -336,41 +336,72 @@ /** * @param elementSymbol First char must be upper case, second char accepts upper or lower case - * @return elementNumber + * @return elementNumber = atomicNumber + IsotopeNumber*256 */ - public static byte elementNumberFromSymbol(String elementSymbol) { + public static short elementNumberFromSymbol(String elementSymbol) { if (htElementMap == null) { Hashtable map = new Hashtable(); - for (int elementNumber = elementNumberMax; --elementNumber >= 0; ) { + for (int elementNumber = elementNumberMax; --elementNumber >= 0;) { String symbol = elementSymbols[elementNumber]; Integer boxed = new Integer(elementNumber); map.put(symbol, boxed); - if (symbol.length() == 2) { - symbol = - "" + symbol.charAt(0) + Character.toUpperCase(symbol.charAt(1)); - map.put(symbol, boxed); - } - if (elementNumber == 1) { - // special case for D = deuterium - // - // We can put in a special table for these in the future - // if there are more 'element symbol aliases' - map.put("D", boxed); - } + if (symbol.length() == 2) + map.put(symbol.toUpperCase(), boxed); } + for (int i = altElementMax; --i >= firstIsotope;) { + String symbol = altElementSymbols[i]; + Integer boxed = new Integer(altElementNumbers[i]); + map.put(symbol, boxed); + if (symbol.length() == 2) + map.put(symbol.toUpperCase(), boxed); + } htElementMap = map; } if (elementSymbol == null) return 0; - Integer boxedAtomicNumber = (Integer)htElementMap.get(elementSymbol); + Integer boxedAtomicNumber = (Integer) htElementMap.get(elementSymbol); if (boxedAtomicNumber != null) - return (byte)boxedAtomicNumber.intValue(); + return (short) boxedAtomicNumber.intValue(); Logger.error("" + elementSymbol + "' is not a recognized symbol"); return 0; } + + /** + * @param elementNumber may be atomicNumber + isotopeNumber*256 + * @return elementSymbol + */ + public final static String elementSymbolFromNumber(int elementNumber) { + //Isotopes as atomicNumber + IsotopeNumber * 256 + if (elementNumber >= elementNumberMax) { + for (int j = altElementMax; --j >= 0;) + if (elementNumber == altElementNumbers[j]) + return altElementSymbols[j]; + elementNumber %= 256; + } + if (elementNumber < 0 || elementNumber >= elementNumberMax) + elementNumber = 0; + return elementSymbols[elementNumber]; + } - public final static String elementNames[] = { - "unknown", + /** + * @param elementNumber may be atomicNumber + isotopeNumber*256 + * @return elementName + */ + public final static String elementNameFromNumber(int elementNumber) { + //Isotopes as atomicNumber + IsotopeNumber * 256 + if (elementNumber >= elementNumberMax) { + for (int j = altElementMax; --j >= 0;) + if (elementNumber == altElementNumbers[j]) + return altElementNames[j]; + elementNumber %= 256; + } + if (elementNumber < 0 || elementNumber >= elementNumberMax) + elementNumber = 0; + return elementNames[elementNumber]; + } + + private final static String elementNames[] = { + "unknown", // 0 "hydrogen", // 1 "helium", // 2 "lithium", // 3 @@ -482,21 +513,68 @@ "meitnerium" // 109 }; - public final static byte[] alternateElementNumbers = { + /** + * @param i index into altElementNames + * @return elementName + */ + public final static String altElementNameFromIndex(int i) { + return altElementNames[i]; + } + + /** + * @param i index into altElementNumbers + * @return elementNumber (may be atomicNumber + isotopeNumber*256) + */ + public final static short altElementNumberFromIndex(int i) { + return altElementNumbers[i]; + } + + /** + * @param atomicAndIsotopeNumber (may be atomicNumber + isotopeNumber*256) + * @return index into altElementNumbers + */ + public final static int altElementIndexFromNumber(int atomicAndIsotopeNumber) { + for (int i = 0; i < altElementMax; i++) + if (altElementNumbers[i] == atomicAndIsotopeNumber) + return i; + return 0; + } + + private final static short[] altElementNumbers = { 0, 13, 16, 55, + 1 + (2 << 8), // D = 1 + 2*256 <-- firstIsotope + 1 + (3 << 8), // T = 1 + 3*256 }; - public final static String[] alternateElementNames = { + private final static int firstIsotope = 4; + + private final static String[] altElementSymbols = { + "Xx", + "Al", + "S", + "Cs", + "D", + "T" + }; + + private final static String[] altElementNames = { "dummy", "aluminium", "sulphur", "caesium", + "deuterium", + "tritium" }; - + /** + * length of the altElementSymbols, altElementNames, altElementNumbers arrays + */ + final static int altElementMax = altElementNumbers.length; + + /** * Default table of van der Waals Radii. * values are stored as MAR -- Milli Angstrom Radius * Used for spacefill rendering of atoms. @@ -1270,6 +1348,15 @@ 0xFFE00038, // Bh 107 0xFFE6002E, // Hs 108 0xFFEB0026, // Mt 109 +}; + + public final static int[] altArgbsCpk = { + 0xFFFF1493, // Xx 0 + 0xFFBFA6A6, // Al 13 + 0xFFFFFF30, // S 16 + 0xFF57178F, // Cs 55 + 0xFFD9FFFF, // D 2H (He color) + 0xFFCC80FF, // T 3H (Li color) }; public final static int[] argbsCpkRasmol = { Modified: trunk/Jmol/src/org/jmol/viewer/ModelManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/ModelManager.java 2006-09-20 08:53:04 UTC (rev 5618) +++ trunk/Jmol/src/org/jmol/viewer/ModelManager.java 2006-09-20 15:41:14 UTC (rev 5619) @@ -591,11 +591,8 @@ } String getElementName(int i) { - try { - return JmolConstants.elementNames[frame.getAtomAt(i).getElementNumber()]; - } catch (Exception e) { - return ""; - } + return JmolConstants.elementNameFromNumber(frame.getAtomAt(i) + .getAtomicAndIsotopeNumber()); } String getAtomName(int i) { @@ -792,9 +789,9 @@ BitSet bsThis = new BitSet(); for (int i = getAtomCount(); --i >= 0;) if (bs.get(i)) - bsThis.set(frame.getAtomAt(i).elementNumber); + bsThis.set(frame.getAtomAt(i).getElementNumber()); for (int i = getAtomCount(); --i >= 0;) - if (bsThis.get(frame.getAtomAt(i).elementNumber)) + if (bsThis.get(frame.getAtomAt(i).getElementNumber())) bsResult.set(i); return bsResult; } Modified: trunk/Jmol/src/org/jmol/viewer/Token.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Token.java 2006-09-20 08:53:04 UTC (rev 5618) +++ trunk/Jmol/src/org/jmol/viewer/Token.java 2006-09-20 15:41:14 UTC (rev 5619) @@ -687,7 +687,7 @@ "atomno", new Token(atomno, "atomno"), "elemno", tokenElemno, - "_e", tokenElemno, + "_e", new Token(element, "element"), "resno", new Token(resno, "resno"), "temperature", new Token(temperature, "temperature"), "relativetemperature", null, This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2006-09-20 18:57:57
|
Revision: 5620 http://svn.sourceforge.net/jmol/?rev=5620&view=rev Author: hansonr Date: 2006-09-20 11:57:45 -0700 (Wed, 20 Sep 2006) Log Message: ----------- deuterium/tritium isotope support Modified Paths: -------------- trunk/Jmol/src/org/jmol/popup/JmolPopup.java trunk/Jmol/src/org/jmol/viewer/Atom.java trunk/Jmol/src/org/jmol/viewer/Frame.java trunk/Jmol/src/org/jmol/viewer/JmolConstants.java trunk/Jmol/src/org/jmol/viewer/ModelManager.java Modified: trunk/Jmol/src/org/jmol/popup/JmolPopup.java =================================================================== --- trunk/Jmol/src/org/jmol/popup/JmolPopup.java 2006-09-20 15:41:14 UTC (rev 5619) +++ trunk/Jmol/src/org/jmol/popup/JmolPopup.java 2006-09-20 18:57:45 UTC (rev 5620) @@ -78,7 +78,6 @@ return; removeAll(elementsComputedMenu); for (int i = 0; i < JmolConstants.elementNumberMax; ++i) { - //no isotopes here for now if (elementsPresentBitSet.get(i)) { String elementName = JmolConstants.elementNameFromNumber(i); String elementSymbol = JmolConstants.elementSymbolFromNumber(i); @@ -87,6 +86,17 @@ addMenuItem(elementsComputedMenu, entryName, script); } } + for (int i = JmolConstants.firstIsotope; i < JmolConstants.altElementMax; ++i) { + int n = JmolConstants.elementNumberMax + i; + if (elementsPresentBitSet.get(n)) { + n = JmolConstants.altElementNumberFromIndex(i); + String elementName = JmolConstants.elementNameFromNumber(n); + String elementSymbol = JmolConstants.elementSymbolFromNumber(n); + String entryName = elementSymbol + " - " + elementName; + String script = "select " + elementName; + addMenuItem(elementsComputedMenu, entryName, script); + } + } } void updateAaresiduesComputedMenu(BitSet groupsPresentBitSet) { Modified: trunk/Jmol/src/org/jmol/viewer/Atom.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Atom.java 2006-09-20 15:41:14 UTC (rev 5619) +++ trunk/Jmol/src/org/jmol/viewer/Atom.java 2006-09-20 18:57:45 UTC (rev 5620) @@ -993,7 +993,7 @@ strT = getAtomName(); break; case 'e': - strT = JmolConstants.elementSymbolFromNumber(atomicAndIsotopeNumber); + strT = getElementSymbol(); break; case 'x': floatT = x; @@ -1299,19 +1299,4 @@ return group.isPyrimidine(); } - //////////////////////////////////////////////////////////////// - - Hashtable getPublicProperties() { - Hashtable ht = new Hashtable(); - ht.put("element", getElementSymbol()); - 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())); - ht.put("radius", new Double(getRadius())); - ht.put("atomNumber", new Integer(getAtomNumber())); - return ht; - } } Modified: trunk/Jmol/src/org/jmol/viewer/Frame.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Frame.java 2006-09-20 15:41:14 UTC (rev 5619) +++ trunk/Jmol/src/org/jmol/viewer/Frame.java 2006-09-20 18:57:45 UTC (rev 5620) @@ -2091,8 +2091,13 @@ void findElementsPresent() { elementsPresent = new BitSet(); - for (int i = atomCount; --i >= 0;) - elementsPresent.set(atoms[i].getElementNumber()); + for (int i = atomCount; --i >= 0;) { + int n = atoms[i].getAtomicAndIsotopeNumber(); + if (n >= 256) + n = JmolConstants.elementNumberMax + + JmolConstants.altElementIndexFromNumber(n); + elementsPresent.set(n); + } } BitSet getElementsPresentBitSet() { Modified: trunk/Jmol/src/org/jmol/viewer/JmolConstants.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2006-09-20 15:41:14 UTC (rev 5619) +++ trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2006-09-20 18:57:45 UTC (rev 5620) @@ -338,7 +338,7 @@ * @param elementSymbol First char must be upper case, second char accepts upper or lower case * @return elementNumber = atomicNumber + IsotopeNumber*256 */ - public static short elementNumberFromSymbol(String elementSymbol) { + public final static short elementNumberFromSymbol(String elementSymbol) { if (htElementMap == null) { Hashtable map = new Hashtable(); for (int elementNumber = elementNumberMax; --elementNumber >= 0;) { @@ -539,7 +539,7 @@ return i; return 0; } - + private final static short[] altElementNumbers = { 0, 13, @@ -549,8 +549,6 @@ 1 + (3 << 8), // T = 1 + 3*256 }; - private final static int firstIsotope = 4; - private final static String[] altElementSymbols = { "Xx", "Al", @@ -569,10 +567,24 @@ "tritium" }; + public final static int[] altArgbsCpk = { + 0xFFFF1493, // Xx 0 + 0xFFBFA6A6, // Al 13 + 0xFFFFFF30, // S 16 + 0xFF57178F, // Cs 55 + 0xFFD9FFFF, // D 2H (He color) + 0xFFCC80FF, // T 3H (Li color) + }; + /** + * first entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arrays + */ + public final static int firstIsotope = 4; + + /** * length of the altElementSymbols, altElementNames, altElementNumbers arrays */ - final static int altElementMax = altElementNumbers.length; + public final static int altElementMax = altElementNumbers.length; /** * Default table of van der Waals Radii. @@ -1350,15 +1362,6 @@ 0xFFEB0026, // Mt 109 }; - public final static int[] altArgbsCpk = { - 0xFFFF1493, // Xx 0 - 0xFFBFA6A6, // Al 13 - 0xFFFFFF30, // S 16 - 0xFF57178F, // Cs 55 - 0xFFD9FFFF, // D 2H (He color) - 0xFFCC80FF, // T 3H (Li color) - }; - public final static int[] argbsCpkRasmol = { 0x00FF1493 + ( 0 << 24), // Xx 0 0x00FFFFFF + ( 1 << 24), // H 1 @@ -2255,7 +2258,7 @@ // "@solvent _g>=70 & _g<=74", // water or ions "@hoh water", - "@water _g>=70 & _g<=72, oxygen & connected(2, hydrogen), hydrogen & connected(oxygen & connected(2, hydrogen))", + "@water _g>=70 & _g<=72, oxygen & connected(2, hydrogen or deuterium or tritium), (hydrogen or deuterium and tritium) & connected(oxygen & connected(2, hydrogen or deuterium or tritium))", "@ions _g=73,_g=74", // Modified: trunk/Jmol/src/org/jmol/viewer/ModelManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/ModelManager.java 2006-09-20 15:41:14 UTC (rev 5619) +++ trunk/Jmol/src/org/jmol/viewer/ModelManager.java 2006-09-20 18:57:45 UTC (rev 5620) @@ -789,9 +789,9 @@ BitSet bsThis = new BitSet(); for (int i = getAtomCount(); --i >= 0;) if (bs.get(i)) - bsThis.set(frame.getAtomAt(i).getElementNumber()); + bsThis.set(getElementNumber(i)); for (int i = getAtomCount(); --i >= 0;) - if (bsThis.get(frame.getAtomAt(i).getElementNumber())) + if (bsThis.get(getElementNumber(i))) bsResult.set(i); return bsResult; } @@ -1041,7 +1041,7 @@ Hashtable info = new Hashtable(); getAtomIdentityInfo(i, info); info.put("element", getElementName(i)); - info.put("elemno", new Integer(atom.getElementNumber())); + info.put("elemno", new Integer(getElementNumber(i))); info.put("x", new Float(getAtomX(i))); info.put("y", new Float(getAtomY(i))); info.put("z", new Float(getAtomZ(i))); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2006-09-21 01:52:00
|
Revision: 5627 http://svn.sourceforge.net/jmol/?rev=5627&view=rev Author: hansonr Date: 2006-09-20 18:51:49 -0700 (Wed, 20 Sep 2006) Log Message: ----------- cartoonRocket fix for erratic behavior of rockets when small Modified Paths: -------------- trunk/Jmol/src/org/jmol/g3d/Cylinder3D.java trunk/Jmol/src/org/jmol/viewer/CartoonRenderer.java trunk/Jmol/src/org/jmol/viewer/MpsRenderer.java Modified: trunk/Jmol/src/org/jmol/g3d/Cylinder3D.java =================================================================== --- trunk/Jmol/src/org/jmol/g3d/Cylinder3D.java 2006-09-20 22:53:13 UTC (rev 5626) +++ trunk/Jmol/src/org/jmol/g3d/Cylinder3D.java 2006-09-21 01:51:49 UTC (rev 5627) @@ -112,6 +112,7 @@ void renderBits(short colixA, short colixB, byte endcaps, int diameter, float xA, float yA, float zA, float xB, float yB, float zB) { + // oops -- problem here if diameter < 0 is that we may have already clipped it! int r = diameter / 2 + 1; int codeMinA = line3d.clipCode((int)xA - r, (int)yA - r, (int)zA - r); int codeMaxA = line3d.clipCode((int)xA + r, (int)yA + r, (int)zA + r); @@ -129,7 +130,6 @@ Graphics3D.isColixTranslucent(colixB), (int)xA, (int)yA, (int)zA, (int)dxB, (int)dyB, (int)dzB, notClipped); return; } - //System.out.println("cyl "+diameter+" "+this.diameter); if (diameter > 0) { this.diameter = diameter; this.xAf = xA; this.yAf = yA; this.zAf = zA; Modified: trunk/Jmol/src/org/jmol/viewer/CartoonRenderer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/CartoonRenderer.java 2006-09-20 22:53:13 UTC (rev 5626) +++ trunk/Jmol/src/org/jmol/viewer/CartoonRenderer.java 2006-09-21 01:51:49 UTC (rev 5627) @@ -124,17 +124,16 @@ isNucleicPolymer ? 1f / 1000 : 0.5f / 1000); ribbonBottomScreens = calcScreens(leadMidpoints, wingVectors, mads, isNucleicPolymer ? 0f : -0.5f / 1000); - if (!renderAsRockets || isNucleicPolymer || isCarbohydratePolymer) - return true; - cordMidPoints = calcRopeMidPoints((AminoPolymer) polymer, newRockets); + if (!isNucleicPolymer) + calcRopeMidPoints((AminoPolymer) polymer, newRockets); getScreens(); clearPending(); return true; } - Point3f[] calcRopeMidPoints(AminoPolymer aminopolymer, boolean isNewStyle) { + void calcRopeMidPoints(AminoPolymer aminopolymer, boolean isNewStyle) { int midPointCount = monomerCount + 1; - Point3f[] cordMidPoints = viewer.allocTempPoints(midPointCount); + cordMidPoints = viewer.allocTempPoints(midPointCount); ProteinStructure proteinstructurePrev = null; Point3f point; for (int i = 0; i < monomerCount; ++i) { @@ -161,7 +160,6 @@ point.set(proteinstructurePrev.getAxisEndPoint()); else aminopolymer.getLeadMidPoint(monomerCount, point); - return cordMidPoints; } void getScreens() { @@ -263,7 +261,7 @@ lastWasHelix = isHelix; } } - renderPending(true); + renderPendingRocketSegment(true); viewer.freeTempScreens(screens); viewer.freeTempPoints(cordMidPoints); viewer.freeTempPoints(screensf); @@ -289,7 +287,7 @@ ++endIndexPending; return; } - renderPending(isEnd); + renderPendingRocketSegment(isEnd); } proteinstructurePending = proteinstructure; startIndexPending = endIndexPending = proteinstructure.getIndex(monomer); @@ -302,7 +300,7 @@ Point3f screenB = new Point3f(); Point3f screenC = new Point3f(); - void renderPending(boolean isEnd) { + void renderPendingRocketSegment(boolean isEnd) { if (!tPending) return; tPending = false; @@ -310,14 +308,14 @@ Point3f[] segments = proteinstructurePending.getSegments(); boolean tEnd = (endIndexPending == proteinstructurePending .getMonomerCount() - 1); - renderPendingHelix(segments[startIndexPending], + renderPendingRocketSegment(segments[startIndexPending], segments[endIndexPending], segments[endIndexPending + 1], tEnd, startIndexPending == 0); //System.out.println("renderP " + startIndexPending + " " + endIndexPending // + " " + tEnd + " " + isEnd); } } - void renderPendingHelix(Point3f pointStart, Point3f pointBeforeEnd, + void renderPendingRocketSegment(Point3f pointStart, Point3f pointBeforeEnd, Point3f pointEnd, boolean tEnd, boolean isEnd) { viewer.transformPoint(pointStart, screenA); viewer.transformPoint(pointEnd, screenB); @@ -332,6 +330,7 @@ screenC, screenB); lastDiameter=coneDiameter; } else { + // System.out.println(screenB + " " + screenC + " " + diameter + " diam" ); g3d.fillCylinderBits(colixPending, Graphics3D.ENDCAPS_FLAT, diameter, screenB, screenC); lastDiameter = Integer.MAX_VALUE; @@ -342,9 +341,17 @@ screenB = screenC; screenC = t; } - //System.out.println("cartoonrender diameter a b "+diameter+screenA+screenB); - g3d.fillCylinderBits(colixPending, Graphics3D.ENDCAPS_FLAT, (diameter == lastDiameter ? -1 : diameter), +/* + * well this was an idea that appears to be too complicated for now at least -- + * when drawing a cylinder draw just the beginning and the end rather than each + * segment. So.... back to the original for now. + * + * g3d.fillCylinderBits(colixPending, Graphics3D.ENDCAPS_FLAT, (diameter == lastDiameter ? -1 : diameter), screenA, screenB); +*/ + g3d.fillCylinderBits(colixPending, Graphics3D.ENDCAPS_FLAT, diameter, + screenA, screenB); + lastDiameter = diameter; } Modified: trunk/Jmol/src/org/jmol/viewer/MpsRenderer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/MpsRenderer.java 2006-09-20 22:53:13 UTC (rev 5626) +++ trunk/Jmol/src/org/jmol/viewer/MpsRenderer.java 2006-09-21 01:51:49 UTC (rev 5627) @@ -98,8 +98,13 @@ if (! isSpecials[iNext1]) madEnd = (mads[iNext1] + madThis) / 2; } - int diameterBeg = + int diameterBeg = 0; + try{ + diameterBeg = viewer.scaleToScreen(leadMidpointScreens[i].z, madBeg); + }catch (Exception e) { + System.out.println(i); + } int diameterEnd = viewer.scaleToScreen(leadMidpointScreens[iNext1].z, madEnd); int diameterMid = This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2006-09-22 15:09:26
|
Revision: 5654 http://svn.sourceforge.net/jmol/?rev=5654&view=rev Author: hansonr Date: 2006-09-22 08:09:20 -0700 (Fri, 22 Sep 2006) Log Message: ----------- unnecessary comments out Modified Paths: -------------- trunk/Jmol/src/org/jmol/applet/Jmol.java trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/applet/Jmol.java =================================================================== --- trunk/Jmol/src/org/jmol/applet/Jmol.java 2006-09-22 15:05:13 UTC (rev 5653) +++ trunk/Jmol/src/org/jmol/applet/Jmol.java 2006-09-22 15:09:20 UTC (rev 5654) @@ -823,7 +823,7 @@ } public void showConsole(boolean showConsole) { - Logger.info("JmolApplet.showConsole(" + showConsole + ")"); + //Logger.info("JmolApplet.showConsole(" + showConsole + ")"); if (jvm12 != null) jvm12.showConsole(showConsole); } Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2006-09-22 15:05:13 UTC (rev 5653) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2006-09-22 15:09:20 UTC (rev 5654) @@ -117,11 +117,12 @@ Logger.info(JmolConstants.copyright + "\nJmol Version " + getJmolVersion() + "\njava.vendor:" + strJavaVendor + "\njava.version:" + strJavaVersion - + "\nos.name:" + strOSName); - Logger.info(htmlName + " jvm11orGreater=" + jvm11orGreater + + "\nos.name:" + strOSName + "\n" + htmlName); +/* + Logger.info("jvm11orGreater=" + jvm11orGreater + "\njvm12orGreater=" + jvm12orGreater + "\njvm14orGreater=" + jvm14orGreater); - +*/ g3d = new Graphics3D(awtComponent); eval = new Eval(this); statusManager = new StatusManager(this); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2006-09-22 17:58:22
|
Revision: 5655 http://svn.sourceforge.net/jmol/?rev=5655&view=rev Author: hansonr Date: 2006-09-22 10:58:05 -0700 (Fri, 22 Sep 2006) Log Message: ----------- first draft isosurface MEP calculation. minor optimization of QM calculation. Modified Paths: -------------- trunk/Jmol/src/org/jmol/quantum/QuantumCalculation.java trunk/Jmol/src/org/jmol/viewer/Eval.java trunk/Jmol/src/org/jmol/viewer/Isosurface.java Added Paths: ----------- trunk/Jmol/src/org/jmol/quantum/MepCalculation.java Added: trunk/Jmol/src/org/jmol/quantum/MepCalculation.java =================================================================== --- trunk/Jmol/src/org/jmol/quantum/MepCalculation.java (rev 0) +++ trunk/Jmol/src/org/jmol/quantum/MepCalculation.java 2006-09-22 17:58:05 UTC (rev 5655) @@ -0,0 +1,174 @@ +/* $RCSfile$ + * $Author: hansonr $ + * $Date: 2006-05-13 19:17:06 -0500 (Sat, 13 May 2006) $ + * $Revision: 5114 $ + * + * Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org + * + * Contact: mi...@jm... + * + * 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.quantum; + +import javax.vecmath.Point3f; + +import org.jmol.viewer.Atom; + +/* + * a simple molecular electrostatic potential cube generator + * just using q/r here + * + * http://teacher.pas.rochester.edu/phy122/Lecture_Notes/Chapter25/Chapter25.html + * + * applying some of the tricks in QuantumCalculation for speed + * + */ +public class MepCalculation { + + final static float bohr_per_angstrom = 1 / 0.52918f; + + public static int MAX_GRID = 40; + + // grid coordinates relative t o charge center in Bohr + float[] X = new float[MAX_GRID]; + float[] Y = new float[MAX_GRID]; + float[] Z = new float[MAX_GRID]; + + // grid coordinate squares relative to charge center in Bohr + float[] X2 = new float[MAX_GRID]; + float[] Y2 = new float[MAX_GRID]; + float[] Z2 = new float[MAX_GRID]; + + Atom[] atoms; + float[] mepCharges; + + Point3f[] atomCoordBohr; + // absolute grid coordinates in Bohr + float[][] xyzBohr = new float[MAX_GRID][3]; + + float[][][] voxelData; + int[] countsXYZ; + float[] originBohr = new float[3]; + float[] stepBohr = new float[3]; + + public MepCalculation() { + } + + public MepCalculation(Atom[] atoms, float[] mepCharges) { + this.atoms = atoms; + this.mepCharges = mepCharges; + } + + public void createMepCube(float[][][] voxelData, int[] countsXYZ, + float[] originXYZ, float[] stepsXYZ) { + this.voxelData = voxelData; + this.countsXYZ = countsXYZ; + setupCoordinates(originXYZ, stepsXYZ); + processMep(); + } + + private void setupCoordinates(float[] originXYZ, float[] stepsXYZ) { + + // all coordinates come in as angstroms, not bohr, and are converted here into bohr + + for (int i = 3; --i >= 0;) { + originBohr[i] = originXYZ[i] * bohr_per_angstrom; + stepBohr[i] = stepsXYZ[i] * bohr_per_angstrom; + } + for (int i = 3; --i >= 0;) { + xyzBohr[0][i] = originBohr[i]; + int n = countsXYZ[i]; + float inc = stepBohr[i]; + for (int j = 0; ++j < n;) + xyzBohr[j][i] = xyzBohr[j - 1][i] + inc; + } + /* + * allowing null atoms allows for selectively removing + * atoms from the rendering. Maybe a first time this has ever been done? + * + */ + atomCoordBohr = new Point3f[atoms.length]; + for (int i = 0; i < atoms.length; i++) { + if (atoms[i] == null) + continue; + atomCoordBohr[i] = new Point3f(atoms[i]); + atomCoordBohr[i].scale(bohr_per_angstrom); + } + } + + private void processMep() { + setMinMax(); + int firstAtom = 0; + int lastAtom = atomCoordBohr.length; + for (int i = 0; i < lastAtom; i++) + if (atomCoordBohr[i] != null) { + firstAtom = i; + break; + } + for (int i = lastAtom; --i >= firstAtom;) + if (atomCoordBohr[i] != null) { + lastAtom = i + 1; + break; + } + + for (int atomIndex = firstAtom; atomIndex < lastAtom; atomIndex++) { + if (atomCoordBohr[atomIndex] == null) + continue; + float x = atomCoordBohr[atomIndex].x; + float y = atomCoordBohr[atomIndex].y; + float z = atomCoordBohr[atomIndex].z; + float charge = mepCharges[atomIndex]; + for (int i = countsXYZ[0]; --i >= 0;) { + X2[i] = X[i] = xyzBohr[i][0] - x; + X2[i] *= X[i]; + } + for (int i = countsXYZ[1]; --i >= 0;) { + Y2[i] = Y[i] = xyzBohr[i][1] - y; + Y2[i] *= Y[i]; + } + for (int i = countsXYZ[2]; --i >= 0;) { + Z2[i] = Z[i] = xyzBohr[i][2] - z; + Z2[i] *= Z[i]; + } + for (int ix = xMax; --ix >= xMin;) { + for (int iy = yMax; --iy >= yMin;) + for (int iz = zMax; --iz >= zMin;) { + float d2 = X2[ix] + Y2[iy] + Z2[iz]; + voxelData[ix][iy][iz] += (d2 == 0 ? charge + * Float.POSITIVE_INFINITY : charge / (float) Math.sqrt(d2)); + } + } + } + } + + int xMin; + int xMax; + int yMin; + int yMax; + int zMin; + int zMax; + + private void setMinMax() { + // optimization will come later + xMin = 0; + yMin = 0; + zMin = 0; + xMax = countsXYZ[0]; + yMax = countsXYZ[1]; + zMax = countsXYZ[2]; + } + +} Modified: trunk/Jmol/src/org/jmol/quantum/QuantumCalculation.java =================================================================== --- trunk/Jmol/src/org/jmol/quantum/QuantumCalculation.java 2006-09-22 15:09:20 UTC (rev 5654) +++ trunk/Jmol/src/org/jmol/quantum/QuantumCalculation.java 2006-09-22 17:58:05 UTC (rev 5655) @@ -246,16 +246,19 @@ + nGaussians + " atom=" + atomIndex); if (atomIndex != lastAtom && atomCoordBohr[atomIndex] != null) { //Logger.