Clazz.declarePackage("J.jvxl.readers");
Clazz.load(["JU.P3", "J.jvxl.readers.AtomDataReader", "JU.P4", "$.V3"], "J.jvxl.readers.IsoSolventReader", ["java.util.Hashtable", "JU.BS", "$.Lst", "$.Measure", "J.jvxl.data.MeshData", "JU.BSUtil", "$.Logger", "$.MeshSurface", "$.TempArray"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.cavityRadius = 0;
this.envelopeRadius = 0;
this.dots = null;
this.doCalculateTroughs = false;
this.isCavity = false;
this.isPocket = false;
this.iter = null;
this.bsSurfacePoints = null;
this.bsSurfaceDone = null;
this.bsLocale = null;
this.htEdges = null;
this.vEdges = null;
this.vFaces = null;
this.ptS1 = null;
this.ptS2 = null;
this.vTemp = null;
this.plane = null;
this.ptTemp2 = null;
this.vTemp2 = null;
this.p = null;
this.bsAtomMinMax = null;
this.isSurfacePoint = false;
this.iAtomSurface = 0;
this.nTest = 0;
if (!Clazz.isClassDefined("J.jvxl.readers.IsoSolventReader.Edge")) {
J.jvxl.readers.IsoSolventReader.$IsoSolventReader$Edge$ ();
}
if (!Clazz.isClassDefined("J.jvxl.readers.IsoSolventReader.Face")) {
J.jvxl.readers.IsoSolventReader.$IsoSolventReader$Face$ ();
}
this.rAS = 0;
this.rBS = 0;
this.rAS2 = 0;
this.rBS2 = 0;
this.dAB = 0;
this.dAB2 = 0;
this.ecosASB2 = 0;
Clazz.instantialize(this, arguments);}, J.jvxl.readers, "IsoSolventReader", J.jvxl.readers.AtomDataReader);
Clazz.prepareFields (c$, function(){
this.ptS1 =  new JU.P3();
this.ptS2 =  new JU.P3();
this.vTemp =  new JU.V3();
this.plane =  new JU.P4();
this.ptTemp2 =  new JU.P3();
this.vTemp2 =  new JU.V3();
this.p =  new JU.P3();
});
Clazz.makeConstructor(c$, 
function(){
Clazz.superConstructor (this, J.jvxl.readers.IsoSolventReader, []);
});
Clazz.overrideMethod(c$, "init", 
function(sg){
this.initADR(sg);
}, "J.jvxl.readers.SurfaceGenerator");
Clazz.overrideMethod(c$, "readVolumeParameters", 
function(isMapData){
this.setup(isMapData);
this.initializeVolumetricData();
this.volumeData.setUnitVectors();
this.vl0 = this.volumeData.volumetricVectorLengths[0];
this.vl1 = this.volumeData.volumetricVectorLengths[1];
this.vl2 = this.volumeData.volumetricVectorLengths[2];
if (this.isProgressive) {
this.volumeData.getYzCount();
this.bsAtomMinMax =  new Array(this.nPointsX);
this.getAtomMinMax(null, this.bsAtomMinMax);
this.voxelSource =  Clazz.newIntArray (this.volumeData.nPoints, 0);
}return true;
}, "~B");
Clazz.overrideMethod(c$, "setup", 
function(isMapData){
this.setup2();
if (this.contactPair == null) {
this.cavityRadius = this.params.cavityRadius;
this.envelopeRadius = this.params.envelopeRadius;
this.sr = this.params.solventRadius;
this.point = this.params.point;
this.isCavity = (this.params.isCavity && this.meshDataServer != null);
this.isPocket = (this.params.pocket != null && this.meshDataServer != null);
this.doCalculateTroughs = (!isMapData && this.sg.atomDataServer != null && !this.isCavity && this.sr > 0 && (this.dataType == 1195 || this.dataType == 1203));
this.doUseIterator = this.doCalculateTroughs;
