/** * Returns whether a bond is unsaturated. A bond is unsaturated if * <b>both</b> Atoms in the bond are unsaturated. */ public boolean isUnsaturated(IBond bond, IAtomContainer atomContainer) throws CDKException { IAtom[] atoms = BondManipulator.getAtomArray(bond); boolean isUnsaturated = true; for (int i = 0; i < atoms.length; i++) { isUnsaturated = isUnsaturated && !isSaturated(atoms[i], atomContainer); } return isUnsaturated; }
/** * Returns whether a bond is saturated. A bond is saturated if * <b>both</b> Atoms in the bond are saturated. */ public boolean isSaturated(IBond bond, IAtomContainer atomContainer) throws CDKException { IAtom[] atoms = BondManipulator.getAtomArray(bond); boolean isSaturated = true; for (int i = 0; i < atoms.length; i++) { isSaturated = isSaturated && isSaturated(atoms[i], atomContainer); } return isSaturated; }
/** * Returns whether a bond is saturated. A bond is saturated if * <b>both</b> Atoms in the bond are saturated. */ public boolean isSaturated(IBond bond, IAtomContainer atomContainer) throws CDKException { IAtom[] atoms = BondManipulator.getAtomArray(bond); boolean isSaturated = true; for (int i = 0; i < atoms.length; i++) { isSaturated = isSaturated && isSaturated(atoms[i], atomContainer); } return isSaturated; }
/** * Returns whether a bond is unsaturated. A bond is unsaturated if * <b>both</b> Atoms in the bond are unsaturated. */ public boolean isUnsaturated(IBond bond, IAtomContainer atomContainer) throws CDKException { IAtom[] atoms = BondManipulator.getAtomArray(bond); boolean isUnsaturated = true; for (int i = 0; i < atoms.length; i++) { isUnsaturated = isUnsaturated && !isSaturated(atoms[i], atomContainer); } return isUnsaturated; }
/** * Returns whether a bond is unsaturated. A bond is unsaturated if * <b>all</b> Atoms in the bond are unsaturated. */ public boolean isUnsaturated(IBond bond, IAtomContainer atomContainer) throws CDKException { logger.debug("isBondUnsaturated?: ", bond); IAtom[] atoms = BondManipulator.getAtomArray(bond); boolean isUnsaturated = true; for (int i = 0; i < atoms.length && isUnsaturated; i++) { isUnsaturated = isUnsaturated && !isSaturated(atoms[i], atomContainer); } logger.debug("Bond is unsaturated?: ", isUnsaturated); return isUnsaturated; }
/** * Returns whether a bond is unsaturated. A bond is unsaturated if * <b>all</b> Atoms in the bond are unsaturated. */ public boolean isUnsaturated(IBond bond, IAtomContainer atomContainer) throws CDKException { logger.debug("isBondUnsaturated?: ", bond); IAtom[] atoms = BondManipulator.getAtomArray(bond); boolean isUnsaturated = true; for (int i = 0; i < atoms.length && isUnsaturated; i++) { isUnsaturated = isUnsaturated && !isSaturated(atoms[i], atomContainer); } logger.debug("Bond is unsaturated?: ", isUnsaturated); return isUnsaturated; }
/** * Returns whether a bond is saturated. A bond is saturated if * <b>both</b> Atoms in the bond are saturated. */ public boolean isSaturated(IBond bond, IAtomContainer atomContainer) throws CDKException { logger.debug("isBondSaturated?: ", bond); IAtom[] atoms = BondManipulator.getAtomArray(bond); boolean isSaturated = true; for (int i = 0; i < atoms.length; i++) { logger.debug("isSaturated(Bond, AC): atom I=", i); isSaturated = isSaturated && isSaturated(atoms[i], atomContainer); } logger.debug("isSaturated(Bond, AC): result=", isSaturated); return isSaturated; }