("processSTO center " + atomCoordBohr[atomIndex]); + float x = atomCoordBohr[atomIndex].x; + float y = atomCoordBohr[atomIndex].y; + float z = atomCoordBohr[atomIndex].z; for (int i = countsXYZ[0]; --i >= 0;) { - X2[i] = X[i] = xyzBohr[i][0] - atomCoordBohr[atomIndex].x; + X2[i] = X[i] = xyzBohr[i][0] - x; X2[i] *= X[i]; } for (int i = countsXYZ[1]; --i >= 0;) { - Y2[i] = Y[i] = xyzBohr[i][1] - atomCoordBohr[atomIndex].y; + Y2[i] = Y[i] = xyzBohr[i][1] - y; Y2[i] *= Y[i]; } for (int i = countsXYZ[2]; --i >= 0;) { - Z2[i] = Z[i] = xyzBohr[i][2] - atomCoordBohr[atomIndex].z; + Z2[i] = Z[i] = xyzBohr[i][2] - z; Z2[i] *= Z[i]; } } Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-22 15:09:20 UTC (rev 5654) +++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-22 17:58:05 UTC (rev 5655) @@ -4819,6 +4819,10 @@ boolean surfaceObjectSeen = false; float[] nlmZ = new float[5]; String str; + int modelIndex = viewer.getDisplayModelIndex(); + if (modelIndex < 0) + evalError("the isosurface command requires that only one model be displayed"); + for (int i = 1; i < statementLength; ++i) { String propertyName = null; Object propertyValue = null; @@ -5102,6 +5106,18 @@ setMoData(JmolConstants.SHAPE_ISOSURFACE, moNumber, null); surfaceObjectSeen = true; continue; + case Token.mep: + float[] partialCharges = null; + try { + partialCharges = viewer.getFrame().partialCharges; + } catch (Exception e) { + } + if (partialCharges == null) + evalError("No partial charges were read from the file; Jmol needs these to render the MEP data."); + surfaceObjectSeen = true; + propertyName = "mep"; + propertyValue = partialCharges; + break; case Token.sasurface: case Token.solvent: surfaceObjectSeen = true; Modified: trunk/Jmol/src/org/jmol/viewer/Isosurface.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Isosurface.java 2006-09-22 15:09:20 UTC (rev 5654) +++ trunk/Jmol/src/org/jmol/viewer/Isosurface.java 2006-09-22 17:58:05 UTC (rev 5655) @@ -110,6 +110,7 @@ import org.jmol.g3d.Graphics3D; import org.jmol.quantum.QuantumCalculation; +import org.jmol.quantum.MepCalculation; class Isosurface extends MeshCollection { @@ -131,6 +132,7 @@ final static float defaultMappedDataMin = 0f; final static float defaultMappedDataMax = 1.0f; final static float defaultCutoff = 0.02f; + final static float defaultMepCutoff = 0.05f; final static float defaultOrbitalCutoff = 0.14f; final static float defaultQMOrbitalCutoff = 0.050f; // WebMO final static int defaultContourCount = 11; //odd is better @@ -158,6 +160,8 @@ float resolution; boolean insideOut; //no longer does anything now that we are forcing 2-sided triangles + float[] mepCharges; + int qmOrbitalType; int qmOrbitalCount; final static int QM_TYPE_UNKNOWN = 0; @@ -165,6 +169,7 @@ final static int QM_TYPE_SLATER = 2; Hashtable moData; float[] moCoefficients; + boolean precalculateVoxelData; Vector functionXYinfo; String lcaoType; @@ -201,6 +206,7 @@ final static int SURFACE_SASURFACE = 12 | IS_SOLVENTTYPE | NO_ANISOTROPY; final static int SURFACE_MOLECULARORBITAL = 13; final static int SURFACE_ATOMICORBITAL = 14; + final static int SURFACE_MEP = 15 | NO_ANISOTROPY; final static int SURFACE_FILE = 16; float solventRadius; @@ -607,6 +613,24 @@ } } + if ("mep" == propertyName) { + mepCharges = (float[]) value; + isEccentric = isAnisotropic = false; + dataType = SURFACE_MEP; + if (state == STATE_DATA_READ) { + propertyName = "mapColor"; + } else { + colorBySign = true; + colorByPhase = true; + colorPhase = 0; + if (cutoff == Float.MAX_VALUE) + cutoff = defaultMepCutoff; + isCutoffAbsolute = (cutoff > 0 && !isPositiveOnly); + isBicolorMap = true; + propertyName = "getSurface"; + } + } + if ("hydrogenOrbital" == propertyName) { dataType = SURFACE_ATOMICORBITAL; float[] nlmZ = (float[]) value; @@ -1035,6 +1059,9 @@ case SURFACE_FUNCTIONXY: setupFunctionXY(); break; + case SURFACE_MEP: + setupMep(); + break; case SURFACE_FILE: default: readTitleLines(); @@ -1253,6 +1280,8 @@ } if (dataType == SURFACE_MOLECULARORBITAL) generateQuantumCube(); + else if (dataType == SURFACE_MEP) + generateMepCube(); else Logger.error("code error -- isPrecalculation, but how?"); if (isMapData || thePlane != null) @@ -1301,6 +1330,7 @@ voxelValue = getPsi(x, y, z); break; case SURFACE_MOLECULARORBITAL: + case SURFACE_MEP: voxelValue = strip[z]; //precalculated break; case SURFACE_FUNCTIONXY: @@ -4038,6 +4068,106 @@ } } + /////// molecular electrostatic potential /////// + + int mep_gridMax = MepCalculation.MAX_GRID; + float mep_ptsPerAngstrom = 3f; + float mep_marginAngstroms = 1f; // may have to adjust this + int mep_nAtoms; + + Atom[] mep_atoms; + + void setupMep() { + Atom[] atoms = frame.atoms; + Point3f xyzMin = new Point3f(Float.MAX_VALUE, Float.MAX_VALUE, + Float.MAX_VALUE); + Point3f xyzMax = new Point3f(-Float.MAX_VALUE, -Float.MAX_VALUE, + -Float.MAX_VALUE); + int modelIndex = viewer.getDisplayModelIndex(); + int iAtom = 0; + int nSelected = 0; + int nAtoms = viewer.getAtomCount(); + for (int i = 0; i < nAtoms; i++) + if (atoms[i].modelIndex == modelIndex) { + ++iAtom; + if (bsSelected != null && bsSelected.get(i)) + ++nSelected; + } + mep_nAtoms = iAtom; + if (nSelected > 0) + Logger.info(nSelected + " of " + mep_nAtoms + + " atoms will be used in the orbital calculation"); + if (mep_nAtoms > 0) + mep_atoms = new Atom[mep_nAtoms]; + iAtom = 0; + for (int i = 0; i < nAtoms; i++) { + Atom atom = atoms[i]; + if (atom.modelIndex != modelIndex) + continue; + Point3f pt = new Point3f(atom); + if (nSelected == 0 || bsSelected.get(i)) { + float rA = atom.getVanderwaalsRadiusFloat() + mep_marginAngstroms; + if (pt.x - rA < xyzMin.x) + xyzMin.x = pt.x - rA; + if (pt.x + rA > xyzMax.x) + xyzMax.x = pt.x + rA; + if (pt.y - rA < xyzMin.y) + xyzMin.y = pt.y - rA; + if (pt.y + rA > xyzMax.y) + xyzMax.y = pt.y + rA; + if (pt.z - rA < xyzMin.z) + xyzMin.z = pt.z - rA; + if (pt.z + rA > xyzMax.z) + xyzMax.z = pt.z + rA; + mep_atoms[iAtom++] = atom; + } else { + ++iAtom; + } + } + if (!Float.isNaN(scale)) { + Vector3f v = new Vector3f(xyzMax); + v.sub(xyzMin); + v.scale(0.5f); + xyzMin.add(v); + v.scale(scale); + xyzMax.set(xyzMin); + xyzMax.add(v); + xyzMin.sub(v); + } + + Logger.info("MEP range bohr " + xyzMin + " to " + xyzMax); + jvxlFileHeader = "MEP range bohr " + xyzMin + " to " + xyzMax + "\n"; + + int maxGrid = mep_gridMax; + + setVoxelRange(0, xyzMin.x, xyzMax.x, mep_ptsPerAngstrom, maxGrid); + setVoxelRange(1, xyzMin.y, xyzMax.y, mep_ptsPerAngstrom, maxGrid); + setVoxelRange(2, xyzMin.z, xyzMax.z, mep_ptsPerAngstrom, maxGrid); + jvxlFileHeader += jvxlGetVolumeHeader(iAtom); + Point3f pt = new Point3f(); + for (int i = 0; i < nAtoms; i++) { + Atom atom = atoms[i]; + if (atom.modelIndex != modelIndex) + continue; + pt.set(atom); + pt.scale(1 / ANGSTROMS_PER_BOHR); + jvxlFileHeader += atom.getAtomicAndIsotopeNumber() + " " + + atom.getAtomicAndIsotopeNumber() + ".0 " + pt.x + " " + pt.y + " " + + pt.z + "\n"; + } + atomCount = -Integer.MAX_VALUE; + negativeAtomCount = false; + precalculateVoxelData = true; + } + + void generateMepCube() { + float[] origin = { volumetricOrigin.x, volumetricOrigin.y, + volumetricOrigin.z }; + MepCalculation m = new MepCalculation(mep_atoms, mepCharges); + m.createMepCube(voxelData, voxelCounts, origin, + volumetricVectorLengths); + } + ///// solvent-accessible, solvent-excluded surface ////// float solvent_ptsPerAngstrom = 2f; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2006-09-24 08:27:16
|
Revision: 5689 http://svn.sourceforge.net/jmol/?rev=5689&view=rev Author: nicove Date: 2006-09-24 01:26:55 -0700 (Sun, 24 Sep 2006) Log Message: ----------- i18n Modified Paths: -------------- trunk/Jmol/src/org/jmol/popup/JmolPopup.java trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po Modified: trunk/Jmol/src/org/jmol/popup/JmolPopup.java =================================================================== --- trunk/Jmol/src/org/jmol/popup/JmolPopup.java 2006-09-24 07:01:15 UTC (rev 5688) +++ trunk/Jmol/src/org/jmol/popup/JmolPopup.java 2006-09-24 08:26:55 UTC (rev 5689) @@ -24,6 +24,7 @@ package org.jmol.popup; import org.jmol.api.*; +import org.jmol.i18n.GT; import org.jmol.viewer.JmolConstants; import java.awt.Component; import java.awt.event.ActionEvent; @@ -125,13 +126,19 @@ viewer.getBooleanProperty("hideNameInPopup") ? hiddenModelSetName : modelSetName); enableMenu(modelSetInfoMenu, true); - addMenuItem(modelSetInfoMenu, "atoms:" + viewer.getAtomCount()); - addMenuItem(modelSetInfoMenu, "bonds:" + viewer.getBondCount()); + addMenuItem(modelSetInfoMenu, + GT._("atoms: {0}", new Object[] { new Integer(viewer.getAtomCount()) })); + addMenuItem(modelSetInfoMenu, + GT._("bonds: {0}", new Object[] { new Integer(viewer.getBondCount()) })); addMenuSeparator(modelSetInfoMenu); - addMenuItem(modelSetInfoMenu, "groups:" + viewer.getGroupCount()); - addMenuItem(modelSetInfoMenu, "chains:" + viewer.getChainCount()); - addMenuItem(modelSetInfoMenu, "polymers:" + viewer.getPolymerCount()); - addMenuItem(modelSetInfoMenu, "models:" + viewer.getModelCount()); + addMenuItem(modelSetInfoMenu, + GT._("groups: {0}", new Object[] { new Integer(viewer.getGroupCount()) })); + addMenuItem(modelSetInfoMenu, + GT._("chains: {0}", new Object[] { new Integer(viewer.getChainCount()) })); + addMenuItem(modelSetInfoMenu, + GT._("polymers: {0}", new Object[] { new Integer(viewer.getPolymerCount()) })); + addMenuItem(modelSetInfoMenu, + GT._("models: {0}", new Object[] { new Integer(viewer.getModelCount()) })); if (viewer.showModelSetDownload() && !viewer.getBooleanProperty("hideNameInPopup")) { addMenuSeparator(modelSetInfoMenu); @@ -152,24 +159,25 @@ addMenuItem(aboutMenu, viewer.getJavaVendor()); addMenuItem(aboutMenu, viewer.getJavaVersion()); addMenuSeparator(aboutMenu); - addMenuItem(aboutMenu, "Java memory usage"); + addMenuItem(aboutMenu, GT._("Java memory usage")); Runtime runtime = Runtime.getRuntime(); runtime.gc(); long mbTotal = convertToMegabytes(runtime.totalMemory()); long mbFree = convertToMegabytes(runtime.freeMemory()); long mbMax = convertToMegabytes(maxMemoryForNewerJvm()); - addMenuItem(aboutMenu, "" + mbTotal + " Mb total"); - addMenuItem(aboutMenu, "" + mbFree + " Mb free"); + addMenuItem(aboutMenu, GT._("{0} Mb total", new Object[] { new Long(mbTotal) })); + addMenuItem(aboutMenu, GT._("{0} Mb free", new Object[] { new Long(mbFree) })); if (mbMax > 0) - addMenuItem(aboutMenu, "" + mbMax + " Mb maximum"); + addMenuItem(aboutMenu, GT._("{0} Mb maximum", new Object[] { new Long(mbMax) })); else - addMenuItem(aboutMenu, "unknown maximum"); + addMenuItem(aboutMenu, GT._("unknown maximum")); int availableProcessors = availableProcessorsForNewerJvm(); if (availableProcessors > 0) - addMenuItem(aboutMenu, "" + availableProcessors + - (availableProcessors == 1 ? " processor" : " processors")); + addMenuItem(aboutMenu, (availableProcessors == 1) ? + GT._("1 processor") : + GT._("{0} processors", new Object[] { new Integer(availableProcessors) } )); else - addMenuItem(aboutMenu, "unknown processor count"); + addMenuItem(aboutMenu, GT._("unknown processor count")); } private long convertToMegabytes(long num) { Modified: trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java =================================================================== --- trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java 2006-09-24 07:01:15 UTC (rev 5688) +++ trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java 2006-09-24 08:26:55 UTC (rev 5689) @@ -761,11 +761,11 @@ { "bondMenu", GT._("Bonds") }, { "bondNone", GT._("Off") }, { "bondWireframe", GT._("On") }, - { "bond100", "0.10 \u00C5" }, - { "bond150", "0.15 \u00C5" }, - { "bond200", "0.20 \u00C5" }, - { "bond250", "0.25 \u00C5" }, - { "bond300", "0.30 \u00C5" }, + { "bond100", GT._("{0} \u00C5", new Object[] { "0.10" })}, + { "bond150", GT._("{0} \u00C5", new Object[] { "0.15" }) }, + { "bond200", GT._("{0} \u00C5", new Object[] { "0.20" }) }, + { "bond250", GT._("{0} \u00C5", new Object[] { "0.25" }) }, + { "bond300", GT._("{0} \u00C5", new Object[] { "0.30" }) }, { "hbondMenu", GT._("Hydrogen Bonds") }, { "hbondNone", GT._("Off") }, @@ -773,22 +773,22 @@ { "hbondWireframe", GT._("On") }, { "hbondSidechain", GT._("Set H-Bonds Side Chain") }, { "hbondBackbone", GT._("Set H-Bonds Backbone") }, - { "hbond100", "0.10 \u00C5" }, - { "hbond150", "0.15 \u00C5" }, - { "hbond200", "0.20 \u00C5" }, - { "hbond250", "0.25 \u00C5" }, - { "hbond300", "0.30 \u00C5" }, + { "hbond100", GT._("{0} \u00C5", new Object[] { "0.10" }) }, + { "hbond150", GT._("{0} \u00C5", new Object[] { "0.15" }) }, + { "hbond200", GT._("{0} \u00C5", new Object[] { "0.20" }) }, + { "hbond250", GT._("{0} \u00C5", new Object[] { "0.25" }) }, + { "hbond300", GT._("{0} \u00C5", new Object[] { "0.30" }) }, { "ssbondMenu", GT._("Disulfide Bonds") }, { "ssbondNone", GT._("Off") }, { "ssbondWireframe", GT._("On") }, { "ssbondSidechain", GT._("Set SS-Bonds Side Chain") }, { "ssbondBackbone", GT._("Set SS-Bonds Backbone") }, - { "ssbond100", "0.10 \u00C5" }, - { "ssbond150", "0.15 \u00C5" }, - { "ssbond200", "0.20 \u00C5" }, - { "ssbond250", "0.25 \u00C5" }, - { "ssbond300", "0.30 \u00C5" }, + { "ssbond100", GT._("{0} \u00C5", new Object[] { "0.10" }) }, + { "ssbond150", GT._("{0} \u00C5", new Object[] { "0.15" }) }, + { "ssbond200", GT._("{0} \u00C5", new Object[] { "0.20" }) }, + { "ssbond250", GT._("{0} \u00C5", new Object[] { "0.25" }) }, + { "ssbond300", GT._("{0} \u00C5", new Object[] { "0.30" }) }, { "structureMenu", GT._("Structures") }, { "structureNone", GT._("Off") }, @@ -801,8 +801,8 @@ { "vectorOff", GT._("Off") }, { "vectorOn", GT._("On") }, { "vector3", GT._("{0} pixels", new Object[]{ "3" }) }, - { "vector005", "0.05 \u00C5" }, - { "vector01", "0.1 \u00C5" }, + { "vector005", GT._("{0} \u00C5", new Object[] { "0.05" })}, + { "vector01", GT._("{0} \u00C5", new Object[] { "0.10" })}, { "vectorScale02", GT._("Scale {0}", new Object[]{ "0.2" }) }, { "vectorScale05", GT._("Scale {0}", new Object[]{ "0.5" }) }, { "vectorScale1", GT._("Scale {0}", new Object[]{ "1" }) }, @@ -920,7 +920,7 @@ { "colorSSbondWhite", GT._("White") }, { "colorSSbondCyan", GT._("Cyan") }, - { "colorBackboneMenu", "Backbone" }, + { "colorBackboneMenu", GT._("Backbone") }, { "colorBackboneInherit", GT._("Inherit") }, { "colorBackboneSchemeMenu", GT._("By Scheme") }, @@ -1066,7 +1066,7 @@ { "spinx50", "50" }, { "setSpinYMenu", GT._("Set Y Rate") }, - { "spiny0", "set spin y 0" }, + { "spiny0", "0" }, { "spiny5", "5" }, { "spiny10", "10" }, { "spiny20", "20" }, @@ -1158,12 +1158,12 @@ { "axes5p", GT._("{0} px", new Object[]{ "5" }) }, { "axes10p", GT._("{0} px", new Object[] { "10" }) }, - { "axesByAngstromMenu", "Angstrom Width" }, - { "axes10a", "0.10 \u00C5" }, - { "axes20a", "0.20 \u00C5" }, - { "axes25a", "0.25 \u00C5" }, - { "axes50a", "0.50 \u00C5" }, - { "axes100a", "1.0 \u00C5" }, + { "axesByAngstromMenu", GT._("Angstrom Width") }, + { "axes10a", GT._("{0} \u00C5", new Object[]{ "0.10" })}, + { "axes20a", GT._("{0} \u00C5", new Object[]{ "0.20" })}, + { "axes25a", GT._("{0} \u00C5", new Object[]{ "0.25" })}, + { "axes50a", GT._("{0} \u00C5", new Object[]{ "0.50" })}, + { "axes100a", GT._("{0} \u00C5", new Object[]{ "1.0" })}, { "colorAxesMenu", GT._("Color") }, { "colorAxesGray", GT._("Gray") }, @@ -1175,18 +1175,18 @@ { "bbcageOff", GT._("Hide") }, { "bbcageDotted", GT._("Dotted") }, - { "bbcageByPixelMenu", "Pixel Width" }, + { "bbcageByPixelMenu", GT._("Pixel Width") }, { "bbcage1p", GT._("{0} px", new Object[]{ "1" }) }, { "bbcage3p", GT._("{0} px", new Object[]{ "3" }) }, { "bbcage5p", GT._("{0} px", new Object[]{ "5" }) }, { "bbcage10p", GT._("{0} px", new Object[]{ "10" }) }, { "bbcageByAngstromMenu", GT._("Angstrom Width") }, - { "bbcage10a", "0.10 \u00C5" }, - { "bbcage20a", "0.20 \u00C5" }, - { "bbcage25a", "0.25 \u00C5" }, - { "bbcage50a", "0.50 \u00C5" }, - { "bbcage100a", "1.0 \u00C5" }, + { "bbcage10a", GT._("{0} \u00C5", new Object[]{ "0.10" })}, + { "bbcage20a", GT._("{0} \u00C5", new Object[]{ "0.20" })}, + { "bbcage25a", GT._("{0} \u00C5", new Object[]{ "0.25" })}, + { "bbcage50a", GT._("{0} \u00C5", new Object[]{ "0.50" })}, + { "bbcage100a", GT._("1.0 \u00C5", new Object[]{ "1.0" })}, { "colorBbcageMenu", GT._("Color") }, { "colorBbcageGray", GT._("Gray") }, @@ -1204,12 +1204,12 @@ { "uccage5p", GT._("{0} px", new Object[]{ "5" }) }, { "uccage10p", GT._("{0} px", new Object[]{ "10" }) }, - { "uccageByAngstromMenu", "Angstrom Width" }, - { "uccage10a", "0.10 \u00C5" }, - { "uccage20a", "0.20 \u00C5" }, - { "uccage25a", "0.25 \u00C5" }, - { "uccage50a", "0.50 \u00C5" }, - { "uccage100a", "1.0 \u00C5" }, + { "uccageByAngstromMenu", GT._("Angstrom Width") }, + { "uccage10a", GT._("{0} \u00C5", new Object[] { "0.10" })}, + { "uccage20a", GT._("{0} \u00C5", new Object[] { "0.20" })}, + { "uccage25a", GT._("{0} \u00C5", new Object[] { "0.25" })}, + { "uccage50a", GT._("{0} \u00C5", new Object[] { "0.50" })}, + { "uccage100a", GT._("{0} \u00C5", new Object[] { "1.0" })}, { "colorUccageMenu", GT._("Color") }, { "colorUccageGray", GT._("Gray") }, Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot 2006-09-24 07:01:15 UTC (rev 5688) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot 2006-09-24 08:26:55 UTC (rev 5689) @@ -8,12 +8,12 @@ msgstr "" "Project-Id-Version: PACKAGE VERSION\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-21 21:19+0200\n" +"POT-Creation-Date: 2006-09-24 10:22+0200\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n" "Language-Team: LANGUAGE <LL...@li...>\n" "MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=CHARSET\n" +"Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" #: org/jmol/applet/Console.java:76 @@ -34,6 +34,72 @@ msgid "File Error:" msgstr "" +#: org/jmol/popup/JmolPopup.java:130 +#, java-format +msgid "atoms: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:132 +#, java-format +msgid "bonds: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:135 +#, java-format +msgid "groups: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:137 +#, java-format +msgid "chains: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:139 +#, java-format +msgid "polymers: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:141 +#, java-format +msgid "models: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:162 +msgid "Java memory usage" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:168 +#, java-format +msgid "{0} Mb total" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:169 +#, java-format +msgid "{0} Mb free" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:171 +#, java-format +msgid "{0} Mb maximum" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:173 +msgid "unknown maximum" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:177 +msgid "1 processor" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:178 +#, java-format +msgid "{0} processors" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:180 +msgid "unknown processor count" +msgstr "" + #: org/jmol/popup/PopupResourceBundle.java:685 msgid "No atoms loaded" msgstr "" @@ -70,6 +136,7 @@ #: org/jmol/popup/PopupResourceBundle.java:708 #: org/jmol/popup/PopupResourceBundle.java:750 #: org/jmol/popup/PopupResourceBundle.java:795 +#: org/jmol/popup/PopupResourceBundle.java:923 msgid "Backbone" msgstr "" @@ -269,6 +336,41 @@ msgid "On" msgstr "" +#: org/jmol/popup/PopupResourceBundle.java:764 +#: org/jmol/popup/PopupResourceBundle.java:765 +#: org/jmol/popup/PopupResourceBundle.java:766 +#: org/jmol/popup/PopupResourceBundle.java:767 +#: org/jmol/popup/PopupResourceBundle.java:768 +#: org/jmol/popup/PopupResourceBundle.java:776 +#: org/jmol/popup/PopupResourceBundle.java:777 +#: org/jmol/popup/PopupResourceBundle.java:778 +#: org/jmol/popup/PopupResourceBundle.java:779 +#: org/jmol/popup/PopupResourceBundle.java:780 +#: org/jmol/popup/PopupResourceBundle.java:787 +#: org/jmol/popup/PopupResourceBundle.java:788 +#: org/jmol/popup/PopupResourceBundle.java:789 +#: org/jmol/popup/PopupResourceBundle.java:790 +#: org/jmol/popup/PopupResourceBundle.java:791 +#: org/jmol/popup/PopupResourceBundle.java:804 +#: org/jmol/popup/PopupResourceBundle.java:805 +#: org/jmol/popup/PopupResourceBundle.java:1162 +#: org/jmol/popup/PopupResourceBundle.java:1163 +#: org/jmol/popup/PopupResourceBundle.java:1164 +#: org/jmol/popup/PopupResourceBundle.java:1165 +#: org/jmol/popup/PopupResourceBundle.java:1166 +#: org/jmol/popup/PopupResourceBundle.java:1185 +#: org/jmol/popup/PopupResourceBundle.java:1186 +#: org/jmol/popup/PopupResourceBundle.java:1187 +#: org/jmol/popup/PopupResourceBundle.java:1188 +#: org/jmol/popup/PopupResourceBundle.java:1208 +#: org/jmol/popup/PopupResourceBundle.java:1209 +#: org/jmol/popup/PopupResourceBundle.java:1210 +#: org/jmol/popup/PopupResourceBundle.java:1211 +#: org/jmol/popup/PopupResourceBundle.java:1212 +#, java-format +msgid "{0} Å" +msgstr "" + #: org/jmol/popup/PopupResourceBundle.java:770 #: org/jmol/popup/PopupResourceBundle.java:897 msgid "Hydrogen Bonds" @@ -940,6 +1042,7 @@ msgstr "" #: org/jmol/popup/PopupResourceBundle.java:1155 +#: org/jmol/popup/PopupResourceBundle.java:1178 #: org/jmol/popup/PopupResourceBundle.java:1201 msgid "Pixel Width" msgstr "" @@ -960,6 +1063,12 @@ msgid "{0} px" msgstr "" +#: org/jmol/popup/PopupResourceBundle.java:1161 +#: org/jmol/popup/PopupResourceBundle.java:1184 +#: org/jmol/popup/PopupResourceBundle.java:1207 +msgid "Angstrom Width" +msgstr "" + #: org/jmol/popup/PopupResourceBundle.java:1169 #: org/jmol/popup/PopupResourceBundle.java:1192 #: org/jmol/popup/PopupResourceBundle.java:1215 @@ -978,8 +1087,8 @@ msgid "Boundbox" msgstr "" -#: org/jmol/popup/PopupResourceBundle.java:1184 -msgid "Angstrom Width" +#: org/jmol/popup/PopupResourceBundle.java:1189 +msgid "1.0 Å" msgstr "" #: org/jmol/popup/PopupResourceBundle.java:1193 Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po 2006-09-24 07:01:15 UTC (rev 5688) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po 2006-09-24 08:26:55 UTC (rev 5689) @@ -6,12 +6,12 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-21 21:19+0200\n" +"POT-Creation-Date: 2006-09-24 10:22+0200\n" "PO-Revision-Date: 2006-01-30 03:37+0100\n" "Last-Translator: Toni Hermoso Pulido <to...@so...>\n" "Language-Team: Catalan <Jmo...@li...