/**
* Procedure required by the CDOInterface. This function is only supposed to be called by the JCFL
* library
*/
public void endObject(String objectType) {
logger.debug("END: " + objectType);
if (objectType.equals("Molecule")) {
eventReader.fireFrameRead();
clearData();
} else if (objectType.equals("Atom")) {
currentMolecule.addAtom(currentAtom);
} else if (objectType.equals("Bond")) {
logger.debug("Bond(" + bond_id + "): " + bond_a1 + ", " + bond_a2 + ", " + bond_order);
if (bond_a1 > currentMolecule.getAtomCount() || bond_a2 > currentMolecule.getAtomCount()) {
logger.error(
"Cannot add bond between at least one non-existant atom: "
+ bond_a1
+ " and "
+ bond_a2);
} else {
IAtom a1 = currentMolecule.getAtom(bond_a1);
IAtom a2 = currentMolecule.getAtom(bond_a2);
IBond b = builder.newBond(a1, a2, bond_order);
if (bond_id != null) b.setID(bond_id);
if (bond_stereo != -99) {
b.setStereo(bond_stereo);
}
currentMolecule.addBond(b);
}
}
}
public Object clone() throws CloneNotSupportedException {
Object clone = null;
try {
clone = super.clone();
} catch (Exception exception) {
logger.error("Could not clone DebugAtomContainer: " + exception.getMessage(), exception);
logger.debug(exception);
}
return clone;
}
private IChemFile readChemFile() throws CDKException {
IChemSequence seq = file.getBuilder().newChemSequence();
IChemModel model = file.getBuilder().newChemModel();
IMoleculeSet containerSet = file.getBuilder().newMoleculeSet();
IMolecule container = file.getBuilder().newMolecule();
int lineNumber = 0;
try {
String line = input.readLine();
while (input.ready() && line != null) {
logger.debug((lineNumber++) + ": ", line);
String command = null;
if (isCommand(line)) {
command = getCommand(line);
int lineCount = getContentLinesCount(line);
if ("ATOMS".equals(command)) {
processAtomsBlock(lineCount, container);
} else if ("BONDS".equals(command)) {
processBondsBlock(lineCount, container);
} else if ("IDENT".equals(command)) {
processIdentBlock(lineCount, container);
} else if ("NAME".equals(command)) {
processNameBlock(lineCount, container);
} else {
// skip lines
logger.warn("Dropping block: ", command);
for (int i = 0; i < lineCount; i++) input.readLine();
}
} else {
logger.warn("Unexpected content at line: ", lineNumber);
}
line = input.readLine();
}
containerSet.addAtomContainer(container);
model.setMoleculeSet(containerSet);
seq.addChemModel(model);
file.addChemSequence(seq);
} catch (Exception exception) {
String message = "Error while parsing CTX file: " + exception.getMessage();
logger.error(message);
logger.debug(exception);
throw new CDKException(message, exception);
}
return file;
}
/**
* Choose any possible quadruple of the set of atoms in ac and establish all of the possible
* bonding schemes according to Faulon's equations.