this.getAtoms(this.params.bsSelected, this.doAddHydrogens, true, false, false, true, false, NaN, null);
if (this.isCavity || this.isPocket) this.dots = this.meshDataServer.calculateGeodesicSurface(this.bsMySelected, this.envelopeRadius);
this.setHeader("solvent/molecular surface", this.params.calculationType);
if (this.havePlane || !isMapData) {
var r = Math.max(this.params.solventExtendedAtomRadius, this.params.solventRadius);
var minPtsPerAng = (r >= 1 ? 1.5 / r : 0);
if (minPtsPerAng > 0) System.out.println("IsoSolventReader.minPtsPerAng=" + minPtsPerAng);
this.setRanges(this.params.solvent_ptsPerAngstrom, this.params.solvent_gridMax, minPtsPerAng);
this.volumeData.getYzCount();
this.margin = this.volumeData.maxGrid * 2.0;
}if (this.bsNearby != null) this.bsMySelected.or(this.bsNearby);
} else if (!isMapData) {
this.setVolumeData();
}if (!this.doCalculateTroughs) {
if (isMapData) {
this.precalculateVoxelData = false;
this.volumeData.sr = this;
} else if (!this.isCavity) {
this.isProgressive = this.isXLowToHigh = true;
}}if (this.thisAtomSet == null) this.thisAtomSet = JU.BSUtil.setAll(this.myAtomCount);
}, "~B");
Clazz.overrideMethod(c$, "generateCube", 
function(){
if (this.isCavity && this.params.theProperty != null) return;
if (this.isCavity && this.dataType != 1207 && this.dataType != 1208) {
this.params.vertexSource = null;
this.newVoxelDataCube();
this.resetVoxelData(3.4028235E38);
this.markSphereVoxels(this.cavityRadius, this.params.distance);
this.generateSolventCavity();
this.resetVoxelData(3.4028235E38);
this.markSphereVoxels(0, NaN);
} else {
this.voxelSource =  Clazz.newIntArray (this.volumeData.nPoints, 0);
this.generateSolventCube();
}this.unsetVoxelData();
var info = this.params.slabInfo;
if (info != null) for (var i = 0; i < info.size(); i++) if ((info.get(i)[2]).booleanValue() && Clazz.instanceOf(info.get(i)[0],"JU.P4")) {
this.volumeData.capData(info.get(i)[0], this.params.cutoff);
info.removeItemAt(i--);
}
});
Clazz.overrideMethod(c$, "getSurfacePointAndFraction", 
function(cutoff, isCutoffAbsolute, valueA, valueB, pointA, edgeVector, x, y, z, vA0, vB0, fReturn, ptReturn){
var vA = this.marchingCubes.getLinearOffset(x, y, z, vA0);
var vB = this.marchingCubes.getLinearOffset(x, y, z, vB0);
this.isSurfacePoint = (this.bsSurfaceVoxels != null && (this.bsSurfaceVoxels.get(vA) || this.bsSurfaceVoxels.get(vB)));
if (this.voxelSource != null) {
var vs = Math.abs(Float.isNaN(valueB) || valueA < valueB ? this.voxelSource[vA] : this.voxelSource[vB]);
if (vs > 0) this.iAtomSurface = this.atomIndex[vs - 1];
}if (J.jvxl.readers.IsoSolventReader.testLinear || this.voxelSource == null || this.voxelSource[vA] == 0 || this.voxelSource[vA] != this.voxelSource[vB]) return this.getSPF(cutoff, isCutoffAbsolute, valueA, valueB, pointA, edgeVector, x, y, z, vA, vB, fReturn, ptReturn);
var fraction = fReturn[0] = JU.MeshSurface.getSphericalInterpolationFraction((this.voxelSource[vA] < 0 ? this.sr : this.atomRadius[this.voxelSource[vA] - 1]), valueA, valueB, edgeVector.length());