>\n" "MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" +"Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "X-Poedit-Language: Catalan\n" "X-Poedit-Country: ANDORRA\n" @@ -36,6 +36,72 @@ msgid "File Error:" msgstr "Error de fitxer:" +#: org/jmol/popup/JmolPopup.java:130 +#, java-format +msgid "atoms: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:132 +#, java-format +msgid "bonds: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:135 +#, java-format +msgid "groups: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:137 +#, fuzzy, java-format +msgid "chains: {0}" +msgstr "Escala {0}" + +#: org/jmol/popup/JmolPopup.java:139 +#, java-format +msgid "polymers: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:141 +#, java-format +msgid "models: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:162 +msgid "Java memory usage" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:168 +#, java-format +msgid "{0} Mb total" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:169 +#, java-format +msgid "{0} Mb free" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:171 +#, java-format +msgid "{0} Mb maximum" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:173 +msgid "unknown maximum" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:177 +msgid "1 processor" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:178 +#, java-format +msgid "{0} processors" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:180 +msgid "unknown processor count" +msgstr "" + #: org/jmol/popup/PopupResourceBundle.java:685 msgid "No atoms loaded" msgstr "No s'ha carregat cap àtom" @@ -72,6 +138,7 @@ #: org/jmol/popup/PopupResourceBundle.java:708 #: org/jmol/popup/PopupResourceBundle.java:750 #: org/jmol/popup/PopupResourceBundle.java:795 +#: org/jmol/popup/PopupResourceBundle.java:923 msgid "Backbone" msgstr "Esquelet" @@ -274,6 +341,41 @@ msgid "On" msgstr "Sí" +#: org/jmol/popup/PopupResourceBundle.java:764 +#: org/jmol/popup/PopupResourceBundle.java:765 +#: org/jmol/popup/PopupResourceBundle.java:766 +#: org/jmol/popup/PopupResourceBundle.java:767 +#: org/jmol/popup/PopupResourceBundle.java:768 +#: org/jmol/popup/PopupResourceBundle.java:776 +#: org/jmol/popup/PopupResourceBundle.java:777 +#: org/jmol/popup/PopupResourceBundle.java:778 +#: org/jmol/popup/PopupResourceBundle.java:779 +#: org/jmol/popup/PopupResourceBundle.java:780 +#: org/jmol/popup/PopupResourceBundle.java:787 +#: org/jmol/popup/PopupResourceBundle.java:788 +#: org/jmol/popup/PopupResourceBundle.java:789 +#: org/jmol/popup/PopupResourceBundle.java:790 +#: org/jmol/popup/PopupResourceBundle.java:791 +#: org/jmol/popup/PopupResourceBundle.java:804 +#: org/jmol/popup/PopupResourceBundle.java:805 +#: org/jmol/popup/PopupResourceBundle.java:1162 +#: org/jmol/popup/PopupResourceBundle.java:1163 +#: org/jmol/popup/PopupResourceBundle.java:1164 +#: org/jmol/popup/PopupResourceBundle.java:1165 +#: org/jmol/popup/PopupResourceBundle.java:1166 +#: org/jmol/popup/PopupResourceBundle.java:1185 +#: org/jmol/popup/PopupResourceBundle.java:1186 +#: org/jmol/popup/PopupResourceBundle.java:1187 +#: org/jmol/popup/PopupResourceBundle.java:1188 +#: org/jmol/popup/PopupResourceBundle.java:1208 +#: org/jmol/popup/PopupResourceBundle.java:1209 +#: org/jmol/popup/PopupResourceBundle.java:1210 +#: org/jmol/popup/PopupResourceBundle.java:1211 +#: org/jmol/popup/PopupResourceBundle.java:1212 +#, fuzzy, java-format +msgid "{0} Å" +msgstr "{0} px" + #: org/jmol/popup/PopupResourceBundle.java:770 #: org/jmol/popup/PopupResourceBundle.java:897 msgid "Hydrogen Bonds" @@ -960,6 +1062,7 @@ msgstr "Puntejat" #: org/jmol/popup/PopupResourceBundle.java:1155 +#: org/jmol/popup/PopupResourceBundle.java:1178 #: org/jmol/popup/PopupResourceBundle.java:1201 msgid "Pixel Width" msgstr "Amplada del píxel" @@ -980,6 +1083,12 @@ msgid "{0} px" msgstr "{0} px" +#: org/jmol/popup/PopupResourceBundle.java:1161 +#: org/jmol/popup/PopupResourceBundle.java:1184 +#: org/jmol/popup/PopupResourceBundle.java:1207 +msgid "Angstrom Width" +msgstr "Amplada de l'àngstrom" + #: org/jmol/popup/PopupResourceBundle.java:1169 #: org/jmol/popup/PopupResourceBundle.java:1192 #: org/jmol/popup/PopupResourceBundle.java:1215 @@ -998,9 +1107,9 @@ msgid "Boundbox" msgstr "Quadre" -#: org/jmol/popup/PopupResourceBundle.java:1184 -msgid "Angstrom Width" -msgstr "Amplada de l'àngstrom" +#: org/jmol/popup/PopupResourceBundle.java:1189 +msgid "1.0 Å" +msgstr "" #: org/jmol/popup/PopupResourceBundle.java:1193 msgid "Salmon" Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po 2006-09-24 07:01:15 UTC (rev 5688) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po 2006-09-24 08:26:55 UTC (rev 5689) @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: JmolApplet 10\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-21 21:19+0200\n" +"POT-Creation-Date: 2006-09-24 10:22+0200\n" "PO-Revision-Date: 2006-04-14 18:00+0100\n" "Last-Translator: Sebastian Lisken <sebastianlisken at users.sourceforge." "net>\n" @@ -38,6 +38,72 @@ msgid "File Error:" msgstr "Datei-Fehler:" +#: org/jmol/popup/JmolPopup.java:130 +#, java-format +msgid "atoms: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:132 +#, java-format +msgid "bonds: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:135 +#, java-format +msgid "groups: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:137 +#, fuzzy, java-format +msgid "chains: {0}" +msgstr "Skalierung {0}" + +#: org/jmol/popup/JmolPopup.java:139 +#, java-format +msgid "polymers: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:141 +#, java-format +msgid "models: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:162 +msgid "Java memory usage" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:168 +#, java-format +msgid "{0} Mb total" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:169 +#, java-format +msgid "{0} Mb free" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:171 +#, java-format +msgid "{0} Mb maximum" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:173 +msgid "unknown maximum" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:177 +msgid "1 processor" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:178 +#, java-format +msgid "{0} processors" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:180 +msgid "unknown processor count" +msgstr "" + #: org/jmol/popup/PopupResourceBundle.java:685 msgid "No atoms loaded" msgstr "Keine Atome geladen" @@ -74,6 +140,7 @@ #: org/jmol/popup/PopupResourceBundle.java:708 #: org/jmol/popup/PopupResourceBundle.java:750 #: org/jmol/popup/PopupResourceBundle.java:795 +#: org/jmol/popup/PopupResourceBundle.java:923 msgid "Backbone" msgstr "Primärstruktur" @@ -276,6 +343,41 @@ msgid "On" msgstr "An" +#: org/jmol/popup/PopupResourceBundle.java:764 +#: org/jmol/popup/PopupResourceBundle.java:765 +#: org/jmol/popup/PopupResourceBundle.java:766 +#: org/jmol/popup/PopupResourceBundle.java:767 +#: org/jmol/popup/PopupResourceBundle.java:768 +#: org/jmol/popup/PopupResourceBundle.java:776 +#: org/jmol/popup/PopupResourceBundle.java:777 +#: org/jmol/popup/PopupResourceBundle.java:778 +#: org/jmol/popup/PopupResourceBundle.java:779 +#: org/jmol/popup/PopupResourceBundle.java:780 +#: org/jmol/popup/PopupResourceBundle.java:787 +#: org/jmol/popup/PopupResourceBundle.java:788 +#: org/jmol/popup/PopupResourceBundle.java:789 +#: org/jmol/popup/PopupResourceBundle.java:790 +#: org/jmol/popup/PopupResourceBundle.java:791 +#: org/jmol/popup/PopupResourceBundle.java:804 +#: org/jmol/popup/PopupResourceBundle.java:805 +#: org/jmol/popup/PopupResourceBundle.java:1162 +#: org/jmol/popup/PopupResourceBundle.java:1163 +#: org/jmol/popup/PopupResourceBundle.java:1164 +#: org/jmol/popup/PopupResourceBundle.java:1165 +#: org/jmol/popup/PopupResourceBundle.java:1166 +#: org/jmol/popup/PopupResourceBundle.java:1185 +#: org/jmol/popup/PopupResourceBundle.java:1186 +#: org/jmol/popup/PopupResourceBundle.java:1187 +#: org/jmol/popup/PopupResourceBundle.java:1188 +#: org/jmol/popup/PopupResourceBundle.java:1208 +#: org/jmol/popup/PopupResourceBundle.java:1209 +#: org/jmol/popup/PopupResourceBundle.java:1210 +#: org/jmol/popup/PopupResourceBundle.java:1211 +#: org/jmol/popup/PopupResourceBundle.java:1212 +#, fuzzy, java-format +msgid "{0} Å" +msgstr "{0} px" + #: org/jmol/popup/PopupResourceBundle.java:770 #: org/jmol/popup/PopupResourceBundle.java:897 msgid "Hydrogen Bonds" @@ -961,6 +1063,7 @@ msgstr "Gepunktet" #: org/jmol/popup/PopupResourceBundle.java:1155 +#: org/jmol/popup/PopupResourceBundle.java:1178 #: org/jmol/popup/PopupResourceBundle.java:1201 msgid "Pixel Width" msgstr "Pixelbreite" @@ -981,6 +1084,12 @@ msgid "{0} px" msgstr "{0} px" +#: org/jmol/popup/PopupResourceBundle.java:1161 +#: org/jmol/popup/PopupResourceBundle.java:1184 +#: org/jmol/popup/PopupResourceBundle.java:1207 +msgid "Angstrom Width" +msgstr "Ångström-Breite" + #: org/jmol/popup/PopupResourceBundle.java:1169 #: org/jmol/popup/PopupResourceBundle.java:1192 #: org/jmol/popup/PopupResourceBundle.java:1215 @@ -999,9 +1108,9 @@ msgid "Boundbox" msgstr "" -#: org/jmol/popup/PopupResourceBundle.java:1184 -msgid "Angstrom Width" -msgstr "Ångström-Breite" +#: org/jmol/popup/PopupResourceBundle.java:1189 +msgid "1.0 Å" +msgstr "" #: org/jmol/popup/PopupResourceBundle.java:1193 msgid "Salmon" Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po 2006-09-24 07:01:15 UTC (rev 5688) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po 2006-09-24 08:26:55 UTC (rev 5689) @@ -2,12 +2,12 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-21 21:19+0200\n" +"POT-Creation-Date: 2006-09-24 10:22+0200\n" "PO-Revision-Date: 2006-09-24 01:26+0100\n" "Last-Translator: Angel Herráez <ang...@ua...>\n" "Language-Team: Spanish <Jmo...@li...>\n" "MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" +"Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "X-Poedit-Language: Spanish\n" "X-Poedit-Country: SPAIN\n" @@ -35,6 +35,72 @@ msgid "File Error:" msgstr "Error de archivo:" +#: org/jmol/popup/JmolPopup.java:130 +#, java-format +msgid "atoms: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:132 +#, java-format +msgid "bonds: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:135 +#, java-format +msgid "groups: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:137 +#, fuzzy, java-format +msgid "chains: {0}" +msgstr "Escala {0}" + +#: org/jmol/popup/JmolPopup.java:139 +#, java-format +msgid "polymers: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:141 +#, java-format +msgid "models: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:162 +msgid "Java memory usage" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:168 +#, java-format +msgid "{0} Mb total" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:169 +#, java-format +msgid "{0} Mb free" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:171 +#, java-format +msgid "{0} Mb maximum" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:173 +msgid "unknown maximum" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:177 +msgid "1 processor" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:178 +#, java-format +msgid "{0} processors" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:180 +msgid "unknown processor count" +msgstr "" + #: org/jmol/popup/PopupResourceBundle.java:685 msgid "No atoms loaded" msgstr "Ningún átomo cargado" @@ -71,6 +137,7 @@ #: org/jmol/popup/PopupResourceBundle.java:708 #: org/jmol/popup/PopupResourceBundle.java:750 #: org/jmol/popup/PopupResourceBundle.java:795 +#: org/jmol/popup/PopupResourceBundle.java:923 msgid "Backbone" msgstr "Esqueleto" @@ -270,6 +337,41 @@ msgid "On" msgstr "Sí" +#: org/jmol/popup/PopupResourceBundle.java:764 +#: org/jmol/popup/PopupResourceBundle.java:765 +#: org/jmol/popup/PopupResourceBundle.java:766 +#: org/jmol/popup/PopupResourceBundle.java:767 +#: org/jmol/popup/PopupResourceBundle.java:768 +#: org/jmol/popup/PopupResourceBundle.java:776 +#: org/jmol/popup/PopupResourceBundle.java:777 +#: org/jmol/popup/PopupResourceBundle.java:778 +#: org/jmol/popup/PopupResourceBundle.java:779 +#: org/jmol/popup/PopupResourceBundle.java:780 +#: org/jmol/popup/PopupResourceBundle.java:787 +#: org/jmol/popup/PopupResourceBundle.java:788 +#: org/jmol/popup/PopupResourceBundle.java:789 +#: org/jmol/popup/PopupResourceBundle.java:790 +#: org/jmol/popup/PopupResourceBundle.java:791 +#: org/jmol/popup/PopupResourceBundle.java:804 +#: org/jmol/popup/PopupResourceBundle.java:805 +#: org/jmol/popup/PopupResourceBundle.java:1162 +#: org/jmol/popup/PopupResourceBundle.java:1163 +#: org/jmol/popup/PopupResourceBundle.java:1164 +#: org/jmol/popup/PopupResourceBundle.java:1165 +#: org/jmol/popup/PopupResourceBundle.java:1166 +#: org/jmol/popup/PopupResourceBundle.java:1185 +#: org/jmol/popup/PopupResourceBundle.java:1186 +#: org/jmol/popup/PopupResourceBundle.java:1187 +#: org/jmol/popup/PopupResourceBundle.java:1188 +#: org/jmol/popup/PopupResourceBundle.java:1208 +#: org/jmol/popup/PopupResourceBundle.java:1209 +#: org/jmol/popup/PopupResourceBundle.java:1210 +#: org/jmol/popup/PopupResourceBundle.java:1211 +#: org/jmol/popup/PopupResourceBundle.java:1212 +#, fuzzy, java-format +msgid "{0} Å" +msgstr "{0} px" + #: org/jmol/popup/PopupResourceBundle.java:770 #: org/jmol/popup/PopupResourceBundle.java:897 msgid "Hydrogen Bonds" @@ -941,6 +1043,7 @@ msgstr "Punteados" #: org/jmol/popup/PopupResourceBundle.java:1155 +#: org/jmol/popup/PopupResourceBundle.java:1178 #: org/jmol/popup/PopupResourceBundle.java:1201 msgid "Pixel Width" msgstr "Grosor en píxeles" @@ -961,6 +1064,12 @@ msgid "{0} px" msgstr "{0} px" +#: org/jmol/popup/PopupResourceBundle.java:1161 +#: org/jmol/popup/PopupResourceBundle.java:1184 +#: org/jmol/popup/PopupResourceBundle.java:1207 +msgid "Angstrom Width" +msgstr "Grosor en ángstroms" + #: org/jmol/popup/PopupResourceBundle.java:1169 #: org/jmol/popup/PopupResourceBundle.java:1192 #: org/jmol/popup/PopupResourceBundle.java:1215 @@ -979,9 +1088,9 @@ msgid "Boundbox" msgstr "Caja" -#: org/jmol/popup/PopupResourceBundle.java:1184 -msgid "Angstrom Width" -msgstr "Grosor en ángstroms" +#: org/jmol/popup/PopupResourceBundle.java:1189 +msgid "1.0 Å" +msgstr "" #: org/jmol/popup/PopupResourceBundle.java:1193 msgid "Salmon" @@ -1081,36 +1190,49 @@ #~ msgid "Except Solvent" #~ msgstr "Excepto disolvente" + #~ msgid "Except Water" #~ msgstr "Excepto agua" + #~ msgid "Other" #~ msgstr "Otros" + #~ msgid "Lipid" #~ msgstr "Lípidos" + #~ msgid "pick " #~ msgstr "elige" + #~ msgid "Nanometers" #~ msgstr "Nanómetros" + #~ msgid "Angstroms" #~ msgstr "Angstroms" + #~ msgid "Picometers" #~ msgstr "Picómetros" + #~ msgid "Open" #~ msgstr "Abrir" + #~ msgid "Close" #~ msgstr "Cerrar" + #~ msgid "Jmol Molecular Visualization http://www.jmol.org" #~ msgstr "Jmol, visualización molecular http://www.jmol.org" + #~ msgid "Jmol script completed" #~ msgstr "Guión de Jmol completado" + #~ msgid "Name hidden" #~ msgstr "Nombre oculto" + #~ msgid "Wireframe Rotation" #~ msgstr "Rotación como alambres" + #~ msgid "" #~ "Jmol Applet. Part of the OpenScience project. See http://www.jmol.org " #~ "for more information" #~ msgstr "" #~ "Miniaplicación Jmol, parte del proyecto OpenScience; para más " #~ "información, vea http://www.jmol.org" - Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po 2006-09-24 07:01:15 UTC (rev 5688) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po 2006-09-24 08:26:55 UTC (rev 5689) @@ -6,7 +6,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-21 21:19+0200\n" +"POT-Creation-Date: 2006-09-24 10:22+0200\n" "PO-Revision-Date: 2006-03-17 20:19+0100\n" "Last-Translator: Ivo Sarak <iv...@ra...>\n" "Language-Team: Estonian <Jmo...@li...>\n" @@ -37,6 +37,72 @@ msgid "File Error:" msgstr "Faili viga:" +#: org/jmol/popup/JmolPopup.java:130 +#, java-format +msgid "atoms: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:132 +#, java-format +msgid "bonds: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:135 +#, java-format +msgid "groups: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:137 +#, fuzzy, java-format +msgid "chains: {0}" +msgstr "Skaala {0}" + +#: org/jmol/popup/JmolPopup.java:139 +#, java-format +msgid "polymers: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:141 +#, java-format +msgid "models: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:162 +msgid "Java memory usage" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:168 +#, java-format +msgid "{0} Mb total" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:169 +#, java-format +msgid "{0} Mb free" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:171 +#, java-format +msgid "{0} Mb maximum" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:173 +msgid "unknown maximum" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:177 +msgid "1 processor" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:178 +#, java-format +msgid "{0} processors" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:180 +msgid "unknown processor count" +msgstr "" + #: org/jmol/popup/PopupResourceBundle.java:685 msgid "No atoms loaded" msgstr "Ei ühtegi aatomit" @@ -73,6 +139,7 @@ #: org/jmol/popup/PopupResourceBundle.java:708 #: org/jmol/popup/PopupResourceBundle.java:750 #: org/jmol/popup/PopupResourceBundle.java:795 +#: org/jmol/popup/PopupResourceBundle.java:923 msgid "Backbone" msgstr "Selgroog" @@ -275,6 +342,41 @@ msgid "On" msgstr "Sees" +#: org/jmol/popup/PopupResourceBundle.java:764 +#: org/jmol/popup/PopupResourceBundle.java:765 +#: org/jmol/popup/PopupResourceBundle.java:766 +#: org/jmol/popup/PopupResourceBundle.java:767 +#: org/jmol/popup/PopupResourceBundle.java:768 +#: org/jmol/popup/PopupResourceBundle.java:776 +#: org/jmol/popup/PopupResourceBundle.java:777 +#: org/jmol/popup/PopupResourceBundle.java:778 +#: org/jmol/popup/PopupResourceBundle.java:779 +#: org/jmol/popup/PopupResourceBundle.java:780 +#: org/jmol/popup/PopupResourceBundle.java:787 +#: org/jmol/popup/PopupResourceBundle.java:788 +#: org/jmol/popup/PopupResourceBundle.java:789 +#: org/jmol/popup/PopupResourceBundle.java:790 +#: org/jmol/popup/PopupResourceBundle.java:791 +#: org/jmol/popup/PopupResourceBundle.java:804 +#: org/jmol/popup/PopupResourceBundle.java:805 +#: org/jmol/popup/PopupResourceBundle.java:1162 +#: org/jmol/popup/PopupResourceBundle.java:1163 +#: org/jmol/popup/PopupResourceBundle.java:1164 +#: org/jmol/popup/PopupResourceBundle.java:1165 +#: org/jmol/popup/PopupResourceBundle.java:1166 +#: org/jmol/popup/PopupResourceBundle.java:1185 +#: org/jmol/popup/PopupResourceBundle.java:1186 +#: org/jmol/popup/PopupResourceBundle.java:1187 +#: org/jmol/popup/PopupResourceBundle.java:1188 +#: org/jmol/popup/PopupResourceBundle.java:1208 +#: org/jmol/popup/PopupResourceBundle.java:1209 +#: org/jmol/popup/PopupResourceBundle.java:1210 +#: org/jmol/popup/PopupResourceBundle.java:1211 +#: org/jmol/popup/PopupResourceBundle.java:1212 +#, fuzzy, java-format +msgid "{0} Å" +msgstr "{0} px" + #: org/jmol/popup/PopupResourceBundle.java:770 #: org/jmol/popup/PopupResourceBundle.java:897 msgid "Hydrogen Bonds" @@ -961,6 +1063,7 @@ msgstr "Punktiir" #: org/jmol/popup/PopupResourceBundle.java:1155 +#: org/jmol/popup/PopupResourceBundle.java:1178 #: org/jmol/popup/PopupResourceBundle.java:1201 msgid "Pixel Width" msgstr "Pikseli Laius" @@ -981,6 +1084,12 @@ msgid "{0} px" msgstr "{0} px" +#: org/jmol/popup/PopupResourceBundle.java:1161 +#: org/jmol/popup/PopupResourceBundle.java:1184 +#: org/jmol/popup/PopupResourceBundle.java:1207 +msgid "Angstrom Width" +msgstr "Angstromi Laius" + #: org/jmol/popup/PopupResourceBundle.java:1169 #: org/jmol/popup/PopupResourceBundle.java:1192 #: org/jmol/popup/PopupResourceBundle.java:1215 @@ -999,9 +1108,9 @@ msgid "Boundbox" msgstr "Boundbox" -#: org/jmol/popup/PopupResourceBundle.java:1184 -msgid "Angstrom Width" -msgstr "Angstromi Laius" +#: org/jmol/popup/PopupResourceBundle.java:1189 +msgid "1.0 Å" +msgstr "" #: org/jmol/popup/PopupResourceBundle.java:1193 msgid "Salmon" Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po 2006-09-24 07:01:15 UTC (rev 5688) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po 2006-09-24 08:26:55 UTC (rev 5689) @@ -7,12 +7,12 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-21 21:19+0200\n" +"POT-Creation-Date: 2006-09-24 10:22+0200\n" "PO-Revision-Date: 2006-04-14 18:11+0100\n" "Last-Translator: Nicolas Vervelle <ni...@us...>\n" "Language-Team: French <Jmo...@li...>\n" "MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" +"Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "X-Poedit-Language: French\n" "X-Poedit-Country: France\n" @@ -41,6 +41,72 @@ msgid "File Error:" msgstr "Erreur de Fichier:" +#: org/jmol/popup/JmolPopup.java:130 +#, java-format +msgid "atoms: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:132 +#, java-format +msgid "bonds: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:135 +#, java-format +msgid "groups: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:137 +#, fuzzy, java-format +msgid "chains: {0}" +msgstr "Echelle {0}" + +#: org/jmol/popup/JmolPopup.java:139 +#, java-format +msgid "polymers: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:141 +#, java-format +msgid "models: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:162 +msgid "Java memory usage" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:168 +#, java-format +msgid "{0} Mb total" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:169 +#, java-format +msgid "{0} Mb free" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:171 +#, java-format +msgid "{0} Mb maximum" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:173 +msgid "unknown maximum" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:177 +msgid "1 processor" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:178 +#, java-format +msgid "{0} processors" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:180 +msgid "unknown processor count" +msgstr "" + #: org/jmol/popup/PopupResourceBundle.java:685 msgid "No atoms loaded" msgstr "Aucun atome chargé" @@ -77,6 +143,7 @@ #: org/jmol/popup/PopupResourceBundle.java:708 #: org/jmol/popup/PopupResourceBundle.java:750 #: org/jmol/popup/PopupResourceBundle.java:795 +#: org/jmol/popup/PopupResourceBundle.java:923 msgid "Backbone" msgstr "Squelette" @@ -279,6 +346,41 @@ msgid "On" msgstr "On" +#: org/jmol/popup/PopupResourceBundle.java:764 +#: org/jmol/popup/PopupResourceBundle.java:765 +#: org/jmol/popup/PopupResourceBundle.java:766 +#: org/jmol/popup/PopupResourceBundle.java:767 +#: org/jmol/popup/PopupResourceBundle.java:768 +#: org/jmol/popup/PopupResourceBundle.java:776 +#: org/jmol/popup/PopupResourceBundle.java:777 +#: org/jmol/popup/PopupResourceBundle.java:778 +#: org/jmol/popup/PopupResourceBundle.java:779 +#: org/jmol/popup/PopupResourceBundle.java:780 +#: org/jmol/popup/PopupResourceBundle.java:787 +#: org/jmol/popup/PopupResourceBundle.java:788 +#: org/jmol/popup/PopupResourceBundle.java:789 +#: org/jmol/popup/PopupResourceBundle.java:790 +#: org/jmol/popup/PopupResourceBundle.java:791 +#: org/jmol/popup/PopupResourceBundle.java:804 +#: org/jmol/popup/PopupResourceBundle.java:805 +#: org/jmol/popup/PopupResourceBundle.java:1162 +#: org/jmol/popup/PopupResourceBundle.java:1163 +#: org/jmol/popup/PopupResourceBundle.java:1164 +#: org/jmol/popup/PopupResourceBundle.java:1165 +#: org/jmol/popup/PopupResourceBundle.java:1166 +#: org/jmol/popup/PopupResourceBundle.java:1185 +#: org/jmol/popup/PopupResourceBundle.java:1186 +#: org/jmol/popup/PopupResourceBundle.java:1187 +#: org/jmol/popup/PopupResourceBundle.java:1188 +#: org/jmol/popup/PopupResourceBundle.java:1208 +#: org/jmol/popup/PopupResourceBundle.java:1209 +#: org/jmol/popup/PopupResourceBundle.java:1210 +#: org/jmol/popup/PopupResourceBundle.java:1211 +#: org/jmol/popup/PopupResourceBundle.java:1212 +#, fuzzy, java-format +msgid "{0} Å" +msgstr "{0} px" + #: org/jmol/popup/PopupResourceBundle.java:770 #: org/jmol/popup/PopupResourceBundle.java:897 msgid "Hydrogen Bonds" @@ -965,6 +1067,7 @@ msgstr "Pointillé" #: org/jmol/popup/PopupResourceBundle.java:1155 +#: org/jmol/popup/PopupResourceBundle.java:1178 #: org/jmol/popup/PopupResourceBundle.java:1201 msgid "Pixel Width" msgstr "Largeur en Pixels" @@ -985,6 +1088,12 @@ msgid "{0} px" msgstr "{0} px" +#: org/jmol/popup/PopupResourceBundle.java:1161 +#: org/jmol/popup/PopupResourceBundle.java:1184 +#: org/jmol/popup/PopupResourceBundle.java:1207 +msgid "Angstrom Width" +msgstr "Largeur en Angströms" + #: org/jmol/popup/PopupResourceBundle.java:1169 #: org/jmol/popup/PopupResourceBundle.java:1192 #: org/jmol/popup/PopupResourceBundle.java:1215 @@ -1003,9 +1112,9 @@ msgid "Boundbox" msgstr "Boîte englobante" -#: org/jmol/popup/PopupResourceBundle.java:1184 -msgid "Angstrom Width" -msgstr "Largeur en Angströms" +#: org/jmol/popup/PopupResourceBundle.java:1189 +msgid "1.0 Å" +msgstr "" #: org/jmol/popup/PopupResourceBundle.java:1193 msgid "Salmon" Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po 2006-09-24 07:01:15 UTC (rev 5688) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po 2006-09-24 08:26:55 UTC (rev 5689) @@ -7,7 +7,7 @@ msgstr "" "Project-Id-Version: nl\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-21 21:19+0200\n" +"POT-Creation-Date: 2006-09-24 10:22+0200\n" "PO-Revision-Date: 2006-09-18 20:32+0100\n" "Last-Translator: Egon Willighagen <eg...@jm...>\n" "Language-Team: Nederlands <kde...@kd...>\n" @@ -41,6 +41,72 @@ msgid "File Error:" msgstr "Bestandsfout:" +#: org/jmol/popup/JmolPopup.java:130 +#, java-format +msgid "atoms: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:132 +#, java-format +msgid "bonds: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:135 +#, java-format +msgid "groups: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:137 +#, fuzzy, java-format +msgid "chains: {0}" +msgstr "Schaal {0}" + +#: org/jmol/popup/JmolPopup.java:139 +#, java-format +msgid "polymers: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:141 +#, java-format +msgid "models: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:162 +msgid "Java memory usage" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:168 +#, java-format +msgid "{0} Mb total" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:169 +#, java-format +msgid "{0} Mb free" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:171 +#, java-format +msgid "{0} Mb maximum" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:173 +msgid "unknown maximum" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:177 +msgid "1 processor" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:178 +#, java-format +msgid "{0} processors" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:180 +msgid "unknown processor count" +msgstr "" + #: org/jmol/popup/PopupResourceBundle.java:685 msgid "No atoms loaded" msgstr "Geen atomen geladen" @@ -77,6 +143,7 @@ #: org/jmol/popup/PopupResourceBundle.java:708 #: org/jmol/popup/PopupResourceBundle.java:750 #: org/jmol/popup/PopupResourceBundle.java:795 +#: org/jmol/popup/PopupResourceBundle.java:923 msgid "Backbone" msgstr "Backbone" @@ -279,6 +346,41 @@ msgid "On" msgstr "Aan" +#: org/jmol/popup/PopupResourceBundle.java:764 +#: org/jmol/popup/PopupResourceBundle.java:765 +#: org/jmol/popup/PopupResourceBundle.java:766 +#: org/jmol/popup/PopupResourceBundle.java:767 +#: org/jmol/popup/PopupResourceBundle.java:768 +#: org/jmol/popup/PopupResourceBundle.java:776 +#: org/jmol/popup/PopupResourceBundle.java:777 +#: org/jmol/popup/PopupResourceBundle.java:778 +#: org/jmol/popup/PopupResourceBundle.java:779 +#: org/jmol/popup/PopupResourceBundle.java:780 +#: org/jmol/popup/PopupResourceBundle.java:787 +#: org/jmol/popup/PopupResourceBundle.java:788 +#: org/jmol/popup/PopupResourceBundle.java:789 +#: org/jmol/popup/PopupResourceBundle.java:790 +#: org/jmol/popup/PopupResourceBundle.java:791 +#: org/jmol/popup/PopupResourceBundle.java:804 +#: org/jmol/popup/PopupResourceBundle.java:805 +#: org/jmol/popup/PopupResourceBundle.java:1162 +#: org/jmol/popup/PopupResourceBundle.java:1163 +#: org/jmol/popup/PopupResourceBundle.java:1164 +#: org/jmol/popup/PopupResourceBundle.java:1165 +#: org/jmol/popup/PopupResourceBundle.java:1166 +#: org/jmol/popup/PopupResourceBundle.java:1185 +#: org/jmol/popup/PopupResourceBundle.java:1186 +#: org/jmol/popup/PopupResourceBundle.java:1187 +#: org/jmol/popup/PopupResourceBundle.java:1188 +#: org/jmol/popup/PopupResourceBundle.java:1208 +#: org/jmol/popup/PopupResourceBundle.java:1209 +#: org/jmol/popup/PopupResourceBundle.java:1210 +#: org/jmol/popup/PopupResourceBundle.java:1211 +#: org/jmol/popup/PopupResourceBundle.java:1212 +#, fuzzy, java-format +msgid "{0} Å" +msgstr "{0} px" + #: org/jmol/popup/PopupResourceBundle.java:770 #: org/jmol/popup/PopupResourceBundle.java:897 msgid "Hydrogen Bonds" @@ -950,6 +1052,7 @@ msgstr "Puntjes" #: org/jmol/popup/PopupResourceBundle.java:1155 +#: org/jmol/popup/PopupResourceBundle.java:1178 #: org/jmol/popup/PopupResourceBundle.java:1201 msgid "Pixel Width" msgstr "Puntgrootte" @@ -970,6 +1073,12 @@ msgid "{0} px" msgstr "{0} px" +#: org/jmol/popup/PopupResourceBundle.java:1161 +#: org/jmol/popup/PopupResourceBundle.java:1184 +#: org/jmol/popup/PopupResourceBundle.java:1207 +msgid "Angstrom Width" +msgstr "Angstrombreedte" + #: org/jmol/popup/PopupResourceBundle.java:1169 #: org/jmol/popup/PopupResourceBundle.java:1192 #: org/jmol/popup/PopupResourceBundle.java:1215 @@ -988,9 +1097,9 @@ msgid "Boundbox" msgstr "Boundbox" -#: org/jmol/popup/PopupResourceBundle.java:1184 -msgid "Angstrom Width" -msgstr "Angstrombreedte" +#: org/jmol/popup/PopupResourceBundle.java:1189 +msgid "1.0 Å" +msgstr "" #: org/jmol/popup/PopupResourceBundle.java:1193 msgid "Salmon" Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po 2006-09-24 07:01:15 UTC (rev 5688) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po 2006-09-24 08:26:55 UTC (rev 5689) @@ -6,7 +6,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-21 21:19+0200\n" +"POT-Creation-Date: 2006-09-24 10:22+0200\n" "PO-Revision-Date: 2005-12-20 07:44-0000\n" "Last-Translator: Metro <por...