*/
public static List sample(IMolecule ac) {
logger.debug("RandomGenerator->mutate() Start");
List structures = new ArrayList();
int nrOfAtoms = ac.getAtomCount();
double a11 = 0, a12 = 0, a22 = 0, a21 = 0;
double b11 = 0, lowerborder = 0, upperborder = 0;
double b12 = 0;
double b21 = 0;
double b22 = 0;
double[] cmax = new double[4];
double[] cmin = new double[4];
IAtomContainer newAc = null;
IAtom ax1 = null, ax2 = null, ay1 = null, ay2 = null;
IBond b1 = null, b2 = null, b3 = null, b4 = null;
// int[] choices = new int[3];
/* We need at least two non-zero bonds in order to be successful */
int nonZeroBondsCounter = 0;
for (int x1 = 0; x1 < nrOfAtoms; x1++) {
for (int x2 = x1 + 1; x2 < nrOfAtoms; x2++) {
for (int y1 = x2 + 1; y1 < nrOfAtoms; y1++) {
for (int y2 = y1 + 1; y2 < nrOfAtoms; y2++) {
nonZeroBondsCounter = 0;
ax1 = ac.getAtom(x1);
ay1 = ac.getAtom(y1);
ax2 = ac.getAtom(x2);
ay2 = ac.getAtom(y2);
/* Get four bonds for these four atoms */
b1 = ac.getBond(ax1, ay1);
if (b1 != null) {
a11 = BondManipulator.destroyBondOrder(b1.getOrder());
nonZeroBondsCounter++;
} else {
a11 = 0;
}
b2 = ac.getBond(ax1, ay2);
if (b2 != null) {
a12 = BondManipulator.destroyBondOrder(b2.getOrder());
nonZeroBondsCounter++;
} else {
a12 = 0;
}
b3 = ac.getBond(ax2, ay1);
if (b3 != null) {
a21 = BondManipulator.destroyBondOrder(b3.getOrder());
nonZeroBondsCounter++;
} else {
a21 = 0;
}
b4 = ac.getBond(ax2, ay2);
if (b4 != null) {
a22 = BondManipulator.destroyBondOrder(b4.getOrder());
nonZeroBondsCounter++;
} else {
a22 = 0;
}
if (nonZeroBondsCounter > 1) {
/* Compute the range for b11 (see Faulons formulae for details) */
cmax[0] = 0;
cmax[1] = a11 - a22;
cmax[2] = a11 + a12 - 3;
cmax[3] = a11 + a21 - 3;
cmin[0] = 3;
cmin[1] = a11 + a12;
cmin[2] = a11 + a21;
cmin[3] = a11 - a22 + 3;
lowerborder = MathTools.max(cmax);
upperborder = MathTools.min(cmin);
for (b11 = lowerborder; b11 <= upperborder; b11++) {
if (b11 != a11) {
b12 = a11 + a12 - b11;
b21 = a11 + a21 - b11;
b22 = a22 - a11 + b11;
logger.debug("Trying atom combination : " + x1 + ":" + x2 + ":" + y1 + ":" + y2);
try {
newAc = (IAtomContainer) ac.clone();
change(newAc, x1, y1, x2, y2, b11, b12, b21, b22);
if (ConnectivityChecker.isConnected(newAc)) {
structures.add(newAc);
} else {
logger.debug("not connected");
}
} catch (CloneNotSupportedException e) {
logger.error("Cloning exception: " + e.getMessage());
logger.debug(e);
}
}
}
}
}
}
}
}
return structures;
}
/**
* Procedure required by the CDOInterface. This function is only supposed to be called by the JCFL
* library
*/
public void setObjectProperty(String objectType, String propertyType, String propertyValue) {
logger.debug("objectType: " + objectType);
logger.debug("propType: " + propertyType);
logger.debug("property: " + propertyValue);
if (objectType == null) {
logger.error("Cannot add property for null object");
return;
}
if (propertyType == null) {
logger.error("Cannot add property for null property type");
return;
}
if (propertyValue == null) {
logger.warn("Will not add null property");
return;
}
if (objectType.equals("Molecule")) {
if (propertyType.equals("id")) {
currentMolecule.setID(propertyValue);
} else if (propertyType.equals("inchi")) {
currentMolecule.setProperty("iupac.nist.chemical.identifier", propertyValue);
}
} else if (objectType.equals("PseudoAtom")) {
if (propertyType.equals("label")) {
if (!(currentAtom instanceof IPseudoAtom)) {
currentAtom = builder.newPseudoAtom(currentAtom);
}
((IPseudoAtom) currentAtom).setLabel(propertyValue);
}
} else if (objectType.equals("Atom")) {
if (propertyType.equals("type")) {
if (propertyValue.equals("R") && !(currentAtom instanceof IPseudoAtom)) {
