@Override
public void initShape() {
super.initShape();
myType = "axes";
font3d = g3d.getFont3D(JmolConstants.AXES_DEFAULT_FONTSIZE);
int axesMode = viewer.getAxesMode();
if (fixedOrigin == null) originPoint.set(0, 0, 0);
else originPoint.set(fixedOrigin);
if (axesMode == JmolConstants.AXES_MODE_UNITCELL && modelSet.getCellInfos() != null) {
SymmetryInterface unitcell = viewer.getCurrentUnitCell();
if (unitcell != null && unitcell.haveUnitCell()) {
Point3f[] vectors = unitcell.getUnitCellVertices();
Point3f offset = unitcell.getCartesianOffset();
if (fixedOrigin == null) {
originPoint.set(offset);
} else {
offset = fixedOrigin;
}
scale = viewer.getAxesScale() / 2f;
// We must divide by 2 because that is the default for ALL axis types.
// Not great, but it will have to do.
axisPoints[0].scaleAdd(scale, vectors[4], offset);
axisPoints[1].scaleAdd(scale, vectors[2], offset);
axisPoints[2].scaleAdd(scale, vectors[1], offset);
return;
}
} else if (axesMode == JmolConstants.AXES_MODE_BOUNDBOX) {
if (fixedOrigin == null) originPoint.set(viewer.getBoundBoxCenter());
}
setScale(viewer.getAxesScale() / 2f);
}
public void applySymmetryAndSetTrajectory() throws Exception {
if (iHaveUnitCell && doCheckUnitCell) {
atomSetCollection.setCoordinatesAreFractional(iHaveFractionalCoordinates);
atomSetCollection.setNotionalUnitCell(
notionalUnitCell, matUnitCellOrientation, unitCellOffset);
atomSetCollection.setAtomSetSpaceGroupName(spaceGroup);
atomSetCollection.setSymmetryRange(symmetryRange);
if (doConvertToFractional || fileCoordinatesAreFractional) {
atomSetCollection.setLatticeCells(
latticeCells, applySymmetryToBonds, doPackUnitCell, supercell);
if (ignoreFileSpaceGroupName || !iHaveSymmetryOperators) {
if (!merging || symmetry == null) getSymmetry();
if (symmetry.createSpaceGroup(
desiredSpaceGroupIndex,
(spaceGroup.indexOf("!") >= 0 ? "P1" : spaceGroup),
notionalUnitCell)) {
atomSetCollection.setAtomSetSpaceGroupName(symmetry.getSpaceGroupName());
atomSetCollection.applySymmetry(symmetry);
}
} else {
atomSetCollection.applySymmetry();
}
}
if (iHaveFractionalCoordinates && merging && symmetry != null) {
// when merging (with appendNew false), we must return cartesians
atomSetCollection.toCartesian(symmetry);
atomSetCollection.setCoordinatesAreFractional(false);
// We no longer allow merging of multiple-model files
// when the file to be appended has fractional coordinates and vibrations
addVibrations = false;
}
}
if (isTrajectory) atomSetCollection.setTrajectory();
initializeSymmetry();
}
private void checkUnitCellOffset() {
if (symmetry == null || fileOffsetFractional == null) return;
fileOffset.set(fileOffsetFractional);
if (unitCellOffsetFractional != fileCoordinatesAreFractional) {
if (unitCellOffsetFractional) symmetry.toCartesian(fileOffset, false);
else symmetry.toFractional(fileOffset, false);
}
}
public void setAtomCoord(Atom atom) {
// fileScaling is used by the PLOT command to
// put data into PDB format, preserving name/residue information,
// and still get any xyz data into the allotted column space.
if (fileScaling != null) {
atom.x = atom.x * fileScaling.x + fileOffset.x;
atom.y = atom.y * fileScaling.y + fileOffset.y;
atom.z = atom.z * fileScaling.z + fileOffset.z;
}
if (doConvertToFractional && !fileCoordinatesAreFractional && symmetry != null) {
if (!symmetry.haveUnitCell()) symmetry.setUnitCell(notionalUnitCell);
symmetry.toFractional(atom, false);
iHaveFractionalCoordinates = true;
}
doCheckUnitCell = true;
}
private void setSymmetry(boolean setOperators) {
double[][] a;
// Part 1: Get sigma_nu
// van Smaalen, p. 92.