@gm...>\n" "Language-Team: Portugal@Folding <Jmo...@li...>\n" @@ -37,6 +37,72 @@ msgid "File Error:" msgstr "Erro no ficheiro..." +#: org/jmol/popup/JmolPopup.java:130 +#, java-format +msgid "atoms: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:132 +#, java-format +msgid "bonds: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:135 +#, java-format +msgid "groups: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:137 +#, fuzzy, java-format +msgid "chains: {0}" +msgstr "Escala 0.2" + +#: org/jmol/popup/JmolPopup.java:139 +#, java-format +msgid "polymers: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:141 +#, java-format +msgid "models: {0}" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:162 +msgid "Java memory usage" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:168 +#, java-format +msgid "{0} Mb total" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:169 +#, java-format +msgid "{0} Mb free" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:171 +#, java-format +msgid "{0} Mb maximum" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:173 +msgid "unknown maximum" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:177 +msgid "1 processor" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:178 +#, java-format +msgid "{0} processors" +msgstr "" + +#: org/jmol/popup/JmolPopup.java:180 +msgid "unknown processor count" +msgstr "" + #: org/jmol/popup/PopupResourceBundle.java:685 msgid "No atoms loaded" msgstr "Nenhum átomo foi carregado" @@ -73,6 +139,7 @@ #: org/jmol/popup/PopupResourceBundle.java:708 #: org/jmol/popup/PopupResourceBundle.java:750 #: org/jmol/popup/PopupResourceBundle.java:795 +#: org/jmol/popup/PopupResourceBundle.java:923 msgid "Backbone" msgstr "Esqueleto/Cadeia principal/raiz" @@ -275,6 +342,41 @@ msgid "On" msgstr "On" +#: org/jmol/popup/PopupResourceBundle.java:764 +#: org/jmol/popup/PopupResourceBundle.java:765 +#: org/jmol/popup/PopupResourceBundle.java:766 +#: org/jmol/popup/PopupResourceBundle.java:767 +#: org/jmol/popup/PopupResourceBundle.java:768 +#: org/jmol/popup/PopupResourceBundle.java:776 +#: org/jmol/popup/PopupResourceBundle.java:777 +#: org/jmol/popup/PopupResourceBundle.java:778 +#: org/jmol/popup/PopupResourceBundle.java:779 +#: org/jmol/popup/PopupResourceBundle.java:780 +#: org/jmol/popup/PopupResourceBundle.java:787 +#: org/jmol/popup/PopupResourceBundle.java:788 +#: org/jmol/popup/PopupResourceBundle.java:789 +#: org/jmol/popup/PopupResourceBundle.java:790 +#: org/jmol/popup/PopupResourceBundle.java:791 +#: org/jmol/popup/PopupResourceBundle.java:804 +#: org/jmol/popup/PopupResourceBundle.java:805 +#: org/jmol/popup/PopupResourceBundle.java:1162 +#: org/jmol/popup/PopupResourceBundle.java:1163 +#: org/jmol/popup/PopupResourceBundle.java:1164 +#: org/jmol/popup/PopupResourceBundle.java:1165 +#: org/jmol/popup/PopupResourceBundle.java:1166 +#: org/jmol/popup/PopupResourceBundle.java:1185 +#: org/jmol/popup/PopupResourceBundle.java:1186 +#: org/jmol/popup/PopupResourceBundle.java:1187 +#: org/jmol/popup/PopupResourceBundle.java:1188 +#: org/jmol/popup/PopupResourceBundle.java:1208 +#: org/jmol/popup/PopupResourceBundle.java:1209 +#: org/jmol/popup/PopupResourceBundle.java:1210 +#: org/jmol/popup/PopupResourceBundle.java:1211 +#: org/jmol/popup/PopupResourceBundle.java:1212 +#, fuzzy, java-format +msgid "{0} Å" +msgstr "1opx" + #: org/jmol/popup/PopupResourceBundle.java:770 #: org/jmol/popup/PopupResourceBundle.java:897 msgid "Hydrogen Bonds" @@ -960,6 +1062,7 @@ msgstr "Tracejado" #: org/jmol/popup/PopupResourceBundle.java:1155 +#: org/jmol/popup/PopupResourceBundle.java:1178 #: org/jmol/popup/PopupResourceBundle.java:1201 msgid "Pixel Width" msgstr "Tamanho do pixel" @@ -980,6 +1083,12 @@ msgid "{0} px" msgstr "1opx" +#: org/jmol/popup/PopupResourceBundle.java:1161 +#: org/jmol/popup/PopupResourceBundle.java:1184 +#: org/jmol/popup/PopupResourceBundle.java:1207 +msgid "Angstrom Width" +msgstr "Tamanho Angstrom" + #: org/jmol/popup/PopupResourceBundle.java:1169 #: org/jmol/popup/PopupResourceBundle.java:1192 #: org/jmol/popup/PopupResourceBundle.java:1215 @@ -998,9 +1107,9 @@ msgid "Boundbox" msgstr "Caixa de ligação" -#: org/jmol/popup/PopupResourceBundle.java:1184 -msgid "Angstrom Width" -msgstr "Tamanho Angstrom" +#: org/jmol/popup/PopupResourceBundle.java:1189 +msgid "1.0 Å" +msgstr "" #: org/jmol/popup/PopupResourceBundle.java:1193 msgid "Salmon" This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2006-09-24 13:30:24
|
Revision: 5692 http://svn.sourceforge.net/jmol/?rev=5692&view=rev Author: egonw Date: 2006-09-24 06:30:07 -0700 (Sun, 24 Sep 2006) Log Message: ----------- Fixed string: MB instead of Mb, HETATM instead of HETATOM Modified Paths: -------------- trunk/Jmol/src/org/jmol/popup/JmolPopup.java trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po Modified: trunk/Jmol/src/org/jmol/popup/JmolPopup.java =================================================================== --- trunk/Jmol/src/org/jmol/popup/JmolPopup.java 2006-09-24 12:19:14 UTC (rev 5691) +++ trunk/Jmol/src/org/jmol/popup/JmolPopup.java 2006-09-24 13:30:07 UTC (rev 5692) @@ -165,10 +165,10 @@ long mbTotal = convertToMegabytes(runtime.totalMemory()); long mbFree = convertToMegabytes(runtime.freeMemory()); long mbMax = convertToMegabytes(maxMemoryForNewerJvm()); - addMenuItem(aboutMenu, GT._("{0} Mb total", new Object[] { new Long(mbTotal) })); - addMenuItem(aboutMenu, GT._("{0} Mb free", new Object[] { new Long(mbFree) })); + addMenuItem(aboutMenu, GT._("{0} MB total", new Object[] { new Long(mbTotal) })); + addMenuItem(aboutMenu, GT._("{0} MB free", new Object[] { new Long(mbFree) })); if (mbMax > 0) - addMenuItem(aboutMenu, GT._("{0} Mb maximum", new Object[] { new Long(mbMax) })); + addMenuItem(aboutMenu, GT._("{0} MB maximum", new Object[] { new Long(mbMax) })); else addMenuItem(aboutMenu, GT._("unknown maximum")); int availableProcessors = availableProcessorsForNewerJvm(); Modified: trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java =================================================================== --- trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java 2006-09-24 12:19:14 UTC (rev 5691) +++ trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java 2006-09-24 13:30:07 UTC (rev 5692) @@ -717,7 +717,7 @@ { "U", "U" }, { "heteroMenu", GT._("Hetero") }, - { "allHetero", GT._("All PDB \"HETATOM\"") }, + { "allHetero", GT._("All PDB \"HETATM\"") }, { "Solvent", GT._("All Solvent") }, { "Water", GT._("All Water") }, { "nonWaterSolvent", GT._("Nonaqueous Solvent") + " (solvent and not water)" }, Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot 2006-09-24 12:19:14 UTC (rev 5691) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot 2006-09-24 13:30:07 UTC (rev 5692) @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: PACKAGE VERSION\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-24 10:22+0200\n" +"POT-Creation-Date: 2006-09-24 15:23+0200\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n" "Language-Team: LANGUAGE <LL...@li...>\n" @@ -70,17 +70,17 @@ #: org/jmol/popup/JmolPopup.java:168 #, java-format -msgid "{0} Mb total" +msgid "{0} MB total" msgstr "" #: org/jmol/popup/JmolPopup.java:169 #, java-format -msgid "{0} Mb free" +msgid "{0} MB free" msgstr "" #: org/jmol/popup/JmolPopup.java:171 #, java-format -msgid "{0} Mb maximum" +msgid "{0} MB maximum" msgstr "" #: org/jmol/popup/JmolPopup.java:173 @@ -201,7 +201,7 @@ msgstr "" #: org/jmol/popup/PopupResourceBundle.java:720 -msgid "All PDB \"HETATOM\"" +msgid "All PDB \"HETATM\"" msgstr "" #: org/jmol/popup/PopupResourceBundle.java:721 Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po 2006-09-24 12:19:14 UTC (rev 5691) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po 2006-09-24 13:30:07 UTC (rev 5692) @@ -6,7 +6,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-24 10:22+0200\n" +"POT-Creation-Date: 2006-09-24 15:23+0200\n" "PO-Revision-Date: 2006-01-30 03:37+0100\n" "Last-Translator: Toni Hermoso Pulido <to...@so...>\n" "Language-Team: Catalan <Jmo...@li...>\n" @@ -72,17 +72,17 @@ #: org/jmol/popup/JmolPopup.java:168 #, java-format -msgid "{0} Mb total" +msgid "{0} MB total" msgstr "" #: org/jmol/popup/JmolPopup.java:169 #, java-format -msgid "{0} Mb free" +msgid "{0} MB free" msgstr "" #: org/jmol/popup/JmolPopup.java:171 #, java-format -msgid "{0} Mb maximum" +msgid "{0} MB maximum" msgstr "" #: org/jmol/popup/JmolPopup.java:173 @@ -204,7 +204,7 @@ msgstr "hetero" #: org/jmol/popup/PopupResourceBundle.java:720 -msgid "All PDB \"HETATOM\"" +msgid "All PDB \"HETATM\"" msgstr "" #: org/jmol/popup/PopupResourceBundle.java:721 Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po 2006-09-24 12:19:14 UTC (rev 5691) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po 2006-09-24 13:30:07 UTC (rev 5692) @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: JmolApplet 10\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-24 10:22+0200\n" +"POT-Creation-Date: 2006-09-24 15:23+0200\n" "PO-Revision-Date: 2006-04-14 18:00+0100\n" "Last-Translator: Sebastian Lisken <sebastianlisken at users.sourceforge." "net>\n" @@ -74,17 +74,17 @@ #: org/jmol/popup/JmolPopup.java:168 #, java-format -msgid "{0} Mb total" +msgid "{0} MB total" msgstr "" #: org/jmol/popup/JmolPopup.java:169 #, java-format -msgid "{0} Mb free" +msgid "{0} MB free" msgstr "" #: org/jmol/popup/JmolPopup.java:171 #, java-format -msgid "{0} Mb maximum" +msgid "{0} MB maximum" msgstr "" #: org/jmol/popup/JmolPopup.java:173 @@ -206,7 +206,7 @@ msgstr "Hetero" #: org/jmol/popup/PopupResourceBundle.java:720 -msgid "All PDB \"HETATOM\"" +msgid "All PDB \"HETATM\"" msgstr "" #: org/jmol/popup/PopupResourceBundle.java:721 Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po 2006-09-24 12:19:14 UTC (rev 5691) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po 2006-09-24 13:30:07 UTC (rev 5692) @@ -2,7 +2,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-24 10:22+0200\n" +"POT-Creation-Date: 2006-09-24 15:23+0200\n" "PO-Revision-Date: 2006-09-24 01:26+0100\n" "Last-Translator: Angel Herráez <ang...@ua...>\n" "Language-Team: Spanish <Jmo...@li...>\n" @@ -71,17 +71,17 @@ #: org/jmol/popup/JmolPopup.java:168 #, java-format -msgid "{0} Mb total" +msgid "{0} MB total" msgstr "" #: org/jmol/popup/JmolPopup.java:169 #, java-format -msgid "{0} Mb free" +msgid "{0} MB free" msgstr "" #: org/jmol/popup/JmolPopup.java:171 #, java-format -msgid "{0} Mb maximum" +msgid "{0} MB maximum" msgstr "" #: org/jmol/popup/JmolPopup.java:173 @@ -202,7 +202,8 @@ msgstr "Grupos \"hetero\"" #: org/jmol/popup/PopupResourceBundle.java:720 -msgid "All PDB \"HETATOM\"" +#, fuzzy +msgid "All PDB \"HETATM\"" msgstr "Todos los \"HETATM\" de PDB" #: org/jmol/popup/PopupResourceBundle.java:721 Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po 2006-09-24 12:19:14 UTC (rev 5691) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po 2006-09-24 13:30:07 UTC (rev 5692) @@ -6,7 +6,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-24 10:22+0200\n" +"POT-Creation-Date: 2006-09-24 15:23+0200\n" "PO-Revision-Date: 2006-03-17 20:19+0100\n" "Last-Translator: Ivo Sarak <iv...@ra...>\n" "Language-Team: Estonian <Jmo...@li...>\n" @@ -73,17 +73,17 @@ #: org/jmol/popup/JmolPopup.java:168 #, java-format -msgid "{0} Mb total" +msgid "{0} MB total" msgstr "" #: org/jmol/popup/JmolPopup.java:169 #, java-format -msgid "{0} Mb free" +msgid "{0} MB free" msgstr "" #: org/jmol/popup/JmolPopup.java:171 #, java-format -msgid "{0} Mb maximum" +msgid "{0} MB maximum" msgstr "" #: org/jmol/popup/JmolPopup.java:173 @@ -205,7 +205,7 @@ msgstr "hetero" #: org/jmol/popup/PopupResourceBundle.java:720 -msgid "All PDB \"HETATOM\"" +msgid "All PDB \"HETATM\"" msgstr "" #: org/jmol/popup/PopupResourceBundle.java:721 Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po 2006-09-24 12:19:14 UTC (rev 5691) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po 2006-09-24 13:30:07 UTC (rev 5692) @@ -7,7 +7,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-24 10:22+0200\n" +"POT-Creation-Date: 2006-09-24 15:23+0200\n" "PO-Revision-Date: 2006-04-14 18:11+0100\n" "Last-Translator: Nicolas Vervelle <ni...@us...>\n" "Language-Team: French <Jmo...@li...>\n" @@ -77,17 +77,17 @@ #: org/jmol/popup/JmolPopup.java:168 #, java-format -msgid "{0} Mb total" +msgid "{0} MB total" msgstr "" #: org/jmol/popup/JmolPopup.java:169 #, java-format -msgid "{0} Mb free" +msgid "{0} MB free" msgstr "" #: org/jmol/popup/JmolPopup.java:171 #, java-format -msgid "{0} Mb maximum" +msgid "{0} MB maximum" msgstr "" #: org/jmol/popup/JmolPopup.java:173 @@ -209,7 +209,7 @@ msgstr "Hétéro" #: org/jmol/popup/PopupResourceBundle.java:720 -msgid "All PDB \"HETATOM\"" +msgid "All PDB \"HETATM\"" msgstr "" #: org/jmol/popup/PopupResourceBundle.java:721 Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po 2006-09-24 12:19:14 UTC (rev 5691) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po 2006-09-24 13:30:07 UTC (rev 5692) @@ -7,7 +7,7 @@ msgstr "" "Project-Id-Version: nl\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-24 10:22+0200\n" +"POT-Creation-Date: 2006-09-24 15:23+0200\n" "PO-Revision-Date: 2006-09-24 14:11+0100\n" "Last-Translator: Egon Willighagen <eg...@jm...>\n" "Language-Team: Nederlands <jmo...@li...>\n" @@ -34,7 +34,8 @@ msgstr "" "Jmol Applet versie {0} {1}.\n" " \n" -"Onderdeel van het OpenScience project. Zie http://www.jmol.org voor meer informatie." +"Onderdeel van het OpenScience project. Zie http://www.jmol.org voor meer " +"informatie." #: org/jmol/applet/Jmol.java:712 msgid "File Error:" @@ -75,18 +76,18 @@ msgstr "Geheugengebruik Java" #: org/jmol/popup/JmolPopup.java:168 -#, java-format -msgid "{0} Mb total" +#, fuzzy, java-format +msgid "{0} MB total" msgstr "{0} Mb totaal" #: org/jmol/popup/JmolPopup.java:169 -#, java-format -msgid "{0} Mb free" +#, fuzzy, java-format +msgid "{0} MB free" msgstr "{0} Mb vrij" #: org/jmol/popup/JmolPopup.java:171 -#, java-format -msgid "{0} Mb maximum" +#, fuzzy, java-format +msgid "{0} MB maximum" msgstr "{0} Mb maximaal" #: org/jmol/popup/JmolPopup.java:173 @@ -207,7 +208,8 @@ msgstr "Hetero-groepen" #: org/jmol/popup/PopupResourceBundle.java:720 -msgid "All PDB \"HETATOM\"" +#, fuzzy +msgid "All PDB \"HETATM\"" msgstr "Alle PDB \"HETATOM\"" #: org/jmol/popup/PopupResourceBundle.java:721 @@ -1195,36 +1197,49 @@ #~ msgid "Except Solvent" #~ msgstr "Behalve Oplosmiddel" + #~ msgid "Except Water" #~ msgstr "Behalve Water" + #~ msgid "Other" #~ msgstr "Anders" + #~ msgid "Lipid" #~ msgstr "Lipide" + #~ msgid "pick " #~ msgstr "selecteer" + #~ msgid "Nanometers" #~ msgstr "Nanometers" + #~ msgid "Angstroms" #~ msgstr "Angstroms" + #~ msgid "Picometers" #~ msgstr "Picometers" + #~ msgid "Open" #~ msgstr "Openen" + #~ msgid "Close" #~ msgstr "Sluiten" + #~ msgid "Jmol Molecular Visualization http://www.jmol.org" #~ msgstr "Jmol Moleculaire Visualisatie http://www.jmol.org" + #~ msgid "Jmol script completed" #~ msgstr "Jmol script is klaar" + #~ msgid "Name hidden" #~ msgstr "Naam verborgen" + #~ msgid "Wireframe Rotation" #~ msgstr "Draadmodelrotatie" + #~ msgid "" #~ "Jmol Applet. Part of the OpenScience project. See http://www.jmol.org " #~ "for more information" #~ msgstr "" #~ "Jmol Applet. Onderdeel van het OpenScience project. Zie http://www.jmol." #~ "org voor meer informatie." - Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po 2006-09-24 12:19:14 UTC (rev 5691) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po 2006-09-24 13:30:07 UTC (rev 5692) @@ -6,7 +6,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-24 10:22+0200\n" +"POT-Creation-Date: 2006-09-24 15:23+0200\n" "PO-Revision-Date: 2005-12-20 07:44-0000\n" "Last-Translator: Metro <por...@gm...>\n" "Language-Team: Portugal@Folding <Jmo...@li...>\n" @@ -73,17 +73,17 @@ #: org/jmol/popup/JmolPopup.java:168 #, java-format -msgid "{0} Mb total" +msgid "{0} MB total" msgstr "" #: org/jmol/popup/JmolPopup.java:169 #, java-format -msgid "{0} Mb free" +msgid "{0} MB free" msgstr "" #: org/jmol/popup/JmolPopup.java:171 #, java-format -msgid "{0} Mb maximum" +msgid "{0} MB maximum" msgstr "" #: org/jmol/popup/JmolPopup.java:173 @@ -205,7 +205,7 @@ msgstr "hetero" #: org/jmol/popup/PopupResourceBundle.java:720 -msgid "All PDB \"HETATOM\"" +msgid "All PDB \"HETATM\"" msgstr "" #: org/jmol/popup/PopupResourceBundle.java:721 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2006-09-24 14:59:14
|
Revision: 5697 http://svn.sourceforge.net/jmol/?rev=5697&view=rev Author: nicove Date: 2006-09-24 07:58:55 -0700 (Sun, 24 Sep 2006) Log Message: ----------- i18n Modified Paths: -------------- trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java trunk/Jmol/src/org/jmol/translation/Jmol/fr.po trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po Modified: trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java =================================================================== --- trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java 2006-09-24 14:50:53 UTC (rev 5696) +++ trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java 2006-09-24 14:58:55 UTC (rev 5697) @@ -1186,7 +1186,7 @@ { "bbcage20a", GT._("{0} \u00C5", new Object[]{ "0.20" })}, { "bbcage25a", GT._("{0} \u00C5", new Object[]{ "0.25" })}, { "bbcage50a", GT._("{0} \u00C5", new Object[]{ "0.50" })}, - { "bbcage100a", GT._("1.0 \u00C5", new Object[]{ "1.0" })}, + { "bbcage100a", GT._("{0} \u00C5", new Object[]{ "1.0" })}, { "colorBbcageMenu", GT._("Color") }, { "colorBbcageGray", GT._("Gray") }, Modified: trunk/Jmol/src/org/jmol/translation/Jmol/fr.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/Jmol/fr.po 2006-09-24 14:50:53 UTC (rev 5696) +++ trunk/Jmol/src/org/jmol/translation/Jmol/fr.po 2006-09-24 14:58:55 UTC (rev 5697) @@ -8,7 +8,7 @@ "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" "POT-Creation-Date: 2006-09-23 21:53+0200\n" -"PO-Revision-Date: 2006-02-19 17:18+0100\n" +"PO-Revision-Date: 2006-09-24 16:31+0100\n" "Last-Translator: Nicolas Vervelle <ni...@us...>\n" "Language-Team: French <Jmo...@li...>\n" "MIME-Version: 1.0\n" @@ -552,9 +552,8 @@ #: org/openscience/jmol/app/GuiMap.java:157 #: org/openscience/jmol/app/Jmol.java:468 -#, fuzzy msgid "Jmol Java Console" -msgstr "Console Jmol" +msgstr "Console Java Jmol" #: org/openscience/jmol/app/GuiMap.java:158 msgid "Hydrogens" @@ -573,9 +572,8 @@ msgstr "Prévisualisation (redémarrage de Jmol nécessaire)" #: org/openscience/jmol/app/GuiMap.java:165 -#, fuzzy msgid "Clear console button (needs restarting Jmol)" -msgstr "Prévisualisation (redémarrage de Jmol nécessaire)" +msgstr "Bouton Effacer dans la console (redémarrage de Jmol nécessaire)" #: org/openscience/jmol/app/GuiMap.java:166 #: org/openscience/jmol/app/GuiMap.java:167 @@ -628,8 +626,7 @@ #: org/openscience/jmol/app/Jmol.java:127 msgid "Error starting Jmol: the property 'user.home' is not defined." -msgstr "" -"Erreur au démarrage de Jmol: la propriété 'user.home' n'est pas définie." +msgstr "Erreur au démarrage de Jmol: la propriété 'user.home' n'est pas définie." #: org/openscience/jmol/app/Jmol.java:156 msgid "Initializing 3D display..." @@ -709,8 +706,7 @@ #: org/openscience/jmol/app/Jmol.java:391 msgid "The -D options are as follows (defaults in parathesis):" -msgstr "" -"Les options -D sont les suivantes (valeurs par défaut entre parenthèses):" +msgstr "Les options -D sont les suivantes (valeurs par défaut entre parenthèses):" #: org/openscience/jmol/app/Jmol.java:456 msgid "Executing script..." @@ -778,12 +774,8 @@ msgstr "Racine du nom de fichier" #: org/openscience/jmol/app/PovrayDialog.java:162 -msgid "" -"Single frame: eg 'caffine' -> 'caffine.pov'; Multiple frame: eg 'caffine' -> " -"'caffine_1.pov', 'caffine_2.pov'" -msgstr "" -"Une seule trame: 'caffine' -> 'caffine.pov'; Plusieurs trames: 'caffine' -> " -"'caffine_1.pov', 'caffine_2.pov'" +msgid "Single frame: eg 'caffine' -> 'caffine.pov'; Multiple frame: eg 'caffine' -> 'caffine_1.pov', 'caffine_2.pov'" +msgstr "Une seule trame: 'caffine' -> 'caffine.pov'; Plusieurs trames: 'caffine' -> 'caffine_1.pov', 'caffine_2.pov'" #: org/openscience/jmol/app/PovrayDialog.java:172 msgid "Working Directory" @@ -819,9 +811,7 @@ #: org/openscience/jmol/app/PovrayDialog.java:223 msgid "Render each model (not only the currently displayed one)" -msgstr "" -"Crée une image pour chaque modèle (pas seulement pour celui actuellement " -"affiché)" +msgstr "Crée une image pour chaque modèle (pas seulement pour celui actuellement affiché)" #: org/openscience/jmol/app/PovrayDialog.java:232 msgid "Turn on POV-Ray anti-aliasing" @@ -829,8 +819,7 @@ #: org/openscience/jmol/app/PovrayDialog.java:234 msgid "Use povray's slower but higher quality anti-aliasing mode" -msgstr "" -"Utiliser l'anti-aliasing de povray, plus lent mais de meilleure qualité" +msgstr "Utiliser l'anti-aliasing de povray, plus lent mais de meilleure qualité" #: org/openscience/jmol/app/PovrayDialog.java:243 msgid "Display While Rendering" @@ -1056,9 +1045,8 @@ msgstr "Ouvrir" #: org/openscience/jmol/app/ScriptWindow.java:64 -#, fuzzy msgid "Jmol Script Console" -msgstr "Console Jmol" +msgstr "Console Script Jmol" #: org/openscience/jmol/app/ScriptWindow.java:83 msgid "Run" @@ -1083,69 +1071,48 @@ #, fuzzy #~ msgid "atoms selected" #~ msgstr "groupe d'atomes" - #~ msgid "Jmol executing script ..." #~ msgstr "Exécution du script par Jmol..." - #~ msgid "Rasmol Scripts" #~ msgstr "Scripts Rasmol" - #~ msgid "Wi&reframe Rotation" #~ msgstr "Rotation &fil de fer" - #~ msgid "Wireframe Rotation" #~ msgstr "Rotation fil de fer" - #~ msgid "Colors" #~ msgstr "Couleurs" - #~ msgid "Background" #~ msgstr "Arrière-plan" - #~ msgid "Set the Background Color" #~ msgstr "Régler la couleur d'Arrière-plan" - #~ msgid "Background Color" #~ msgstr "Couleur d'Arrière-plan" - #~ msgid "Picked Atoms" #~ msgstr "Atomes Choisis" - #~ msgid "Set the Color for Picked Atoms" #~ msgstr "Régler la Couleur pour les Atomes Choisis" - #~ msgid "Picked Atom Color" #~ msgstr "Couleur de l'Atome Choisi" - #~ msgid "Text" #~ msgstr "Texte" - #~ msgid "Set the Color for Text" #~ msgstr "Régler la Couleur pour le Texte" - #~ msgid "Text Color" #~ msgstr "Couleur du Texte" - #~ msgid "Set the Color for Bonds" #~ msgstr "Régler la Couleur pour les Liens" - #~ msgid "Bond Color" #~ msgstr "Couleur des Liens" - #~ msgid "Vectors" #~ msgstr "Vecteurs" - #~ msgid "Set the Vector Color" #~ msgstr "Régler la Couleur de Vecteur" - #~ msgid "Vector Color" #~ msgstr "Couleur de Vecteur" - #~ msgid "Color for distance, angle, & torsion measurements" #~ msgstr "Couleur pour les mesures de distance, angle & torsion" - #~ msgid "Measurements Color" #~ msgstr "Couleur des Mesures" - #~ msgid "Loading plugins..." #~ msgstr "Chargement des plugins..." + Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot 2006-09-24 14:50:53 UTC (rev 5696) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot 2006-09-24 14:58:55 UTC (rev 5697) @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: PACKAGE VERSION\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-24 15:23+0200\n" +"POT-Creation-Date: 2006-09-24 16:41+0200\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n" "Language-Team: LANGUAGE <LL...@li...