public void setIsPDB() {
atomSetCollection.setGlobalBoolean(AtomSetCollection.GLOBAL_ISPDB);
atomSetCollection.setAtomSetAuxiliaryInfo("isPDB", Boolean.TRUE);
if (htParams.get("pdbNoHydrogens") != null)
atomSetCollection.setAtomSetCollectionAuxiliaryInfo(
"pdbNoHydrogens", htParams.get("pdbNoHydrogens"));
}
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;
}
private void setError(Throwable e) {
e.printStackTrace();
if (line == null)
atomSetCollection.errorMessage =
"Unexpected end of file after line " + --ptLine + ":\n" + prevline;
else
atomSetCollection.errorMessage =
"Error reading file at line " + ptLine + ":\n" + line + "\n" + e.getMessage();
}
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;
}
protected int cloneLastAtomSet(int atomCount, Point3f[] pts) throws Exception {
int lastAtomCount = atomSetCollection.getLastAtomSetAtomCount();
atomSetCollection.cloneLastAtomSet(atomCount, pts);
if (atomSetCollection.haveUnitCell) {
iHaveUnitCell = true;
doCheckUnitCell = true;
spaceGroup = previousSpaceGroup;
notionalUnitCell = previousUnitCell;
}
return lastAtomCount;
}
@SuppressWarnings("unchecked")
public void setMOData(Map<String, Object> moData) {
atomSetCollection.setAtomSetAuxiliaryInfo("moData", moData);
if (moData == null) return;
List<Map<String, Object>> orbitals = (List<Map<String, Object>>) moData.get("mos");
if (orbitals != null)
Logger.info(
orbitals.size()
+ " molecular orbitals read in model "
+ atomSetCollection.getAtomSetCount());
}
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);
}
/**
* @param atom
* @param iAtom
* @return true if we want this atom
*/
protected boolean filterAtom(Atom atom, int iAtom) {
if (!haveAtomFilter) return true;
// cif, mdtop, pdb, gromacs, pqr
boolean isOK = checkFilter(atom, filter1);
if (filter2 != null) isOK |= checkFilter(atom, filter2);
if (isOK && filterEveryNth) isOK = (((nFiltered++) % filterN) == 0);
bsFilter.set(iAtom >= 0 ? iAtom : atomSetCollection.getAtomCount(), isOK);
return isOK;
}
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 newAtomSet(String name) {
if (atomSetCollection.getCurrentAtomSetIndex() >= 0) {
atomSetCollection.newAtomSet();
atomSetCollection.setCollectionName(
"<collection of " + (atomSetCollection.getCurrentAtomSetIndex() + 1) + " models>");
} else {
atomSetCollection.setCollectionName(name);
}
atomSetCollection.setAtomSetAuxiliaryInfo(
"name", name, Math.max(0, atomSetCollection.getCurrentAtomSetIndex()));
}
protected void addSites(Map<String, Map<String, Object>> htSites) {
atomSetCollection.setAtomSetAuxiliaryInfo("pdbSites", htSites);
String sites = "";
for (Map.Entry<String, Map<String, Object>> entry : htSites.entrySet()) {
String name = entry.getKey();
Map<String, Object> htSite = entry.getValue();
char ch;
for (int i = name.length(); --i >= 0; )
if (!Character.isLetterOrDigit(ch = name.charAt(i)) && ch != '\'')
name = name.substring(0, i) + "_" + name.substring(i + 1);
// String seqNum = (String) htSite.get("seqNum");
String groups = (String) htSite.get("groups");
if (groups.length() == 0) continue;
addSiteScript("@site_" + name + " " + groups);
// addJmolScript("@" + seqNum + " " + groups);
addSiteScript("site_" + name + " = \"" + groups + "\".split(\",\")");
sites += (sites == "" ? "" : ",") + "site_" + name;
}
addSiteScript("site_list = \"" + sites + "\".split(\",\")");
}
/**
* Extracts a block of frequency data from a file. This block may be of two types -- either X Y Z
* across a row or each of X Y Z on a separate line. Data is presumed to be in fixed FORTRAN-like
* column format, not space-separated columns.
