@Override
public boolean hasNext() {
if (ibond == bondCount) return false;
while ((bond = bonds[ibond++]) == null
|| (bsAtoms != null && (!bsAtoms.get(bond.atomIndex1) || !bsAtoms.get(bond.atomIndex2))))
if (ibond == bondCount) return false;
return true;
}
private void getStateAtoms(SB sb) {
BS bsDone = new BS();
Map<String, BS> temp = new Hashtable<String, BS>();
Map<String, BS> temp2 = new Hashtable<String, BS>();
for (Ellipsoid e : atomEllipsoids.values()) {
int iType = e.tensor.iType;
if (bsDone.get(iType + 1)) continue;
bsDone.set(iType + 1);
boolean isADP = (e.tensor.iType == Tensor.TYPE_ADP);
String cmd = (isADP ? null : "Ellipsoids set " + PT.esc(e.tensor.type));
for (Ellipsoid e2 : atomEllipsoids.values()) {
if (e2.tensor.iType != iType || isADP && !e2.isOn) continue;
int i = e2.tensor.atomIndex1;
//
BSUtil.setMapBitSet(
temp,
i,
i,
(isADP
? "Ellipsoids " + e2.percent
: cmd
+ " scale "
+ e2.scale
+ (e2.options == null ? "" : " options " + PT.esc(e2.options))
+ (e2.isOn ? " ON" : " OFF")));
if (e2.colix != C.INHERIT_ALL)
BSUtil.setMapBitSet(
temp2, i, i, getColorCommand(cmd, e2.pid, e2.colix, translucentAllowed));
}
}
sb.append(vwr.getCommands(temp, temp2, "select"));
}
public void resetTransPolygons() {
boolean isTranslucent = C.isColixTranslucent(colix);
float translucentLevel = C.getColixTranslucencyFractional(colix);
for (int i = 0; i < pc; i++)
if (bsTransPolygons.get(i)) {
if (!setABC(i)) continue;
vcs[iA] = C.getColixTranslucent3(vcs[iA], isTranslucent, translucentLevel);
vcs[iB] = C.getColixTranslucent3(vcs[iB], isTranslucent, translucentLevel);
vcs[iC] = C.getColixTranslucent3(vcs[iC], isTranslucent, translucentLevel);
}
bsTransPolygons = null;
polygonTranslucencies = null;
}
private void setVis(Map<?, Ellipsoid> ellipsoids, BS bs, Atom[] atoms) {
for (Ellipsoid e : ellipsoids.values()) {
Tensor t = e.tensor;
boolean isOK = (t != null && e.isValid && e.isOn);
if (isOK && t.atomIndex1 >= 0) {
if (t.iType == Tensor.TYPE_ADP) {
boolean isModTensor = t.isModulated;
boolean isUnmodTensor = t.isUnmodulated;
boolean isModAtom = ms.isModulated(t.atomIndex1);
isOK = (!isModTensor && !isUnmodTensor || isModTensor == isModAtom);
}
atoms[t.atomIndex1].setShapeVisibility(vf, true);
}
e.visible = isOK && (e.modelIndex < 0 || bs.get(e.modelIndex));
}
}
private boolean initializePolymer(BioShape bioShape) {
BS bsDeleted = vwr.getDeletedAtoms();
if (vwr.ms.isJmolDataFrameForModel(bioShape.modelIndex)) {
controlPoints = bioShape.bioPolymer.getControlPoints(true, 0, false);
} else {
controlPoints =
bioShape.bioPolymer.getControlPoints(isTraceAlpha, sheetSmoothing, invalidateSheets);
}
monomerCount = bioShape.monomerCount;
bsRenderMesh = BS.newN(monomerCount);
monomers = bioShape.monomers;
reversed = bioShape.bioPolymer.reversed;
leadAtomIndices = bioShape.bioPolymer.getLeadAtomIndices();
bsVisible.clearAll();
boolean haveVisible = false;
if (invalidateMesh) bioShape.falsifyMesh();
for (int i = monomerCount; --i >= 0; ) {
if ((monomers[i].shapeVisibilityFlags & myVisibilityFlag) == 0
|| ms.isAtomHidden(leadAtomIndices[i])
|| bsDeleted != null && bsDeleted.get(leadAtomIndices[i])) continue;
Atom lead = ms.at[leadAtomIndices[i]];
if (!g3d.isInDisplayRange(lead.sX, lead.sY)) continue;
bsVisible.set(i);
haveVisible = true;
}
if (!haveVisible) return false;
ribbonBorder = vwr.getBoolean(T.ribbonborder);
// note that we are not treating a PhosphorusPolymer
// as nucleic because we are not calculating the wing
// vector correctly.