ptReturn.scaleAdd2(fraction, edgeVector, pointA);
var diff = valueB - valueA;
return valueA + fraction * diff;
}, "~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");
Clazz.overrideMethod(c$, "addVertexCopy", 
function(vertexXYZ, value, assocVertex, asCopy){
var i = this.addVC(vertexXYZ, value, assocVertex, asCopy);
if (i < 0) return i;
if (this.isSurfacePoint) this.bsSurfacePoints.set(i);
if (this.params.vertexSource != null) this.params.vertexSource[i] = this.iAtomSurface;
return i;
}, "JU.T3,~N,~N,~B");
Clazz.overrideMethod(c$, "selectPocket", 
function(doExclude){
if (this.meshDataServer != null) this.meshDataServer.fillMeshData(this.meshData, 1, null);
var v = this.meshData.vs;
var nVertices = this.meshData.vc;
var vv = this.meshData.vvs;
var nDots = this.dots.length;
for (var i = 0; i < nVertices; i++) {
for (var j = 0; j < nDots; j++) {
if (this.dots[j].distance(v[i]) < this.envelopeRadius) {
vv[i] = NaN;
continue;
}}
}
this.meshData.getSurfaceSet();
var nSets = this.meshData.nSets;
var pocketSet = JU.BS.newN(nSets);
var ss;
for (var i = 0; i < nSets; i++) if ((ss = this.meshData.surfaceSet[i]) != null) for (var j = ss.nextSetBit(0); j >= 0; j = ss.nextSetBit(j + 1)) if (Float.isNaN(this.meshData.vvs[j])) {
pocketSet.set(i);
break;
}

for (var i = 0; i < nSets; i++) if (this.meshData.surfaceSet[i] != null && pocketSet.get(i) == doExclude) this.meshData.invalidateSurfaceSet(i);

this.updateSurfaceData();
if (!doExclude) this.meshData.surfaceSet = null;
if (this.meshDataServer != null) {
this.meshDataServer.fillMeshData(this.meshData, 3, null);
this.meshData =  new J.jvxl.data.MeshData();
}}, "~B");
Clazz.overrideMethod(c$, "postProcessVertices", 
function(){
this.setVertexSource();
if (this.doCalculateTroughs && this.bsSurfacePoints != null) {
var bsAll =  new JU.BS();
var bsSurfaces = this.meshData.getSurfaceSet();
var bsSources = null;
var volumes = (this.isPocket ? null : J.jvxl.data.MeshData.calculateVolumeOrArea(this.meshData, null, false, false));
var minVolume = (this.isCavity ? (1.5 * 3.141592653589793 * Math.pow(this.sr, 3)) : 0);
var maxVolume = 0;
var maxIsNegative = false;
if (volumes != null && !this.isCavity) for (var i = 0; i < this.meshData.nSets; i++) {
var v = volumes[i];
if (Math.abs(v) > maxVolume) {
maxVolume = Math.abs(v);
maxIsNegative = (v < 0);
}}
var factor = (maxIsNegative ? -1 : 1);
for (var i = 0; i < this.meshData.nSets; i++) {
var bss = bsSurfaces[i];
if (bss.intersects(this.bsSurfacePoints)) {
if (volumes == null || volumes[i] * factor > minVolume) if (this.params.vertexSource != null) {
var bs =  new JU.BS();
if (bsSources == null) bsSources =  new Array(bsSurfaces.length);
for (var j = bss.nextSetBit(0); j >= 0; j = bss.nextSetBit(j + 1)) {
var iatom = this.params.vertexSource[j];
if (iatom < 0) continue;
if (bsAll.get(iatom)) {
this.meshData.invalidateSurfaceSet(i);
break;
}bs.set(iatom);
}
bsAll.or(bs);
continue;
