private static void replaceReferencesWithClones(final IChemModel chemModel)
throws CDKException {
// we make references in products/reactants clones, since same compounds
// in different reactions need separate layout (different positions etc)
if (chemModel.getReactionSet() != null) {
for (final IReaction reaction : chemModel.getReactionSet()
.reactions()) {
int i = 0;
final IAtomContainerSet products = reaction.getProducts();
for (final IAtomContainer product : products.atomContainers()) {
try {
products.replaceAtomContainer(i, product.clone());
} catch (final CloneNotSupportedException e) {
}
i++;
}
i = 0;
final IAtomContainerSet reactants = reaction.getReactants();
for (final IAtomContainer reactant : reactants.atomContainers()) {
try {
reactants.replaceAtomContainer(i, reactant.clone());
} catch (final CloneNotSupportedException e) {
}
i++;
}
}
}
}
/** {@inheritDoc} */
@Override
@TestMethod("testEmptyReaction")
public IRenderingElement generate(IReaction reaction, RendererModel model) {
if (!model.getParameter(ShowReactionBoxes.class).getValue()) return null;
double separation =
model.getParameter(BondLength.class).getValue()
/ model.getParameter(Scale.class).getValue();
Rectangle2D totalBounds = BoundsCalculator.calculateBounds(reaction);
if (totalBounds == null) return null;
ElementGroup diagram = new ElementGroup();
Color foregroundColor =
model.getParameter(BasicSceneGenerator.ForegroundColor.class).getValue();
diagram.add(
new RectangleElement(
totalBounds.getMinX() - separation,
totalBounds.getMinY() - separation,
totalBounds.getMaxX() + separation,
totalBounds.getMaxY() + separation,
foregroundColor));
if (reaction.getID() != null) {
diagram.add(
new TextElement(
(totalBounds.getMinX() + totalBounds.getMaxX()) / 2,
totalBounds.getMinY() - separation,
reaction.getID(),
foregroundColor));
}
return diagram;
}
private double caclModelScale(IReaction rxn) {
List<IAtomContainer> mols = new ArrayList<>();
for (IAtomContainer mol : rxn.getReactants().atomContainers()) mols.add(mol);
for (IAtomContainer mol : rxn.getProducts().atomContainers()) mols.add(mol);
for (IAtomContainer mol : rxn.getAgents().atomContainers()) mols.add(mol);
return caclModelScale(mols);
}
private synchronized double calRelation(IReaction reaction, IMappingAlgorithm theory) {
try {
Map<Integer, IAtomContainer> educts =
synchronizedSortedMap(new TreeMap<Integer, IAtomContainer>());
for (int i = 0; i < reaction.getReactantCount(); i++) {
educts.put(i, reaction.getReactants().getAtomContainer(i));
}
Map<Integer, IAtomContainer> products =
synchronizedSortedMap(new TreeMap<Integer, IAtomContainer>());
for (int i = 0; i < reaction.getProductCount(); i++) {
products.put(i, reaction.getProducts().getAtomContainer(i));
}
GameTheoryMatrix EDSH = new GameTheoryMatrix(theory, reaction, removeHydrogen);
IGameTheory gameTheory = make(theory, reaction, removeHydrogen, educts, products, EDSH);
this.reactionBlastMolMapping = gameTheory.getReactionMolMapping();
EDSH.Clear();
return gameTheory.getDelta();
} catch (Exception e) {
logger.error(e);
return -1;
}
}
public String toString() {
StringBuffer buffer = new StringBuffer(32);
buffer.append("ReactionSet(");
buffer.append(this.hashCode());
buffer.append(", R=").append(getReactionCount()).append(", ");
for (IReaction reaction : reactions()) {
buffer.append(reaction.toString());
}
buffer.append(')');
return buffer.toString();
}
private static void setReactionIDs(final IChemModel chemModel) {
// we give all reactions an ID, in case they have none
// IDs are needed for handling in JCP
final IReactionSet reactionSet = chemModel.getReactionSet();
if (reactionSet != null) {
int i = 0;
for (final IReaction reaction : reactionSet.reactions()) {
if (reaction.getID() == null) {
reaction.setID("Reaction " + ++i);
}
}
}
}
// ~--- constructors -------------------------------------------------------
GameTheoryMin(
IReaction reaction,
boolean removeHydrogen,
Map<Integer, IAtomContainer> _educts,
Map<Integer, IAtomContainer> _products,
GameTheoryMatrix rpsh)
throws Exception {
if (DEBUG) {
out.println("I am MIN MIX");
}
this.canonLabeler = new SmilesMoleculeLabeller();
this.removeHydrogen = removeHydrogen;
this.reaction = reaction;
this.educts = _educts;
this.products = _products;
this.reactionName = reaction.getID();
this.eductList = synchronizedList(rpsh.getEductCounter());
this.productList = synchronizedList(rpsh.getProductCounter());
this.mh = rpsh.getMatrixHolder();
setReactionMolMapping(rpsh.getReactionMolMapping());
winner = new ChooseWinner(eductList, productList);
this._dirSuffix = super.getSuffix();
ReactionIsomorphismHandler RIH = new ReactionIsomorphismHandler(mh, eductList, productList);
if (RIH.getIsomorphismFlag()) {
// System.out.println("ISOMORPHISM");
mh = RIH.getMatrixHolder();
GenerateIsoMorphismMapping();
} else {
GenerateMapping(false);
}
}
private Bounds generateReactionConditions(IReaction chemObj, Color fg, double scale) {
String title = chemObj.getProperty(CDKConstants.REACTION_CONDITIONS);
if (title == null || title.isEmpty()) return new Bounds();
return new Bounds(
MarkedElement.markup(
StandardGenerator.embedText(font, title, fg, 1 / scale), "conditions"));
}
/** {@inheritDoc} */
@Override
@TestMethod("testEmptyReaction")
public IRenderingElement generate(IReaction reaction, RendererModel model) {
Rectangle2D totalBoundsReactants = BoundsCalculator.calculateBounds(reaction.getReactants());
Rectangle2D totalBoundsProducts = BoundsCalculator.calculateBounds(reaction.getProducts());
if (totalBoundsReactants == null || totalBoundsProducts == null) return null;
double separation =
model.getParameter(BondLength.class).getValue()
/ model.getParameter(Scale.class).getValue();
Color foregroundColor =
model.getParameter(BasicSceneGenerator.ForegroundColor.class).getValue();
return new ArrowElement(
totalBoundsReactants.getMaxX() + separation,
totalBoundsReactants.getCenterY(),
totalBoundsProducts.getMinX() - separation,
totalBoundsReactants.getCenterY(),
1 / model.getParameter(Scale.class).getValue(),
true,
foregroundColor);
}
@Override
public void store(IReaction reaction) {
String id = reaction.getID();
File file = new File(reactionDir, id + ".rxn");
try {
FileWriter writer = new FileWriter(file);
rxnWriter = new MDLV2000RXNWriter(writer);
// rxnWriter.setWriter(writer);
rxnWriter.write(reaction);
// writer.flush();
// writer.close();
rxnWriter.close();
} catch (CDKException | IOException e) {
e.printStackTrace();
}
}
/**
* @param removeHydrogen
* @param reaction
* @param algorithm
*/
public CalculationProcess(
boolean removeHydrogen, IReaction reaction, IMappingAlgorithm algorithm) {
/*
* This case handles rings cases where 6 membered ring reduces to 5 membered rings Example KEGG reaction R01432
* of Isomerase class
*/
super(reaction);
// System.out.println("I am CalculationProcess");
this.removeHydrogen = removeHydrogen;
logger.debug("\n|++++++++++++++++++++++++++++|");
logger.debug("Performing Atom-Atom Mapping ....... " + reaction.getID() + " .......");
logger.debug("\n|++++++++++++++++++++++++++++|");
this.algorithm = algorithm;
run();
}
@Test
public void testReaction() throws Exception {
String cmlString =
"<reaction>"
+ "<reactantList><reactant><molecule id='react'/></reactant></reactantList>"
+ "<productList><product><molecule id='product'/></product></productList>"
+ "<substanceList><substance><molecule id='water'/></substance></substanceList>"
+ "</reaction>";
IChemFile chemFile = parseCMLString(cmlString);
IReaction reaction = checkForSingleReactionFile(chemFile);
Assert.assertEquals(1, reaction.getReactantCount());
Assert.assertEquals(1, reaction.getProductCount());
Assert.assertEquals(1, reaction.getAgents().getMoleculeCount());
Assert.assertEquals("react", reaction.getReactants().getMolecule(0).getID());
Assert.assertEquals("product", reaction.getProducts().getMolecule(0).getID());
Assert.assertEquals("water", reaction.getAgents().getMolecule(0).getID());
}
private IReaction readReaction(IChemObjectBuilder builder) throws CDKException {
IReaction reaction = builder.newInstance(IReaction.class);
readLine(); // first line should be $RXN
readLine(); // second line
readLine(); // third line
readLine(); // fourth line
int reactantCount = 0;
int productCount = 0;
boolean foundCOUNTS = false;
while (isReady() && !foundCOUNTS) {
String command = readCommand();
if (command.startsWith("COUNTS")) {
StringTokenizer tokenizer = new StringTokenizer(command);
try {
tokenizer.nextToken();
reactantCount = Integer.valueOf(tokenizer.nextToken()).intValue();
logger.info("Expecting " + reactantCount + " reactants in file");
productCount = Integer.valueOf(tokenizer.nextToken()).intValue();
logger.info("Expecting " + productCount + " products in file");
} catch (Exception exception) {
logger.debug(exception);
throw new CDKException("Error while counts line of RXN file", exception);
}
foundCOUNTS = true;
} else {
logger.warn("Waiting for COUNTS line, but found: " + command);
}
}
// now read the reactants
for (int i = 1; i <= reactantCount; i++) {
StringBuffer molFile = new StringBuffer();
String announceMDLFileLine = readCommand();
if (!announceMDLFileLine.equals("BEGIN REACTANT")) {
String error = "Excepted start of reactant, but found: " + announceMDLFileLine;
logger.error(error);
throw new CDKException(error);
}
String molFileLine = "";
while (!molFileLine.endsWith("END REACTANT")) {
molFileLine = readLine();
molFile.append(molFileLine);
molFile.append(System.getProperty("line.separator"));
}
;
try {
// read MDL molfile content
MDLV3000Reader reader =
new MDLV3000Reader(new StringReader(molFile.toString()), super.mode);
IAtomContainer reactant =
(IAtomContainer) reader.read(builder.newInstance(IAtomContainer.class));
// add reactant
reaction.addReactant(reactant);
} catch (Exception exception) {
String error = "Error while reading reactant: " + exception.getMessage();
logger.error(error);
logger.debug(exception);
throw new CDKException(error, exception);
}
}
// now read the products
for (int i = 1; i <= productCount; i++) {
StringBuffer molFile = new StringBuffer();
String announceMDLFileLine = readCommand();
if (!announceMDLFileLine.equals("BEGIN PRODUCT")) {
String error = "Excepted start of product, but found: " + announceMDLFileLine;
logger.error(error);
throw new CDKException(error);
}
String molFileLine = "";
while (!molFileLine.endsWith("END PRODUCT")) {
molFileLine = readLine();
molFile.append(molFileLine);
molFile.append(System.getProperty("line.separator"));
}
;
try {
// read MDL molfile content
MDLV3000Reader reader = new MDLV3000Reader(new StringReader(molFile.toString()));
IAtomContainer product =
(IAtomContainer) reader.read(builder.newInstance(IAtomContainer.class));
// add product
reaction.addProduct(product);
} catch (Exception exception) {
String error = "Error while reading product: " + exception.getMessage();
logger.error(error);
logger.debug(exception);
throw new CDKException(error, exception);
}
}
return reaction;
}
/**
* Read a Reaction from a file in MDL RXN format
*
* @return The Reaction that was read from the MDL file.
*/
private IReaction readReaction(IChemObjectBuilder builder) throws CDKException {
IReaction reaction = builder.newReaction();
try {
input.readLine(); // first line should be $RXN
input.readLine(); // second line
input.readLine(); // third line
input.readLine(); // fourth line
} catch (IOException exception) {
logger.debug(exception);
throw new CDKException("Error while reading header of RXN file", exception);
}
int reactantCount = 0;
int productCount = 0;
try {
String countsLine = input.readLine();
/* this line contains the number of reactants
and products */
StringTokenizer tokenizer = new StringTokenizer(countsLine);
reactantCount = Integer.valueOf(tokenizer.nextToken()).intValue();
logger.info("Expecting " + reactantCount + " reactants in file");
productCount = Integer.valueOf(tokenizer.nextToken()).intValue();
logger.info("Expecting " + productCount + " products in file");
} catch (Exception exception) {
logger.debug(exception);
throw new CDKException("Error while counts line of RXN file", exception);
}
// now read the reactants
try {
for (int i = 1; i <= reactantCount; i++) {
StringBuffer molFile = new StringBuffer();
input.readLine(); // announceMDLFileLine
String molFileLine = "";
do {
molFileLine = input.readLine();
molFile.append(molFileLine);
molFile.append(System.getProperty("line.separator"));
} while (!molFileLine.equals("M END"));
// read MDL molfile content
// Changed this to mdlv2000 reader
MDLV2000Reader reader =
new MDLV2000Reader(new StringReader(molFile.toString()), super.mode);
IMolecule reactant = (IMolecule) reader.read(builder.newMolecule());
// add reactant
reaction.addReactant(reactant);
}
} catch (CDKException exception) {
// rethrow exception from MDLReader
throw exception;
} catch (Exception exception) {
logger.debug(exception);
throw new CDKException("Error while reading reactant", exception);
}
// now read the products
try {
for (int i = 1; i <= productCount; i++) {
StringBuffer molFile = new StringBuffer();
input.readLine(); // String announceMDLFileLine =
String molFileLine = "";
do {
molFileLine = input.readLine();
molFile.append(molFileLine);
molFile.append(System.getProperty("line.separator"));
} while (!molFileLine.equals("M END"));
// read MDL molfile content
MDLV2000Reader reader = new MDLV2000Reader(new StringReader(molFile.toString()));
IMolecule product = (IMolecule) reader.read(builder.newMolecule());
// add reactant
reaction.addProduct(product);
}
} catch (CDKException exception) {
// rethrow exception from MDLReader
throw exception;
} catch (Exception exception) {
logger.debug(exception);
throw new CDKException("Error while reading products", exception);
}
// now try to map things, if wanted
logger.info("Reading atom-atom mapping from file");
// distribute all atoms over two AtomContainer's
IAtomContainer reactingSide = builder.newAtomContainer();
java.util.Iterator molecules = reaction.getReactants().molecules().iterator();
while (molecules.hasNext()) {
reactingSide.add((IMolecule) molecules.next());
}
IAtomContainer producedSide = builder.newAtomContainer();
molecules = reaction.getProducts().molecules().iterator();
while (molecules.hasNext()) {
producedSide.add((IMolecule) molecules.next());
}
// map the atoms
int mappingCount = 0;
// IAtom[] reactantAtoms = reactingSide.getAtoms();
// IAtom[] producedAtoms = producedSide.getAtoms();
for (int i = 0; i < reactingSide.getAtomCount(); i++) {
for (int j = 0; j < producedSide.getAtomCount(); j++) {
IAtom eductAtom = reactingSide.getAtom(i);
IAtom productAtom = producedSide.getAtom(j);
if (eductAtom.getID() != null && eductAtom.getID().equals(productAtom.getID())) {
reaction.addMapping(builder.newMapping(eductAtom, productAtom));
mappingCount++;
break;
}
}
}
logger.info("Mapped atom pairs: " + mappingCount);
return reaction;
}
/**
* Depict a reaction.
*
* @param rxn reaction instance
* @return depiction
* @throws CDKException a depiction could not be generated
*/
public Depiction depict(IReaction rxn) throws CDKException {
ensure2dLayout(rxn); // can reorder components!
final Color fgcol =
getParameterValue(StandardGenerator.AtomColor.class)
.getAtomColor(rxn.getBuilder().newInstance(IAtom.class, "C"));
final List<IAtomContainer> reactants = toList(rxn.getReactants());
final List<IAtomContainer> products = toList(rxn.getProducts());
final List<IAtomContainer> agents = toList(rxn.getAgents());
// set ids for tagging elements
int molId = 0;
for (IAtomContainer mol : reactants) {
setIfMissing(mol, MarkedElement.ID_KEY, "mol" + ++molId);
setIfMissing(mol, MarkedElement.CLASS_KEY, "reactant");
}
for (IAtomContainer mol : products) {
setIfMissing(mol, MarkedElement.ID_KEY, "mol" + ++molId);
setIfMissing(mol, MarkedElement.CLASS_KEY, "product");
}
for (IAtomContainer mol : agents) {
setIfMissing(mol, MarkedElement.ID_KEY, "mol" + ++molId);
setIfMissing(mol, MarkedElement.CLASS_KEY, "agent");
}
final Map<IChemObject, Color> myHighlight = new HashMap<>();
if (highlightAtomMap) {
myHighlight.putAll(makeHighlightAtomMap(reactants, products));
}
// user highlight buffer pushes out the atom-map highlight if provided
myHighlight.putAll(highlight);
highlight.clear();
final List<Double> reactantScales = prepareCoords(reactants);
final List<Double> productScales = prepareCoords(products);
final List<Double> agentScales = prepareCoords(agents);
// highlight parts
for (Map.Entry<IChemObject, Color> e : myHighlight.entrySet())
e.getKey().setProperty(StandardGenerator.HIGHLIGHT_COLOR, e.getValue());
// setup the model scale based on bond length
final double scale = this.caclModelScale(rxn);
final DepictionGenerator copy = this.withParam(BasicSceneGenerator.Scale.class, scale);
final RendererModel model = copy.getModel();
// reactant/product/agent element generation, we number the reactants, then products then agents
List<Bounds> reactantBounds = copy.generate(reactants, model, 1);
List<Bounds> productBounds =
copy.generate(toList(rxn.getProducts()), model, rxn.getReactantCount());
List<Bounds> agentBounds =
copy.generate(
toList(rxn.getAgents()), model, rxn.getReactantCount() + rxn.getProductCount());
// remove current highlight buffer
for (IChemObject obj : myHighlight.keySet())
obj.removeProperty(StandardGenerator.HIGHLIGHT_COLOR);
// generate a 'plus' element
Bounds plus = copy.generatePlusSymbol(scale, fgcol);
// reset the coordinates to how they were before we invoked depict
resetCoords(reactants, reactantScales);
resetCoords(products, productScales);
resetCoords(agents, agentScales);
final Bounds emptyBounds = new Bounds();
final Bounds title =
copy.getParameterValue(BasicSceneGenerator.ShowReactionTitle.class)
? copy.generateTitle(rxn, scale)
: emptyBounds;
final List<Bounds> reactantTitles = new ArrayList<>();
final List<Bounds> productTitles = new ArrayList<>();
if (copy.getParameterValue(BasicSceneGenerator.ShowMoleculeTitle.class)) {
for (IAtomContainer reactant : reactants)
reactantTitles.add(copy.generateTitle(reactant, scale));
for (IAtomContainer product : products) productTitles.add(copy.generateTitle(product, scale));
}
final Bounds conditions =
generateReactionConditions(rxn, fgcol, model.get(BasicSceneGenerator.Scale.class));
return new ReactionDepiction(
model,
reactantBounds,
productBounds,
agentBounds,
plus,
rxn.getDirection(),
dimensions,
reactantTitles,
productTitles,
title,
conditions,
fgcol);
}
/**
* Initiates the process for the given mechanism. The atoms to apply are mapped between reactants
* and products.
*
* @param atomContainerSet
* @param atomList The list of atoms taking part in the mechanism. Only allowed two atoms. The
* first atom is the atom which contains the ISingleElectron and the second third is the atom
* which will be removed the first atom
* @param bondList The list of bonds taking part in the mechanism. Only allowed one bond. It is
* the bond which is moved
* @return The Reaction mechanism
*/
@TestMethod(value = "testInitiate_IAtomContainerSet_ArrayList_ArrayList")
public IReaction initiate(
IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)
throws CDKException {
CDKAtomTypeMatcher atMatcher = CDKAtomTypeMatcher.getInstance(atomContainerSet.getBuilder());
if (atomContainerSet.getAtomContainerCount() != 1) {
throw new CDKException("RadicalSiteIonizationMechanism only expects one IMolecule");
}
if (atomList.size() != 3) {
throw new CDKException("RadicalSiteIonizationMechanism expects three atoms in the ArrayList");
}
if (bondList.size() != 2) {
throw new CDKException(
"RadicalSiteIonizationMechanism only expect one bond in the ArrayList");
}
IAtomContainer molecule = atomContainerSet.getAtomContainer(0);
IAtomContainer reactantCloned;
try {
reactantCloned = (IAtomContainer) molecule.clone();
} catch (CloneNotSupportedException e) {
throw new CDKException("Could not clone IMolecule!", e);
}
IAtom atom1 = atomList.get(0); // Atom containing the ISingleElectron
IAtom atom1C = reactantCloned.getAtom(molecule.getAtomNumber(atom1));
IAtom atom2 = atomList.get(1); // Atom
IAtom atom2C = reactantCloned.getAtom(molecule.getAtomNumber(atom2));
IAtom atom3 = atomList.get(2); // Atom to be saved
IAtom atom3C = reactantCloned.getAtom(molecule.getAtomNumber(atom3));
IBond bond1 = bondList.get(0); // Bond to increase the order
int posBond1 = molecule.getBondNumber(bond1);
IBond bond2 = bondList.get(1); // Bond to remove
int posBond2 = molecule.getBondNumber(bond2);
BondManipulator.increaseBondOrder(reactantCloned.getBond(posBond1));
reactantCloned.removeBond(reactantCloned.getBond(posBond2));
List<ISingleElectron> selectron = reactantCloned.getConnectedSingleElectronsList(atom1C);
reactantCloned.removeSingleElectron(selectron.get(selectron.size() - 1));
atom1C.setHybridization(null);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
IAtomType type = atMatcher.findMatchingAtomType(reactantCloned, atom1C);
if (type == null) return null;
atom2C.setHybridization(null);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
type = atMatcher.findMatchingAtomType(reactantCloned, atom2C);
if (type == null) return null;
reactantCloned.addSingleElectron(new SingleElectron(atom3C));
atom3C.setHybridization(null);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
type = atMatcher.findMatchingAtomType(reactantCloned, atom3C);
if (type == null) return null;
IReaction reaction = DefaultChemObjectBuilder.getInstance().newInstance(IReaction.class);
reaction.addReactant(molecule);
/* mapping */
for (IAtom atom : molecule.atoms()) {
IMapping mapping =
DefaultChemObjectBuilder.getInstance()
.newInstance(
IMapping.class, atom, reactantCloned.getAtom(molecule.getAtomNumber(atom)));
reaction.addMapping(mapping);
}
IAtomContainerSet moleculeSetP = ConnectivityChecker.partitionIntoMolecules(reactantCloned);
for (int z = 0; z < moleculeSetP.getAtomContainerCount(); z++)
reaction.addProduct((IAtomContainer) moleculeSetP.getAtomContainer(z));
return reaction;
}