/** * Returns whether a bond is saturated. A bond is saturated if * <b>both</b> Atoms in the bond are saturated. */ public boolean isSaturated(IBond bond, IAtomContainer atomContainer) throws CDKException { logger.debug("isBondSaturated?: ", bond); IAtom[] atoms = BondManipulator.getAtomArray(bond); boolean isSaturated = true; for (int i = 0; i < atoms.length; i++) { logger.debug("isSaturated(Bond, AC): atom I=", i); isSaturated = isSaturated && isSaturated(atoms[i], atomContainer); } logger.debug("isSaturated(Bond, AC): result=", isSaturated); return isSaturated; }
IBond bond1 = g1.getBond(map.getKey()); IBond bond2 = g2.getBond(map.getValue()); IAtom[] atom1 = BondManipulator.getAtomArray(bond1); IAtom[] atom2 = BondManipulator.getAtomArray(bond2); for (int j = 0; j < 2; j++) { List<IBond> bondsConnectedToAtom1j = g1.getConnectedBondsList(atom1[j]);
IBond bond1 = g1.getBond(l.get(i).getId1()); IBond bond2 = g2.getBond(l.get(i).getId2()); IAtom[] atom1 = BondManipulator.getAtomArray(bond1); IAtom[] atom2 = BondManipulator.getAtomArray(bond2); for (int j = 0; j < 2; j++) { List<IBond> bondsConnectedToAtom1j = g1.getConnectedBondsList(atom1[j]);
IBond qBond = graph1.getBond(rMapList.get(i).getId1()); IBond tBond = graph2.getBond(rMapList.get(i).getId2()); IAtom[] qAtoms = BondManipulator.getAtomArray(qBond); IAtom[] tAtoms = BondManipulator.getAtomArray(tBond); for (int j = 0; j < 2; j++) { List<IBond> bondsConnectedToAtom1j = graph1.getConnectedBondsList(qAtoms[j]);
IBond bond1 = g1.getBond(l.get(i).getId1()); IBond bond2 = g2.getBond(l.get(i).getId2()); IAtom[] atom1 = BondManipulator.getAtomArray(bond1); IAtom[] atom2 = BondManipulator.getAtomArray(bond2); for (int j = 0; j < 2; j++) { List<IBond> bondsConnectedToAtom1j = g1.getConnectedBondsList(atom1[j]);
IBond bond1 = g1.getBond(l.get(i).getId1()); IBond bond2 = g2.getBond(l.get(i).getId2()); IAtom[] atom1 = BondManipulator.getAtomArray(bond1); IAtom[] atom2 = BondManipulator.getAtomArray(bond2); for (int j = 0; j < 2; j++) { List<IBond> bondsConnectedToAtom1j = g1.getConnectedBondsList(atom1[j]);
IBond bond1 = g1.getBond(l.get(i).getId1()); IBond bond2 = g2.getBond(l.get(i).getId2()); IAtom[] atom1 = BondManipulator.getAtomArray(bond1); IAtom[] atom2 = BondManipulator.getAtomArray(bond2); for (int j = 0; j < 2; j++) { List<IBond> bondsConnectedToAtom1j = g1.getConnectedBondsList(atom1[j]);
@Test public void testGetAtomArray_IBond() { IAtom atom1 = new Atom(Elements.CARBON); IAtom atom2 = new Atom(Elements.CARBON); IBond bond = new Bond(atom1, atom2, Order.TRIPLE); IAtom[] atoms = BondManipulator.getAtomArray(bond); Assert.assertEquals(2, atoms.length); Assert.assertEquals(atom1, atoms[0]); Assert.assertEquals(atom2, atoms[1]); }
@Override public DescriptorValue calculate(IBond bond, IAtomContainer ac) { ensureIsotopeFactory(); if (bond.getAtomCount() != 2) { return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult( Double.NaN), NAMES, new CDKException("Only 2-center bonds are considered")); } IAtom[] atoms = BondManipulator.getAtomArray(bond); return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult( Math.abs(factory.getElement(atoms[0].getSymbol()).getAtomicNumber() - factory.getElement(atoms[1].getSymbol()).getAtomicNumber())), NAMES); }
IAtom[] atoms = BondManipulator.getAtomArray(bond); IAtom atom = atoms[0]; IAtom partner = atoms[1];
IAtom[] atoms = BondManipulator.getAtomArray(bond); IAtom atom = atoms[0]; IAtom partner = atoms[1];
IAtom[] atoms = BondManipulator.getAtomArray(bond); IAtom atom = atoms[0]; IAtom partner = atoms[1];
IAtom[] atoms = BondManipulator.getAtomArray(bond); IAtom atom = atoms[0]; IAtom partner = atoms[1];