// if/when we do that then this test will become
// isNucleic = bioShape.bioPolymer.isNucleic();
isNucleic = bioShape.bioPolymer instanceof NucleicPolymer;
isCarbohydrate = bioShape.bioPolymer instanceof CarbohydratePolymer;
haveControlPointScreens = false;
wingVectors = bioShape.wingVectors;
meshReady = bioShape.meshReady;
meshes = bioShape.meshes;
mads = bioShape.mads;
colixes = bioShape.colixes;
colixesBack = bioShape.colixesBack;
setStructureTypes();
return true;
}
/**
* @param doFill
* @param i
* @param thisTypeOnly true for Cartoon but not MeshRibbon
*/
protected void renderHermiteRibbon(boolean doFill, int i, boolean thisTypeOnly) {
// cartoons and meshRibbon
setNeighbors(i);
colix = getLeadColix(i);
if (!setBioColix(colix)) return;
colixBack = getLeadColixBack(i);
if (doFill && (aspectRatio != 0 || isExport)) {
if (setMads(i, thisTypeOnly) || isExport) {
try {
if ((meshes[i] == null || !meshReady[i])
&& !createMesh(i, madBeg, madMid, madEnd, aspectRatio, isNucleic ? 4 : 7)) return;
meshes[i].setColix(colix);
meshes[i].setColixBack(colixBack);
bsRenderMesh.set(i);
return;
} catch (Exception e) {
bsRenderMesh.clear(i);
meshes[i] = null;
Logger.error("render mesh error hermiteRibbon: " + e.toString());
// System.out.println(e.getMessage());
}
}
}
g3d.drawHermite7(
doFill,
ribbonBorder,
(reversed.get(i) ? -1 : 1) * (isNucleic ? 4 : 7),
ribbonTopScreens[iPrev],
ribbonTopScreens[i],
ribbonTopScreens[iNext],
ribbonTopScreens[iNext2],
ribbonBottomScreens[iPrev],
ribbonBottomScreens[i],
ribbonBottomScreens[iNext],
ribbonBottomScreens[iNext2],
(int) aspectRatio,
colixBack);
}
private static float checkSlab(
int tokType, T3 v, float val, float distance, P4 plane, T3[] ptCenters, BS bs) {
float d;
switch (tokType) {
case T.decimal:
return (val >= 0 && bs.get((int) val) ? 1 : -1);
case T.min:
d = distance - val;
break;
case T.max:
d = val - distance;
break;
case T.plane:
d = Measure.distanceToPlane(plane, v);
break;
case T.distance:
d = minDist(v, ptCenters) - distance;
break;
default:
d = -minDist(v, ptCenters) - distance;
break;
}
return (Math.abs(d) < 0.0001f ? 0 : d);
}
/**
* @param distance a distance from a plane or point
* @param plane a slabbing plane
* @param ptCenters a set of atoms to measure distance from
* @param vData when not null, this is a query, not an actual slabbing
* @param fData vertex values or other data to overlay
* @param bsSource TODO
* @param meshSurface second surface; not implemented -- still some problems there
* @param andCap to cap this off, crudely only
* @param doClean compact set - draw only
* @param tokType type of slab
* @param isGhost translucent slab, so we mark slabbed triangles
*/
public void getIntersection(
float distance,
P4 plane,
P3[] ptCenters,
Lst<P3[]> vData,
float[] fData,
BS bsSource,
MeshSurface meshSurface,
boolean andCap,
boolean doClean,
int tokType,
boolean isGhost) {
boolean isSlab = (vData == null);
P3[] pts = null;
if (fData == null) {
if (tokType == T.decimal && bsSource != null) {
if (vertexSource == null) return;
fData = new float[vc];
for (int i = 0; i < vc; i++)
