/** * {@inheritDoc} */ @Override public IBond getBond(IAtom atom1, IAtom atom2) { logger.debug("Getting bond for atoms: atom1=" + atom1, " atom2=" + atom2); return super.getBond(atom1, atom2); }
/** * {@inheritDoc} */ @Override public void removeAllBonds() { for (int f = 0; f < getBondCount(); f++) { getBond(f).removeListener(this); } bonds = new IBond[growArraySize]; bondCount = 0; notifyChanged(); }
/** * {@inheritDoc} */ @Override public void removeAllBonds() { for (int f = 0; f < getBondCount(); f++) { getBond(f).removeListener(this); } bonds = new IBond[growArraySize]; bondCount = 0; notifyChanged(); }
/** * {@inheritDoc} */ @Override public int getBondNumber(IAtom atom1, IAtom atom2) { return indexOf(getBond(atom1, atom2)); }
stringContent.append(", #B:").append(getBondCount()); for (int i = 0; i < getBondCount(); i++) { stringContent.append(", ").append(getBond(i).toString());
/** * {@inheritDoc} */ @Override public IBond getBond(int idx) { logger.debug("Getting bond at: ", idx); return super.getBond(idx); }
stringContent.append(", #B:").append(getBondCount()); for (int i = 0; i < getBondCount(); i++) { stringContent.append(", ").append(getBond(i).toString());
/** * {@inheritDoc} */ @Override public int getBondNumber(IAtom atom1, IAtom atom2) { return indexOf(getBond(atom1, atom2)); }
@Test public void testBondPermutation() { AtomContainer ac = new org.openscience.cdk.AtomContainer(); AtomContainer result; String bonds = new String(""); ac.addAtom(new Atom("C")); ac.addAtom(new Atom("N")); ac.addAtom(new Atom("P")); ac.addAtom(new Atom("O")); ac.addAtom(new Atom("S")); ac.addAtom(new Atom("Br")); ac.addBond(0, 1, IBond.Order.SINGLE); ac.addBond(1, 2, IBond.Order.DOUBLE); ac.addBond(2, 3, IBond.Order.TRIPLE); ac.addBond(3, 4, IBond.Order.QUADRUPLE); ac.addBond(4, 5, IBond.Order.SINGLE); // was 5.0 ! AtomContainerBondPermutor acap = new AtomContainerBondPermutor(ac); int counter = 0; while (acap.hasNext()) { counter++; bonds = ""; result = (AtomContainer) acap.next(); for (int f = 0; f < result.getBondCount(); f++) { bonds += result.getBond(f).getOrder(); } //logger.debug(bonds); } Assert.assertEquals(119, counter); }
/** * {@inheritDoc} */ @Override public IBond removeBond(IAtom atom1, IAtom atom2) { int pos = indexOf(getBond(atom1, atom2)); IBond bond = null; if (pos != -1) { bond = bonds[pos]; removeBond(pos); } return bond; }
/** * {@inheritDoc} */ @Override public IBond removeBond(IAtom atom1, IAtom atom2) { int pos = indexOf(getBond(atom1, atom2)); IBond bond = null; if (pos != -1) { bond = bonds[pos]; removeBond(pos); } return bond; }
Assert.assertTrue(bond1.getFlag(CDKConstants.SINGLE_OR_DOUBLE)); Assert.assertTrue(mol.getAtom(0).getFlag(CDKConstants.SINGLE_OR_DOUBLE)); Assert.assertTrue(mol.getBond(0).getFlag(CDKConstants.SINGLE_OR_DOUBLE)); Assert.assertTrue(mol.getFlag(CDKConstants.SINGLE_OR_DOUBLE));