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();
}
public void setSymmetryOperator(String xyz) {
if (ignoreFileSymmetryOperators) return;
atomSetCollection.setLatticeCells(
latticeCells, applySymmetryToBonds, doPackUnitCell, supercell);
if (!atomSetCollection.addSpaceGroupOperation(xyz))
Logger.warn("Skipping symmetry operation " + xyz);
iHaveSymmetryOperators = true;
}
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();
}
}