Logger.info("[subsystem " + code + "]");
Matrix winv = w.inverse();
Logger.info("w=" + w);
Logger.info("w_inv=" + winv);
// w33 w3d van Smaalen, p. 94, Eqn. 4.15
// w =
// wd3 wdd
Matrix w33 = w.getSubmatrix(0, 0, 3, 3);
Matrix wd3 = w.getSubmatrix(3, 0, d, 3);
Matrix w3d = w.getSubmatrix(0, 3, 3, d);
Matrix wdd = w.getSubmatrix(3, 3, d, d);
Matrix sigma = msRdr.getSigma();
// Eqn. 4.16
Matrix sigma_nu = wdd.mul(sigma).add(wd3).mul(w3d.mul(sigma).add(w33).inverse());
Matrix tFactor = wdd.sub(sigma_nu.mul(w3d));
Logger.info("sigma_nu = " + sigma_nu);
// Part 2: Get the new unit cell and symmetry operators
SymmetryInterface s0 = msRdr.cr.asc.getSymmetry();
V3[] vu43 = s0.getUnitCellVectors();
V3[] vr43 = reciprocalsOf(vu43);
// using full matrix math here:
//
// mar3 = just 3x3 matrix of ai* (a*, b*, c*)
// mard3 = full (3+d)x3 matrix of ai* (a*, b*, c*, x4*, x5*,....)
// = [ mard3 | sigma * mard3 ]
//
Matrix mard3 = new Matrix(null, 3 + d, 3);
Matrix mar3 = new Matrix(null, 3, 3);
double[][] mard3a = mard3.getArray();
double[][] mar3a = mar3.getArray();
for (int i = 0; i < 3; i++)
mard3a[i] = mar3a[i] = new double[] {vr43[i + 1].x, vr43[i + 1].y, vr43[i + 1].z};
Matrix sx = sigma.mul(mar3);
a = sx.getArray();
for (int i = 0; i < d; i++) mard3a[i + 3] = a[i];
a = w.mul(mard3).getArray();
// back to vector notation and direct lattice
V3[] uc_nu = new V3[4];
uc_nu[0] = vu43[0]; // origin
for (int i = 0; i < 3; i++)
uc_nu[i + 1] = V3.new3((float) a[i][0], (float) a[i][1], (float) a[i][2]);
uc_nu = reciprocalsOf(uc_nu);
symmetry =
((Symmetry) msRdr.cr.getInterface("org.jmol.symmetry.Symmetry"))
.getUnitCell(uc_nu, false, null);
modMatrices = new Matrix[] {sigma_nu, tFactor};
if (!setOperators) return;
isFinalized = true;
// Part 3: Transform the operators
//
Logger.info("unit cell parameters: " + symmetry.getUnitCellInfo());
symmetry.createSpaceGroup(-1, "[subsystem " + code + "]", new Lst<M4>());
int nOps = s0.getSpaceGroupOperationCount();
for (int iop = 0; iop < nOps; iop++) {
Matrix rv = s0.getOperationRsVs(iop);
Matrix r0 = rv.getRotation();
Matrix v0 = rv.getTranslation();
Matrix r = w.mul(r0).mul(winv);
Matrix v = w.mul(v0);
String code = this.code;
if (isMixed(r)) {
// This operator mixes x4,x5... into x1,x2,x3.
// It is not a pure operation. Instead, it correlates one
// subsystem with another. Our job is to find the other
// subsystem "j" that will satisfy the following condition:
//
// (Wj R Wi_inv).submatrix(0,3,3,d) == all_zeros
//
for (Entry<String, Subsystem> e : msRdr.htSubsystems.entrySet()) {
Subsystem ss = e.getValue();
if (ss == this) continue;
Matrix rj = ss.w.mul(r0).mul(winv);
if (!isMixed(rj)) {
// We have found the corresponding subsystem.
// The result of this operation will be in other system,
// and the operation itself will be used to rotate the modulation.