*
* @param iAtom0 the first atom to be assigned a frequency
* @param atomCount the number of atoms to be assigned
* @param modelAtomCount the number of atoms in each model
* @param ignore the frequencies to ignore because the user has selected only certain vibrations
* to be read or for whatever reason; length serves to set the number of frequencies to be
* read
* @param isWide when TRUE, this is a table that has X Y Z for each mode within the same row; when
* FALSE, this is a table that has X Y Z for each mode on a separate line.
* @param col0 the column in which data starts
* @param colWidth the width of the data columns
* @param atomIndexes an array either null or indicating exactly which atoms get the frequencies
* (used by CrystalReader)
* @param minLineLen
* @param minlineLen TODO
* @throws Exception
*/
protected void fillFrequencyData(
int iAtom0,
int atomCount,
int modelAtomCount,
boolean[] ignore,
boolean isWide,
int col0,
int colWidth,
int[] atomIndexes,
int minLineLen)
throws Exception {
boolean withSymmetry = (modelAtomCount != atomCount);
if (atomIndexes != null) atomCount = atomIndexes.length;
int nLines = (isWide ? atomCount : atomCount * 3);
int nFreq = ignore.length;
String[][] data = new String[nLines][];
fillDataBlock(data, col0, colWidth, minLineLen);
for (int i = 0, atomPt = 0; i < nLines; i++, atomPt++) {
String[] values = data[i];
String[] valuesY = (isWide ? null : data[++i]);
String[] valuesZ = (isWide ? null : data[++i]);
int dataPt = values.length - (isWide ? nFreq * 3 : nFreq) - 1;
for (int j = 0, jj = 0; jj < nFreq; jj++) {
++dataPt;
String x = values[dataPt];
if (x.charAt(0) == ')') // AMPAC reader!
x = x.substring(1);
float vx = parseFloat(x);
float vy = parseFloat(isWide ? values[++dataPt] : valuesY[dataPt]);
float vz = parseFloat(isWide ? values[++dataPt] : valuesZ[dataPt]);
if (ignore[jj]) continue;
int iAtom = (atomIndexes == null ? atomPt : atomIndexes[atomPt]);
if (iAtom < 0) continue;
if (Logger.debugging)
Logger.debug("atom " + iAtom + " vib" + j + ": " + vx + " " + vy + " " + vz);
atomSetCollection.addVibrationVector(
iAtom0 + modelAtomCount * j++ + iAtom, vx, vy, vz, withSymmetry);
}
}
}
public boolean doGetModel(int modelNumber, String title) {
if (title != null
&& nameRequired != null
&& nameRequired.length() > 0
&& title.toUpperCase().indexOf(nameRequired) < 0) return false;
// modelNumber is 1-based, but firstLastStep is 0-based
boolean isOK =
(bsModels == null
? desiredModelNumber < 1 || modelNumber == desiredModelNumber
: modelNumber > lastModelNumber
? false
: modelNumber > 0 && bsModels.get(modelNumber - 1)
|| haveModel
&& firstLastStep != null
&& firstLastStep[1] < 0
&& (firstLastStep[2] < 2
|| (modelNumber - 1 - firstLastStep[0]) % firstLastStep[2] == 0));
if (isOK && desiredModelNumber == 0) atomSetCollection.discardPreviousAtoms();
haveModel |= isOK;
if (isOK) doProcessLines = true;
return isOK;
}
BondIterator(AtomSetCollection atomSetCollection) {
bsAtoms = atomSetCollection.bsAtoms;
bonds = atomSetCollection.getBonds();
bondCount = atomSetCollection.getBondCount();
ibond = 0;
}
protected void finalizeReader() throws Exception {
applySymmetryAndSetTrajectory();
if (loadNote.length() > 0)
atomSetCollection.setAtomSetCollectionAuxiliaryInfo("modelLoadNote", loadNote.toString());
if (doCentralize) atomSetCollection.centralize();
}
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 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();
}
}
protected void set2D() {
// MOL and JME
atomSetCollection.setAtomSetCollectionAuxiliaryInfo("is2D", Boolean.TRUE);
if (!checkFilter("NOMIN"))
atomSetCollection.setAtomSetCollectionAuxiliaryInfo("doMinimize", Boolean.TRUE);
}
