@Test public void testDestroyBondOrder_IBond_Order() { Assert.assertEquals(1.0, BondManipulator.destroyBondOrder(IBond.Order.SINGLE), 0.00001); Assert.assertEquals(2.0, BondManipulator.destroyBondOrder(IBond.Order.DOUBLE), 0.00001); Assert.assertEquals(3.0, BondManipulator.destroyBondOrder(IBond.Order.TRIPLE), 0.00001); Assert.assertEquals(4.0, BondManipulator.destroyBondOrder(IBond.Order.QUADRUPLE), 0.00001); Assert.assertEquals(5.0, BondManipulator.destroyBondOrder(IBond.Order.QUINTUPLE), 0.00001); Assert.assertEquals(6.0, BondManipulator.destroyBondOrder(IBond.Order.SEXTUPLE), 0.00001); }
/** * This method is used if, by some reason, the bond order sum is not set * for an atom. * * @param atom The atom in question * @param mol The molecule that the atom belongs to * @return The bond order sum * @throws CDKException */ private double getAtomBondordersum(IAtom atom, IAtomContainer mol) throws CDKException { double sum = 0; for (IBond bond : mol.bonds()) if (bond.contains(atom)) sum += BondManipulator.destroyBondOrder(bond.getOrder()); return sum; }
/** * This method is used if, by some reason, the bond order sum is not set * for an atom. * * @param atom The atom in question * @param mol The molecule that the atom belongs to * @return The bond order sum * @throws CDKException */ private double getAtomBondordersum(IAtom atom, IAtomContainer mol) throws CDKException { double sum = 0; for (IBond bond : mol.bonds()) if (bond.contains(atom)) sum += BondManipulator.destroyBondOrder(bond.getOrder()); return sum; }
oxNum += BondManipulator.destroyBondOrder(atomContainer.getBond(ca0, ca2j).getOrder());
oxNum += BondManipulator.destroyBondOrder(atomContainer.getBond(ca0, ca2j).getOrder());
oxNum += BondManipulator.destroyBondOrder(atomContainer.getBond(ca0, ca2j).getOrder());
oxNum += BondManipulator.destroyBondOrder(atomContainer.getBond(ca0, ca2j).getOrder());
oxNum += BondManipulator.destroyBondOrder(atomContainer.getBond(ca0, ca2j).getOrder());
oxNum += BondManipulator.destroyBondOrder(atomContainer.getBond(ca0, ca2j).getOrder());
oxNum += BondManipulator.destroyBondOrder(atomContainer.getBond(ca0, ca2j).getOrder());
oxNum += BondManipulator.destroyBondOrder(atomContainer.getBond(ca0, ca2j).getOrder());
else oxNum += BondManipulator .destroyBondOrder(atomContainer.getBond(ai, ((IAtom) ca.get(j))).getOrder());
else oxNum += BondManipulator .destroyBondOrder(atomContainer.getBond(ai, ((IAtom) ca.get(j))).getOrder());
/** * Returns the connection matrix representation of this AtomContainer. * * @param container The AtomContainer for which the matrix is calculated * @return A connection matrix representing this AtomContainer */ public static double[][] getMatrix(IAtomContainer container) { IBond bond = null; int indexAtom1; int indexAtom2; double[][] conMat = new double[container.getAtomCount()][container.getAtomCount()]; for (int f = 0; f < container.getBondCount(); f++) { bond = container.getBond(f); indexAtom1 = container.indexOf(bond.getBegin()); indexAtom2 = container.indexOf(bond.getEnd()); conMat[indexAtom1][indexAtom2] = BondManipulator.destroyBondOrder(bond.getOrder()); conMat[indexAtom2][indexAtom1] = BondManipulator.destroyBondOrder(bond.getOrder()); } return conMat; }
a11 = BondManipulator.destroyBondOrder(b1.getOrder()); nonZeroBondsCounter++; } else { a12 = BondManipulator.destroyBondOrder(b2.getOrder()); nonZeroBondsCounter++; } else { a21 = BondManipulator.destroyBondOrder(b3.getOrder()); nonZeroBondsCounter++; } else { a22 = BondManipulator.destroyBondOrder(b4.getOrder()); nonZeroBondsCounter++; } else {
a11 = BondManipulator.destroyBondOrder(b1.getOrder()); nonZeroBondsCounter++; } else { a12 = BondManipulator.destroyBondOrder(b2.getOrder()); nonZeroBondsCounter++; } else { a21 = BondManipulator.destroyBondOrder(b3.getOrder()); nonZeroBondsCounter++; } else { a22 = BondManipulator.destroyBondOrder(b4.getOrder()); nonZeroBondsCounter++; } else {
a11 = BondManipulator.destroyBondOrder(b1.getOrder()); nonZeroBondsCounter++; } else { a12 = BondManipulator.destroyBondOrder(b2.getOrder()); nonZeroBondsCounter++; } else { a21 = BondManipulator.destroyBondOrder(b3.getOrder()); nonZeroBondsCounter++; } else { a22 = BondManipulator.destroyBondOrder(b4.getOrder()); nonZeroBondsCounter++; } else {
a11 = BondManipulator.destroyBondOrder(b1.getOrder()); nonZeroBondsCounter++; } else { a12 = BondManipulator.destroyBondOrder(b2.getOrder()); nonZeroBondsCounter++; } else { a21 = BondManipulator.destroyBondOrder(b3.getOrder()); nonZeroBondsCounter++; } else { a22 = BondManipulator.destroyBondOrder(b4.getOrder()); nonZeroBondsCounter++; } else {
int bondsToAtom = 0; for (IBond bond : atomContainer.bonds()) if (bond.contains(atom)) bondsToAtom += BondManipulator.destroyBondOrder(bond.getOrder()); int implicitHydrogens; if (atom.getImplicitHydrogenCount() == CDKConstants.UNSET || atom.getImplicitHydrogenCount() == null) {
int bondsToAtom = 0; for (IBond bond : atomContainer.bonds()) if (bond.contains(atom)) bondsToAtom += BondManipulator.destroyBondOrder(bond.getOrder()); int implicitHydrogens; if (atom.getImplicitHydrogenCount() == CDKConstants.UNSET || atom.getImplicitHydrogenCount() == null) {