if ((fData[i] = vertexSource[i]) == -1) System.out.println("meshsurface hmm");
} else {
fData = vvs;
}
}
Map<String, Integer> mapEdge = new Hashtable<String, Integer>();
/*
Vector3f vNorm = null;
Vector3f vBC = null;
Vector3f vAC = null;
Point3f[] pts2 = null;
Vector3f vTemp3 = null;
Point4f planeTemp = null;
boolean isMeshIntersect = (meshSurface != null);
if (isMeshIntersect) {
// NOT IMPLEMENTED
vBC = new Vector3f();
vAC = new Vector3f();
vNorm = new Vector3f();
plane = new Point4f();
planeTemp = new Point4f();
vTemp3 = new Vector3f();
pts2 = new Point3f[] { null, new Point3f(), new Point3f() };
}
*/
if (ptCenters != null || isGhost)
andCap = false; // can only cap faces, and no capping of ghosts
float[] values = new float[2];
float[] fracs = new float[2];
double absD = Math.abs(distance);
float d1, d2, d3, valA, valB, valC;
int sourceA = 0, sourceB = 0, sourceC = 0, setA = 0;
Lst<int[]> iPts = (andCap ? new Lst<int[]>() : null);
if (pc == 0) {
for (int i = mergeVertexCount0; i < vc; i++) {
if (Float.isNaN(fData[i])
|| checkSlab(tokType, vs[i], fData[i], distance, plane, ptCenters, bsSource) > 0)
bsSlabDisplay.clear(i);
}
return;
}
int iLast = pc;
for (int i = mergePolygonCount0; i < iLast; i++) {
if (!setABC(i)) continue;
BS bsSlab = (bsSlabGhost != null && bsSlabGhost.get(i) ? bsSlabGhost : bsSlabDisplay);
int check1 = pis[i][3];
int check2 = (checkCount == 2 ? pis[i][4] : 0);
T3 vA = vs[iA];
T3 vB = vs[iB];
T3 vC = vs[iC];
valA = fData[iA];
valB = fData[iB];
valC = fData[iC];
if (vertexSource != null) {
sourceA = vertexSource[iA];
sourceB = vertexSource[iB];
sourceC = vertexSource[iC];
}
if (vertexSets != null) setA = vertexSets[iA];
d1 =
checkSlab(
tokType,
vA,
valA,
(bsSource == null ? distance : sourceA),
plane,
ptCenters,
bsSource);
d2 =
checkSlab(
tokType,
vB,
valB,
(bsSource == null ? distance : sourceB),
plane,
ptCenters,
bsSource);
d3 =
checkSlab(
tokType,
vC,
valC,
(bsSource == null ? distance : sourceC),
plane,
ptCenters,
bsSource);
int test1 =
(d1 != 0 && d1 < 0 ? 1 : 0) + (d2 != 0 && d2 < 0 ? 2 : 0) + (d3 != 0 && d3 < 0 ? 4 : 0);
/*
if (iA == 955 || iB == 955 || iC == 955) {
System.out.println(i + " " + iA + " " + iB + " " + iC + " "+ d1 + " " + d2 + " " + d3 + " " + test1);
System.out.println("testing messhsurf ");
}
*/
/*
if (isMeshIntersect && test1 != 7 && test1 != 0) {
// NOT IMPLEMENTED
boolean isOK = (d1 == 0 && d2 * d3 >= 0 || d2 == 0 && (d1 * d3) >= 0 || d3 == 0
&& d1 * d2 >= 0);
if (isOK)
continue;
// We have a potential crossing. Now to find the exact point of crossing
// the other isosurface.
if (checkIntersection(vA, vB, vC, meshSurface, pts2, vNorm, vBC, vAC,
plane, planeTemp, vTemp3)) {
iD = addIntersectionVertex(pts2[0], 0, sourceA, mapEdge, -1, -1); // have to choose some source
addPolygon(iA, iB, iD, check1 & 1, check2, 0, bsSlabDisplay);
addPolygon(iD, iB, iC, check1 & 2, check2, 0, bsSlabDisplay);
addPolygon(iA, iD, iC, check1 & 4, check2, 0, bsSlabDisplay);
test1 = 0; // toss original
iLast = polygonCount;
} else {
// process normally for now
// not fully implemented -- need to check other way as well.