>\n" @@ -362,6 +362,7 @@ #: org/jmol/popup/PopupResourceBundle.java:1186 #: org/jmol/popup/PopupResourceBundle.java:1187 #: org/jmol/popup/PopupResourceBundle.java:1188 +#: org/jmol/popup/PopupResourceBundle.java:1189 #: org/jmol/popup/PopupResourceBundle.java:1208 #: org/jmol/popup/PopupResourceBundle.java:1209 #: org/jmol/popup/PopupResourceBundle.java:1210 @@ -1087,10 +1088,6 @@ msgid "Boundbox" msgstr "" -#: org/jmol/popup/PopupResourceBundle.java:1189 -msgid "1.0 Å" -msgstr "" - #: org/jmol/popup/PopupResourceBundle.java:1193 msgid "Salmon" msgstr "" Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po 2006-09-24 14:50:53 UTC (rev 5696) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po 2006-09-24 14:58:55 UTC (rev 5697) @@ -6,7 +6,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-24 15:23+0200\n" +"POT-Creation-Date: 2006-09-24 16:41+0200\n" "PO-Revision-Date: 2006-01-30 03:37+0100\n" "Last-Translator: Toni Hermoso Pulido <to...@so...>\n" "Language-Team: Catalan <Jmo...@li...>\n" @@ -367,6 +367,7 @@ #: org/jmol/popup/PopupResourceBundle.java:1186 #: org/jmol/popup/PopupResourceBundle.java:1187 #: org/jmol/popup/PopupResourceBundle.java:1188 +#: org/jmol/popup/PopupResourceBundle.java:1189 #: org/jmol/popup/PopupResourceBundle.java:1208 #: org/jmol/popup/PopupResourceBundle.java:1209 #: org/jmol/popup/PopupResourceBundle.java:1210 @@ -1107,10 +1108,6 @@ msgid "Boundbox" msgstr "Quadre" -#: org/jmol/popup/PopupResourceBundle.java:1189 -msgid "1.0 Å" -msgstr "" - #: org/jmol/popup/PopupResourceBundle.java:1193 msgid "Salmon" msgstr "Salmó" Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po 2006-09-24 14:50:53 UTC (rev 5696) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po 2006-09-24 14:58:55 UTC (rev 5697) @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: JmolApplet 10\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-24 15:23+0200\n" +"POT-Creation-Date: 2006-09-24 16:41+0200\n" "PO-Revision-Date: 2006-04-14 18:00+0100\n" "Last-Translator: Sebastian Lisken <sebastianlisken at users.sourceforge." "net>\n" @@ -369,6 +369,7 @@ #: org/jmol/popup/PopupResourceBundle.java:1186 #: org/jmol/popup/PopupResourceBundle.java:1187 #: org/jmol/popup/PopupResourceBundle.java:1188 +#: org/jmol/popup/PopupResourceBundle.java:1189 #: org/jmol/popup/PopupResourceBundle.java:1208 #: org/jmol/popup/PopupResourceBundle.java:1209 #: org/jmol/popup/PopupResourceBundle.java:1210 @@ -1108,10 +1109,6 @@ msgid "Boundbox" msgstr "" -#: org/jmol/popup/PopupResourceBundle.java:1189 -msgid "1.0 Å" -msgstr "" - #: org/jmol/popup/PopupResourceBundle.java:1193 msgid "Salmon" msgstr "Lachsrosa" Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po 2006-09-24 14:50:53 UTC (rev 5696) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po 2006-09-24 14:58:55 UTC (rev 5697) @@ -2,7 +2,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-24 15:23+0200\n" +"POT-Creation-Date: 2006-09-24 16:41+0200\n" "PO-Revision-Date: 2006-09-24 01:26+0100\n" "Last-Translator: Angel Herráez <ang...@ua...>\n" "Language-Team: Spanish <Jmo...@li...>\n" @@ -364,6 +364,7 @@ #: org/jmol/popup/PopupResourceBundle.java:1186 #: org/jmol/popup/PopupResourceBundle.java:1187 #: org/jmol/popup/PopupResourceBundle.java:1188 +#: org/jmol/popup/PopupResourceBundle.java:1189 #: org/jmol/popup/PopupResourceBundle.java:1208 #: org/jmol/popup/PopupResourceBundle.java:1209 #: org/jmol/popup/PopupResourceBundle.java:1210 @@ -1089,10 +1090,6 @@ msgid "Boundbox" msgstr "Caja" -#: org/jmol/popup/PopupResourceBundle.java:1189 -msgid "1.0 Å" -msgstr "" - #: org/jmol/popup/PopupResourceBundle.java:1193 msgid "Salmon" msgstr "Salmón" Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po 2006-09-24 14:50:53 UTC (rev 5696) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po 2006-09-24 14:58:55 UTC (rev 5697) @@ -6,7 +6,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-24 15:23+0200\n" +"POT-Creation-Date: 2006-09-24 16:41+0200\n" "PO-Revision-Date: 2006-03-17 20:19+0100\n" "Last-Translator: Ivo Sarak <iv...@ra...>\n" "Language-Team: Estonian <Jmo...@li...>\n" @@ -368,6 +368,7 @@ #: org/jmol/popup/PopupResourceBundle.java:1186 #: org/jmol/popup/PopupResourceBundle.java:1187 #: org/jmol/popup/PopupResourceBundle.java:1188 +#: org/jmol/popup/PopupResourceBundle.java:1189 #: org/jmol/popup/PopupResourceBundle.java:1208 #: org/jmol/popup/PopupResourceBundle.java:1209 #: org/jmol/popup/PopupResourceBundle.java:1210 @@ -1108,10 +1109,6 @@ msgid "Boundbox" msgstr "Boundbox" -#: org/jmol/popup/PopupResourceBundle.java:1189 -msgid "1.0 Å" -msgstr "" - #: org/jmol/popup/PopupResourceBundle.java:1193 msgid "Salmon" msgstr "Kollane" Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po 2006-09-24 14:50:53 UTC (rev 5696) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po 2006-09-24 14:58:55 UTC (rev 5697) @@ -7,8 +7,8 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-24 15:23+0200\n" -"PO-Revision-Date: 2006-04-14 18:11+0100\n" +"POT-Creation-Date: 2006-09-24 16:41+0200\n" +"PO-Revision-Date: 2006-09-24 16:47+0100\n" "Last-Translator: Nicolas Vervelle <ni...@us...>\n" "Language-Team: French <Jmo...@li...>\n" "MIME-Version: 1.0\n" @@ -20,7 +20,7 @@ #: org/jmol/applet/Console.java:76 msgid "press CTRL-ENTER for new line" -msgstr "" +msgstr "Appuyer sur Ctrl+Entrée pour une nouvelle ligne" #: org/jmol/applet/Jmol.java:597 #, java-format @@ -44,68 +44,68 @@ #: org/jmol/popup/JmolPopup.java:130 #, java-format msgid "atoms: {0}" -msgstr "" +msgstr "{0} atomes" #: org/jmol/popup/JmolPopup.java:132 #, java-format msgid "bonds: {0}" -msgstr "" +msgstr "{0} liens" #: org/jmol/popup/JmolPopup.java:135 #, java-format msgid "groups: {0}" -msgstr "" +msgstr "{0} groupes" #: org/jmol/popup/JmolPopup.java:137 -#, fuzzy, java-format +#, java-format msgid "chains: {0}" -msgstr "Echelle {0}" +msgstr "{0} chaînes" #: org/jmol/popup/JmolPopup.java:139 #, java-format msgid "polymers: {0}" -msgstr "" +msgstr "{0} polymères" #: org/jmol/popup/JmolPopup.java:141 #, java-format msgid "models: {0}" -msgstr "" +msgstr "{0} modèles" #: org/jmol/popup/JmolPopup.java:162 msgid "Java memory usage" -msgstr "" +msgstr "Utilisation mémoire de Java" #: org/jmol/popup/JmolPopup.java:168 #, java-format msgid "{0} MB total" -msgstr "" +msgstr "Total de {0} MB" #: org/jmol/popup/JmolPopup.java:169 #, java-format msgid "{0} MB free" -msgstr "" +msgstr "{0} MB libres" #: org/jmol/popup/JmolPopup.java:171 #, java-format msgid "{0} MB maximum" -msgstr "" +msgstr "Maximum de {0} MB" #: org/jmol/popup/JmolPopup.java:173 msgid "unknown maximum" -msgstr "" +msgstr "Maximum inconnu" #: org/jmol/popup/JmolPopup.java:177 msgid "1 processor" -msgstr "" +msgstr "1 processeur" #: org/jmol/popup/JmolPopup.java:178 #, java-format msgid "{0} processors" -msgstr "" +msgstr "{0} processeurs" #: org/jmol/popup/JmolPopup.java:180 msgid "unknown processor count" -msgstr "" +msgstr "Nombre de processeurs inconnu" #: org/jmol/popup/PopupResourceBundle.java:685 msgid "No atoms loaded" @@ -204,31 +204,28 @@ msgstr "Paires AU" #: org/jmol/popup/PopupResourceBundle.java:719 -#, fuzzy msgid "Hetero" msgstr "Hétéro" #: org/jmol/popup/PopupResourceBundle.java:720 msgid "All PDB \"HETATM\"" -msgstr "" +msgstr "Tous les \"HETATM\" PDB" #: org/jmol/popup/PopupResourceBundle.java:721 -#, fuzzy msgid "All Solvent" -msgstr "Solvant" +msgstr "Tout Solvant" #: org/jmol/popup/PopupResourceBundle.java:722 -#, fuzzy msgid "All Water" -msgstr "Eau" +msgstr "Tout Eau" #: org/jmol/popup/PopupResourceBundle.java:723 msgid "Nonaqueous Solvent" -msgstr "" +msgstr "Solvant non-aqueux" #: org/jmol/popup/PopupResourceBundle.java:724 msgid "Nonaqueous HETATM" -msgstr "" +msgstr "HETATM non-aqueux" #: org/jmol/popup/PopupResourceBundle.java:725 msgid "Ligand" @@ -240,7 +237,7 @@ #: org/jmol/popup/PopupResourceBundle.java:727 msgid "None of the above" -msgstr "" +msgstr "Aucun des précédents" #: org/jmol/popup/PopupResourceBundle.java:729 #: org/jmol/popup/PopupResourceBundle.java:1142 @@ -372,14 +369,15 @@ #: org/jmol/popup/PopupResourceBundle.java:1186 #: org/jmol/popup/PopupResourceBundle.java:1187 #: org/jmol/popup/PopupResourceBundle.java:1188 +#: org/jmol/popup/PopupResourceBundle.java:1189 #: org/jmol/popup/PopupResourceBundle.java:1208 #: org/jmol/popup/PopupResourceBundle.java:1209 #: org/jmol/popup/PopupResourceBundle.java:1210 #: org/jmol/popup/PopupResourceBundle.java:1211 #: org/jmol/popup/PopupResourceBundle.java:1212 -#, fuzzy, java-format +#, java-format msgid "{0} Å" -msgstr "{0} px" +msgstr "{0} Å" #: org/jmol/popup/PopupResourceBundle.java:770 #: org/jmol/popup/PopupResourceBundle.java:897 @@ -908,126 +906,112 @@ msgstr "En arrière" #: org/jmol/popup/PopupResourceBundle.java:1111 -#, fuzzy msgid "Measurement" msgstr "Mesures" #: org/jmol/popup/PopupResourceBundle.java:1112 msgid "Double-Click starts all measurements" -msgstr "" +msgstr "Double-clic commence toutes les mesures" #: org/jmol/popup/PopupResourceBundle.java:1113 msgid "Click for distance measurement" -msgstr "" +msgstr "Cliquer pour une mesure de distance" #: org/jmol/popup/PopupResourceBundle.java:1114 msgid "Click for angle measurement" -msgstr "" +msgstr "Cliquer pour une mesure d'angle" #: org/jmol/popup/PopupResourceBundle.java:1115 msgid "Click for torsion (dihedral) measurement" -msgstr "" +msgstr "Cliquer pour une mesure de torsion (dihédrale)" #: org/jmol/popup/PopupResourceBundle.java:1116 -#, fuzzy msgid "Delete measurements" -msgstr "Mesures" +msgstr "Effacer les mesures" #: org/jmol/popup/PopupResourceBundle.java:1117 -#, fuzzy msgid "List measurements" -msgstr "Mesures" +msgstr "Donner la liste des mesures" #: org/jmol/popup/PopupResourceBundle.java:1118 msgid "Distance units nanometers" -msgstr "" +msgstr "Unité pour les distances en nanomètres" #: org/jmol/popup/PopupResourceBundle.java:1119 msgid "Distance units Angstroms" -msgstr "" +msgstr "Unité pour les distances en Angstroms" #: org/jmol/popup/PopupResourceBundle.java:1120 msgid "Distance units picometers" -msgstr "" +msgstr "Unité pour les distances en picomètres" #: org/jmol/popup/PopupResourceBundle.java:1122 msgid "Set picking" msgstr "" #: org/jmol/popup/PopupResourceBundle.java:1124 -#, fuzzy msgid "Center" -msgstr "Centré" +msgstr "Centre" #: org/jmol/popup/PopupResourceBundle.java:1126 -#, fuzzy msgid "Label" -msgstr "Textes" +msgstr "Texte" #: org/jmol/popup/PopupResourceBundle.java:1127 -#, fuzzy msgid "Select atom" -msgstr "Sélectionner" +msgstr "Sélectionner atome" #: org/jmol/popup/PopupResourceBundle.java:1128 -#, fuzzy msgid "Select chain" -msgstr "Sélectionner" +msgstr "Sélectionner chaîne" #: org/jmol/popup/PopupResourceBundle.java:1129 -#, fuzzy msgid "Select element" -msgstr "Sélectionner" +msgstr "Sélectionner élément" #: org/jmol/popup/PopupResourceBundle.java:1130 -#, fuzzy msgid "Select group" -msgstr "Sélectionner" +msgstr "Sélectionner groupe" #: org/jmol/popup/PopupResourceBundle.java:1131 -#, fuzzy msgid "Select molecule" -msgstr "Choisir le mode de sélection" +msgstr "Sélectionner molécule" #: org/jmol/popup/PopupResourceBundle.java:1132 -#, fuzzy msgid "Select site" -msgstr "Sélectionner" +msgstr "Sélectionner site" #: org/jmol/popup/PopupResourceBundle.java:1135 msgid "Show" -msgstr "" +msgstr "Afficher" #: org/jmol/popup/PopupResourceBundle.java:1136 -#, fuzzy msgid "Console" -msgstr "Console..." +msgstr "Console" #: org/jmol/popup/PopupResourceBundle.java:1137 msgid "File Contents" -msgstr "" +msgstr "Contenu du fichier" #: org/jmol/popup/PopupResourceBundle.java:1138 msgid "File Header" -msgstr "" +msgstr "Entête du fichier" #: org/jmol/popup/PopupResourceBundle.java:1139 msgid "Isosurface JVXL data" -msgstr "" +msgstr "Données isosurface au format JVXL" #: org/jmol/popup/PopupResourceBundle.java:1140 -#, fuzzy msgid "Measure" -msgstr "Mesures" +msgstr "Mesure" #: org/jmol/popup/PopupResourceBundle.java:1141 msgid "Molecular orbital JVXL data" -msgstr "" +msgstr "Données orbites moléculaires au format JVXL" #: org/jmol/popup/PopupResourceBundle.java:1143 -#, fuzzy msgid "Orientation" -msgstr "Traductions" +msgstr "Orientation" #: org/jmol/popup/PopupResourceBundle.java:1144 msgid "Space group" @@ -1035,10 +1019,9 @@ #: org/jmol/popup/PopupResourceBundle.java:1145 msgid "Symmetry" -msgstr "" +msgstr "Symétrie" #: org/jmol/popup/PopupResourceBundle.java:1146 -#, fuzzy msgid "Unit cell" msgstr "Cellule unitaire" @@ -1112,10 +1095,6 @@ msgid "Boundbox" msgstr "Boîte englobante" -#: org/jmol/popup/PopupResourceBundle.java:1189 -msgid "1.0 Å" -msgstr "" - #: org/jmol/popup/PopupResourceBundle.java:1193 msgid "Salmon" msgstr "Saumon" @@ -1149,9 +1128,8 @@ msgstr "Options" #: org/jmol/popup/PopupResourceBundle.java:1221 -#, fuzzy msgid "Show Selected Atoms" -msgstr "Afficher les halos de sélection" +msgstr "Afficher les atomes sélectionnés" #: org/jmol/popup/PopupResourceBundle.java:1222 msgid "Show Hydrogens" @@ -1199,16 +1177,15 @@ #: org/jmol/viewer/PickingManager.java:167 msgid "pick one more atom in order to spin the model around an axis" -msgstr "" +msgstr "Choisir un atome supplémentaire pour faire tourner le modèle autour d'un axe" #: org/jmol/viewer/PickingManager.java:168 msgid "pick two atoms in order to spin the model around an axis" -msgstr "" +msgstr "Choisir deux atomes pour faire tourner le modèle autour d'un axe" #: org/jmol/viewer/PickingManager.java:229 -#, fuzzy msgid "atoms selected" -msgstr "Aucun atome chargé" +msgstr "atomes sélectionnés" #: org/jmol/viewer/StatusManager.java:177 msgid "Jmol executing script ..." @@ -1216,39 +1193,28 @@ #~ msgid "Except Solvent" #~ msgstr "Excepté le solvant" - #~ msgid "Except Water" #~ msgstr "Excepté l'eau" - #~ msgid "Other" #~ msgstr "Autre" - #~ msgid "Lipid" #~ msgstr "Lipide" - #~ msgid "Nanometers" #~ msgstr "Nanomètres" - #~ msgid "Angstroms" #~ msgstr "Angströms" - #~ msgid "Picometers" #~ msgstr "Picomètres" - #~ msgid "Open" #~ msgstr "Ouvrir" - #~ msgid "Close" #~ msgstr "Fermer" - #~ msgid "Jmol Molecular Visualization http://www.jmol.org" #~ msgstr "Jmol Visualisation Moléculaire http://www.jmol.org" - #~ msgid "Jmol script completed" #~ msgstr "Script Jmol terminé" - #~ msgid "Name hidden" #~ msgstr "Nom caché" - #~ msgid "Wireframe Rotation" #~ msgstr "Rotation fil de fer" + Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po 2006-09-24 14:50:53 UTC (rev 5696) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po 2006-09-24 14:58:55 UTC (rev 5697) @@ -7,7 +7,7 @@ msgstr "" "Project-Id-Version: nl\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-24 15:23+0200\n" +"POT-Creation-Date: 2006-09-24 16:41+0200\n" "PO-Revision-Date: 2006-09-24 14:11+0100\n" "Last-Translator: Egon Willighagen <eg...@jm...>\n" "Language-Team: Nederlands <jmo...@li...>\n" @@ -370,6 +370,7 @@ #: org/jmol/popup/PopupResourceBundle.java:1186 #: org/jmol/popup/PopupResourceBundle.java:1187 #: org/jmol/popup/PopupResourceBundle.java:1188 +#: org/jmol/popup/PopupResourceBundle.java:1189 #: org/jmol/popup/PopupResourceBundle.java:1208 #: org/jmol/popup/PopupResourceBundle.java:1209 #: org/jmol/popup/PopupResourceBundle.java:1210 @@ -1095,10 +1096,6 @@ msgid "Boundbox" msgstr "Boundbox" -#: org/jmol/popup/PopupResourceBundle.java:1189 -msgid "1.0 Å" -msgstr "1.0 Å" - #: org/jmol/popup/PopupResourceBundle.java:1193 msgid "Salmon" msgstr "Zalm" @@ -1195,6 +1192,9 @@ msgid "Jmol executing script ..." msgstr "Jmol voert script uit ..." +#~ msgid "1.0 Å" +#~ msgstr "1.0 Å" + #~ msgid "Except Solvent" #~ msgstr "Behalve Oplosmiddel" Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po 2006-09-24 14:50:53 UTC (rev 5696) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po 2006-09-24 14:58:55 UTC (rev 5697) @@ -6,7 +6,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-24 15:23+0200\n" +"POT-Creation-Date: 2006-09-24 16:41+0200\n" "PO-Revision-Date: 2005-12-20 07:44-0000\n" "Last-Translator: Metro <por...@gm...>\n" "Language-Team: Portugal@Folding <Jmo...@li...>\n" @@ -368,6 +368,7 @@ #: org/jmol/popup/PopupResourceBundle.java:1186 #: org/jmol/popup/PopupResourceBundle.java:1187 #: org/jmol/popup/PopupResourceBundle.java:1188 +#: org/jmol/popup/PopupResourceBundle.java:1189 #: org/jmol/popup/PopupResourceBundle.java:1208 #: org/jmol/popup/PopupResourceBundle.java:1209 #: org/jmol/popup/PopupResourceBundle.java:1210 @@ -1107,10 +1108,6 @@ msgid "Boundbox" msgstr "Caixa de ligação" -#: org/jmol/popup/PopupResourceBundle.java:1189 -msgid "1.0 Å" -msgstr "" - #: org/jmol/popup/PopupResourceBundle.java:1193 msgid "Salmon" msgstr "Salmão" This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2006-09-24 23:45:51
|
Revision: 5706 http://svn.sourceforge.net/jmol/?rev=5706&view=rev Author: hansonr Date: 2006-09-24 16:45:41 -0700 (Sun, 24 Sep 2006) Log Message: ----------- popup select ---> hetero ---> by HETNAM Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/CifReader.java trunk/Jmol/src/org/jmol/api/JmolViewer.java trunk/Jmol/src/org/jmol/popup/JmolPopup.java trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java trunk/Jmol/src/org/jmol/viewer/Mmset.java trunk/Jmol/src/org/jmol/viewer/ModelManager.java trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/CifReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/CifReader.java 2006-09-24 22:47:55 UTC (rev 5705) +++ trunk/Jmol/src/org/jmol/adapter/smarter/CifReader.java 2006-09-24 23:45:41 UTC (rev 5706) @@ -144,6 +144,8 @@ } else if (key.startsWith("_atom_sites.fract_tran") || key.startsWith("_atom_sites.fract_tran")) { processUnitCellTransformMatrix(); + } else if (key.startsWith("_pdbx_entity_nonpoly")) { + processNonpolyData(); } } } @@ -598,7 +600,7 @@ } //////////////////////////////////////////////////////////////// - // helix and turn structure data + // HETATM identity //////////////////////////////////////////////////////////////// final static byte NONPOLY_ENTITY_ID = 0; @@ -610,10 +612,30 @@ "_pdbx_entity_nonpoly.name", "_pdbx_entity_nonpoly.comp_id", }; + + /** + * + * optional nonloop format -- see 1jsa.cif + * + */ + String[] hetatmData; + void processNonpolyData() { + if (hetatmData == null) + hetatmData = new String[3]; + for (int i = nonpolyFields.length; --i >= 0;) + if (isMatch(key, nonpolyFields[i])) { + hetatmData[i] = data; + break; + } + if (hetatmData[NONPOLY_NAME] == null || hetatmData[NONPOLY_COMP_ID] == null) + return; + addHetero(hetatmData[NONPOLY_COMP_ID], hetatmData[NONPOLY_NAME]); + hetatmData = null; + } /** * - * a HETERO name definition field. Maybe not all hetero? + * a HETERO name definition field. Maybe not all hetero? nonpoly? * * @throws Exception */ @@ -643,13 +665,17 @@ } if (groupName == null || hetName == null) return; - if (htHetero == null) - htHetero = new Hashtable(); - htHetero.put(groupName, hetName); - logger.log("hetero: "+groupName+" "+hetName); + addHetero(groupName, hetName); } } + void addHetero(String groupName, String hetName) { + if (htHetero == null) + htHetero = new Hashtable(); + htHetero.put(groupName, hetName); + logger.log("hetero: "+groupName+" = "+hetName); + } + //////////////////////////////////////////////////////////////// // helix and turn structure data //////////////////////////////////////////////////////////////// Modified: trunk/Jmol/src/org/jmol/api/JmolViewer.java =================================================================== --- trunk/Jmol/src/org/jmol/api/JmolViewer.java 2006-09-24 22:47:55 UTC (rev 5705) +++ trunk/Jmol/src/org/jmol/api/JmolViewer.java 2006-09-24 23:45:41 UTC (rev 5706) @@ -168,6 +168,8 @@ abstract public BitSet getGroupsPresentBitSet(); + abstract public Hashtable getHeteroList(); + abstract public void setPerspectiveDepth(boolean perspectiveDepth); abstract public boolean getPerspectiveDepth(); Modified: trunk/Jmol/src/org/jmol/popup/JmolPopup.java =================================================================== --- trunk/Jmol/src/org/jmol/popup/JmolPopup.java 2006-09-24 22:47:55 UTC (rev 5705) +++ trunk/Jmol/src/org/jmol/popup/JmolPopup.java 2006-09-24 23:45:41 UTC (rev 5706) @@ -32,6 +32,7 @@ import java.util.StringTokenizer; import java.util.BitSet; import java.util.Hashtable; +import java.util.Enumeration; abstract public class JmolPopup { private final static boolean forceAwt = false; @@ -42,6 +43,7 @@ Object elementsComputedMenu; Object aaresiduesComputedMenu; + Object heteroComputedMenu; Object aboutMenu; int aboutMenuBaseCount; Object consoleMenu; @@ -70,6 +72,7 @@ public void updateComputedMenus() { updateElementsComputedMenu(viewer.getElementsPresentBitSet()); + updateHeteroComputedMenu(viewer.getHeteroList()); updateAaresiduesComputedMenu(viewer.getGroupsPresentBitSet()); updateModelSetInfoMenu(); } @@ -99,7 +102,23 @@ } } } - + + void updateHeteroComputedMenu(Hashtable htHetero) { + if (htHetero == null) + return; + removeAll(heteroComputedMenu); + Enumeration e = htHetero.keys(); + while (e.hasMoreElements()) { + String heteroCode = (String) e.nextElement(); + String heteroName = (String) htHetero.get(heteroCode); + if (heteroName.length() > 20) + heteroName = heteroName.substring(0,20) + "..."; + String entryName = heteroCode + " - " + heteroName; + String script = "select " + heteroCode; + addMenuItem(heteroComputedMenu, entryName, script); + } + } + void updateAaresiduesComputedMenu(BitSet groupsPresentBitSet) { if (aaresiduesComputedMenu == null || groupsPresentBitSet == null) return; @@ -203,6 +222,8 @@ elementsComputedMenu = subMenu; else if ("aaresiduesComputedMenu".equals(item)) aaresiduesComputedMenu = subMenu; + else if ("heteroComputedMenu".equals(item)) + heteroComputedMenu = subMenu; else addMenuItems(item, subMenu, popupResourceBundle); if ("aboutMenu".equals(item)) Modified: trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java =================================================================== --- trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java 2006-09-24 22:47:55 UTC (rev 5705) +++ trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java 2006-09-24 23:45:41 UTC (rev 5706) @@ -93,7 +93,7 @@ { "T", "select t" }, { "U", "select u" }, - { "heteroMenu", "allHetero Solvent Water - " + + { "heteroMenu", "heteroComputedMenu - allHetero Solvent Water - " + "Ligand exceptWater nonWaterSolvent" }, { "allHetero", "select hetero" }, { "Solvent", "select solvent" }, @@ -700,7 +700,7 @@ { "negativeCharge", GT._("Acidic Residues (-)") }, { "noCharge", GT._("Uncharged Residues") }, { "aaresiduesComputedMenu", GT._("By Residue Name") }, - + { "heteroComputedMenu", GT._("By HETATM") }, { "nucleicMenu", GT._("Nucleic") }, { "allNucleic", GT._("All") }, { "DNA", GT._("DNA") }, Modified: trunk/Jmol/src/org/jmol/viewer/Mmset.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Mmset.java 2006-09-24 22:47:55 UTC (rev 5705) +++ trunk/Jmol/src/org/jmol/viewer/Mmset.java 2006-09-24 23:45:41 UTC (rev 5706) @@ -27,6 +27,7 @@ import java.util.Properties; import java.util.BitSet; import java.util.Vector; +import java.util.Enumeration; import org.jmol.util.ArrayUtil; @@ -85,6 +86,21 @@ models[i].setConformation(bsConformation); } + Hashtable getHeteroList() { + Hashtable htFull = new Hashtable(); + for (int i = modelCount; --i >= 0;) { + Hashtable ht = (Hashtable) getModelAuxiliaryInfo(i, "hetNames"); + if (ht == null) + continue; + Enumeration e = ht.keys(); + while (e.hasMoreElements()) { + String key = (String) e.nextElement(); + htFull.put(key, ht.get(key)); + } + } + return htFull; + } + void freeze() { for (int i = modelCount; --i >= 0;) { models[i].freeze(); Modified: trunk/Jmol/src/org/jmol/viewer/ModelManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/ModelManager.java 2006-09-24 22:47:55 UTC (rev 5705) +++ trunk/Jmol/src/org/jmol/viewer/ModelManager.java 2006-09-24 23:45:41 UTC (rev 5706) @@ -500,6 +500,10 @@ return (frame == null) ? null : frame.getElementsPresentBitSet(); } + public Hashtable getHeteroList() { + return (frame == null) ? null : frame.mmset.getHeteroList(); + } + BitSet getGroupsPresentBitSet() { return (frame == null) ? null : frame.getGroupsPresentBitSet(); } Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2006-09-24 22:47:55 UTC (rev 5705) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2006-09-24 23:45:41 UTC (rev 5706) @@ -1183,6 +1183,7 @@ transformManager.setFixedRotationCenter(new Point3f(0, 0, 0)); setStatusFileLoaded(0, null, null, null, null, null); refresh(0, "Viewer:clear()"); + System.gc(); } public String getModelSetName() { @@ -1542,6 +1543,10 @@ public BitSet getElementsPresentBitSet() { return modelManager.getElementsPresentBitSet(); } + + public Hashtable getHeteroList() { + return modelManager.getHeteroList(); + } BitSet getVisibleSet() { return modelManager.getVisibleSet(); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2006-09-25 04:29:04
|