}}this.meshData.invalidateSurfaceSet(i);
}
this.updateSurfaceData();
if (this.meshDataServer != null) {
this.meshDataServer.fillMeshData(this.meshData, 3, null);
this.meshData =  new J.jvxl.data.MeshData();
}}if (this.params.thePlane != null && this.params.slabInfo == null) this.params.addSlabInfo(JU.TempArray.getSlabWithinRange(-100, 0));
});
Clazz.defineMethod(c$, "generateSolventCavity", 
function(){
var bs = JU.BS.newN(this.nPointsX * this.nPointsY * this.nPointsZ);
var i = 0;
var nDots = this.dots.length;
var n = 0;
var d;
var r2 = this.envelopeRadius;
for (var x = 0; x < this.nPointsX; ++x) for (var y = 0; y < this.nPointsY; ++y) {
out : for (var z = 0; z < this.nPointsZ; ++z, ++i) if ((d = this.voxelData[x][y][z]) < 3.4028235E38 && d >= this.cavityRadius) {
this.volumeData.voxelPtToXYZ(x, y, z, this.ptV);
for (var j = 0; j < nDots; j++) {
if (this.dots[j].distance(this.ptV) < r2) continue out;
}
bs.set(i);
n++;
}
}

JU.Logger.info("cavities include " + n + " voxel points");
this.atomRadius =  Clazz.newFloatArray (n, 0);
this.atomXyzTruncated =  new Array(n);
for (var x = 0, ipt = 0, apt = 0; x < this.nPointsX; ++x) for (var y = 0; y < this.nPointsY; ++y) for (var z = 0; z < this.nPointsZ; ++z) if (bs.get(ipt++)) {
this.volumeData.voxelPtToXYZ(x, y, z, (this.atomXyzTruncated[apt] =  new JU.P3()));
this.atomRadius[apt++] = this.voxelData[x][y][z];
}


this.myAtomCount = this.firstNearbyAtom = n;
this.thisAtomSet = JU.BSUtil.setAll(this.myAtomCount);
this.rs = null;
this.setRadii();
});
Clazz.defineMethod(c$, "generateSolventCube", 
function(){
if (this.dataType == 1207) return;
this.params.vertexSource =  Clazz.newIntArray (this.volumeData.nPoints, 0);
this.bsSurfaceDone =  new JU.BS();
this.bsSurfaceVoxels =  new JU.BS();
this.bsSurfacePoints =  new JU.BS();
if (this.doCalculateTroughs) {
this.iter = this.sg.atomDataServer.getSelectedAtomIterator(this.bsMySelected, true, false, false);
this.vEdges =  new JU.Lst();
this.bsLocale =  new Array(this.myAtomCount);
this.htEdges =  new java.util.Hashtable();
this.getEdges();
JU.Logger.info(this.vEdges.size() + " edges");
this.vFaces =  new JU.Lst();
this.getFaces();
JU.Logger.info(this.vFaces.size() + " faces");
this.bsLocale = null;
this.htEdges = null;
this.iter.release();
this.iter = null;
this.newVoxelDataCube();
this.resetVoxelData(3.4028235E38);
this.markFaceVoxels(true);
this.markToroidVoxels();
this.validSpheres.or(this.noFaceSpheres);
this.vEdges = null;
this.markFaceVoxels(false);
this.vFaces = null;
} else {
this.newVoxelDataCube();
this.resetVoxelData(3.4028235E38);
}this.markSphereVoxels(0, this.doCalculateTroughs ? 3.4028235E38 : this.params.distance);
this.noFaceSpheres = null;
this.validSpheres = null;
});
Clazz.defineMethod(c$, "getEdges", 
function(){
for (var iatomA = 0; iatomA < this.myAtomCount; iatomA++) this.bsLocale[iatomA] =  new JU.BS();

for (var iatomA = 0; iatomA < this.myAtomCount; iatomA++) {
var ptA = this.atomXyzTruncated[iatomA];