}
}
*/
switch (test1) {
default:
case 7:
case 0:
// all on the same side
break;
case 1:
case 6:
// BC on same side
if (ptCenters == null)
pts =
new P3[] {
interpolatePoint(vA, vB, -d1, d2, valA, valB, values, fracs, 0),
interpolatePoint(vA, vC, -d1, d3, valA, valC, values, fracs, 1)
};
else
pts =
new P3[] {
interpolateSphere(vA, vB, -d1, -d2, absD, valA, valB, values, fracs, 0),
interpolateSphere(vA, vC, -d1, -d3, absD, valA, valC, values, fracs, 1)
};
break;
case 2:
case 5:
// AC on same side
if (ptCenters == null)
pts =
new P3[] {
interpolatePoint(vB, vA, -d2, d1, valB, valA, values, fracs, 1),
interpolatePoint(vB, vC, -d2, d3, valB, valC, values, fracs, 0)
};
else
pts =
new P3[] {
interpolateSphere(vB, vA, -d2, -d1, absD, valB, valA, values, fracs, 1),
interpolateSphere(vB, vC, -d2, -d3, absD, valB, valC, values, fracs, 0)
};
break;
case 3:
case 4:
// AB on same side need A-C, B-C
if (ptCenters == null)
pts =
new P3[] {
interpolatePoint(vC, vA, -d3, d1, valC, valA, values, fracs, 0),
interpolatePoint(vC, vB, -d3, d2, valC, valB, values, fracs, 1)
};
else
pts =
new P3[] {
interpolateSphere(vC, vA, -d3, -d1, absD, valC, valA, values, fracs, 0),
interpolateSphere(vC, vB, -d3, -d2, absD, valC, valB, values, fracs, 1)
};
break;
}
doClear = true;
doGhost = isGhost;
doCap = andCap;
BS bs;
// adjust for minor discrepencies
// for (int j = 0; j < 2; j++)
// if (fracs[j] == 0)
// fracs[1 - j] = (fracs[1 - j] < 0.5 ? 0 : 1);
if (isSlab) {
// iD = iE = -1;
switch (test1) {
// A
// / \
// B---C
case 0:
// all on the same side -- toss
doCap = false;
break;
case 7:
// all on the same side -- keep
continue;
case 1:
case 6:
// 0 A 0
// / \
// 0 -------- 1
// / \
// 1 B-------C 1
boolean tossBC = (test1 == 1);
if (tossBC || isGhost) {
// 1: BC on side to toss -- +tossBC+isGhost -tossBC+isGhost
if (!getDE(fracs, 0, iA, iB, iC, tossBC)) break;
if (iD < 0)
iD = addIntersectionVertex(pts[0], values[0], sourceA, setA, mapEdge, iA, iB);
if (iE < 0)
iE = addIntersectionVertex(pts[1], values[1], sourceA, setA, mapEdge, iA, iC);
bs = (tossBC ? bsSlab : bsSlabGhost);
addPolygonV3(iA, iD, iE, check1 & 5 | 2, check2, 0, bs);
if (!isGhost) break;
}
// BC on side to keep -- -tossBC+isGhost, +tossBC+isGhost
if (!getDE(fracs, 1, iA, iC, iB, tossBC)) break;
bs = (tossBC ? bsSlabGhost : bsSlab);
if (iE < 0) {
iE = addIntersectionVertex(pts[0], values[0], sourceB, setA, mapEdge, iA, iB);
addPolygonV3(iE, iB, iC, check1 & 3, check2, 0, bs);
}
if (iD < 0) {
iD = addIntersectionVertex(pts[1], values[1], sourceC, setA, mapEdge, iA, iC);
addPolygonV3(iD, iE, iC, check1 & 4 | 1, check2, 0, bs);
}
break;
case 5:
case 2:
// A
// \/ \
// /\ \
// B--\--C
// \
//
boolean tossAC = (test1 == 2);
if (tossAC || isGhost) {
// AC on side to toss
if (!getDE(fracs, 0, iB, iC, iA, tossAC)) break;
bs = (tossAC ? bsSlab : bsSlabGhost);