Revision: 5713 http://svn.sourceforge.net/jmol/?rev=5713&view=rev Author: nicove Date: 2006-09-24 21:28:47 -0700 (Sun, 24 Sep 2006) Log Message: ----------- i18n Modified Paths: -------------- trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po trunk/Jmol/src/org/jmol/viewer/Eval.java Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot 2006-09-25 04:22:59 UTC (rev 5712) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/JmolApplet.pot 2006-09-25 04:28:47 UTC (rev 5713) @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: PACKAGE VERSION\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-25 06:12+0200\n" +"POT-Creation-Date: 2006-09-25 06:25+0200\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n" "Language-Team: LANGUAGE <LL...@li...>\n" @@ -1209,89 +1209,86 @@ msgstr "" #: org/jmol/viewer/Eval.java:2143 -msgid "space group " +#, java-format +msgid "space group {0} was not found." msgstr "" -#: org/jmol/viewer/Eval.java:2143 -msgid " was not found." -msgstr "" - -#: org/jmol/viewer/Eval.java:2887 +#: org/jmol/viewer/Eval.java:2888 msgid "\"conformation\" not allowed with background model displayed" msgstr "" -#: org/jmol/viewer/Eval.java:3129 +#: org/jmol/viewer/Eval.java:3130 msgid "Calculate what? hbonds? surface? structure?" msgstr "" -#: org/jmol/viewer/Eval.java:3146 +#: org/jmol/viewer/Eval.java:3147 msgid "surfaces require that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:3357 +#: org/jmol/viewer/Eval.java:3358 msgid "invalid frame control keyword" msgstr "" -#: org/jmol/viewer/Eval.java:3689 +#: org/jmol/viewer/Eval.java:3690 msgid "SET ECHO must follow, not precede, model loading" msgstr "" -#: org/jmol/viewer/Eval.java:4071 +#: org/jmol/viewer/Eval.java:4072 msgid "save what? bonds? orientation? selection?" msgstr "" -#: org/jmol/viewer/Eval.java:4092 +#: org/jmol/viewer/Eval.java:4093 msgid "restore what? bonds? orientation? selection?" msgstr "" -#: org/jmol/viewer/Eval.java:4166 org/jmol/viewer/Eval.java:4789 +#: org/jmol/viewer/Eval.java:4167 org/jmol/viewer/Eval.java:4790 msgid "MO isosurfaces require that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:4170 org/jmol/viewer/Eval.java:4793 +#: org/jmol/viewer/Eval.java:4171 org/jmol/viewer/Eval.java:4794 msgid "no MO basis/coefficient data available for this frame" msgstr "" -#: org/jmol/viewer/Eval.java:4213 +#: org/jmol/viewer/Eval.java:4214 msgid "use \"show ORIENTATION\"" msgstr "" -#: org/jmol/viewer/Eval.java:4218 +#: org/jmol/viewer/Eval.java:4219 msgid "unrecognized SHOW parameter -- use \"getProperty CHAININFO \"" msgstr "" -#: org/jmol/viewer/Eval.java:4220 +#: org/jmol/viewer/Eval.java:4221 msgid "unrecognized SHOW parameter -- use \"getProperty ATOMINFO (selected)\"" msgstr "" -#: org/jmol/viewer/Eval.java:4222 +#: org/jmol/viewer/Eval.java:4223 msgid "" "unrecognized SHOW parameter -- use \"getProperty ATOMINFO (atom expression)" "\"" msgstr "" -#: org/jmol/viewer/Eval.java:4233 +#: org/jmol/viewer/Eval.java:4234 msgid "unrecognized SHOW parameter" msgstr "" -#: org/jmol/viewer/Eval.java:4797 +#: org/jmol/viewer/Eval.java:4798 msgid "no MO coefficient data available" msgstr "" -#: org/jmol/viewer/Eval.java:4799 +#: org/jmol/viewer/Eval.java:4800 msgid "Only one molecular orbital is available in this file" msgstr "" -#: org/jmol/viewer/Eval.java:4801 +#: org/jmol/viewer/Eval.java:4802 #, java-format msgid "An MO index from 1 to {0} is required" msgstr "" -#: org/jmol/viewer/Eval.java:4821 +#: org/jmol/viewer/Eval.java:4822 msgid "the isosurface command requires that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:5113 +#: org/jmol/viewer/Eval.java:5114 msgid "" "No partial charges were read from the file; Jmol needs these to render the " "MEP data." Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po 2006-09-25 04:22:59 UTC (rev 5712) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/ca.po 2006-09-25 04:28:47 UTC (rev 5713) @@ -6,7 +6,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-25 06:12+0200\n" +"POT-Creation-Date: 2006-09-25 06:25+0200\n" "PO-Revision-Date: 2006-01-30 03:37+0100\n" "Last-Translator: Toni Hermoso Pulido <to...@so...>\n" "Language-Team: Catalan <Jmo...@li...>\n" @@ -1231,89 +1231,86 @@ msgstr "" #: org/jmol/viewer/Eval.java:2143 -msgid "space group " +#, java-format +msgid "space group {0} was not found." msgstr "" -#: org/jmol/viewer/Eval.java:2143 -msgid " was not found." -msgstr "" - -#: org/jmol/viewer/Eval.java:2887 +#: org/jmol/viewer/Eval.java:2888 msgid "\"conformation\" not allowed with background model displayed" msgstr "" -#: org/jmol/viewer/Eval.java:3129 +#: org/jmol/viewer/Eval.java:3130 msgid "Calculate what? hbonds? surface? structure?" msgstr "" -#: org/jmol/viewer/Eval.java:3146 +#: org/jmol/viewer/Eval.java:3147 msgid "surfaces require that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:3357 +#: org/jmol/viewer/Eval.java:3358 msgid "invalid frame control keyword" msgstr "" -#: org/jmol/viewer/Eval.java:3689 +#: org/jmol/viewer/Eval.java:3690 msgid "SET ECHO must follow, not precede, model loading" msgstr "" -#: org/jmol/viewer/Eval.java:4071 +#: org/jmol/viewer/Eval.java:4072 msgid "save what? bonds? orientation? selection?" msgstr "" -#: org/jmol/viewer/Eval.java:4092 +#: org/jmol/viewer/Eval.java:4093 msgid "restore what? bonds? orientation? selection?" msgstr "" -#: org/jmol/viewer/Eval.java:4166 org/jmol/viewer/Eval.java:4789 +#: org/jmol/viewer/Eval.java:4167 org/jmol/viewer/Eval.java:4790 msgid "MO isosurfaces require that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:4170 org/jmol/viewer/Eval.java:4793 +#: org/jmol/viewer/Eval.java:4171 org/jmol/viewer/Eval.java:4794 msgid "no MO basis/coefficient data available for this frame" msgstr "" -#: org/jmol/viewer/Eval.java:4213 +#: org/jmol/viewer/Eval.java:4214 msgid "use \"show ORIENTATION\"" msgstr "" -#: org/jmol/viewer/Eval.java:4218 +#: org/jmol/viewer/Eval.java:4219 msgid "unrecognized SHOW parameter -- use \"getProperty CHAININFO \"" msgstr "" -#: org/jmol/viewer/Eval.java:4220 +#: org/jmol/viewer/Eval.java:4221 msgid "unrecognized SHOW parameter -- use \"getProperty ATOMINFO (selected)\"" msgstr "" -#: org/jmol/viewer/Eval.java:4222 +#: org/jmol/viewer/Eval.java:4223 msgid "" "unrecognized SHOW parameter -- use \"getProperty ATOMINFO (atom expression)" "\"" msgstr "" -#: org/jmol/viewer/Eval.java:4233 +#: org/jmol/viewer/Eval.java:4234 msgid "unrecognized SHOW parameter" msgstr "" -#: org/jmol/viewer/Eval.java:4797 +#: org/jmol/viewer/Eval.java:4798 msgid "no MO coefficient data available" msgstr "" -#: org/jmol/viewer/Eval.java:4799 +#: org/jmol/viewer/Eval.java:4800 msgid "Only one molecular orbital is available in this file" msgstr "" -#: org/jmol/viewer/Eval.java:4801 +#: org/jmol/viewer/Eval.java:4802 #, java-format msgid "An MO index from 1 to {0} is required" msgstr "" -#: org/jmol/viewer/Eval.java:4821 +#: org/jmol/viewer/Eval.java:4822 msgid "the isosurface command requires that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:5113 +#: org/jmol/viewer/Eval.java:5114 msgid "" "No partial charges were read from the file; Jmol needs these to render the " "MEP data." Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po 2006-09-25 04:22:59 UTC (rev 5712) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/de.po 2006-09-25 04:28:47 UTC (rev 5713) @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: JmolApplet 10\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-25 06:12+0200\n" +"POT-Creation-Date: 2006-09-25 06:25+0200\n" "PO-Revision-Date: 2006-04-14 18:00+0100\n" "Last-Translator: Sebastian Lisken <sebastianlisken at users.sourceforge." "net>\n" @@ -1231,89 +1231,86 @@ msgstr "" #: org/jmol/viewer/Eval.java:2143 -msgid "space group " +#, java-format +msgid "space group {0} was not found." msgstr "" -#: org/jmol/viewer/Eval.java:2143 -msgid " was not found." -msgstr "" - -#: org/jmol/viewer/Eval.java:2887 +#: org/jmol/viewer/Eval.java:2888 msgid "\"conformation\" not allowed with background model displayed" msgstr "" -#: org/jmol/viewer/Eval.java:3129 +#: org/jmol/viewer/Eval.java:3130 msgid "Calculate what? hbonds? surface? structure?" msgstr "" -#: org/jmol/viewer/Eval.java:3146 +#: org/jmol/viewer/Eval.java:3147 msgid "surfaces require that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:3357 +#: org/jmol/viewer/Eval.java:3358 msgid "invalid frame control keyword" msgstr "" -#: org/jmol/viewer/Eval.java:3689 +#: org/jmol/viewer/Eval.java:3690 msgid "SET ECHO must follow, not precede, model loading" msgstr "" -#: org/jmol/viewer/Eval.java:4071 +#: org/jmol/viewer/Eval.java:4072 msgid "save what? bonds? orientation? selection?" msgstr "" -#: org/jmol/viewer/Eval.java:4092 +#: org/jmol/viewer/Eval.java:4093 msgid "restore what? bonds? orientation? selection?" msgstr "" -#: org/jmol/viewer/Eval.java:4166 org/jmol/viewer/Eval.java:4789 +#: org/jmol/viewer/Eval.java:4167 org/jmol/viewer/Eval.java:4790 msgid "MO isosurfaces require that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:4170 org/jmol/viewer/Eval.java:4793 +#: org/jmol/viewer/Eval.java:4171 org/jmol/viewer/Eval.java:4794 msgid "no MO basis/coefficient data available for this frame" msgstr "" -#: org/jmol/viewer/Eval.java:4213 +#: org/jmol/viewer/Eval.java:4214 msgid "use \"show ORIENTATION\"" msgstr "" -#: org/jmol/viewer/Eval.java:4218 +#: org/jmol/viewer/Eval.java:4219 msgid "unrecognized SHOW parameter -- use \"getProperty CHAININFO \"" msgstr "" -#: org/jmol/viewer/Eval.java:4220 +#: org/jmol/viewer/Eval.java:4221 msgid "unrecognized SHOW parameter -- use \"getProperty ATOMINFO (selected)\"" msgstr "" -#: org/jmol/viewer/Eval.java:4222 +#: org/jmol/viewer/Eval.java:4223 msgid "" "unrecognized SHOW parameter -- use \"getProperty ATOMINFO (atom expression)" "\"" msgstr "" -#: org/jmol/viewer/Eval.java:4233 +#: org/jmol/viewer/Eval.java:4234 msgid "unrecognized SHOW parameter" msgstr "" -#: org/jmol/viewer/Eval.java:4797 +#: org/jmol/viewer/Eval.java:4798 msgid "no MO coefficient data available" msgstr "" -#: org/jmol/viewer/Eval.java:4799 +#: org/jmol/viewer/Eval.java:4800 msgid "Only one molecular orbital is available in this file" msgstr "" -#: org/jmol/viewer/Eval.java:4801 +#: org/jmol/viewer/Eval.java:4802 #, java-format msgid "An MO index from 1 to {0} is required" msgstr "" -#: org/jmol/viewer/Eval.java:4821 +#: org/jmol/viewer/Eval.java:4822 msgid "the isosurface command requires that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:5113 +#: org/jmol/viewer/Eval.java:5114 msgid "" "No partial charges were read from the file; Jmol needs these to render the " "MEP data." Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po 2006-09-25 04:22:59 UTC (rev 5712) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/es.po 2006-09-25 04:28:47 UTC (rev 5713) @@ -2,7 +2,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-25 06:12+0200\n" +"POT-Creation-Date: 2006-09-25 06:25+0200\n" "PO-Revision-Date: 2006-09-25 00:32+0100\n" "Last-Translator: Angel Herráez <ang...@ua...>\n" "Language-Team: Spanish <Jmo...@li...>\n" @@ -1212,90 +1212,86 @@ msgstr "" #: org/jmol/viewer/Eval.java:2143 -#, fuzzy -msgid "space group " -msgstr "Grupo espacial" - -#: org/jmol/viewer/Eval.java:2143 -msgid " was not found." +#, java-format +msgid "space group {0} was not found." msgstr "" -#: org/jmol/viewer/Eval.java:2887 +#: org/jmol/viewer/Eval.java:2888 msgid "\"conformation\" not allowed with background model displayed" msgstr "" -#: org/jmol/viewer/Eval.java:3129 +#: org/jmol/viewer/Eval.java:3130 msgid "Calculate what? hbonds? surface? structure?" msgstr "" -#: org/jmol/viewer/Eval.java:3146 +#: org/jmol/viewer/Eval.java:3147 msgid "surfaces require that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:3357 +#: org/jmol/viewer/Eval.java:3358 msgid "invalid frame control keyword" msgstr "" -#: org/jmol/viewer/Eval.java:3689 +#: org/jmol/viewer/Eval.java:3690 msgid "SET ECHO must follow, not precede, model loading" msgstr "" -#: org/jmol/viewer/Eval.java:4071 +#: org/jmol/viewer/Eval.java:4072 msgid "save what? bonds? orientation? selection?" msgstr "" -#: org/jmol/viewer/Eval.java:4092 +#: org/jmol/viewer/Eval.java:4093 msgid "restore what? bonds? orientation? selection?" msgstr "" -#: org/jmol/viewer/Eval.java:4166 org/jmol/viewer/Eval.java:4789 +#: org/jmol/viewer/Eval.java:4167 org/jmol/viewer/Eval.java:4790 msgid "MO isosurfaces require that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:4170 org/jmol/viewer/Eval.java:4793 +#: org/jmol/viewer/Eval.java:4171 org/jmol/viewer/Eval.java:4794 msgid "no MO basis/coefficient data available for this frame" msgstr "" -#: org/jmol/viewer/Eval.java:4213 +#: org/jmol/viewer/Eval.java:4214 msgid "use \"show ORIENTATION\"" msgstr "" -#: org/jmol/viewer/Eval.java:4218 +#: org/jmol/viewer/Eval.java:4219 msgid "unrecognized SHOW parameter -- use \"getProperty CHAININFO \"" msgstr "" -#: org/jmol/viewer/Eval.java:4220 +#: org/jmol/viewer/Eval.java:4221 msgid "unrecognized SHOW parameter -- use \"getProperty ATOMINFO (selected)\"" msgstr "" -#: org/jmol/viewer/Eval.java:4222 +#: org/jmol/viewer/Eval.java:4223 msgid "" "unrecognized SHOW parameter -- use \"getProperty ATOMINFO (atom expression)" "\"" msgstr "" -#: org/jmol/viewer/Eval.java:4233 +#: org/jmol/viewer/Eval.java:4234 msgid "unrecognized SHOW parameter" msgstr "" -#: org/jmol/viewer/Eval.java:4797 +#: org/jmol/viewer/Eval.java:4798 msgid "no MO coefficient data available" msgstr "" -#: org/jmol/viewer/Eval.java:4799 +#: org/jmol/viewer/Eval.java:4800 msgid "Only one molecular orbital is available in this file" msgstr "" -#: org/jmol/viewer/Eval.java:4801 +#: org/jmol/viewer/Eval.java:4802 #, java-format msgid "An MO index from 1 to {0} is required" msgstr "" -#: org/jmol/viewer/Eval.java:4821 +#: org/jmol/viewer/Eval.java:4822 msgid "the isosurface command requires that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:5113 +#: org/jmol/viewer/Eval.java:5114 msgid "" "No partial charges were read from the file; Jmol needs these to render the " "MEP data." @@ -1317,6 +1313,10 @@ msgid "Jmol executing script ..." msgstr "Jmol ejecutando un guión..." +#, fuzzy +#~ msgid "space group " +#~ msgstr "Grupo espacial" + #~ msgid "Except Solvent" #~ msgstr "Excepto disolvente" Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po 2006-09-25 04:22:59 UTC (rev 5712) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/et.po 2006-09-25 04:28:47 UTC (rev 5713) @@ -6,7 +6,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-25 06:12+0200\n" +"POT-Creation-Date: 2006-09-25 06:25+0200\n" "PO-Revision-Date: 2006-03-17 20:19+0100\n" "Last-Translator: Ivo Sarak <iv...@ra...>\n" "Language-Team: Estonian <Jmo...@li...>\n" @@ -1232,89 +1232,86 @@ msgstr "" #: org/jmol/viewer/Eval.java:2143 -msgid "space group " +#, java-format +msgid "space group {0} was not found." msgstr "" -#: org/jmol/viewer/Eval.java:2143 -msgid " was not found." -msgstr "" - -#: org/jmol/viewer/Eval.java:2887 +#: org/jmol/viewer/Eval.java:2888 msgid "\"conformation\" not allowed with background model displayed" msgstr "" -#: org/jmol/viewer/Eval.java:3129 +#: org/jmol/viewer/Eval.java:3130 msgid "Calculate what? hbonds? surface? structure?" msgstr "" -#: org/jmol/viewer/Eval.java:3146 +#: org/jmol/viewer/Eval.java:3147 msgid "surfaces require that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:3357 +#: org/jmol/viewer/Eval.java:3358 msgid "invalid frame control keyword" msgstr "" -#: org/jmol/viewer/Eval.java:3689 +#: org/jmol/viewer/Eval.java:3690 msgid "SET ECHO must follow, not precede, model loading" msgstr "" -#: org/jmol/viewer/Eval.java:4071 +#: org/jmol/viewer/Eval.java:4072 msgid "save what? bonds? orientation? selection?" msgstr "" -#: org/jmol/viewer/Eval.java:4092 +#: org/jmol/viewer/Eval.java:4093 msgid "restore what? bonds? orientation? selection?" msgstr "" -#: org/jmol/viewer/Eval.java:4166 org/jmol/viewer/Eval.java:4789 +#: org/jmol/viewer/Eval.java:4167 org/jmol/viewer/Eval.java:4790 msgid "MO isosurfaces require that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:4170 org/jmol/viewer/Eval.java:4793 +#: org/jmol/viewer/Eval.java:4171 org/jmol/viewer/Eval.java:4794 msgid "no MO basis/coefficient data available for this frame" msgstr "" -#: org/jmol/viewer/Eval.java:4213 +#: org/jmol/viewer/Eval.java:4214 msgid "use \"show ORIENTATION\"" msgstr "" -#: org/jmol/viewer/Eval.java:4218 +#: org/jmol/viewer/Eval.java:4219 msgid "unrecognized SHOW parameter -- use \"getProperty CHAININFO \"" msgstr "" -#: org/jmol/viewer/Eval.java:4220 +#: org/jmol/viewer/Eval.java:4221 msgid "unrecognized SHOW parameter -- use \"getProperty ATOMINFO (selected)\"" msgstr "" -#: org/jmol/viewer/Eval.java:4222 +#: org/jmol/viewer/Eval.java:4223 msgid "" "unrecognized SHOW parameter -- use \"getProperty ATOMINFO (atom expression)" "\"" msgstr "" -#: org/jmol/viewer/Eval.java:4233 +#: org/jmol/viewer/Eval.java:4234 msgid "unrecognized SHOW parameter" msgstr "" -#: org/jmol/viewer/Eval.java:4797 +#: org/jmol/viewer/Eval.java:4798 msgid "no MO coefficient data available" msgstr "" -#: org/jmol/viewer/Eval.java:4799 +#: org/jmol/viewer/Eval.java:4800 msgid "Only one molecular orbital is available in this file" msgstr "" -#: org/jmol/viewer/Eval.java:4801 +#: org/jmol/viewer/Eval.java:4802 #, java-format msgid "An MO index from 1 to {0} is required" msgstr "" -#: org/jmol/viewer/Eval.java:4821 +#: org/jmol/viewer/Eval.java:4822 msgid "the isosurface command requires that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:5113 +#: org/jmol/viewer/Eval.java:5114 msgid "" "No partial charges were read from the file; Jmol needs these to render the " "MEP data." Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po 2006-09-25 04:22:59 UTC (rev 5712) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/fr.po 2006-09-25 04:28:47 UTC (rev 5713) @@ -7,7 +7,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-25 06:12+0200\n" +"POT-Creation-Date: 2006-09-25 06:25+0200\n" "PO-Revision-Date: 2006-09-24 16:47+0100\n" "Last-Translator: Nicolas Vervelle <ni...@us...>\n" "Language-Team: French <Jmo...@li...>\n" @@ -1218,89 +1218,86 @@ msgstr "" #: org/jmol/viewer/Eval.java:2143 -msgid "space group " +#, java-format +msgid "space group {0} was not found." msgstr "" -#: org/jmol/viewer/Eval.java:2143 -msgid " was not found." -msgstr "" - -#: org/jmol/viewer/Eval.java:2887 +#: org/jmol/viewer/Eval.java:2888 msgid "\"conformation\" not allowed with background model displayed" msgstr "" -#: org/jmol/viewer/Eval.java:3129 +#: org/jmol/viewer/Eval.java:3130 msgid "Calculate what? hbonds? surface? structure?" msgstr "" -#: org/jmol/viewer/Eval.java:3146 +#: org/jmol/viewer/Eval.java:3147 msgid "surfaces require that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:3357 +#: org/jmol/viewer/Eval.java:3358 msgid "invalid frame control keyword" msgstr "" -#: org/jmol/viewer/Eval.java:3689 +#: org/jmol/viewer/Eval.java:3690 msgid "SET ECHO must follow, not precede, model loading" msgstr "" -#: org/jmol/viewer/Eval.java:4071 +#: org/jmol/viewer/Eval.java:4072 msgid "save what? bonds? orientation? selection?" msgstr "" -#: org/jmol/viewer/Eval.java:4092 +#: org/jmol/viewer/Eval.java:4093 msgid "restore what? bonds? orientation? selection?" msgstr "" -#: org/jmol/viewer/Eval.java:4166 org/jmol/viewer/Eval.java:4789 +#: org/jmol/viewer/Eval.java:4167 org/jmol/viewer/Eval.java:4790 msgid "MO isosurfaces require that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:4170 org/jmol/viewer/Eval.java:4793 +#: org/jmol/viewer/Eval.java:4171 org/jmol/viewer/Eval.java:4794 msgid "no MO basis/coefficient data available for this frame" msgstr "" -#: org/jmol/viewer/Eval.java:4213 +#: org/jmol/viewer/Eval.java:4214 msgid "use \"show ORIENTATION\"" msgstr "" -#: org/jmol/viewer/Eval.java:4218 +#: org/jmol/viewer/Eval.java:4219 msgid "unrecognized SHOW parameter -- use \"getProperty CHAININFO \"" msgstr "" -#: org/jmol/viewer/Eval.java:4220 +#: org/jmol/viewer/Eval.java:4221 msgid "unrecognized SHOW parameter -- use \"getProperty ATOMINFO (selected)\"" msgstr "" -#: org/jmol/viewer/Eval.java:4222 +#: org/jmol/viewer/Eval.java:4223 msgid "" "unrecognized SHOW parameter -- use \"getProperty ATOMINFO (atom expression)" "\"" msgstr "" -#: org/jmol/viewer/Eval.java:4233 +#: org/jmol/viewer/Eval.java:4234 msgid "unrecognized SHOW parameter" msgstr "" -#: org/jmol/viewer/Eval.java:4797 +#: org/jmol/viewer/Eval.java:4798 msgid "no MO coefficient data available" msgstr "" -#: org/jmol/viewer/Eval.java:4799 +#: org/jmol/viewer/Eval.java:4800 msgid "Only one molecular orbital is available in this file" msgstr "" -#: org/jmol/viewer/Eval.java:4801 +#: org/jmol/viewer/Eval.java:4802 #, java-format msgid "An MO index from 1 to {0} is required" msgstr "" -#: org/jmol/viewer/Eval.java:4821 +#: org/jmol/viewer/Eval.java:4822 msgid "the isosurface command requires that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:5113 +#: org/jmol/viewer/Eval.java:5114 msgid "" "No partial charges were read from the file; Jmol needs these to render the " "MEP data." Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po 2006-09-25 04:22:59 UTC (rev 5712) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/nl.po 2006-09-25 04:28:47 UTC (rev 5713) @@ -7,7 +7,7 @@ msgstr "" "Project-Id-Version: nl\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-25 06:12+0200\n" +"POT-Creation-Date: 2006-09-25 06:25+0200\n" "PO-Revision-Date: 2006-09-24 14:11+0100\n" "Last-Translator: Egon Willighagen <eg...@jm...>\n" "Language-Team: Nederlands <jmo...@li...>\n" @@ -1219,90 +1219,86 @@ msgstr "" #: org/jmol/viewer/Eval.java:2143 -#, fuzzy -msgid "space group " -msgstr "Ruimtegroep" - -#: org/jmol/viewer/Eval.java:2143 -msgid " was not found." +#, java-format +msgid "space group {0} was not found." msgstr "" -#: org/jmol/viewer/Eval.java:2887 +#: org/jmol/viewer/Eval.java:2888 msgid "\"conformation\" not allowed with background model displayed" msgstr "" -#: org/jmol/viewer/Eval.java:3129 +#: org/jmol/viewer/Eval.java:3130 msgid "Calculate what? hbonds? surface? structure?" msgstr "" -#: org/jmol/viewer/Eval.java:3146 +#: org/jmol/viewer/Eval.java:3147 msgid "surfaces require that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:3357 +#: org/jmol/viewer/Eval.java:3358 msgid "invalid frame control keyword" msgstr "" -#: org/jmol/viewer/Eval.java:3689 +#: org/jmol/viewer/Eval.java:3690 msgid "SET ECHO must follow, not precede, model loading" msgstr "" -#: org/jmol/viewer/Eval.java:4071 +#: org/jmol/viewer/Eval.java:4072 msgid "save what? bonds? orientation? selection?" msgstr "" -#: org/jmol/viewer/Eval.java:4092 +#: org/jmol/viewer/Eval.java:4093 msgid "restore what? bonds? orientation? selection?" msgstr "" -#: org/jmol/viewer/Eval.java:4166 org/jmol/viewer/Eval.java:4789 +#: org/jmol/viewer/Eval.java:4167 org/jmol/viewer/Eval.java:4790 msgid "MO isosurfaces require that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:4170 org/jmol/viewer/Eval.java:4793 +#: org/jmol/viewer/Eval.java:4171 org/jmol/viewer/Eval.java:4794 msgid "no MO basis/coefficient data available for this frame" msgstr "" -#: org/jmol/viewer/Eval.java:4213 +#: org/jmol/viewer/Eval.java:4214 msgid "use \"show ORIENTATION\"" msgstr "" -#: org/jmol/viewer/Eval.java:4218 +#: org/jmol/viewer/Eval.java:4219 msgid "unrecognized SHOW parameter -- use \"getProperty CHAININFO \"" msgstr "" -#: org/jmol/viewer/Eval.java:4220 +#: org/jmol/viewer/Eval.java:4221 msgid "unrecognized SHOW parameter -- use \"getProperty ATOMINFO (selected)\"" msgstr "" -#: org/jmol/viewer/Eval.java:4222 +#: org/jmol/viewer/Eval.java:4223 msgid "" "unrecognized SHOW parameter -- use \"getProperty ATOMINFO (atom expression)" "\"" msgstr "" -#: org/jmol/viewer/Eval.java:4233 +#: org/jmol/viewer/Eval.java:4234 msgid "unrecognized SHOW parameter" msgstr "" -#: org/jmol/viewer/Eval.java:4797 +#: org/jmol/viewer/Eval.java:4798 msgid "no MO coefficient data available" msgstr "" -#: org/jmol/viewer/Eval.java:4799 +#: org/jmol/viewer/Eval.java:4800 msgid "Only one molecular orbital is available in this file" msgstr "" -#: org/jmol/viewer/Eval.java:4801 +#: org/jmol/viewer/Eval.java:4802 #, java-format msgid "An MO index from 1 to {0} is required" msgstr "" -#: org/jmol/viewer/Eval.java:4821 +#: org/jmol/viewer/Eval.java:4822 msgid "the isosurface command requires that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:5113 +#: org/jmol/viewer/Eval.java:5114 msgid "" "No partial charges were read from the file; Jmol needs these to render the " "MEP data." @@ -1324,6 +1320,10 @@ msgid "Jmol executing script ..." msgstr "Jmol voert script uit ..." +#, fuzzy +#~ msgid "space group " +#~ msgstr "Ruimtegroep" + #~ msgid "1.0 Å" #~ msgstr "1.0 Å" Modified: trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po =================================================================== --- trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po 2006-09-25 04:22:59 UTC (rev 5712) +++ trunk/Jmol/src/org/jmol/translation/JmolApplet/pt.po 2006-09-25 04:28:47 UTC (rev 5713) @@ -6,7 +6,7 @@ msgstr "" "Project-Id-Version: Jmol\n" "Report-Msgid-Bugs-To: jmo...@li...\n" -"POT-Creation-Date: 2006-09-25 06:12+0200\n" +"POT-Creation-Date: 2006-09-25 06:25+0200\n" "PO-Revision-Date: 2005-12-20 07:44-0000\n" "Last-Translator: Metro <por...@gm...>\n" "Language-Team: Portugal@Folding <Jmo...@li...>\n" @@ -1231,89 +1231,86 @@ msgstr "" #: org/jmol/viewer/Eval.java:2143 -msgid "space group " +#, java-format +msgid "space group {0} was not found." msgstr "" -#: org/jmol/viewer/Eval.java:2143 -msgid " was not found." -msgstr "" - -#: org/jmol/viewer/Eval.java:2887 +#: org/jmol/viewer/Eval.java:2888 msgid "\"conformation\" not allowed with background model displayed" msgstr "" -#: org/jmol/viewer/Eval.java:3129 +#: org/jmol/viewer/Eval.java:3130 msgid "Calculate what? hbonds? surface? structure?" msgstr "" -#: org/jmol/viewer/Eval.java:3146 +#: org/jmol/viewer/Eval.java:3147 msgid "surfaces require that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:3357 +#: org/jmol/viewer/Eval.java:3358 msgid "invalid frame control keyword" msgstr "" -#: org/jmol/viewer/Eval.java:3689 +#: org/jmol/viewer/Eval.java:3690 msgid "SET ECHO must follow, not precede, model loading" msgstr "" -#: org/jmol/viewer/Eval.java:4071 +#: org/jmol/viewer/Eval.java:4072 msgid "save what? bonds? orientation? selection?" msgstr "" -#: org/jmol/viewer/Eval.java:4092 +#: org/jmol/viewer/Eval.java:4093 msgid "restore what? bonds? orientation? selection?" msgstr "" -#: org/jmol/viewer/Eval.java:4166 org/jmol/viewer/Eval.java:4789 +#: org/jmol/viewer/Eval.java:4167 org/jmol/viewer/Eval.java:4790 msgid "MO isosurfaces require that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:4170 org/jmol/viewer/Eval.java:4793 +#: org/jmol/viewer/Eval.java:4171 org/jmol/viewer/Eval.java:4794 msgid "no MO basis/coefficient data available for this frame" msgstr "" -#: org/jmol/viewer/Eval.java:4213 +#: org/jmol/viewer/Eval.java:4214 msgid "use \"show ORIENTATION\"" msgstr "" -#: org/jmol/viewer/Eval.java:4218 +#: org/jmol/viewer/Eval.java:4219 msgid "unrecognized SHOW parameter -- use \"getProperty CHAININFO \"" msgstr "" -#: org/jmol/viewer/Eval.java:4220 +#: org/jmol/viewer/Eval.java:4221 msgid "unrecognized SHOW parameter -- use \"getProperty ATOMINFO (selected)\"" msgstr "" -#: org/jmol/viewer/Eval.java:4222 +#: org/jmol/viewer/Eval.java:4223 msgid "" "unrecognized SHOW parameter -- use \"getProperty ATOMINFO (atom expression)" "\"" msgstr "" -#: org/jmol/viewer/Eval.java:4233 +#: org/jmol/viewer/Eval.java:4234 msgid "unrecognized SHOW parameter" msgstr "" -#: org/jmol/viewer/Eval.java:4797 +#: org/jmol/viewer/Eval.java:4798 msgid "no MO coefficient data available" msgstr "" -#: org/jmol/viewer/Eval.java:4799 +#: org/jmol/viewer/Eval.java:4800 msgid "Only one molecular orbital is available in this file" msgstr "" -#: org/jmol/viewer/Eval.java:4801 +#: org/jmol/viewer/Eval.java:4802 #, java-format msgid "An MO index from 1 to {0} is required" msgstr "" -#: org/jmol/viewer/Eval.java:4821 +#: org/jmol/viewer/Eval.java:4822 msgid "the isosurface command requires that only one model be displayed" msgstr "" -#: org/jmol/viewer/Eval.java:5113 +#: org/jmol/viewer/Eval.java:5114 msgid "" "No partial charges were read from the file; Jmol needs these to render the " "MEP data." Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-25 04:22:59 UTC (rev 5712) +++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-25 04:28:47 UTC (rev 5713) @@ -2140,7 +2140,8 @@ } else { iGroup = viewer.getSpaceGroupIndexFromName(spacegroup); if (iGroup == -1) - evalError(GT._("space group " + spacegroup + " was not found.")); + evalError(GT._("space group {0} was not found.", + new Object[] { spacegroup })); } p = new int[5]; for (int j = 0; j < 4; j++) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2006-09-26 06:48:32