currentAtom = builder.newPseudoAtom(currentAtom);
}
currentAtom.setSymbol(propertyValue);
} else if (propertyType.equals("x2")) {
Point2d coord = currentAtom.getPoint2d();
if (coord == null) coord = new Point2d();
coord.x = Double.parseDouble(propertyValue);
currentAtom.setPoint2d(coord);
} else if (propertyType.equals("y2")) {
Point2d coord = currentAtom.getPoint2d();
if (coord == null) coord = new Point2d();
coord.y = Double.parseDouble(propertyValue);
currentAtom.setPoint2d(coord);
} else if (propertyType.equals("x3")) {
Point3d coord = currentAtom.getPoint3d();
if (coord == null) coord = new Point3d();
coord.x = Double.parseDouble(propertyValue);
currentAtom.setPoint3d(coord);
} else if (propertyType.equals("y3")) {
Point3d coord = currentAtom.getPoint3d();
if (coord == null) coord = new Point3d();
coord.y = Double.parseDouble(propertyValue);
currentAtom.setPoint3d(coord);
} else if (propertyType.equals("z3")) {
Point3d coord = currentAtom.getPoint3d();
if (coord == null) coord = new Point3d();
coord.z = Double.parseDouble(propertyValue);
currentAtom.setPoint3d(coord);
} else if (propertyType.equals("xFract")) {
Point3d coord = currentAtom.getFractionalPoint3d();
if (coord == null) coord = new Point3d();
coord.x = Double.parseDouble(propertyValue);
currentAtom.setFractionalPoint3d(coord);
} else if (propertyType.equals("yFract")) {
Point3d coord = currentAtom.getFractionalPoint3d();
if (coord == null) coord = new Point3d();
coord.y = Double.parseDouble(propertyValue);
currentAtom.setFractionalPoint3d(coord);
} else if (propertyType.equals("zFract")) {
Point3d coord = currentAtom.getFractionalPoint3d();
if (coord == null) coord = new Point3d();
coord.z = Double.parseDouble(propertyValue);
currentAtom.setFractionalPoint3d(coord);
} else if (propertyType.equals("formalCharge")) {
currentAtom.setFormalCharge(Integer.parseInt(propertyValue));
} else if (propertyType.equals("charge") || propertyType.equals("partialCharge")) {
currentAtom.setCharge(Double.parseDouble(propertyValue));
} else if (propertyType.equals("hydrogenCount")) {
currentAtom.setHydrogenCount(Integer.parseInt(propertyValue));
} else if (propertyType.equals("dictRef")) {
currentAtom.setProperty("org.openscience.cdk.dict", propertyValue);
} else if (propertyType.equals("atomicNumber")) {
currentAtom.setAtomicNumber(Integer.parseInt(propertyValue));
} else if (propertyType.equals("massNumber")) {
currentAtom.setMassNumber((int) Double.parseDouble(propertyValue));
} else if (propertyType.equals("id")) {
logger.debug("id: ", propertyValue);
currentAtom.setID(propertyValue);
atomEnumeration.put(propertyValue, numberOfAtoms);
}
} else if (objectType.equals("Bond")) {
if (propertyType.equals("atom1")) {
bond_a1 = Integer.parseInt(propertyValue);
} else if (propertyType.equals("atom2")) {
bond_a2 = Integer.parseInt(propertyValue);
} else if (propertyType.equals("id")) {
logger.debug("id: " + propertyValue);
bond_id = propertyValue;
} else if (propertyType.equals("order")) {
try {
Double order = Double.parseDouble(propertyValue);
if (order == 1.0) {
bond_order = IBond.Order.SINGLE;
} else if (order == 2.0) {
bond_order = IBond.Order.DOUBLE;
} else if (order == 3.0) {
bond_order = IBond.Order.TRIPLE;
} else if (order == 4.0) {
bond_order = IBond.Order.QUADRUPLE;
} else {
bond_order = IBond.Order.SINGLE;
}
} catch (Exception e) {
logger.error("Cannot convert to double: " + propertyValue);
bond_order = IBond.Order.SINGLE;
}
} else if (propertyType.equals("stereo")) {
if (propertyValue.equals("H")) {
bond_stereo = CDKConstants.STEREO_BOND_DOWN;
} else if (propertyValue.equals("W")) {
bond_stereo = CDKConstants.STEREO_BOND_UP;
}
}
}
logger.debug("Object property set...");
}