/** * Increment the bond order of this bond. * * @param bond The bond whose order is to be incremented * @see #increaseBondOrder(org.openscience.cdk.interfaces.IBond.Order) * @see #decreaseBondOrder(org.openscience.cdk.interfaces.IBond.Order) * @see #decreaseBondOrder(org.openscience.cdk.interfaces.IBond) */ public static void increaseBondOrder(IBond bond) { bond.setOrder(increaseBondOrder(bond.getOrder())); }
/** * Increment the bond order of this bond. * * @param bond The bond whose order is to be incremented * @see #increaseBondOrder(org.openscience.cdk.interfaces.IBond.Order) * @see #decreaseBondOrder(org.openscience.cdk.interfaces.IBond.Order) * @see #decreaseBondOrder(org.openscience.cdk.interfaces.IBond) */ public static void increaseBondOrder(IBond bond) { bond.setOrder(increaseBondOrder(bond.getOrder())); }
@Test public void testIncreaseBondOrder_IBond_Order() { Assert.assertEquals(IBond.Order.DOUBLE, BondManipulator.increaseBondOrder(IBond.Order.SINGLE)); Assert.assertEquals(IBond.Order.TRIPLE, BondManipulator.increaseBondOrder(IBond.Order.DOUBLE)); Assert.assertEquals(IBond.Order.QUADRUPLE, BondManipulator.increaseBondOrder(IBond.Order.TRIPLE)); Assert.assertEquals(IBond.Order.QUINTUPLE, BondManipulator.increaseBondOrder(IBond.Order.QUADRUPLE)); Assert.assertEquals(IBond.Order.SEXTUPLE, BondManipulator.increaseBondOrder(IBond.Order.QUINTUPLE)); Assert.assertEquals(IBond.Order.SEXTUPLE, BondManipulator.increaseBondOrder(IBond.Order.SEXTUPLE)); }
/** * This method decides the highest bond order that the bond can have and set * it to that. * * @param bond The bond to be investigated * @param atomContainer The {@link IAtomContainer} that contains the bond * @throws CDKEXception when the bond cannot be further increased */ private void setMaxBondOrder(IBond bond, IAtomContainer atomContainer) throws CDKException { if (bondOrderCanBeIncreased(bond, atomContainer)) { if (bond.getOrder() != IBond.Order.QUADRUPLE) bond.setOrder(BondManipulator.increaseBondOrder(bond.getOrder())); else throw new CDKException("Can't increase a quadruple bond!"); } }
/** * This method decides the highest bond order that the bond can have and set * it to that. * * @param bond The bond to be investigated * @param atomContainer The {@link IAtomContainer} that contains the bond * @throws CDKEXception when the bond cannot be further increased */ private void setMaxBondOrder(IBond bond, IAtomContainer atomContainer) throws CDKException { if (bondOrderCanBeIncreased(bond, atomContainer)) { if (bond.getOrder() != IBond.Order.QUADRUPLE) bond.setOrder(BondManipulator.increaseBondOrder(bond.getOrder())); else throw new CDKException("Can't increase a quadruple bond!"); } }
@Test public void testIncreaseBondOrder_IBond() { IBond bond = new Bond(); bond.setOrder(IBond.Order.SINGLE); BondManipulator.increaseBondOrder(bond); Assert.assertEquals(IBond.Order.DOUBLE, bond.getOrder()); BondManipulator.increaseBondOrder(bond); Assert.assertEquals(IBond.Order.TRIPLE, bond.getOrder()); BondManipulator.increaseBondOrder(bond); Assert.assertEquals(IBond.Order.QUADRUPLE, bond.getOrder()); BondManipulator.increaseBondOrder(bond); Assert.assertEquals(IBond.Order.QUINTUPLE, bond.getOrder()); BondManipulator.increaseBondOrder(bond); Assert.assertEquals(IBond.Order.SEXTUPLE, bond.getOrder()); BondManipulator.increaseBondOrder(bond); Assert.assertEquals(IBond.Order.SEXTUPLE, bond.getOrder()); }