// ss.code will be used to mark any atom created by this operation as
// part of the other system.
r = rj;
v = ss.w.mul(v0);
code = ss.code;
break;
}
}
}
String jf = symmetry.addOp(code, r, v, sigma_nu);
Logger.info(
this.code + "." + (iop + 1) + (this.code.equals(code) ? " " : ">" + code + " ") + jf);
}
}
public void checkLineForScript() {
if (line.indexOf("Jmol") >= 0) {
if (line.indexOf("Jmol PDB-encoded data") >= 0) {
atomSetCollection.setAtomSetCollectionAuxiliaryInfo("jmolData", line);
if (!line.endsWith("#noautobond")) line += "#noautobond";
}
if (line.indexOf("Jmol data min") >= 0) {
Logger.info(line);
// The idea here is to use a line such as the following:
//
// REMARK 6 Jmol data min = {-1 -1 -1} max = {1 1 1}
// unScaledXyz = xyz / {10 10 10} + {0 0 0}
// plotScale = {100 100 100}
//
// to pass on to Jmol how to graph non-molecular data.
// The format allows for the actual data to be linearly transformed
// so that it fits into the PDB format for x, y, and z coordinates.
// This adapter will then unscale the data and also pass on to
// Jmol the unit cell equivalent that takes the actual data (which
// will be considered the fractional coordinates) to Jmol coordinates,
// which will be a cube centered at {0 0 0} and ranging from {-100 -100 -100}
// to {100 100 100}.
//
// Jmol 12.0.RC23 uses this to pass through the adapter a quaternion,
// ramachandran, or other sort of plot.
float[] data = new float[15];
parseStringInfestedFloatArray(
line.substring(10).replace('=', ' ').replace('{', ' ').replace('}', ' '), data);
Point3f minXYZ = new Point3f(data[0], data[1], data[2]);
Point3f maxXYZ = new Point3f(data[3], data[4], data[5]);
fileScaling = new Point3f(data[6], data[7], data[8]);
fileOffset = new Point3f(data[9], data[10], data[11]);
Point3f plotScale = new Point3f(data[12], data[13], data[14]);
if (plotScale.x <= 0) plotScale.x = 100;
if (plotScale.y <= 0) plotScale.y = 100;
if (plotScale.z <= 0) plotScale.z = 100;
if (fileScaling.y == 0) fileScaling.y = 1;
if (fileScaling.z == 0) fileScaling.z = 1;
setFractionalCoordinates(true);
latticeCells = new int[3];
atomSetCollection.setLatticeCells(latticeCells, true, false, supercell);
setUnitCell(
plotScale.x * 2 / (maxXYZ.x - minXYZ.x),
plotScale.y * 2 / (maxXYZ.y - minXYZ.y),
plotScale.z * 2 / (maxXYZ.z == minXYZ.z ? 1 : maxXYZ.z - minXYZ.z),
90,
90,
90);
/*
unitCellOffset = new Point3f(minXYZ);
symmetry.toCartesian(unitCellOffset);
System.out.println(unitCellOffset);
unitCellOffset = new Point3f(maxXYZ);
symmetry.toCartesian(unitCellOffset);
System.out.println(unitCellOffset);
*/
unitCellOffset = new Point3f(plotScale);
unitCellOffset.scale(-1);
symmetry.toFractional(unitCellOffset, false);
unitCellOffset.scaleAdd(-1f, minXYZ, unitCellOffset);
symmetry.setUnitCellOffset(unitCellOffset);
/*
Point3f pt = new Point3f(minXYZ);
symmetry.toCartesian(pt);
System.out.println("ASCR minXYZ " + pt);
pt.set(maxXYZ);
symmetry.toCartesian(pt);
System.out.println("ASCR maxXYZ " + pt);
*/
atomSetCollection.setAtomSetCollectionAuxiliaryInfo(
"jmolDataScaling", new Point3f[] {minXYZ, maxXYZ, plotScale});
}
}
if (line.endsWith("#noautobond")) {
line = line.substring(0, line.lastIndexOf('#')).trim();
atomSetCollection.setNoAutoBond();
}
int pt = line.indexOf("jmolscript:");
if (pt >= 0) {
String script = line.substring(pt + 11, line.length());
if (script.indexOf("#") >= 0) {
script = script.substring(0, script.indexOf("#"));
}
addJmolScript(script);
line = line.substring(0, pt).trim();
}
}