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[Jmol-commits] CVS: Jmol/src/org/jmol/viewer Sasurface1.java,1.22,1.23
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From: Miguel <mig...@us...> - 2005-09-19 15:44:38
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Update of /cvsroot/jmol/Jmol/src/org/jmol/viewer In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv16238/src/org/jmol/viewer Modified Files: Sasurface1.java Log Message: cleanup + fixed grandparent inheritance for saddles Index: Sasurface1.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/jmol/viewer/Sasurface1.java,v retrieving revision 1.22 retrieving revision 1.23 diff -u -r1.22 -r1.23 --- Sasurface1.java 19 Sep 2005 14:29:15 -0000 1.22 +++ Sasurface1.java 19 Sep 2005 15:44:30 -0000 1.23 @@ -114,6 +114,7 @@ IntInt2ObjHash htToruses; + int[] edgeVertexesT; int[] edgeVertexesAT; int[] edgeVertexesBT; @@ -124,6 +125,7 @@ final Point3f pointT = new Point3f(); final Point3f pointT1 = new Point3f(); final Point3f zeroPointT = new Point3f(); + final Point3f centerPointT = new Point3f(); final Point3f centerPointAT = new Point3f(); final Point3f centerPointBT = new Point3f(); @@ -164,6 +166,7 @@ geodesicNeighborVertexes = g3d.getGeodesicNeighborVertexes(geodesicRenderingLevel); + edgeVertexesT = Bmp.allocateBitmap(geodesicVertexCount); edgeVertexesAT = Bmp.allocateBitmap(geodesicVertexCount); edgeVertexesBT = Bmp.allocateBitmap(geodesicVertexCount); } @@ -218,6 +221,10 @@ torus.clipVertexMaps(); + } + + for (int i = torusCount; --i >= 0; ) { + Torus torus = toruses[i]; torus.stitchWithGeodesics(); // torus.checkTorusSegments(); torus.connectWithGeodesics(); @@ -335,7 +342,6 @@ setProperty("translucencySaddle", value, bs); } if ("colorConvex" == propertyName) { - System.out.println("Surface.setProperty('colorConvex')"); short colix = Graphics3D.getColix(value); for (int i = atomCount; --i >= 0; ) if (bs.get(i)) @@ -521,35 +527,6 @@ final Point3f projectedPointT = new Point3f(); final Vector3f projectedVectorT = new Vector3f(); - void clipGeodesic(boolean isEdgeA, Point3f geodesicCenter, float radius, - Point3f planePoint, Vector3f axisUnitVector, - int[] vertexMap) { - centerVectorT.sub(geodesicCenter, planePoint); - float dotCenter = centerVectorT.dot(axisUnitVector); - if (isEdgeA) - dotCenter = -dotCenter; - if (dotCenter >= radius) // all points are visible - return; - if (dotCenter < -radius) { // all points are clipped - Bmp.clearBitmap(vertexMap); - return; - } - - calcClippingPlaneCenter(geodesicCenter, axisUnitVector, - planePoint, planeCenterT); - - for (int i = -1; (i = Bmp.nextSetBit(vertexMap, i + 1)) >= 0; ) { - vertexPointT.scaleAdd(radius, geodesicVertexVectors[i], - geodesicCenter); - vertexVectorT.sub(vertexPointT, planePoint); - float dot = vertexVectorT.dot(axisUnitVector); - if (isEdgeA) - dot = -dot; - if (dot < 0) - Bmp.clearBit(vertexMap, i); - } - } - int[] bmpNotClipped; void findClippedGeodesicEdge(boolean isEdgeA, @@ -591,11 +568,13 @@ } } } + /* System.out.println("findClippedGeodesicEdge is returning edgeVertexMap:"); for (int v = -1; (v = Bmp.nextSetBit(edgeVertexMap, v + 1)) >= 0; ) { System.out.print("" + v + " "); } System.out.println(""); + */ } /* @@ -673,9 +652,11 @@ final Vector3f vector90T = new Vector3f(); final Point3f planeCenterT = new Point3f(); - void projectGeodesicPoints(Point3f geodesicCenter, float radius, - Point3f planeCenter, Vector3f axisUnitVector, - Point3f planeZeroPoint, int[] edgeVertexMap) { + void projectAndSortGeodesicPoints(Point3f geodesicCenter, float radius, + Point3f planeCenter, + Vector3f axisUnitVector, + Point3f planeZeroPoint, + int[] edgeVertexMap) { Vector3f vector0T = this.vector0T; Vector3f vector90T = this.vector90T; Point3f vertexPointT = this.vertexPointT; @@ -706,6 +687,7 @@ projectedDistancesT[projectedCountT] = distance * radiansPerAngstrom; ++projectedCountT; } + sortProjectedVertexes(); } void calcClippingPlaneCenter(Point3f axisPoint, Vector3f axisUnitVector, @@ -725,10 +707,11 @@ return angle; } - void sortProjectedVertexes(int projectedCount, - short[] projectedVertexes, - float[] projectedAngles, - float[] projectedDistances) { + void sortProjectedVertexes() { + int projectedCount = projectedCountT; + short[] projectedVertexes = projectedVertexesT; + float[] projectedAngles = projectedAnglesT; + float[] projectedDistances = projectedDistancesT; for (int i = projectedCount; --i > 0; ) for (int j = i; --j >= 0; ) if (projectedAngles[j] > projectedAngles[i]) { @@ -1422,17 +1405,40 @@ } void clipVertexMaps() { - clipConvexMap(true); - clipConvexMap(false); + clipVertexMap(true); + clipVertexMap(false); } - void clipConvexMap(boolean isEdgeA) { + void clipVertexMap(boolean isEdgeA) { int ix = isEdgeA ? ixA : ixB; Atom atom = frame.atoms[ix]; calcZeroPoint(isEdgeA, zeroPointT); clipGeodesic(isEdgeA, atom.point3f, atom.getVanderwaalsRadiusFloat(), - zeroPointT, axisUnitVector, - convexVertexMaps[ix]); + zeroPointT, convexVertexMaps[ix]); + } + + void clipGeodesic(boolean isEdgeA, Point3f geodesicCenter, float radius, + Point3f planePoint, int[] geodesicVertexMap) { + centerVectorT.sub(geodesicCenter, planePoint); + float dotCenter = centerVectorT.dot(axisUnitVector); + if (isEdgeA) + dotCenter = -dotCenter; + if (dotCenter >= radius) // all points are visible + return; + if (dotCenter < -radius) { // all points are clipped + Bmp.clearBitmap(geodesicVertexMap); + return; + } + for (int i = -1; (i = Bmp.nextSetBit(geodesicVertexMap, i + 1)) >= 0; ) { + vertexPointT.scaleAdd(radius, geodesicVertexVectors[i], + geodesicCenter); + vertexVectorT.sub(vertexPointT, planePoint); + float dot = vertexVectorT.dot(axisUnitVector); + if (isEdgeA) + dot = -dot; + if (dot < 0) + Bmp.clearBit(geodesicVertexMap, i); + } } void calcZeroPoint(boolean edgeA, Point3f zeroPoint) { @@ -1449,6 +1455,13 @@ zeroPoint.add(t); } + void calcZeroAndCenterPoints(boolean edgeA, Point3f atomCenter, + Point3f zeroPoint, Point3f centerPoint) { + calcZeroPoint(edgeA, zeroPoint); + calcClippingPlaneCenter(atomCenter, axisUnitVector, zeroPoint, + centerPoint); + } + void calcClippingPlaneCenterPoints(Point3f centerPointA, Point3f centerPointB) { calcZeroPoint(true, zeroPointT); @@ -1464,55 +1477,24 @@ void stitchWithGeodesics() { System.out.println("torus.stitchWithGeodesics()"); - calcClippingPlaneCenterPoints(centerPointAT, centerPointBT); - Atom atomA = frame.atoms[ixA]; - Atom atomB = frame.atoms[ixB]; - - findClippedGeodesicEdge(true, atomA.point3f, - atomA.getVanderwaalsRadiusFloat(), - centerPointAT, axisUnitVector, - edgeVertexesAT); - Bmp.and(edgeVertexesAT, convexVertexMaps[ixA]); - if (Bmp.countBits(edgeVertexesAT) > 0) { - calcZeroPoint(true, zeroPointT); - projectGeodesicPoints(atomA.point3f, atomA.getVanderwaalsRadiusFloat(), - centerPointAT, axisUnitVector, - zeroPointT, - edgeVertexesAT); - sortProjectedVertexes(projectedCountT, projectedVertexesT, - projectedAnglesT, projectedDistancesT); - for (int i = 0; i < projectedCountT; ++i) { - System.out.println("" + i + " : " + - projectedVertexesT[i] + " : " + - projectedAnglesT[i] + " @ " + - projectedDistancesT[i]); - } - stitchSegmentsWithSortedProjectedVertexes(projectedCountT, - projectedVertexesT, - projectedAnglesT, - projectedDistancesT, - true); - } + stitchWithGeodesic(true); + stitchWithGeodesic(false); + } - findClippedGeodesicEdge(false, atomB.point3f, - atomB.getVanderwaalsRadiusFloat(), - centerPointBT, axisUnitVector, - edgeVertexesBT); - Bmp.and(edgeVertexesBT, convexVertexMaps[ixB]); - System.out.println("B after the AND edgeVertexMap:"); - for (int v = -1; (v = Bmp.nextSetBit(edgeVertexesBT, v + 1)) >= 0; ) { - System.out.print("" + v + " "); - } - System.out.println(""); - if (Bmp.countBits(edgeVertexesBT) > 0) { - calcZeroPoint(false, zeroPointT); - projectGeodesicPoints(atomB.point3f, atomB.getVanderwaalsRadiusFloat(), - centerPointBT, axisUnitVector, - zeroPointT, - edgeVertexesBT); - sortProjectedVertexes(projectedCountT, projectedVertexesT, - projectedAnglesT, projectedDistancesT); - System.out.println("the Sorted B's"); + void stitchWithGeodesic(boolean isEdgeA) { + int ix = isEdgeA ? ixA : ixB; + Atom atom = frame.atoms[ix]; + float atomRadius = atom.getVanderwaalsRadiusFloat(); + Point3f atomCenter = atom.point3f; + calcZeroAndCenterPoints(isEdgeA, atomCenter, zeroPointT, centerPointT); + findClippedGeodesicEdge(isEdgeA, atomCenter, atomRadius, + centerPointT, axisUnitVector, + edgeVertexesT); + Bmp.and(edgeVertexesT, convexVertexMaps[ix]); + if (Bmp.countBits(edgeVertexesT) > 0) { + projectAndSortGeodesicPoints(atomCenter, atomRadius, + centerPointT, axisUnitVector, zeroPointT, + edgeVertexesT); for (int i = 0; i < projectedCountT; ++i) { System.out.println("" + i + " : " + projectedVertexesT[i] + " : " + @@ -1523,7 +1505,7 @@ projectedVertexesT, projectedAnglesT, projectedDistancesT, - false); + isEdgeA); } } |