private Object finish() {
String s = (String) htParams.get("loadState");
atomSetCollection.setAtomSetCollectionAuxiliaryInfo("loadState", s == null ? "" : s);
s = (String) htParams.get("smilesString");
if (s != null) atomSetCollection.setAtomSetCollectionAuxiliaryInfo("smilesString", s);
if (!htParams.containsKey("templateAtomCount"))
htParams.put("templateAtomCount", Integer.valueOf(atomSetCollection.getAtomCount()));
if (htParams.containsKey("bsFilter"))
htParams.put(
"filteredAtomCount",
Integer.valueOf(BitSetUtil.cardinalityOf((BitSet) htParams.get("bsFilter"))));
if (!calculationType.equals("?"))
atomSetCollection.setAtomSetCollectionAuxiliaryInfo("calculationType", calculationType);
String name = atomSetCollection.getFileTypeName();
String fileType = name;
if (fileType.indexOf("(") >= 0) fileType = fileType.substring(0, fileType.indexOf("("));
for (int i = atomSetCollection.getAtomSetCount(); --i >= 0; ) {
atomSetCollection.setAtomSetAuxiliaryInfo("fileName", filePath, i);
atomSetCollection.setAtomSetAuxiliaryInfo("fileType", fileType, i);
}
atomSetCollection.freeze(reverseModels);
if (atomSetCollection.errorMessage != null)
return atomSetCollection.errorMessage + "\nfor file " + filePath + "\ntype " + name;
if ((atomSetCollection.bsAtoms == null
? atomSetCollection.getAtomCount()
: atomSetCollection.bsAtoms.cardinality())
== 0
&& fileType.indexOf("DataOnly") < 0)
return "No atoms found\nfor file " + filePath + "\ntype " + name;
return atomSetCollection;
}
public void setIsPDB() {
atomSetCollection.setGlobalBoolean(AtomSetCollection.GLOBAL_ISPDB);
atomSetCollection.setAtomSetAuxiliaryInfo("isPDB", Boolean.TRUE);
if (htParams.get("pdbNoHydrogens") != null)
atomSetCollection.setAtomSetCollectionAuxiliaryInfo(
"pdbNoHydrogens", htParams.get("pdbNoHydrogens"));
}
protected void addSiteScript(String script) {
if (siteScript == null) siteScript = "";
else if (!siteScript.endsWith(";")) siteScript += ";";
siteScript += script;
atomSetCollection.setAtomSetCollectionAuxiliaryInfo(
"sitescript", siteScript); // checked in ScriptEvaluator.load()
}
protected void addJmolScript(String script) {
Logger.info("#jmolScript: " + script);
if (previousScript == null) previousScript = "";
else if (!previousScript.endsWith(";")) previousScript += ";";
previousScript += script;
atomSetCollection.setAtomSetCollectionAuxiliaryInfo("jmolscript", previousScript);
}
public void setTransform(
float x1, float y1, float z1, float x2, float y2, float z2, float x3, float y3, float z3) {
if (matrixRotate != null || !doSetOrientation) return;
matrixRotate = new Matrix3f();
Vector3f v = new Vector3f();
// rows in Sygress/CAChe and Spartan become columns here
v.set(x1, y1, z1);
v.normalize();
matrixRotate.setColumn(0, v);
v.set(x2, y2, z2);
v.normalize();
matrixRotate.setColumn(1, v);
v.set(x3, y3, z3);
v.normalize();
matrixRotate.setColumn(2, v);
atomSetCollection.setAtomSetCollectionAuxiliaryInfo(
"defaultOrientationMatrix", new Matrix3f(matrixRotate));
// first two matrix column vectors define quaternion X and XY plane
Quaternion q = new Quaternion(matrixRotate);
atomSetCollection.setAtomSetCollectionAuxiliaryInfo("defaultOrientationQuaternion", q);
Logger.info("defaultOrientationMatrix = " + matrixRotate);
}
protected void set2D() {
// MOL and JME
atomSetCollection.setAtomSetCollectionAuxiliaryInfo("is2D", Boolean.TRUE);
if (!checkFilter("NOMIN"))
atomSetCollection.setAtomSetCollectionAuxiliaryInfo("doMinimize", Boolean.TRUE);
}
protected void finalizeReader() throws Exception {
applySymmetryAndSetTrajectory();
if (loadNote.length() > 0)
atomSetCollection.setAtomSetCollectionAuxiliaryInfo("modelLoadNote", loadNote.toString());
if (doCentralize) atomSetCollection.centralize();
}
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();
}
}
