private void processIdentBlock(int lineCount, IAtomContainer container) throws IOException {
String identifier = "";
for (int i = 0; i < lineCount; i++) {
identifier = identifier + input.readLine().trim();
}
container.setID(identifier);
}
private synchronized void UpdateMapping() throws Exception {
boolean[][] FlagMatrix = winner.getFlagMatrix();
ReactionContainer reactionStructureInformationContainer = mh.getReactionContainer();
for (int iIndex = 0; iIndex < reactionStructureInformationContainer.getEductCount(); iIndex++) {
for (int jIndex = 0;
jIndex < reactionStructureInformationContainer.getProductCount();
jIndex++) {
int substrateIndex = iIndex;
int productIndex = jIndex;
IAtomContainer ac1 = reactionStructureInformationContainer.getEduct(substrateIndex);
IAtomContainer ac2 = reactionStructureInformationContainer.getProduct(productIndex);
if (FlagMatrix[substrateIndex][productIndex]) {
// updateFlag=true;
BitSet a_BitSet =
reactionStructureInformationContainer.getFingerPrintofEduct(
substrateIndex); // a_BitSet=EDUCT
BitSet b_BitSet =
reactionStructureInformationContainer.getFingerPrintofProduct(
productIndex); // b_BitSet=PRODUCT
/*
* Choose this function if you want JMCS to run
*/
ac1.setID(this.eductList.get(substrateIndex));
ac2.setID(this.productList.get(productIndex));
IGraphMatching graphMatching =
new GraphMatching(reactionName, ac1, ac2, _dirSuffix, removeHydrogen);
boolean mcsMatch =
graphMatching.mcsMatch(
mh, removeHydrogen, substrateIndex, productIndex, a_BitSet, b_BitSet);
if (DEBUG) {
out.println(
"Mol Size E: " + ac1.getAtomCount() + " , Mol Size P: " + ac2.getAtomCount());
}
if (mcsMatch) {
if (DEBUG) {
out.println(eductList.get(substrateIndex) + " <=> " + productList.get(productIndex));
}
delta += graphMatching.removeMatchedAtomsAndUpdateAAM(reaction);
List<MolMapping> rMap =
getReactionMolMapping()
.getMapping(
reactionName,
this.eductList.get(substrateIndex),
this.productList.get(productIndex));
for (MolMapping map : rMap) {
map.setReactionMapping(true);
IAtomContainer mol = graphMatching.getMatchedPart();
mol = canonLabeler.getCanonicalMolecule(mol);
CDKSMILES cdkSmiles = new CDKSMILES(mol, true, false);
map.setMatchedSMILES(cdkSmiles.getCanonicalSMILES(), ++stepIndex);
}
}
IAtomContainer remainingEduct = graphMatching.getRemainingEduct();
IAtomContainer remainingProduct = graphMatching.getRemainingProduct();
reactionStructureInformationContainer.putEduct(substrateIndex, remainingEduct);
reactionStructureInformationContainer.putProduct(productIndex, remainingProduct);
reactionStructureInformationContainer.setEductModified(substrateIndex, true);
reactionStructureInformationContainer.setProductModified(productIndex, true);
}
}
}
}
/**
* 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...");
}