Java IAtomContainer.getBond方法代码示例

import org.openscience.cdk.interfaces.IAtomContainer; //导入方法依赖的package包/类
/**
 *  Append the symbol for the bond order between <code>a1</code> and <code>a2</code>
 *  to the <code>line</code>.
 *
 *@param  line           the StringBuffer that the bond symbol is appended to.
 *@param  a1             Atom participating in the bond.
 *@param  a2             Atom participating in the bond.
 *@param  atomContainer  the AtomContainer that the SMILES string is generated
 *      for.
  	 *@param useAromaticity				true=aromaticity or sp2 will trigger lower case letters, wrong=only sp2
 */
private void parseBond(StringBuffer line, IAtom a1, IAtom a2, IAtomContainer atomContainer, boolean useAromaticity)
{
	//logger.debug("in parseBond()");
	if (useAromaticity && a1.getFlag(CDKConstants.ISAROMATIC) && a2.getFlag(CDKConstants.ISAROMATIC))
	{
		return;
	}
	if (atomContainer.getBond(a1, a2) == null)
	{
		return;
	}
	IBond.Order type = atomContainer.getBond(a1, a2).getOrder();
	if (type == IBond.Order.SINGLE) {
	} else if (type == IBond.Order.DOUBLE) {
		line.append("=");
	} else if (type == IBond.Order.TRIPLE) {
		line.append("#");
	} else {
		// //logger.debug("Unknown bond type");
	}
}
 

import org.openscience.cdk.interfaces.IAtomContainer; //导入方法依赖的package包/类
private void makeGraph(IAtomContainer base){
	graph = new SparseUndirectedGraph();
	for(int i=0; i<base.getAtomCount(); i++){
		graph.add(i);
		atomsToNodes.put(base.getAtom(i), i);
		nodesToAtoms.put(i, base.getAtom(i));
		for(int j=0; j<i; j++){
			IBond bond = base.getBond(base.getAtom(i), base.getAtom(j));
			if(  bond != null){
				Edge newEdge = new SimpleEdge(i,j);
				bondsToEdges.put(bond, newEdge);
				edgesToBonds.put(newEdge, bond);
				graph.add( newEdge);
			}
		}
	}
}
 

import org.openscience.cdk.interfaces.IAtomContainer; //导入方法依赖的package包/类
private boolean isCOOHPOOHSOOHGroup(IAtom a, IAtomContainer mol) {
	int falseNeighbor = 0;
	boolean doubleBondSeen = false;
	boolean singleBondSeen = false;
	boolean hydrogenSeen = false;

	for (final IAtom n : mol.getConnectedAtomsList(a)) {
		if (!n.getAtomicNumber().equals(8)) {
			if (falseNeighbor == 1) {
				return false;
			} else {
				falseNeighbor++;
			}
		} else {
			// Oxygen neighbor check bond type
			final IBond b = mol.getBond(a, n);
			if (b.getOrder().equals(IBond.Order.SINGLE)) {
				if (!singleBondSeen) {
					singleBondSeen = true;
					if (n.getImplicitHydrogenCount() > 0)
						hydrogenSeen = true;
				} else {
					return false;
				}
			} else if (b.getOrder().equals(IBond.Order.DOUBLE)) {
				if (!doubleBondSeen) {
					doubleBondSeen = true;
				} else {
					return false;
				}
			}
		}
	}
	if (doubleBondSeen && singleBondSeen && hydrogenSeen) {
		return true;
	} else {
		return false;
	}
}
 

import org.openscience.cdk.interfaces.IAtomContainer; //导入方法依赖的package包/类
public static BondRef[] getBondRefs(IAtomContainer mol) {

        final int numAtoms = mol.getAtomCount();
        final int numBonds = mol.getBondCount();
        BondRef[] bonds    = new BondRef[numBonds];

        final Map<IAtom, AtomRef> atomCache = new IdentityHashMap<>(mol.getAtomCount());

        for (int i = 0; i < numAtoms; i++) {
            final IAtom atom = mol.getAtom(i);
            final AtomRef atomrf = new AtomRef(i,
                                               atom,
                                               new ArrayList<BondRef>());
            atomCache.put(atomrf.atom, atomrf);
        }
        for (int i = 0; i < numBonds; i++) {
            final IBond   bond    = mol.getBond(i);
            AtomRef       beg     = atomCache.get(bond.getAtom(0));
            AtomRef       end     = atomCache.get(bond.getAtom(1));
            final BondRef bondref = new BondRef(bond, i, beg, end);
            beg.bonds.add(bondref);
            end.bonds.add(bondref);
            bonds[i] = bondref;
        }

        return bonds;
    }
 

import org.openscience.cdk.interfaces.IAtomContainer; //导入方法依赖的package包/类
public static AtomRef[] getAtomRefs(IAtomContainer mol) {

        final int numAtoms = mol.getAtomCount();
        final int numBonds = mol.getBondCount();
        AtomRef[] atoms    = new AtomRef[numAtoms];

        final Map<IAtom, AtomRef> atomCache = new IdentityHashMap<>(mol.getAtomCount());

        for (int i = 0; i < numAtoms; i++) {
            final IAtom atom = mol.getAtom(i);
            final AtomRef atomrf = new AtomRef(i,
                                               atom,
                                               new ArrayList<BondRef>());
            atomCache.put(atomrf.atom, atomrf);
            atoms[i] = atomrf;
        }
        for (int i = 0; i < numBonds; i++) {
            final IBond   bond    = mol.getBond(i);
            AtomRef       beg     = atomCache.get(bond.getAtom(0));
            AtomRef       end     = atomCache.get(bond.getAtom(1));
            final BondRef bondref = new BondRef(bond, i, beg, end);
            beg.bonds.add(bondref);
            end.bonds.add(bondref);
        }

        return atoms;
    }