@Test public void testGetBondOrderSum() { IChemObject object = newChemObject(); IRing r = object.getBuilder().newInstance(IRing.class, 5, "C"); Assert.assertEquals(5, r.getBondOrderSum()); BondManipulator.increaseBondOrder(r.getBond(0)); Assert.assertEquals(6, r.getBondOrderSum()); BondManipulator.increaseBondOrder(r.getBond(0)); Assert.assertEquals(7, r.getBondOrderSum()); BondManipulator.increaseBondOrder(r.getBond(4)); Assert.assertEquals(8, r.getBondOrderSum()); }
int posBond1 = molecule.indexOf(bond1); BondManipulator.increaseBondOrder(reactantCloned.getBond(posBond1));
int posBond1 = molecule.indexOf(bond1); BondManipulator.increaseBondOrder(reactantCloned.getBond(posBond1));
BondManipulator.increaseBondOrder(reactantCloned.getBond(posBond2)); reactantCloned.removeBond(reactantCloned.getBond(posBond3)); IBond newBond = molecule.getBuilder().newInstance(IBond.class, atom1C, atom4C, IBond.Order.SINGLE);
BondManipulator.increaseBondOrder(reactantCloned.getBond(posBond2)); reactantCloned.removeBond(reactantCloned.getBond(posBond3)); IBond newBond = molecule.getBuilder().newInstance(IBond.class, atom1C, atom4C, IBond.Order.SINGLE);
int posBond2 = molecule.indexOf(bond2); BondManipulator.increaseBondOrder(reactantCloned.getBond(posBond1)); reactantCloned.removeBond(reactantCloned.getBond(posBond2));
int posBond2 = molecule.indexOf(bond2); BondManipulator.increaseBondOrder(reactantCloned.getBond(posBond1)); reactantCloned.removeBond(reactantCloned.getBond(posBond2));
int posBond2 = molecule.indexOf(bond2); BondManipulator.increaseBondOrder(reactantCloned.getBond(posBond1)); if (bond2.getOrder() == IBond.Order.SINGLE) reactantCloned.removeBond(reactantCloned.getBond(posBond2));
bond = atomContainer.getBond(atom, partner); logger.debug("Bond order was " + bond.getOrder()); BondManipulator.increaseBondOrder(bond); logger.debug("Bond order now " + bond.getOrder()); break; bond = atomContainer.getBond(atom, partner); logger.debug("Bond order was " + bond.getOrder()); BondManipulator.increaseBondOrder(bond); logger.debug("Bond order now " + bond.getOrder()); break;
int bondiP = reactant.indexOf(bondi); if (bondi.getOrder() == IBond.Order.SINGLE) BondManipulator.increaseBondOrder(reactantCloned.getBond(bondiP)); else BondManipulator.decreaseBondOrder(reactantCloned.getBond(bondiP));
if (BondManipulator.isLowerOrder(bond.getOrder(), aType2.getMaxBondOrder()) && BondManipulator.isLowerOrder(bond.getOrder(), aType1.getMaxBondOrder())) { bond.setOrder(BondManipulator.increaseBondOrder(bond.getOrder())); logger.debug("Bond order now ", bond.getOrder()); return true;
if (BondManipulator.isLowerOrder(bond.getOrder(), aType2.getMaxBondOrder()) && BondManipulator.isLowerOrder(bond.getOrder(), aType1.getMaxBondOrder())) { bond.setOrder(BondManipulator.increaseBondOrder(bond.getOrder())); logger.debug("Bond order now ", bond.getOrder()); return true;
} else if (BondManipulator.isLowerOrder(bond.getOrder(), aType2.getMaxBondOrder()) && BondManipulator.isLowerOrder(bond.getOrder(), aType1.getMaxBondOrder())) { BondManipulator.increaseBondOrder(bond); logger.debug("Bond order now " + bond.getOrder()); bondOrderIncreased = true;
} else if (BondManipulator.isLowerOrder(bond.getOrder(), aType2.getMaxBondOrder()) && BondManipulator.isLowerOrder(bond.getOrder(), aType1.getMaxBondOrder())) { BondManipulator.increaseBondOrder(bond); logger.debug("Bond order now " + bond.getOrder()); bondOrderIncreased = true;