|
Revision: 5729 http://svn.sourceforge.net/jmol/?rev=5729&view=rev Author: hansonr Date: 2006-09-25 23:48:23 -0700 (Mon, 25 Sep 2006) Log Message: ----------- _12C, _13C, _14C, _14N, _15N support xyzi format allows "13C" etc. for element name select carbon # all isotopes select _C # all isotopes select _13C # only C-13 Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java trunk/Jmol/src/org/jmol/adapter/smarter/CubeReader.java trunk/Jmol/src/org/jmol/adapter/smarter/XyzReader.java trunk/Jmol/src/org/jmol/util/Parser.java trunk/Jmol/src/org/jmol/viewer/Eval.java trunk/Jmol/src/org/jmol/viewer/JmolConstants.java trunk/Jmol/src/org/jmol/viewer/Token.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2006-09-26 04:36:52 UTC (rev 5728) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2006-09-26 06:48:23 UTC (rev 5729) @@ -91,6 +91,7 @@ SmarterJmolAdapter.PATH_SEPARATOR); } + /** * Creates an AtomSetCollection based on an array of AtomSetCollection * @@ -105,6 +106,14 @@ } /** + * Just sets the overall file type after the fact. + * @param type + */ + void setFileTypeName(String type) { + fileTypeName = type; + } + + /** * Appends an AtomSetCollection * * @param collectionIndex collection index for new model number Modified: trunk/Jmol/src/org/jmol/adapter/smarter/CubeReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/CubeReader.java 2006-09-26 04:36:52 UTC (rev 5728) +++ trunk/Jmol/src/org/jmol/adapter/smarter/CubeReader.java 2006-09-26 06:48:23 UTC (rev 5729) @@ -77,9 +77,9 @@ readAtomCountAndOrigin(); readVoxelVectors(); readAtoms(); + readExtraLine(); /* volumetric data is no longer read here - readExtraLine(); readVoxelData(); atomSetCollection.volumetricOrigin = origin; atomSetCollection.volumetricSurfaceVectors = voxelVectors; @@ -109,7 +109,7 @@ negativeAtomCount = true; } } - + void readVoxelVectors() throws Exception { readVoxelVector(0); readVoxelVector(1); @@ -138,13 +138,17 @@ } } - /* - void readExtraLine() throws Exception { if (negativeAtomCount) line = reader.readLine(); + int nSurfaces = parseInt(line); + if (nSurfaces != Integer.MIN_VALUE && nSurfaces < 0) + atomSetCollection.setFileTypeName("jvxl"); } + /* + + void readVoxelData() throws Exception { String line = ""; ichNextParse = 0; Modified: trunk/Jmol/src/org/jmol/adapter/smarter/XyzReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/XyzReader.java 2006-09-26 04:36:52 UTC (rev 5728) +++ trunk/Jmol/src/org/jmol/adapter/smarter/XyzReader.java 2006-09-26 06:48:23 UTC (rev 5729) @@ -26,17 +26,18 @@ import java.io.BufferedReader; +import org.jmol.viewer.JmolConstants; + /** * Minnesota SuperComputer Center XYZ file format * - * - * * simple symmetry extension via load command: * 9/2006 ha...@st... * * setAtomCoord(atom) * applySymmetry() * + * extended to read XYZI files (Bob's invention -- allows isotope numbers) * */ @@ -102,7 +103,16 @@ for (int i = 0; i < modelAtomCount; ++i) { String line = reader.readLine(); Atom atom = atomSetCollection.addNewAtom(); - atom.elementSymbol = parseToken(line); + int isotope = parseInt(line); + String str = parseToken(line); + // xyzI + if (isotope == Integer.MIN_VALUE) { + atom.elementSymbol = str; + } else { + str = str.substring((""+isotope).length()); + atom.elementNumber = (short)((isotope << 8) + JmolConstants.elementNumberFromSymbol(str)); + atomSetCollection.setFileTypeName("xyzi"); + } atom.x = parseFloat(line, ichNextParse); atom.y = parseFloat(line, ichNextParse); atom.z = parseFloat(line, ichNextParse); Modified: trunk/Jmol/src/org/jmol/util/Parser.java =================================================================== --- trunk/Jmol/src/org/jmol/util/Parser.java 2006-09-26 04:36:52 UTC (rev 5728) +++ trunk/Jmol/src/org/jmol/util/Parser.java 2006-09-26 06:48:23 UTC (rev 5729) @@ -109,6 +109,11 @@ return value; } + /** + * parses a string for an integer + * @param str + * @return integer or Integer.MIN_VALUE + */ public int parseInt(String str) { return parseIntChecked(str, 0, str.length()); } Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-26 04:36:52 UTC (rev 5728) +++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-26 06:48:23 UTC (rev 5729) @@ -292,29 +292,40 @@ predefine(JmolConstants.predefinedSets[iPredef]); // Now, define all the elements as predefined sets // hydrogen is handled specially, so don't define it + + int firstIsotope = JmolConstants.firstIsotope; + // name ==> e_=n for all standard elements for (int i = JmolConstants.elementNumberMax; --i > 1;) { String definition = "@" + JmolConstants.elementNameFromNumber(i) + " _e=" + i; predefine(definition); } - for (int i = JmolConstants.altElementMax; --i >= 0;) { - String definition = "@" + JmolConstants.altElementNameFromIndex(i) - + " _e=" + JmolConstants.altElementNumberFromIndex(i); - predefine(definition); - } + // _Xx ==> name for of all elements, isotope-blind for (int i = JmolConstants.elementNumberMax; --i >= 1;) { - String definition = "@_" + JmolConstants.elementSymbolFromNumber(i) + " " - + JmolConstants.elementNameFromNumber(i); + String definition = "@_" + JmolConstants.elementSymbolFromNumber(i) + + " " + JmolConstants.elementNameFromNumber(i); predefine(definition); } - for (int i = JmolConstants.altElementMax; --i >= JmolConstants.firstIsotope;) { - String definition = "@_" + JmolConstants.altElementSymbolFromIndex(i) + // name ==> _e=nn for each alternative element + for (int i = firstIsotope; --i >= 0;) { + String definition = "@" + JmolConstants.altElementNameFromIndex(i) + " _e=" + JmolConstants.altElementNumberFromIndex(i); predefine(definition); - definition = "@_" + JmolConstants.altIsotopeSymbolFromIndex(i) + " _e=" - + JmolConstants.altElementNumberFromIndex(i); - predefine(definition); } + // these variables _e, _x can't be more than two characters + // name ==> _isotope=iinn for each isotope + // _T ==> _isotope=iinn for each isotope + // _3H ==> _isotope=iinn for each isotope + for (int i = JmolConstants.altElementMax; --i >= firstIsotope;) { + String def = " element=" + JmolConstants.altElementNumberFromIndex(i); + String definition = "@_" + JmolConstants.altElementSymbolFromIndex(i); + predefine(definition + def); + definition = "@_" + JmolConstants.altIsotopeSymbolFromIndex(i); + predefine(definition + def); + definition = "@" + JmolConstants.altElementNameFromIndex(i); + if (definition.length() > 1) + predefine(definition + def); + } } void predefine(String script) { Modified: trunk/Jmol/src/org/jmol/viewer/JmolConstants.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2006-09-26 04:36:52 UTC (rev 5728) +++ trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2006-09-26 06:48:23 UTC (rev 5729) @@ -562,8 +562,11 @@ 13, 16, 55, - 1 + (2 << 8), // D = 1 + 2*256 <-- firstIsotope - 1 + (3 << 8), // T = 1 + 3*256 + (2 << 8) + 1, // D = 2*256 + 1 <-- firstIsotope + (3 << 8) + 1, // T = 3*256 + 1 + (13 << 8) + 6, // 13C + (14 << 8) + 6, // 14C + (15 << 8) + 7, // 15N }; private final static String[] altElementSymbols = { @@ -572,7 +575,10 @@ "S", "Cs", "D", - "T" + "T", + "13C", + "14C", + "15N", }; private final static String[] altElementNames = { @@ -581,7 +587,10 @@ "sulphur", "caesium", "deuterium", - "tritium" + "tritium", + "", + "", + "", }; public final static int[] altArgbsCpk = { @@ -591,6 +600,9 @@ 0xFF57178F, // Cs 55 0xFFFFFFC0, // D 2H 0xFFFFFFA0, // T 3H + 0xFF505050, // 13C 6 - darker + 0xFF404040, // 14C 6 - darker still + 0xFF105050, // 15N 7 - darker }; /** @@ -2248,6 +2260,8 @@ // main isotope // "@_1H _H & !(_2H,_3H)", + "@_12C _C & !(_13C,_14C)", + "@_14N _N & !(_15N)", // // protein related // Modified: trunk/Jmol/src/org/jmol/viewer/Token.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Token.java 2006-09-26 04:36:52 UTC (rev 5728) +++ trunk/Jmol/src/org/jmol/viewer/Token.java 2006-09-26 06:48:23 UTC (rev 5729) @@ -311,6 +311,8 @@ final static int altloc = expression | 21; final static int insertion = expression | 22; + + // miguel 2005 01 01 // these are used to demark the beginning and end of expressions // they do not exist in the source code, but are emitted by the @@ -688,7 +690,8 @@ "atomno", new Token(atomno, "atomno"), "elemno", tokenElemno, - "_e", new Token(element, "element"), + "_e", null, + "element", new Token(element, "element"), "resno", new Token(resno, "resno"), "temperature", new Token(temperature, "temperature"), "relativetemperature", null, @@ -702,7 +705,6 @@ "polymerlength",new Token(polymerLength, "polymerlength"), "site", new Token(site, "site"), "symop", new Token(symop, "symop"), - "element", new Token(element, "element"), "off", new Token(off, 0, "off"), "false", null, "on", tokenOn, This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2006-09-26 08:12:27
|
Revision: 5730 http://svn.sourceforge.net/jmol/?rev=5730&view=rev Author: hansonr Date: 2006-09-26 01:12:15 -0700 (Tue, 26 Sep 2006) Log Message: ----------- generalized pattern matcher for isotopes xyzi reader moving isotopes over 1 bit so every single possible element fits. Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/XyzReader.java trunk/Jmol/src/org/jmol/api/JmolAdapter.java trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java trunk/Jmol/src/org/jmol/smiles/SmilesParser.java trunk/Jmol/src/org/jmol/viewer/Atom.java trunk/Jmol/src/org/jmol/viewer/Frame.java trunk/Jmol/src/org/jmol/viewer/JmolConstants.java trunk/Jmol/src/org/jmol/viewer/PatternMatcher.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/XyzReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/XyzReader.java 2006-09-26 06:48:23 UTC (rev 5729) +++ trunk/Jmol/src/org/jmol/adapter/smarter/XyzReader.java 2006-09-26 08:12:15 UTC (rev 5730) @@ -110,7 +110,7 @@ atom.elementSymbol = str; } else { str = str.substring((""+isotope).length()); - atom.elementNumber = (short)((isotope << 8) + JmolConstants.elementNumberFromSymbol(str)); + atom.elementNumber = (short)((isotope << 7) + JmolConstants.elementNumberFromSymbol(str)); atomSetCollection.setFileTypeName("xyzi"); } atom.x = parseFloat(line, ichNextParse); Modified: trunk/Jmol/src/org/jmol/api/JmolAdapter.java =================================================================== --- trunk/Jmol/src/org/jmol/api/JmolAdapter.java 2006-09-26 06:48:23 UTC (rev 5729) +++ trunk/Jmol/src/org/jmol/api/JmolAdapter.java 2006-09-26 08:12:15 UTC (rev 5730) @@ -393,7 +393,7 @@ public BitSet getAtomSymmetry() { return null; } public int getAtomSite() { return Integer.MIN_VALUE; } abstract public Object getUniqueID(); - public int getElementNumber() { return -1; } // may be atomicNumber + isotopeNumber*256 + public int getElementNumber() { return -1; } // may be atomicNumber + isotopeNumber*128 public String getElementSymbol() { return null; } public String getAtomName() { return null; } public int getFormalCharge() { return 0; } Modified: trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java =================================================================== --- trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java 2006-09-26 06:48:23 UTC (rev 5729) +++ trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java 2006-09-26 08:12:15 UTC (rev 5730) @@ -24,6 +24,8 @@ package org.jmol.smiles; +import org.jmol.viewer.JmolConstants; + /** * This class represents an atom in a <code>SmilesMolecule</code>. */ @@ -32,6 +34,7 @@ private int number; private String symbol; private int atomicMass; + private boolean isNatural = true; private int charge; private int hydrogenCount; private int matchingAtom; @@ -190,8 +193,23 @@ public void setAtomicMass(int mass) { this.atomicMass = mass; } + + /** + * Sets if this should match the unidentified mass symbol + * + */ + public void setMatchNatural() { + isNatural = JmolConstants.isNaturalIsotope(atomicMass + symbol); + } /** + * + * @return if it should match a natural element "H" "C" + */ + public boolean getMatchNatural() { + return isNatural; + } + /** * Returns the charge of the atom. * * @return Charge. Modified: trunk/Jmol/src/org/jmol/smiles/SmilesParser.java =================================================================== --- trunk/Jmol/src/org/jmol/smiles/SmilesParser.java 2006-09-26 06:48:23 UTC (rev 5729) +++ trunk/Jmol/src/org/jmol/smiles/SmilesParser.java 2006-09-26 08:12:15 UTC (rev 5730) @@ -404,6 +404,7 @@ } newAtom.setSymbol(atomSymbol); newAtom.setAtomicMass(atomicMass); + newAtom.setMatchNatural(); newAtom.setCharge(charge); newAtom.setChiralClass(chiralClass); newAtom.setChiralOrder(chiralOrder); Modified: trunk/Jmol/src/org/jmol/viewer/Atom.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Atom.java 2006-09-26 06:48:23 UTC (rev 5729) +++ trunk/Jmol/src/org/jmol/viewer/Atom.java 2006-09-26 08:12:15 UTC (rev 5730) @@ -410,11 +410,11 @@ } short getElementNumber() { - return (short) (atomicAndIsotopeNumber % 256); + return (short) (atomicAndIsotopeNumber % 128); } short getIsotopeNumber() { - return (short) (atomicAndIsotopeNumber >> 8); + return (short) (atomicAndIsotopeNumber >> 7); } short getAtomicAndIsotopeNumber() { @@ -581,15 +581,15 @@ } short getVanderwaalsMar() { - return JmolConstants.vanderwaalsMars[atomicAndIsotopeNumber % 256]; + return JmolConstants.vanderwaalsMars[atomicAndIsotopeNumber % 128]; } float getVanderwaalsRadiusFloat() { - return JmolConstants.vanderwaalsMars[atomicAndIsotopeNumber % 256] / 1000f; + return JmolConstants.vanderwaalsMars[atomicAndIsotopeNumber % 128] / 1000f; } short getBondingMar() { - return JmolConstants.getBondingMar(atomicAndIsotopeNumber % 256, + return JmolConstants.getBondingMar(atomicAndIsotopeNumber % 128, formalChargeAndFlags >> 3); } Modified: trunk/Jmol/src/org/jmol/viewer/Frame.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Frame.java 2006-09-26 06:48:23 UTC (rev 5729) +++ trunk/Jmol/src/org/jmol/viewer/Frame.java 2006-09-26 08:12:15 UTC (rev 5730) @@ -153,7 +153,7 @@ if (atomList.get(i)) { nAtoms++; int n = atoms[i].getAtomicAndIsotopeNumber(); - if (n < 256) { + if (n < 128) { elementCounts[n]++; if (elementCounts[n] == 1) nElements++; @@ -2126,7 +2126,7 @@ elementsPresent = new BitSet(); for (int i = atomCount; --i >= 0;) { int n = atoms[i].getAtomicAndIsotopeNumber(); - if (n >= 256) + if (n >= 128) n = JmolConstants.elementNumberMax + JmolConstants.altElementIndexFromNumber(n); elementsPresent.set(n); Modified: trunk/Jmol/src/org/jmol/viewer/JmolConstants.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2006-09-26 06:48:23 UTC (rev 5729) +++ trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2006-09-26 08:12:15 UTC (rev 5730) @@ -336,7 +336,7 @@ /** * @param elementSymbol First char must be upper case, second char accepts upper or lower case - * @return elementNumber = atomicNumber + IsotopeNumber*256 + * @return elementNumber = atomicNumber + IsotopeNumber*128 */ public final static short elementNumberFromSymbol(String elementSymbol) { if (htElementMap == null) { @@ -367,16 +367,16 @@ } /** - * @param elementNumber may be atomicNumber + isotopeNumber*256 + * @param elementNumber may be atomicNumber + isotopeNumber*128 * @return elementSymbol */ public final static String elementSymbolFromNumber(int elementNumber) { - //Isotopes as atomicNumber + IsotopeNumber * 256 + //Isotopes as atomicNumber + IsotopeNumber * 128 if (elementNumber >= elementNumberMax) { for (int j = altElementMax; --j >= 0;) if (elementNumber == altElementNumbers[j]) return altElementSymbols[j]; - elementNumber %= 256; + elementNumber %= 128; } if (elementNumber < 0 || elementNumber >= elementNumberMax) elementNumber = 0; @@ -384,16 +384,16 @@ } /** - * @param elementNumber may be atomicNumber + isotopeNumber*256 + * @param elementNumber may be atomicNumber + isotopeNumber*128 * @return elementName */ public final static String elementNameFromNumber(int elementNumber) { - //Isotopes as atomicNumber + IsotopeNumber * 256 + //Isotopes as atomicNumber + IsotopeNumber * 128 if (elementNumber >= elementNumberMax) { for (int j = altElementMax; --j >= 0;) if (elementNumber == altElementNumbers[j]) return altElementNames[j]; - elementNumber %= 256; + elementNumber %= 128; } if (elementNumber < 0 || elementNumber >= elementNumberMax) elementNumber = 0; @@ -523,7 +523,7 @@ /** * @param i index into altElementNumbers - * @return elementNumber (may be atomicNumber + isotopeNumber*256) + * @return elementNumber (may be atomicNumber + isotopeNumber*128) */ public final static short altElementNumberFromIndex(int i) { return altElementNumbers[i]; @@ -543,11 +543,11 @@ */ public final static String altIsotopeSymbolFromIndex(int i) { int code = altElementNumbers[i]; - return (code >> 8) + elementSymbolFromNumber(code % 256); + return (code >> 8) + elementSymbolFromNumber(code ); } /** - * @param atomicAndIsotopeNumber (may be atomicNumber + isotopeNumber*256) + * @param atomicAndIsotopeNumber (may be atomicNumber + isotopeNumber*128) * @return index into altElementNumbers */ public final static int altElementIndexFromNumber(int atomicAndIsotopeNumber) { @@ -557,18 +557,26 @@ return 0; } + // add as we go + private final static String naturalIsotopes = "1H,12C,14N,"; + + public final static boolean isNaturalIsotope(String isotopeSymbol) { + return (naturalIsotopes.indexOf(isotopeSymbol + ",") >= 0); + } + private final static short[] altElementNumbers = { 0, 13, 16, 55, - (2 << 8) + 1, // D = 2*256 + 1 <-- firstIsotope - (3 << 8) + 1, // T = 3*256 + 1 - (13 << 8) + 6, // 13C - (14 << 8) + 6, // 14C - (15 << 8) + 7, // 15N + (2 << 7) + 1, // D = 2*128 + 1 <-- firstIsotope + (3 << 7) + 1, // T = 3*128 + 1 + (13 << 7) + 6, // 13C + (14 << 7) + 6, // 14C + (15 << 7) + 7, // 15N }; + private final static String[] altElementSymbols = { "Xx", "Al", @@ -605,6 +613,7 @@ 0xFF105050, // 15N 7 - darker }; + /** * first entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arrays */ Modified: trunk/Jmol/src/org/jmol/viewer/PatternMatcher.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/PatternMatcher.java 2006-09-26 06:48:23 UTC (rev 5729) +++ trunk/Jmol/src/org/jmol/viewer/PatternMatcher.java 2006-09-26 08:12:15 UTC (rev 5730) @@ -148,19 +148,33 @@ Atom atom = frame.getAtomAt(i); // Check symbol -- not isotope-sensitive - String s = patternAtom.getSymbol(); + String targetSym = patternAtom.getSymbol(); int n = atom.getElementNumber(); - if (s != "*" && s != JmolConstants.elementSymbolFromNumber(n)) + if (targetSym != "*" && targetSym != JmolConstants.elementSymbolFromNumber(n)) return; - // Check atomic mass for [2H] [3H] only + //nothing more needs to be done here + //this is fully generalized + //to match int targetMass = patternAtom.getAtomicMass(); - if (n == 1 && targetMass > 0) { - int atomMass = atom.getIsotopeNumber(); - // allow Jmol H to match H or [1H] - if (atomMass != targetMass && (atomMass != 0 || targetMass != 1)) - return; + if (targetMass > 0) { + // smiles indicates [13C] or [12C] + int isotopeMass = atom.getIsotopeNumber(); + if (isotopeMass != targetMass) { + if (isotopeMass > 0) { + //both are indicating and not the same + //no match: 12C != 13C + return; + } + // we let "C" match only [12C] (naturl) + // If it is not listed in JmolConstants as natural, + // then we it will consider it unmatched + if(!patternAtom.getMatchNatural()) + return; + // if here, we must have "C"/[12C]; "N"/[14N]; "H"/[1H] + // we use the convention that no label is natural + } } // Check charge if (patternAtom.getCharge() != atom.getFormalCharge()) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2006-09-26 19:16:41
|
