void generateSolventCube(boolean isFirstPass) {
float distance = params.distance;
float rA, rB;
Point3f ptA;
Point3f ptY0 = new Point3f(), ptZ0 = new Point3f();
Point3i pt0 = new Point3i(), pt1 = new Point3i();
float value = Float.MAX_VALUE;
if (Logger.debugging)
Logger.startTimer();
for (int x = 0; x < nPointsX; ++x)
for (int y = 0; y < nPointsY; ++y)
for (int z = 0; z < nPointsZ; ++z)
voxelData[x][y][z] = value;
if (dataType == Parameters.SURFACE_NOMAP)
return;
int atomCount = myAtomCount;
float maxRadius = 0;
float r0 = (isFirstPass && isCavity ? cavityRadius : 0);
boolean isWithin = (isFirstPass && distance != Float.MAX_VALUE && point != null);
AtomIndexIterator iter = (doCalculateTroughs ?
atomDataServer.getSelectedAtomIterator(bsMySelected, true, false) : null);
for (int iAtom = 0; iAtom < atomCount; iAtom++) {
ptA = atomXyz[iAtom];
rA = atomRadius[iAtom];
if (rA > maxRadius)
maxRadius = rA;
if (isWithin && ptA.distance(point) > distance + rA + 0.5)
continue;
boolean isNearby = (iAtom >= firstNearbyAtom);
float rA0 = rA + r0;
setGridLimitsForAtom(ptA, rA0, pt0, pt1);
volumeData.voxelPtToXYZ(pt0.x, pt0.y, pt0.z, ptXyzTemp);
for (int i = pt0.x; i < pt1.x; i++) {
ptY0.set(ptXyzTemp);
for (int j = pt0.y; j < pt1.y; j++) {
ptZ0.set(ptXyzTemp);
for (int k = pt0.z; k < pt1.z; k++) {
float v = ptXyzTemp.distance(ptA) - rA;
if ((r0 == 0 || v <= rA0) && v < voxelData[i][j][k]) {
voxelData[i][j][k] = (isNearby || isWithin
&& ptXyzTemp.distance(point) > distance ? Float.NaN : v);
}
ptXyzTemp.add(volumetricVectors[2]);
}
ptXyzTemp.set(ptZ0);
ptXyzTemp.add(volumetricVectors[1]);
}
ptXyzTemp.set(ptY0);
ptXyzTemp.add(volumetricVectors[0]);
}
}
if (isCavity && isFirstPass)
return;
if (doCalculateTroughs) {
Point3i ptA0 = new Point3i();
Point3i ptB0 = new Point3i();
Point3i ptA1 = new Point3i();
Point3i ptB1 = new Point3i();
for (int iAtom = 0; iAtom < firstNearbyAtom - 1; iAtom++)
if (atomNo[iAtom] > 0) {
ptA = atomXyz[iAtom];
rA = atomRadius[iAtom] + solventRadius;
int iatomA = atomIndex[iAtom];