var rA = this.rs[iatomA];
this.sg.atomDataServer.setIteratorForAtom(this.iter, this.atomIndex[iatomA], rA + this.maxRS);
while (this.iter.hasNext()) {
var iB = this.iter.next();
var iatomB = this.myIndex[iB];
if (iatomA >= this.firstNearbyAtom && iatomB >= this.firstNearbyAtom) continue;
var ptB = this.atomXyzTruncated[iatomB];
var rB = this.rs[iatomB];
var dAB = ptA.distance(ptB);
if (dAB >= rA + rB) continue;
var edge = Clazz.innerTypeInstance(J.jvxl.readers.IsoSolventReader.Edge, this, null, this, iatomA, iatomB, dAB);
this.vEdges.addLast(edge);
this.bsLocale[iatomA].set(iatomB);
this.bsLocale[iatomB].set(iatomA);
this.htEdges.put(edge.toString(), edge);
}
}
});
Clazz.defineMethod(c$, "findEdge", 
function(i, j){
return this.htEdges.get(i < j ? i + "_" + j : j + "_" + i);
}, "~N,~N");
Clazz.defineMethod(c$, "getFaces", 
function(){
var bs =  new JU.BS();
this.params.surfaceAtoms = this.validSpheres =  new JU.BS();
this.noFaceSpheres = JU.BSUtil.setAll(this.myAtomCount);
for (var i = this.vEdges.size(); --i >= 0; ) {
var edge = this.vEdges.get(i);
var ia = edge.ia;
var ib = edge.ib;
bs.clearAll();
bs.or(this.bsLocale[ia]);
bs.and(this.bsLocale[ib]);
for (var ic = bs.nextSetBit(ib + 1); ic >= 0; ic = bs.nextSetBit(ic + 1)) {
if (this.getSolventPoints(edge, ia, ib, ic)) {
var f;
var isOK = false;
if ((f = this.validateFace(ia, ib, ic, edge, this.ptS1)) != null) {
this.vFaces.addLast(f);
isOK = true;
}if ((f = this.validateFace(ia, ib, ic, edge, this.ptS2)) != null) {
this.vFaces.addLast(f);
isOK = true;
}if (isOK) {
this.noFaceSpheres.clear(ia);
this.noFaceSpheres.clear(ib);
this.noFaceSpheres.clear(ic);
}}}
}
});
Clazz.defineMethod(c$, "validateFace", 
function(ia, ib, ic, edge, ptS){
this.sg.atomDataServer.setIteratorForPoint(this.iter, this.modelIndex, ptS, this.maxRS);
var isValid = true;
while (this.iter.hasNext()) {
var iia = this.iter.next();
var iatom = this.myIndex[iia];
if (iatom == ia || iatom == ib || iatom == ic) continue;
var d = this.atomData.atoms[iia].distance(ptS);
if (d < this.atomData.atomRadius[iia] + this.sr) {
isValid = false;
break;
}}
var bc = this.findEdge(ib, ic);
var ca = this.findEdge(ia, ic);
var f = (isValid ? Clazz.innerTypeInstance(J.jvxl.readers.IsoSolventReader.Face, this, null, ia, ib, ic, ptS) : null);
edge.addFace(f);
bc.addFace(f);
ca.addFace(f);
if (!isValid) return null;
this.validSpheres.set(ia);
this.validSpheres.set(ib);
this.validSpheres.set(ic);
return f;
}, "~N,~N,~N,J.jvxl.readers.IsoSolventReader.Edge,JU.P3");
Clazz.defineMethod(c$, "markFaceVoxels", 
function(firstPass){
var bsThisPass =  new JU.BS();
var v0 = this.volumetricVectors[0];
var v1 = this.volumetricVectors[1];
var v2 = this.volumetricVectors[2];
for (var fi = this.vFaces.size(); --fi >= 0; ) {
var f = this.vFaces.get(fi);
var ptA = this.atomXyzTruncated[f.ia];
var ptB = this.atomXyzTruncated[f.ib];
var ptC = this.atomXyzTruncated[f.ic];
var ptS = f.pS;
this.setGridLimitsForAtom(ptS, this.sr, this.pt0, this.pt1);
this.volumeData.voxelPtToXYZ(this.pt0.x, this.pt0.y, this.pt0.z, this.ptV);
for (var i = this.pt0.x; i < this.pt1.x; i++, this.ptV.add2(v0, this.ptY0)) {
this.ptY0.setT(this.ptV);
for (var j = this.pt0.y; j < this.pt1.y; j++, this.ptV.add2(v1, this.ptZ0)) {
this.ptZ0.setT(this.ptV);
for (var k = this.pt0.z; k < this.pt1.z; k++, this.ptV.add(v2)) {
var value = this.sr - this.ptV.distance(ptS);
var v = this.voxelData[i][j][k];
var ipt = this.volumeData.getPointIndex(i, j, k);
if (firstPass && value > 0) this.bsSurfaceDone.set(ipt);
if (JU.Measure.isInTetrahedron(this.ptV, ptA, ptB, ptC, ptS, this.plane, this.vTemp, this.vTemp2, false)) {
if (!firstPass ? !this.bsSurfaceDone.get(ipt) && value < 0 && value > -this.volumeData.maxGrid * 1.8 && (value > v) == bsThisPass.get(ipt) : (value > 0 && (v < 0 || v == 3.4028235E38 || (value > v) == bsThisPass.get(ipt)))) {
bsThisPass.set(ipt);
this.setVoxel(i, j, k, ipt, value);
if (this.voxelSource != null) this.voxelSource[ipt] = -1 - f.ia;
if (value > 0) {
this.bsSurfaceVoxels.set(ipt);
}}}}
}
}
}
}, "~B");
Clazz.defineMethod(c$, "markToroidVoxels", 
function(){
var v0 = this.volumetricVectors[0];
var v1 = this.volumetricVectors[1];
var v2 = this.volumetricVectors[2];
for (var ei = this.vEdges.size(); --ei >= 0; ) {
var edge = this.vEdges.get(ei);
if (!edge.isValid()) continue;
var ia = edge.ia;
var ib = edge.ib;
var ptA = this.atomXyzTruncated[ia];
var ptB = this.atomXyzTruncated[ib];
this.rAS = this.rs[ia];
this.rBS = this.rs[ib];
this.rAS2 = this.rs2[ia];
this.rBS2 = this.rs2[ib];
this.dAB = edge.d;
this.dAB2 = edge.d2;
this.ecosASB2 = edge.cosASB2;
this.setGridLimitsForAtom(edge, edge.maxr, this.pt0, this.pt1);
this.volumeData.voxelPtToXYZ(this.pt0.x, this.pt0.y, this.pt0.z, this.ptV);
for (var i = this.pt0.x; i < this.pt1.x; i++, this.ptV.add2(v0, this.ptY0)) {
this.ptY0.setT(this.ptV);
for (var j = this.pt0.y; j < this.pt1.y; j++, this.ptV.add2(v1, this.ptZ0)) {
this.ptZ0.setT(this.ptV);
for (var k = this.pt0.z; k < this.pt1.z; k++, this.ptV.add(v2)) {
var dVS = this.checkSpecialVoxel(ptA, ptB, this.ptV);
if (Float.isNaN(dVS)) continue;
var value = this.sr - dVS;
if (value < this.voxelData[i][j][k]) {
var ipt = this.volumeData.getPointIndex(i, j, k);
this.setVoxel(i, j, k, ipt, value);
if (this.voxelSource != null) this.voxelSource[ipt] = -1 - ia;
}}
}
}
}
});
Clazz.overrideMethod(c$, "unsetVoxelData", 
function(){
if (!this.havePlane) {
this.unsetVoxelData2();
return;
}if (this.isProgressive) for (var i = 0; i < this.yzCount; i++) {
if (this.thisPlane[i] < 0.001) {
} else {
this.thisPlane[i] = 0.001;
}}
 else for (var x = 0; x < this.nPointsX; ++x) for (var y = 0; y < this.nPointsY; ++y) for (var z = 0; z < this.nPointsZ; ++z) if (this.voxelData[x][y][z] < 0.001) {
} else {
this.voxelData[x][y][z] = 0.001;
}


});
Clazz.defineMethod(c$, "getSolventPoints", 
function(edge, ia, ib, ic){
var rAS = this.rs[ia];
var v = edge.v;
var cosAngleBAS = (edge.d2 + this.rs2[ia] - this.rs2[ib]) / (2 * edge.d * rAS);
var angleBAS = Math.acos(cosAngleBAS);
this.p.scaleAdd2(cosAngleBAS * rAS, v, this.atomXyzTruncated[ia]);
JU.Measure.getPlaneThroughPoint(this.p, v, this.plane);
var dPS = (Math.sin(angleBAS) * rAS);
var ptC = this.atomXyzTruncated[ic];
var rCS = this.rs[ic];
var dCT = JU.Measure.distanceToPlane(this.plane, ptC);
if (Math.abs(dCT) >= rCS * 0.9) return false;
this.ptTemp.scaleAdd2(-dCT, v, ptC);
var dpT = this.p.distance(this.ptTemp);
var dsp2 = dPS * dPS;
var dST2 = this.rs2[ic] - dCT * dCT;
var cosTheta = (dsp2 + dpT * dpT - dST2) / (2 * dPS * dpT);
if (Math.abs(cosTheta) >= 0.99) return false;
var vXS = this.vTemp2;
vXS.sub2(this.ptTemp, this.p);
vXS.normalize();
this.ptTemp.scaleAdd2(dPS * cosTheta, vXS, this.p);
vXS.cross(v, vXS);
vXS.normalize();
vXS.scale((Math.sqrt(1 - cosTheta * cosTheta) * dPS));
this.ptS1.add2(this.ptTemp, vXS);
this.ptS2.sub2(this.ptTemp, vXS);
return true;
}, "J.jvxl.readers.IsoSolventReader.Edge,~N,~N,~N");
Clazz.defineMethod(c$, "checkSpecialVoxel", 
function(ptA, ptB, ptV){
var dAV = ptA.distance(ptV);
var dAV2 = ptA.distanceSquared(ptV);
var f = this.rAS / dAV;
if (f > 1) {
this.p.set(ptA.x + (ptV.x - ptA.x) * f, ptA.y + (ptV.y - ptA.y) * f, ptA.z + (ptV.z - ptA.z) * f);
return (ptB.distanceSquared(this.p) >= this.rBS2 ? NaN : this.solventDistance(this.rAS, this.rAS2, this.rBS2, dAV, dAV2, ptB.distanceSquared(ptV)));
}var dBV = ptB.distance(ptV);
if ((f = this.rBS / dBV) > 1) {
this.p.set(ptB.x + (ptV.x - ptB.x) * f, ptB.y + (ptV.y - ptB.y) * f, ptB.z + (ptV.z - ptB.z) * f);
return (ptA.distanceSquared(this.p) >= this.rAS2 ? NaN : this.solventDistance(this.rBS, this.rBS2, this.rAS2, dBV, dBV * dBV, dAV2));
}return NaN;
}, "JU.P3,JU.P3,JU.P3");
Clazz.defineMethod(c$, "solventDistance", 
function(rAS, rAS2, rBS2, dAV, dAV2, dBV2){
var angleVAB = Math.acos((dAV2 + this.dAB2 - dBV2) / (2 * dAV * this.dAB));
var angleSAB = Math.acos((rAS2 + this.dAB2 - rBS2) / (2 * rAS * this.dAB));
var dVS2 = (rAS2 + dAV2 - 2 * rAS * dAV * Math.cos(angleSAB - angleVAB));
var dVS = Math.sqrt(dVS2);
return (this.ecosASB2 < (rAS2 + dVS2 - dAV * dAV) / (dVS * rAS) ? dVS : NaN);
}, "~N,~N,~N,~N,~N,~N");
Clazz.defineMethod(c$, "dumpLine", 
function(pt1, pt2, label, color){
this.sg.log("draw ID \"x" + label + (this.nTest++) + "\" " + JU.P3.newP(pt1) + " " + JU.P3.newP(pt2) + " color " + color);
}, "JU.P3,JU.T3,~S,~S");
Clazz.defineMethod(c$, "dumpLine2", 
function(pt1, pt2, label, d, color1, color2){
var pt =  new JU.V3();
pt.setT(pt2);
pt.sub(pt1);
pt.normalize();
pt.scale(d);
pt.add(pt1);
this.sg.log("draw ID \"" + label + (this.nTest++) + "\" " + JU.P3.newP(pt1) + " " + JU.P3.newP(pt) + " color " + color1);
this.sg.log("draw ID \"" + label + (this.nTest++) + "\"" + JU.P3.newP(pt) + " " + JU.P3.newP(pt2) + " color " + color2 + "\"" + label + "\"");
}, "JU.P3,JU.P3,~S,~N,~S,~S");
Clazz.defineMethod(c$, "dumpPoint", 
function(pt, label, color){