Revision: 5734 http://svn.sourceforge.net/jmol/?rev=5734&view=rev Author: hansonr Date: 2006-09-26 12:16:28 -0700 (Tue, 26 Sep 2006) Log Message: ----------- isosurface ionic isosurface vdw cif reader update to read charges Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/CifReader.java trunk/Jmol/src/org/jmol/viewer/Eval.java trunk/Jmol/src/org/jmol/viewer/Isosurface.java trunk/Jmol/src/org/jmol/viewer/Token.java Added Paths: ----------- trunk/Jmol/src/org/jmol/_documents/ionicRadia11.xls Added: trunk/Jmol/src/org/jmol/_documents/ionicRadia11.xls =================================================================== (Binary files differ) Property changes on: trunk/Jmol/src/org/jmol/_documents/ionicRadia11.xls ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Modified: trunk/Jmol/src/org/jmol/adapter/smarter/CifReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/CifReader.java 2006-09-26 17:17:11 UTC (rev 5733) +++ trunk/Jmol/src/org/jmol/adapter/smarter/CifReader.java 2006-09-26 19:16:28 UTC (rev 5734) @@ -309,6 +309,10 @@ atomSetCollection.setAtomSetAuxiliaryInfo("formula", thisFormula); return; } + if (str.startsWith("_atom_type")) { + processAtomTypeLoopBlock(); + return; + } if (str.startsWith("_geom_bond")) { if (doApplySymmetry) //not reading bonds when symmetry is enabled yet skipLoop(); @@ -347,9 +351,70 @@ } //////////////////////////////////////////////////////////////// - // atom data + // atom type data //////////////////////////////////////////////////////////////// + + Hashtable atomTypes; + + final static byte ATOM_TYPE_SYMBOL = 0; + final static byte ATOM_TYPE_OXIDATION_NUMBER = 1; + + final static String[] atomTypeFields = { + "_atom_type_symbol", + "_atom_type_oxidation_number", + }; + + /** + * + * reads the oxidation number and associates it with an atom name, which can + * then later be associated with the right atom indirectly. + * + * @throws Exception + */ + void processAtomTypeLoopBlock() throws Exception { + parseLoopParameters(atomTypeFields); + for (int i = propertyCount; --i >= 0;) + if (!propertyReferenced[i]) { + logger.log("?que? missing _atom_type property:" + i); + skipLoop(); + return; + } + + while (tokenizer.getData()) { + String atomTypeSymbol = null; + float oxidationNumber = Float.NaN; + + for (int i = 0; i < fieldCount; ++i) { + String field = loopData[i]; + if (field.length() == 0) + continue; + char firstChar = field.charAt(0); + if (firstChar == '\0') + continue; + switch (fieldTypes[i]) { + case NONE: + break; + case ATOM_TYPE_SYMBOL: + atomTypeSymbol = field; + break; + case ATOM_TYPE_OXIDATION_NUMBER: + oxidationNumber = parseFloat(field); + break; + } + } + if (atomTypeSymbol == null || Float.isNaN(oxidationNumber)) + continue; + if (atomTypes == null) + atomTypes = new Hashtable(); + atomTypes.put(atomTypeSymbol, new Float(oxidationNumber)); + } + } + + //////////////////////////////////////////////////////////////// + // atom site data + //////////////////////////////////////////////////////////////// + final static byte NONE = -1; final static byte TYPE_SYMBOL = 0; final static byte LABEL = 1; @@ -451,6 +516,13 @@ elementSymbol = "" + ch0; } atom.elementSymbol = elementSymbol; + if (atomTypes != null && atomTypes.containsKey(field)) { + float charge = ((Float) atomTypes.get(field)).floatValue(); + atom.formalCharge = (int) charge; + if (Math.abs(atom.formalCharge - charge) > 0.1) + logger.log("CIF charge on " + field + " was " + charge + + "; rounded to " + atom.formalCharge); + } break; case LABEL: case AUTH_ATOM: Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-26 17:17:11 UTC (rev 5733) +++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-26 19:16:28 UTC (rev 5734) @@ -1219,6 +1219,66 @@ return floatValue; } + /** + * Based on the form of the parameters, returns and encoded radius + * as follows: + * + * script meaning range encoded + * + * +1.2 offset [0 - 10] x + * -1.2 offset 0) x + * 1.2 absolute (0 - 10] x + 10 + * -30% percent (-100 - 0) -x + 100 + * +30% percent (0 x + 1000 + * + * in each case, numbers can be integer or float + * + * @param index + * @param defaultValue a default value or Float.NaN + * @return one of the above possibilities + * @throws ScriptException + */ + float radiusParameter(int index, float defaultValue) throws ScriptException { + if (index >= statementLength) + badArgumentCount(); + float v = Float.NaN; + boolean isOffset = (statement[index].tok == Token.plus); + boolean isPercent = (index + 1 < statementLength + && statement[index + 1].tok == Token.percent); + if (isOffset) + index++; + int tok = (index < statementLength ? statement[index].tok : 0); + switch (tok) { + case Token.integer: + v = statement[index].intValue; + break; + case Token.decimal: + v = ((Float) statement[index].value).floatValue(); + if (v < 0 && ! isPercent) + isOffset = true; + break; + default: + v = defaultValue; + index--; + } + pcLastExpressionInstruction = index + (isPercent ? 1 : 0); + if (Float.isNaN(v)) + numberExpected(); + if (v == 0) + return 0; + if (isPercent) { + if (v <= -100) + invalidArgument(); + v = (v < 0 ? 100 - v : v + 1000); + } else if (isOffset) { + } else { + if (v < 0 || v > 10) + numberOutOfRange(0f, 10f); + v += 10; + } + return v; + } + int floatParameterSet(int i, float[] fparams) throws ScriptException { if (i < statementLength && statement[i].tok == Token.leftbrace) i++; @@ -4896,7 +4956,8 @@ String str; int modelIndex = viewer.getDisplayModelIndex(); if (modelIndex < 0) - evalError(GT._("the isosurface command requires that only one model be displayed")); + evalError(GT + ._("the isosurface command requires that only one model be displayed")); for (int i = 1; i < statementLength; ++i) { String propertyName = null; @@ -4974,6 +5035,16 @@ propertyName = "colorRGB"; propertyValue = new Integer(getArgbParam(i)); break; + case Token.ionic: + propertyName = "ionicRadius"; + propertyValue = new Float(radiusParameter(++i, 0)); + i = pcLastExpressionInstruction; + break; + case Token.vanderwaals: + propertyName = "vdwRadius"; + propertyValue = new Float(radiusParameter(++i, 0)); + i = pcLastExpressionInstruction; + break; case Token.identifier: str = (String) token.value; if (str.equalsIgnoreCase("REMAPPABLE")) { // testing only @@ -5188,7 +5259,8 @@ } catch (Exception e) { } if (partialCharges == null) - evalError(GT._("No partial charges were read from the file; Jmol needs these to render the MEP data.")); + evalError(GT + ._("No partial charges were read from the file; Jmol needs these to render the MEP data.")); surfaceObjectSeen = true; propertyName = "mep"; propertyValue = partialCharges; Modified: trunk/Jmol/src/org/jmol/viewer/Isosurface.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Isosurface.java 2006-09-26 17:17:11 UTC (rev 5733) +++ trunk/Jmol/src/org/jmol/viewer/Isosurface.java 2006-09-26 19:16:28 UTC (rev 5734) @@ -211,6 +211,10 @@ float solventRadius; float solventExtendedAtomRadius; + float solventAtomRadiusFactor; + float solventAtomRadiusAbsolute; + float solventAtomRadiusOffset; + boolean useIonic; boolean addHydrogens; int edgeFractionBase; @@ -542,6 +546,29 @@ drawLcaoCartoon(lcaoType, info[0], info[1]); } + if ("vdwRadius" == propertyName || "ionicRadius" == propertyName) { + useIonic = (propertyName.charAt(0) == 'i'); + float radius = ((Float)value).floatValue(); + /* + * script meaning range encoded + * + * +1.2 offset [0 - 10] x + * -1.2 offset 0) x + * 1.2 absolute (0 - 10] x + 10 + * -30% percent (-100 - 0) -x + 100 + * +30% percent (0 x + 1000 + * + */ + if (radius > 1000) + solventAtomRadiusFactor = (radius - 1000) / 100; + else if (radius > 100) + solventAtomRadiusFactor = 1 -(radius - 100) / 100; + else if (radius > 10) + solventAtomRadiusAbsolute = radius - 10; + else + solventAtomRadiusOffset = radius; + } + if ("solvent" == propertyName || "sasurface" == propertyName) { isEccentric = isAnisotropic = false; //anisotropy[0] = anisotropy[1] = anisotropy[2] = 1f; @@ -551,9 +578,9 @@ dataType = ("sasurface" == propertyName || solventRadius == 0f ? SURFACE_SASURFACE : SURFACE_SOLVENT); if (dataType == SURFACE_SASURFACE) { + solventExtendedAtomRadius = solventRadius; Logger.info("creating solvent-accessible surface with radius " - + solventRadius); - solventExtendedAtomRadius = solventRadius; + + solventExtendedAtomRadius); solventRadius = 0f; } else { Logger.info("creating solvent-excluded surface with radius " @@ -807,6 +834,12 @@ isBicolorMap = isCutoffAbsolute = isPositiveOnly = false; precalculateVoxelData = false; bsIgnore = null; + solventExtendedAtomRadius = 0; + solventAtomRadiusFactor = 1; + solventAtomRadiusAbsolute = 0; + solventAtomRadiusOffset = 0; + useIonic = false; + jvxlInitFlags(); initState(); } @@ -4201,7 +4234,7 @@ int firstSet = -1; int lastSet = 0; for (int i = 0; i < nAtoms; i++) - if ((bsIgnore == null || !bsIgnore.get(i)) + if ((bsIgnore == null || !bsIgnore.get(i)) && (nSelected == 0 || bsSelected.get(i))) { if (solvent_modelIndex < 0) solvent_modelIndex = atoms[i].modelIndex; @@ -4224,15 +4257,19 @@ solvent_atomRadius = new float[iAtom + nH]; solvent_ptAtom = new Point3f[iAtom + nH]; atomNo = new int[iAtom + nH]; - float r = JmolConstants.vanderwaalsMars[1] / 1000f - + solventExtendedAtomRadius; + + float r = (solventAtomRadiusAbsolute > 0 ? solventAtomRadiusAbsolute + : JmolConstants.vanderwaalsMars[1] / 1000f); + r *= solventAtomRadiusFactor; + r += solventExtendedAtomRadius + solventAtomRadiusOffset; + for (int i = 0; i < nH; i++) { atomNo[i] = 1; solvent_atomRadius[i] = r; solvent_ptAtom[i] = hAtoms[i]; if (logMessages) Logger.debug("draw {" + hAtoms[i].x + " " + hAtoms[i].y + " " - + hAtoms[i].z + "};"); + + hAtoms[i].z + "};"); } iAtom = nH; for (int i = firstSet; i <= lastSet; i++) { @@ -4240,8 +4277,12 @@ continue; atomNo[iAtom] = atoms[i].getElementNumber(); solvent_ptAtom[iAtom] = atoms[i]; - solvent_atomRadius[iAtom++] = atoms[i].getVanderwaalsRadiusFloat() - + solventExtendedAtomRadius; + r = (solventAtomRadiusAbsolute > 0 ? solventAtomRadiusAbsolute + : useIonic ? atoms[i].getBondingRadiusFloat() : atoms[i] + .getVanderwaalsRadiusFloat()); + r *= solventAtomRadiusFactor; + solvent_atomRadius[iAtom++] = r + solventExtendedAtomRadius + + solventAtomRadiusOffset; } } solvent_nAtoms = solvent_firstNearbyAtom = iAtom; @@ -4281,8 +4322,8 @@ for (int i = 0; i < solvent_nAtoms; i++) { pt.set(solvent_ptAtom[i]); pt.scale(1 / ANGSTROMS_PER_BOHR); - jvxlFileHeader += atomNo[i] + " " + atomNo[i] + ".0 " - + pt.x + " " + pt.y + " " + pt.z + "\n"; + jvxlFileHeader += atomNo[i] + " " + atomNo[i] + ".0 " + pt.x + " " + pt.y + + " " + pt.z + "\n"; } atomCount = -Integer.MAX_VALUE; negativeAtomCount = false; @@ -4297,6 +4338,14 @@ pt = atoms[i]; float rA = atoms[i].getVanderwaalsRadiusFloat() + solventExtendedAtomRadius; + + rA = (solventAtomRadiusAbsolute > 0 ? solventAtomRadiusAbsolute + : useIonic ? atoms[i].getBondingRadiusFloat() : atoms[i] + .getVanderwaalsRadiusFloat()); + rA *= solventAtomRadiusFactor; + rA += solventExtendedAtomRadius + solventAtomRadiusOffset; + + if (pt.x + rA > xyzMin.x && pt.x - rA < xyzMax.x && pt.y + rA > xyzMin.y && pt.y - rA < xyzMax.y && pt.z + rA > xyzMin.z && pt.z - rA < xyzMax.z) { @@ -4313,7 +4362,8 @@ solvent_nAtoms += nNearby; solvent_atomRadius = (float[]) ArrayUtil.setLength(solvent_atomRadius, solvent_nAtoms); - solvent_ptAtom = (Point3f[]) ArrayUtil.setLength(solvent_ptAtom, solvent_nAtoms); + solvent_ptAtom = (Point3f[]) ArrayUtil.setLength(solvent_ptAtom, + solvent_nAtoms); iAtom = solvent_firstNearbyAtom; for (int i = firstSet; i <= lastSet; i++) { Modified: trunk/Jmol/src/org/jmol/viewer/Token.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Token.java 2006-09-26 17:17:11 UTC (rev 5733) +++ trunk/Jmol/src/org/jmol/viewer/Token.java 2006-09-26 19:16:28 UTC (rev 5734) @@ -773,6 +773,7 @@ "fill", new Token(fill, "fill"), "nofill", new Token(nofill, "nofill"), "vanderwaals", new Token(vanderwaals, "vanderwaals"), + "vdw", null, "ionic", new Token(ionic, "ionic"), "resume", new Token(resume, "resume"), "next", new Token(next, "next"), This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2006-09-30 15:16:58
|
Revision: 5778 http://svn.sourceforge.net/jmol/?rev=5778&view=rev Author: hansonr Date: 2006-09-30 08:16:53 -0700 (Sat, 30 Sep 2006) Log Message: ----------- critical bug fix -- Shelx reader Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/ShelxReader.java trunk/Jmol/src/org/jmol/symmetry/HallInfo.java trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/ShelxReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/ShelxReader.java 2006-09-30 11:17:31 UTC (rev 5777) +++ trunk/Jmol/src/org/jmol/adapter/smarter/ShelxReader.java 2006-09-30 15:16:53 UTC (rev 5778) @@ -58,6 +58,7 @@ String[] sfacElementSymbols; boolean isCmdf = false; + boolean iHaveAtomSet = false; AtomSetCollection readAtomSetCollection(BufferedReader reader) throws Exception { @@ -75,7 +76,7 @@ applySymmetry(); setFractionalCoordinates(true); isCmdf = false; - atomSetCollection.newAtomSet(); + iHaveAtomSet = false; } readLine_loop: while ((line = reader.readLine()) != null) { lineLength = line.trim().length(); @@ -104,7 +105,7 @@ processSupportedRecord(i, line); continue readLine_loop; } - if (readThisModel && !isCmdf) + if (readThisModel && !isCmdf && iHaveAtomSet) assumeAtomRecord(line); } } @@ -118,6 +119,9 @@ void processSupportedRecord(int recordIndex, String line) throws Exception { //Logger.debug(recordIndex+" "+line); + if (!iHaveAtomSet) + atomSetCollection.newAtomSet(); + iHaveAtomSet = true; switch (recordIndex) { case 0: // TITL atomSetCollection.setAtomSetName(parseTrimmed(line, 4)); Modified: trunk/Jmol/src/org/jmol/symmetry/HallInfo.java =================================================================== --- trunk/Jmol/src/org/jmol/symmetry/HallInfo.java 2006-09-30 11:17:31 UTC (rev 5777) +++ trunk/Jmol/src/org/jmol/symmetry/HallInfo.java 2006-09-30 15:16:53 UTC (rev 5778) @@ -198,11 +198,15 @@ if (vectorCode.length() > 0) str += "; vector offset:" + vectorCode; if (rotation != null) - str += "\noperator: " + SymmetryOperation.getXYZFromMatrix(seitzMatrix12ths, allPositive) + str += "\noperator: " + getXYZ(allPositive) + "\nSeitz matrix:\n" + SymmetryOperation.dumpSeitz(seitzMatrix12ths); return str; } + String getXYZ(boolean allPositive) { + return SymmetryOperation.getXYZFromMatrix(seitzMatrix12ths, allPositive); + } + private void getRotationInfo(String code, int prevOrder, char prevAxisType) { this.inputCode = code; this.prevOrder = prevOrder; @@ -370,6 +374,13 @@ this.vectorShift12ths = new Point3i(); } + final static String getHallLatticeEquivalent(int latticeParameter) { + // SHELX LATT --> Hall term + char latticeCode = Translation.getLatticeCode(latticeParameter); + boolean isCentrosymmetric = (latticeParameter > 0); + return (isCentrosymmetric ? "-" : "") + latticeCode + " 1"; + } + final static int getLatticeIndex(char latt) { /* * returns lattice code (1-9, including S and T) for a given lattice type Modified: trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java =================================================================== --- trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2006-09-30 11:17:31 UTC (rev 5777) +++ trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2006-09-30 15:16:53 UTC (rev 5778) @@ -133,7 +133,7 @@ public String dumpInfo() { if (hallInfo == null) hallInfo = new HallInfo(hallSymbol); - generateAllOperators(); + generateAllOperators(null); String str = "\nHermann-Mauguin symbol: " + hmSymbol + (hmSymbolExt.length() > 0 ? ":" + hmSymbolExt : "") + "\ninternational table number: " + intlTableNumber @@ -169,6 +169,10 @@ } public void setLattice(int latticeParameter) { + // implication here is that we do NOT have a Hall symbol. + // so we generate one. + // The idea here is that we can represent any LATT number + // as a simple set of rotation/translation operations this.latticeParameter = latticeParameter; latticeCode = Translation.getLatticeCode(latticeParameter); } @@ -201,7 +205,7 @@ } } if (sg != null) - sg.generateAllOperators(); + sg.generateAllOperators(null); return sg; } @@ -221,7 +225,7 @@ sg = createSpaceGroup(name); } if (sg != null) - sg.generateAllOperators(); + sg.generateAllOperators(null); return sg; } @@ -395,6 +399,11 @@ } public SymmetryOperation[] getFinalOperations(Point3f[] atoms, int atomIndex, int count) { + if (hallInfo == null && latticeParameter != 0) { + HallInfo h = new HallInfo(Translation.getHallLatticeEquivalent(latticeParameter)); + generateAllOperators(h); + } + SymmetryOperation[] finalOperations = new SymmetryOperation[operationCount]; for (int i = 0; i < operationCount; i++) { finalOperations[i] = new SymmetryOperation(operations[i], atoms, atomIndex, count); @@ -453,33 +462,37 @@ } /// operation based on Hall name and unit cell parameters only - - private void generateAllOperators() { - if (operationCount > 0) - return; - operations = new SymmetryOperation[4]; - operationCount = 0; - if (hallInfo == null || hallInfo.nRotations == 0) - hallInfo = new HallInfo(hallSymbol); - setLattice(hallInfo.latticeCode, hallInfo.isCentrosymmetric); + + private void generateAllOperators(HallInfo h) { + if (h == null) { + h = hallInfo; + if (operationCount > 0) + return; + operations = new SymmetryOperation[4]; + operationCount = 0; + if (hallInfo == null || hallInfo.nRotations == 0) + hallInfo = new HallInfo(hallSymbol); + setLattice(hallInfo.latticeCode, hallInfo.isCentrosymmetric); + addOperation(null); + addSymmetry("x,y,z"); + } Matrix4f mat1 = new Matrix4f(); Matrix4f operation = new Matrix4f(); Matrix4f[] newOps = new Matrix4f[7]; for (int i = 0; i < 7; i++) newOps[i] = new Matrix4f(); newOps[0].setIdentity(); - addOperation(null); - addSymmetry("x,y,z"); - for (int i = 0; i < hallInfo.nRotations; i++) { - mat1.set(hallInfo.rotationTerms[i].seitzMatrix12ths); - int nRot = hallInfo.rotationTerms[i].order; + for (int i = 0; i < h.nRotations; i++) { + mat1.set(h.rotationTerms[i].seitzMatrix12ths); + int nRot = h.rotationTerms[i].order; int nOps = operationCount; for (int j = 1; j <= nRot; j++) { - newOps[j].mul(mat1, newOps[0]); + newOps[j].mul(mat1, newOps[0]); newOps[0].set(newOps[j]); for (int k = 0; k < nOps; k++) { operation.mul(newOps[j], operations[k]); - addSymmetry(SymmetryOperation.getXYZFromMatrix(operation, true), operation); + addSymmetry(SymmetryOperation.getXYZFromMatrix(operation, true), + operation); } } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2006-10-01 06:54:55
|
Revision: 5792 http://svn.sourceforge.net/jmol/?rev=5792&view=rev Author: hansonr Date: 2006-09-30 23:54:47 -0700 (Sat, 30 Sep 2006) Log Message: ----------- just rewording to make this clearer what is what. bug in that mouse listeners and hover watcher continue after viewer=null Modified Paths: -------------- trunk/Jmol/src/org/jmol/applet/Jmol.java trunk/Jmol/src/org/jmol/viewer/MouseManager.java trunk/Jmol/src/org/jmol/viewer/MouseManager10.java trunk/Jmol/src/org/jmol/viewer/MouseManager11.java trunk/Jmol/src/org/jmol/viewer/MouseManager14.java trunk/Jmol/src/org/jmol/viewer/RepaintManager.java trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/applet/Jmol.java =================================================================== --- trunk/Jmol/src/org/jmol/applet/Jmol.java 2006-10-01 06:46:08 UTC (rev 5791) +++ trunk/Jmol/src/org/jmol/applet/Jmol.java 2006-10-01 06:54:47 UTC (rev 5792) @@ -157,11 +157,11 @@ // viewer = new JmolViewer(this, new CdkJmolAdapter(null)); viewer = JmolViewer.allocateViewer(appletWrapper, new SmarterJmolAdapter( null)); + viewer.setAppletContext(htmlName, appletWrapper.getDocumentBase(), appletWrapper + .getCodeBase(), getValue("JmolAppletProxy", null)); myStatusListener = new MyStatusListener(); viewer.setJmolStatusListener(myStatusListener); - viewer.setAppletContext(htmlName, appletWrapper.getDocumentBase(), appletWrapper - .getCodeBase(), getValue("JmolAppletProxy", null)); jvm12orGreater = viewer.isJvm12orGreater(); if (jvm12orGreater) Modified: trunk/Jmol/src/org/jmol/viewer/MouseManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/MouseManager.java 2006-10-01 06:46:08 UTC (rev 5791) +++ trunk/Jmol/src/org/jmol/viewer/MouseManager.java 2006-10-01 06:54:47 UTC (rev 5792) @@ -24,7 +24,6 @@ package org.jmol.viewer; -import java.awt.Component; import java.awt.Cursor; import java.awt.Rectangle; import java.awt.Event; @@ -34,7 +33,6 @@ final static int HOVER_TIME = 1000; - Component component; Viewer viewer; Thread hoverWatcherThread; @@ -57,8 +55,7 @@ private static final boolean logMouseEvents = false; - MouseManager(Component component, Viewer viewer) { - this.component = component; + MouseManager(Viewer viewer) { this.viewer = viewer; hoverWatcherThread = new Thread(new HoverWatcher()); hoverWatcherThread.start(); @@ -523,8 +520,11 @@ } } } catch (InterruptedException ie) { - Logger.debug("InterruptedException!"); + Logger.debug("Hover InterruptedException!"); return; + } catch (Exception ie) { + Logger.debug("Hover Exception!" + ie); + return; } } } Modified: trunk/Jmol/src/org/jmol/viewer/MouseManager10.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/MouseManager10.java 2006-10-01 06:46:08 UTC (rev 5791) +++ trunk/Jmol/src/org/jmol/viewer/MouseManager10.java 2006-10-01 06:54:47 UTC (rev 5792) @@ -30,7 +30,7 @@ class MouseManager10 extends MouseManager { MouseManager10(Component component, Viewer viewer) { - super(component, viewer); + super(viewer); //Logger.debug("MouseManager10 implemented"); } Modified: trunk/Jmol/src/org/jmol/viewer/MouseManager11.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/MouseManager11.java 2006-10-01 06:46:08 UTC (rev 5791) +++ trunk/Jmol/src/org/jmol/viewer/MouseManager11.java 2006-10-01 06:54:47 UTC (rev 5792) @@ -33,11 +33,11 @@ class MouseManager11 extends MouseManager implements MouseListener, MouseMotionListener { - MouseManager11(Component component, Viewer viewer) { - super(component, viewer); + MouseManager11(Component display, Viewer viewer) { + super(viewer); //Logger.debug("MouseManager11 implemented"); - component.addMouseListener(this); - component.addMouseMotionListener(this); + display.addMouseListener(this); + display.addMouseMotionListener(this); } boolean handleOldJvm10Event(Event e) { Modified: trunk/Jmol/src/org/jmol/viewer/MouseManager14.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/MouseManager14.java 2006-10-01 06:46:08 UTC (rev 5791) +++ trunk/Jmol/src/org/jmol/viewer/MouseManager14.java 2006-10-01 06:54:47 UTC (rev 5792) @@ -32,10 +32,10 @@ class MouseManager14 extends MouseManager11 implements MouseWheelListener { - MouseManager14(Component component, Viewer viewer) { - super(component, viewer); + MouseManager14(Component display, Viewer viewer) { + super(display, viewer); //Logger.debug("MouseManager14 implemented"); - component.addMouseWheelListener(this); + display.addMouseWheelListener(this); } public void mouseWheelMoved(MouseWheelEvent e) { Modified: trunk/Jmol/src/org/jmol/viewer/RepaintManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/RepaintManager.java 2006-10-01 06:46:08 UTC (rev 5791) +++ trunk/Jmol/src/org/jmol/viewer/RepaintManager.java 2006-10-01 06:54:47 UTC (rev 5792) @@ -116,7 +116,7 @@ if (holdRepaint <= 0) { holdRepaint = 0; repaintPending = true; - viewer.awtComponent.repaint(); + viewer.display.repaint(); } } @@ -125,13 +125,13 @@ return; repaintPending = true; if (holdRepaint == 0) { - viewer.awtComponent.repaint(); + viewer.display.repaint(); } } synchronized void requestRepaintAndWait() { - viewer.awtComponent.repaint(); + viewer.display.repaint(); try { wait(); } catch (InterruptedException e) { Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2006-10-01 06:46:08 UTC (rev 5791) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2006-10-01 06:54:47 UTC (rev 5792) @@ -75,9 +75,13 @@ public class Viewer extends JmolViewer { + public void finalize() { + System.out.println("viewer finalize " + this); + } + StateManager stateManager = new StateManager(this); StateManager.GlobalSettings global = stateManager.globalSettings; - Component awtComponent; + Component display; ColorManager colorManager; PropertyManager propertyManager; StatusManager statusManager; @@ -104,8 +108,9 @@ boolean jvm14orGreater = false; public CommandHistory commandHistory = new CommandHistory(); - Viewer(Component awtComponent, JmolAdapter modelAdapter) { - this.awtComponent = awtComponent; + Viewer(Component display, JmolAdapter modelAdapter) { + System.out.println("Viewer constructor " + this); + this.display = display; this.modelAdapter = modelAdapter; strJavaVendor = System.getProperty("java.vendor"); strOSName = System.getProperty("os.name"); @@ -116,8 +121,7 @@ && strJavaVersion.compareTo("1.1.5") <= 0 && "Mac OS".equals(strOSName))); jvm12orGreater = (strJavaVersion.compareTo("1.2") >= 0); jvm14orGreater = (strJavaVersion.compareTo("1.4") >= 0); - - g3d = new Graphics3D(awtComponent); + g3d = new Graphics3D(display); eval = new Eval(this); statusManager = new StatusManager(this); scriptManager = new ScriptManager(this); @@ -125,23 +129,23 @@ transformManager = new TransformManager(this); selectionManager = new SelectionManager(this); if (jvm14orGreater) - mouseManager = MouseWrapper14.alloc(awtComponent, this); + mouseManager = MouseWrapper14.alloc(display, this); else if (jvm11orGreater) - mouseManager = MouseWrapper11.alloc(awtComponent, this); + mouseManager = MouseWrapper11.alloc(display, this); else - mouseManager = new MouseManager10(awtComponent, this); - fileManager = new FileManager(this, modelAdapter); - repaintManager = new RepaintManager(this); + mouseManager = new MouseManager10(display, this); modelManager = new ModelManager(this); styleManager = new StyleManager(this); propertyManager = new PropertyManager(this); tempManager = new TempManager(this); pickingManager = new PickingManager(this); + fileManager = new FileManager(this, modelAdapter); + repaintManager = new RepaintManager(this); } - public static JmolViewer allocateViewer(Component awtComponent, + public static JmolViewer allocateViewer(Component display, JmolAdapter modelAdapter) { - return new Viewer(awtComponent, modelAdapter); + return new Viewer(display, modelAdapter); } boolean isSilent = false; @@ -203,7 +207,7 @@ } public Component getAwtComponent() { - return awtComponent; + return display; } public boolean handleOldJvm10Event(Event e) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2006-10-04 05:51:36
|
Revision: 5813 http://svn.sourceforge.net/jmol/?rev=5813&view=rev Author: nicove Date: 2006-10-03 22:51:29 -0700 (Tue, 03 Oct 2006) Log Message: ----------- i18n: Ignore Jmol/Messages from the applet Modified Paths: -------------- trunk/Jmol/src/org/jmol/appletwrapper/AppletWrapper.java trunk/Jmol/src/org/jmol/i18n/GT.java Modified: trunk/Jmol/src/org/jmol/appletwrapper/AppletWrapper.java =================================================================== --- trunk/Jmol/src/org/jmol/appletwrapper/AppletWrapper.java 2006-10-04 04:27:05 UTC (rev 5812) +++ trunk/Jmol/src/org/jmol/appletwrapper/AppletWrapper.java 2006-10-04 05:51:29 UTC (rev 5813) @@ -77,6 +77,7 @@ String preloadTextMessage, int preloadThreadCount, String[] preloadClassNames) { + GT.ignoreApplicationBundle(); this.wrappedAppletClassName = wrappedAppletClassName; this.preloadImageName = preloadImageName; this.preloadTextMessage = preloadTextMessage; Modified: trunk/Jmol/src/org/jmol/i18n/GT.java =================================================================== --- trunk/Jmol/src/org/jmol/i18n/GT.java 2006-10-04 04:27:05 UTC (rev 5812) +++ trunk/Jmol/src/org/jmol/i18n/GT.java 2006-10-04 05:51:29 UTC (rev 5813) @@ -28,8 +28,9 @@ import org.jmol.util.Logger; public class GT { - - private static GT getTextWrapper = new GT(); + + private static boolean ignoreApplicationBundle = false; + private static GT getTextWrapper; private ResourceBundle translationResources; private ResourceBundle appletTranslationResources; @@ -46,8 +47,10 @@ } Logger.debug("Instantiating gettext wrapper..."); try { - translationResources = ResourceBundle.getBundle( - "org.jmol.translation.Jmol.Messages"); + if (!ignoreApplicationBundle) { + translationResources = ResourceBundle.getBundle( + "org.jmol.translation.Jmol.Messages"); + } } catch (MissingResourceException mre) { Logger.warn("Translations do not seem to have been installed!"); Logger.warn(mre.getMessage()); @@ -69,12 +72,23 @@ } } + private static GT getTextWrapper() { + if (getTextWrapper == null) { + getTextWrapper = new GT(); + } + return getTextWrapper; + } + + public static void ignoreApplicationBundle() { + ignoreApplicationBundle = true; + } + public static String _(String string) { - return getTextWrapper.getString(string); + return getTextWrapper().getString(string); } public static String _(String string, Object[] objects) { - return getTextWrapper.getString(string, objects); + return getTextWrapper().getString(string, objects); } private String getString(String string) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |