Java IAtomContainer.addAtom方法代码示例

import org.openscience.cdk.interfaces.IAtomContainer; //导入方法依赖的package包/类
public IAtomContainer getStructureAsAromaticIAtomContainer() {
	IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
	IAtomContainer fragmentStructure = builder.newInstance(IAtomContainer.class);
	
	for(int i = 0; i < this.bondsBitArray.getSize(); i++) {
		if(this.bondsBitArray.get(i)) {
			IBond curBond = this.precursorMolecule.getStructureAsIAtomContainer().getBond(i);
			if(this.precursorMolecule.isAromaticBond(i)) curBond.setIsAromatic(true);
			for(IAtom atom : curBond.atoms()) {
				atom.setImplicitHydrogenCount(0);
				if(this.precursorMolecule.isAromaticBond(i)) atom.setIsAromatic(true);
				fragmentStructure.addAtom(atom);
			}
			fragmentStructure.addBond(curBond);
		}
	}
//	loss of hydrogens
//	MoleculeFunctions.prepareAtomContainer(fragmentStructure);
	
	return fragmentStructure;
}
 

import org.openscience.cdk.interfaces.IAtomContainer; //导入方法依赖的package包/类
public IAtomContainer getStructureAsIAtomContainer() {
	IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
	IAtomContainer fragmentStructure = builder.newInstance(IAtomContainer.class);
	
	for(int i = 0; i < this.bondsBitArray.getSize(); i++) {
		if(this.bondsBitArray.get(i)) {
			IBond curBond = this.precursorMolecule.getStructureAsIAtomContainer().getBond(i);
			for(IAtom atom : curBond.atoms()) {
				fragmentStructure.addAtom(atom);
			}
			fragmentStructure.addBond(curBond);
		}
	}
//	loss of hydrogens
//	MoleculeFunctions.prepareAtomContainer(fragmentStructure);
	
	return fragmentStructure;
}
 

import org.openscience.cdk.interfaces.IAtomContainer; //导入方法依赖的package包/类
private ECFPFeature computeIterationForAtom(IAtom atom) throws FingerPrinterException, MoltyperException{
	ECFPFeature oldFeature = featuresOfLastIteration.get(atom);
       IAtomContainer newSubstructure = oldFeature.getNonDeepCloneOfSubstructure();
	List<BondOrderIdentifierTupel> connectivity = new ArrayList<BondOrderIdentifierTupel>();

	for(IAtom connectedAtom: molecule.getConnectedAtomsList(atom)){
		int identifierOfConnectedAtom = featuresOfLastIteration.get(connectedAtom).hashCode();
		//System.out.println("iterate "+connectedAtom.getAtomTypeName()+",id="+identifierOfConnectedAtom+",id="+featuresOfLastIteration.get(connectedAtom).featureToString(true));
		connectivity.add(new BondOrderIdentifierTupel(this.getBondOrder(molecule.getBond(atom,connectedAtom)),identifierOfConnectedAtom));
           IAtomContainer structure = this.featuresOfLastIteration.get(connectedAtom).representedSubstructure();
		for(IAtom a: structure.atoms()){
			if(!newSubstructure.contains(a))
				newSubstructure.addAtom(a);
		}
		for(IBond b: structure.bonds()){
			if(!newSubstructure.contains(b))
				newSubstructure.addBond(b);
		}
	}
	
	ECFPFeature newFeature = new ECFPFeature(this, molecule, atom, newSubstructure, this.iteration,oldFeature.hashCode(), connectivity);
	return newFeature;
}
 

import org.openscience.cdk.interfaces.IAtomContainer; //导入方法依赖的package包/类
private void computeInitialIteration() throws MoltyperException, FingerPrinterException{
	for (IAtom atom : this.molecule.atoms()) {
           IAtomContainer substructure = new AtomContainer();
		substructure.addAtom(atom);
		ECFPVariantFeature ecfpFeature = new ECFPVariantFeature(this, molecule, atom, substructure,
												this.generateExtensionBondList(atom), this.currentIteration,this.getAtomLabel(atom).hashCode(),null);
		this.hashedAtomLabels.put(atom, ecfpFeature.hashCode());
		this.featuresOfLastIteration.put(atom, ecfpFeature);
		this.completeFeatures.add(ecfpFeature);
	}
}
 

import org.openscience.cdk.interfaces.IAtomContainer; //导入方法依赖的package包/类
private void computeInitialIdentifiers() throws FingerPrinterException, MoltyperException{
	for(IAtom atom: molecule.atoms()){
           IAtomContainer substructure = new AtomContainer();
		substructure.addAtom(atom);
		for(IBond bond: molecule.getConnectedBondsList(atom)){
			substructure.addBond(bond);
		}
		//System.out.println("initial "+this.getAtomLabel(atom)+",id="+this.getAtomLabel(atom).hashCode());
		ECFPFeature ecfpFeature = new ECFPFeature(this, molecule, atom, substructure,this.iteration,this.getAtomLabel(atom).hashCode(), null);
		this.featuresOfLastIteration.put(atom, ecfpFeature);
		completeFeatures.add(ecfpFeature);
	}
}
 

import org.openscience.cdk.interfaces.IAtomContainer; //导入方法依赖的package包/类
public IAtomContainer getNonDeepCloneOfSubstructure(){
       IAtomContainer clone = new AtomContainer();
	for(IBond bond: this.substructure.bonds())
		clone.addBond(bond);
	
	for(IAtom atom: this.substructure.atoms())
		clone.addAtom(atom);
	
	return clone;
}
 

import org.openscience.cdk.interfaces.IAtomContainer; //导入方法依赖的package包/类
private IAtom sproutHydrogen(IAtomContainer mol, IAtom focus)
{
  IAtom hydrogen = mol.getBuilder().newAtom();
  hydrogen.setAtomicNumber(1);
  hydrogen.setSymbol("H");
  hydrogen.setImplicitHydrogenCount(0);
  mol.addAtom(hydrogen);
  mol.addBond(mol.indexOf(focus), mol.getAtomCount() - 1, IBond.Order.SINGLE);
  return hydrogen;
}
 

import org.openscience.cdk.interfaces.IAtomContainer; //导入方法依赖的package包/类
private ECFPVariantFeature computeIterationForAtom(IAtom atom) throws FingerPrinterException, MoltyperException {
	final ECFPVariantFeature oldFeature = this.featuresOfLastIteration.get(atom);
	final IAtomContainer newSubstructure = oldFeature.getNonDeepCloneOfSubstructure();
	final int numDanglingBonds = oldFeature.numberOfDanglingBonds();

	final List<BondOrderIdentifierTupel> connections = new ArrayList<BondOrderIdentifierTupel>(numDanglingBonds);
	final Map<IBond, DanglingBond> newConnectionCandidates = new HashMap<IBond, DanglingBond>();

	for (int i = 0; i < numDanglingBonds; i++) {
		final DanglingBond connection = oldFeature.getDanglingBond(i);
		final IAtom connectedAtom = connection.getBond().getAtom(connection.getConnectedAtomPosition());
		final int identifierOfConnectedAtom = this.hashedAtomLabels.get(connectedAtom);
		newSubstructure.addAtom(connectedAtom);
		newSubstructure.addBond(connection.getBond());
		final BondOrderIdentifierTupel boIDtupel=Encoding2DECFP.getNewBondOrderIdentifierTupel(this.getBondOrder(connection.getBond()), identifierOfConnectedAtom);
		connections.add(boIDtupel);

		final ArrayList<DanglingBond> newConnections = this.getConnectionsOfAtom(connection.getBond(), connectedAtom);
		for (final DanglingBond dbond : newConnections) {
			if (!newConnectionCandidates.containsKey(dbond.getBond())) {
				newConnectionCandidates.put(dbond.getBond(), dbond);
			}
		}
	}

	final Iterator<DanglingBond> iter = newConnectionCandidates.values().iterator();
	
	while (iter.hasNext()) {
		final DanglingBond bondToCheck = iter.next();
		if (newSubstructure.contains(bondToCheck.getConnectedAtom())) {
			if (!newSubstructure.contains(bondToCheck.getBond())) {
				newSubstructure.addBond(bondToCheck.getBond());
			}
			iter.remove();
		}
	}
	
	final DanglingBond[] newDanglingBonds = newConnectionCandidates.values().toArray(
			new DanglingBond[newConnectionCandidates.size()]);
	
	final ECFPVariantFeature newFeature = new ECFPVariantFeature(this, molecule, atom, newSubstructure, newDanglingBonds,
			this.currentIteration,oldFeature.hashCode(), connections);
	
	this.featuresOfLastIteration.put(atom, newFeature);
	return newFeature;
}