this.sg.log("draw ID \"" + label + (this.nTest++) + "\"" + JU.P3.newP(pt) + " color " + color);
}, "JU.P3,~S,~S");
Clazz.overrideMethod(c$, "getValueAtPoint", 
function(pt, getSource){
if (this.contactPair != null) return pt.distance(this.contactPair.myAtoms[1]) - this.contactPair.radii[1];
var value = 3.4028235E38;
for (var iAtom = 0; iAtom < this.firstNearbyAtom; iAtom++) {
var r = pt.distance(this.atomXyzTruncated[iAtom]) - this.rs[iAtom];
if (r < value) value = r;
}
return (value == 3.4028235E38 ? NaN : value);
}, "JU.T3,~B");
Clazz.overrideMethod(c$, "discardTempData", 
function(discardAll){
this.rs = null;
this.rs2 = null;
this.discardTempDataSR(discardAll);
}, "~B");
Clazz.overrideMethod(c$, "getPlane", 
function(x){
if (this.yzCount == 0) {
this.initPlanes();
}this.thisX = x;
this.thisPlane = this.yzPlanes[x % 2];
if (this.contactPair == null) {
this.resetPlane(3.4028235E38);
this.thisAtomSet = this.bsAtomMinMax[x];
this.markSphereVoxels(0, this.params.distance);
this.unsetVoxelData();
} else {
this.markPlaneVoxels(this.contactPair.myAtoms[0], this.contactPair.radii[0]);
}return this.thisPlane;
}, "~N");
c$.$IsoSolventReader$Edge$ = function(){
/*if4*/;(function(){
var c$ = Clazz.decorateAsClass(function(){
Clazz.prepareCallback(this, arguments);
this.ia = 0;
this.ib = 0;
this.nFaces = 0;
this.nInvalid = 0;
this.d = 0;
this.d2 = 0;
this.maxr = 0;
this.cosASB2 = 0;
this.v = null;
Clazz.instantialize(this, arguments);}, J.jvxl.readers.IsoSolventReader, "Edge", JU.P3);
Clazz.overrideConstructor(c$, 
function(r, ia, ib, d){
this.ia = Math.min(ia, ib);
this.ib = Math.max(ia, ib);
this.d = d;
this.d2 = d * d;
this.maxr = Math.sqrt(this.d2 / 4 + Math.max(r.rs2[ia], r.rs2[ib]));
this.ave(r.atomXyzTruncated[ia], r.atomXyzTruncated[ib]);
this.cosASB2 = (r.rs2[ia] + r.rs2[ib] - this.d2) / (r.rs[ib] * r.rs[ia]);
this.v = JU.V3.newVsub(r.atomXyzTruncated[ib], r.atomXyzTruncated[ia]);
this.v.normalize();
}, "J.jvxl.readers.IsoSolventReader,~N,~N,~N");
Clazz.defineMethod(c$, "addFace", 
function(f){
this.nFaces++;
if (f == null) {
this.nInvalid++;
return;
}}, "J.jvxl.readers.IsoSolventReader.Face");
Clazz.defineMethod(c$, "isValid", 
function(){
return (this.nFaces == 0 || this.nInvalid != this.nFaces);
});
Clazz.overrideMethod(c$, "toString", 
function(){
return this.ia + "_" + this.ib;
});
/*eoif4*/})();
};
c$.$IsoSolventReader$Face$ = function(){
/*if4*/;(function(){
var c$ = Clazz.decorateAsClass(function(){
Clazz.prepareCallback(this, arguments);
this.ia = 0;
this.ib = 0;
this.ic = 0;
this.pS = null;
Clazz.instantialize(this, arguments);}, J.jvxl.readers.IsoSolventReader, "Face", null);
Clazz.makeConstructor(c$, 
function(ia, ib, ic, pS){
this.ia = ia;
this.ib = ib;
this.ic = ic;
this.pS = JU.P3.newP(pS);
}, "~N,~N,~N,JU.P3");
Clazz.overrideMethod(c$, "toString", 
function(){
return this.ia + "_" + this.ib + "_" + this.ic + "_" + this.pS;
});
/*eoif4*/})();
};
c$.testLinear = false;
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