if (iE < 0)
iE = addIntersectionVertex(pts[0], values[0], sourceB, setA, mapEdge, iB, iA);
if (iD < 0)
iD = addIntersectionVertex(pts[1], values[1], sourceB, setA, mapEdge, iB, iC);
addPolygonV3(iE, iB, iD, check1 & 3 | 4, check2, 0, bs);
if (!isGhost) break;
}
// AC on side to keep
if (!getDE(fracs, 1, iB, iA, iC, tossAC)) break;
bs = (tossAC ? bsSlabGhost : bsSlab);
if (iD < 0) {
iD = addIntersectionVertex(pts[0], values[0], sourceA, setA, mapEdge, iB, iA);
addPolygonV3(iA, iD, iC, check1 & 5, check2, 0, bs);
}
if (iE < 0) {
iE = addIntersectionVertex(pts[1], values[1], sourceC, setA, mapEdge, iB, iC);
addPolygonV3(iD, iE, iC, check1 & 2 | 1, check2, 0, bs);
}
break;
case 4:
case 3:
// A
// / \/
// / /\
// B--/--C
// /
//
boolean tossAB = (test1 == 4);
if (tossAB || isGhost) {
if (!getDE(fracs, 0, iC, iA, iB, tossAB)) break;
if (iD < 0)
iD = addIntersectionVertex(pts[0], values[0], sourceC, setA, mapEdge, iA, iC); // CA
if (iE < 0)
iE = addIntersectionVertex(pts[1], values[1], sourceC, setA, mapEdge, iB, iC); // CB
bs = (tossAB ? bsSlab : bsSlabGhost);
addPolygonV3(iD, iE, iC, check1 & 6 | 1, check2, 0, bs);
if (!isGhost) break;
}
// AB on side to keep
if (!getDE(fracs, 1, iC, iB, iA, tossAB)) break;
bs = (tossAB ? bsSlabGhost : bsSlab);
if (iE < 0) {
iE = addIntersectionVertex(pts[0], values[0], sourceA, setA, mapEdge, iA, iC); // CA
addPolygonV3(iA, iB, iE, check1 & 5, check2, 0, bs);
}
if (iD < 0) {
iD = addIntersectionVertex(pts[1], values[1], sourceB, setA, mapEdge, iB, iC); // CB
addPolygonV3(iE, iB, iD, check1 & 2 | 4, check2, 0, bs);
}
break;
}
if (doClear) {
bsSlab.clear(i);
if (doGhost) bsSlabGhost.set(i);
}
if (doCap) {
iPts.addLast(new int[] {iD, iE});
}
} else if (pts != null) {
vData.addLast(pts);
}
}
if (andCap && iPts.size() > 0) {
P3 center = new P3();
for (int i = iPts.size(); --i >= 0; ) {
int[] ipts = iPts.get(i);
center.add(vs[ipts[0]]);
center.add(vs[ipts[1]]);
}
center.scale(0.5f / iPts.size());
int v0 = addIntersectionVertex(center, 0, -1, setA, mapEdge, -1, -1);
for (int i = iPts.size(); --i >= 0; ) {
int[] ipts = iPts.get(i);
// int p =
addPolygonV3(ipts[0], v0, ipts[1], 0, 0, 0, bsSlabDisplay);
}
}
if (!doClean) return;
BS bsv = new BS();
BS bsp = new BS();
for (int i = 0; i < pc; i++) {
if (pis[i] == null) continue;
bsp.set(i);
for (int j = 0; j < 3; j++) bsv.set(pis[i][j]);
}
int n = 0;
int nPoly = bsp.cardinality();
if (nPoly != pc) {
int[] map = new int[vc];
for (int i = 0; i < vc; i++) if (bsv.get(i)) map[i] = n++;
T3[] vTemp = new P3[n];
n = 0;
for (int i = 0; i < vc; i++) if (bsv.get(i)) vTemp[n++] = vs[i];
int[][] pTemp = AU.newInt2(nPoly);
nPoly = 0;
for (int i = 0; i < pc; i++)
if (pis[i] != null) {
for (int j = 0; j < 3; j++) pis[i][j] = map[pis[i][j]];
pTemp[nPoly++] = pis[i];
}
vs = vTemp;
vc = n;
pis = pTemp;
pc = nPoly;
}
}