private IAtomContainer getAllInOneContainer(IRingSet ringSet) { IAtomContainer resultContainer = ringSet.getBuilder().newInstance(IAtomContainer.class); Iterator<IAtomContainer> containers = RingSetManipulator.getAllAtomContainers(ringSet).iterator(); while (containers.hasNext()) { resultContainer.add((IAtomContainer) containers.next()); } return resultContainer; }
/** * Puts all rings of a ringSet in a single atomContainer * * @param ringSet The ringSet to use * @return The produced atomContainer */ public static IAtomContainer getAllInOneContainer(IRingSet ringSet) { IAtomContainer resultContainer = ringSet.getBuilder().newInstance(IAtomContainer.class); Iterator<IAtomContainer> containers = RingSetManipulator.getAllAtomContainers(ringSet).iterator(); while (containers.hasNext()) { resultContainer.add(containers.next()); } return resultContainer; }
} while (!toremove.isEmpty()); final IRingSet core = rs.getBuilder().newInstance(IRingSet.class); for (IRing ring : ringsystem) core.addAtomContainer(ring);
} while (!toremove.isEmpty()); final IRingSet core = rs.getBuilder().newInstance(IRingSet.class); for (IRing ring : ringsystem) core.addAtomContainer(ring);
@Test @Override public void testIsEmpty() { IRingSet ringSet = (IRingSet) newChemObject(); Assert.assertThat("new ringset should be empty", ringSet.isEmpty(), is(true)); ringSet.addAtomContainer(ringSet.getBuilder().newInstance(IAtomContainer.class)); Assert.assertThat("ringset with an atom container should not be empty", ringSet.isEmpty(), is(not(true))); ringSet.removeAllAtomContainers(); Assert.assertThat("ringset with removed atom containers should be empty", ringSet.isEmpty(), is(true)); }
IRingSet ringset = (IRingSet) newChemObject(); IAtom ring1Atom1 = ringset.getBuilder().newInstance(IAtom.class, "C"); // rather artificial molecule IAtom ring1Atom2 = ringset.getBuilder().newInstance(IAtom.class, "C"); IAtom sharedAtom1 = ringset.getBuilder().newInstance(IAtom.class, "C"); IAtom sharedAtom2 = ringset.getBuilder().newInstance(IAtom.class, "C"); IAtom ring2Atom1 = ringset.getBuilder().newInstance(IAtom.class, "C"); IAtom ring2Atom2 = ringset.getBuilder().newInstance(IAtom.class, "C"); IBond ring1Bond1 = ringset.getBuilder().newInstance(IBond.class, ring1Atom1, ring1Atom2); IBond ring1Bond2 = ringset.getBuilder().newInstance(IBond.class, sharedAtom1, ring1Atom1); IBond ring1Bond3 = ringset.getBuilder().newInstance(IBond.class, sharedAtom2, ring1Atom2); IBond sharedBond = ringset.getBuilder().newInstance(IBond.class, sharedAtom1, sharedAtom2); IBond ring2Bond1 = ringset.getBuilder().newInstance(IBond.class, ring2Atom1, ring2Atom2); IBond ring2Bond2 = ringset.getBuilder().newInstance(IBond.class, sharedAtom1, ring2Atom1); IBond ring2Bond3 = ringset.getBuilder().newInstance(IBond.class, sharedAtom2, ring2Atom2); IRing ring1 = ringset.getBuilder().newInstance(IRing.class); ring1.addAtom(ring1Atom1); ring1.addAtom(ring1Atom2); ring1.addBond(ring1Bond3); ring1.addBond(sharedBond); IRing ring2 = ringset.getBuilder().newInstance(IRing.class); ring2.addAtom(ring2Atom1); ring2.addAtom(ring2Atom2);
IAtom atom = null; IRingSet rings = null; IAtomContainer unplacedPartners = rs.getBuilder().newInstance(IAtomContainer.class); IAtomContainer sharedAtoms = rs.getBuilder().newInstance(IAtomContainer.class); IAtomContainer primaryAtoms = rs.getBuilder().newInstance(IAtomContainer.class); IAtomContainer treatedAtoms = rs.getBuilder().newInstance(IAtomContainer.class); Point2d centerOfRingGravity = null; for (int j = 0; j < rs.getAtomContainerCount(); j++) {
IAtom atom = null; IRingSet rings = null; IAtomContainer unplacedPartners = rs.getBuilder().newInstance(IAtomContainer.class); IAtomContainer sharedAtoms = rs.getBuilder().newInstance(IAtomContainer.class); IAtomContainer primaryAtoms = rs.getBuilder().newInstance(IAtomContainer.class); IAtomContainer treatedAtoms = rs.getBuilder().newInstance(IAtomContainer.class); Point2d centerOfRingGravity = null; for (int j = 0; j < rs.getAtomContainerCount(); j++) {
IRingSet ringset = (IRingSet) newChemObject(); IAtom ring1Atom1 = ringset.getBuilder().newInstance(IAtom.class, "C"); // rather artificial molecule IAtom ring1Atom2 = ringset.getBuilder().newInstance(IAtom.class, "C"); IAtom sharedAtom1 = ringset.getBuilder().newInstance(IAtom.class, "C"); IAtom sharedAtom2 = ringset.getBuilder().newInstance(IAtom.class, "C"); IAtom ring2Atom1 = ringset.getBuilder().newInstance(IAtom.class, "C"); IAtom ring2Atom2 = ringset.getBuilder().newInstance(IAtom.class, "C"); IBond ring1Bond1 = ringset.getBuilder().newInstance(IBond.class, ring1Atom1, ring1Atom2); IBond ring1Bond2 = ringset.getBuilder().newInstance(IBond.class, sharedAtom1, ring1Atom1); IBond ring1Bond3 = ringset.getBuilder().newInstance(IBond.class, sharedAtom2, ring1Atom2); IBond sharedBond = ringset.getBuilder().newInstance(IBond.class, sharedAtom1, sharedAtom2); IBond ring2Bond1 = ringset.getBuilder().newInstance(IBond.class, ring2Atom1, ring2Atom2); IBond ring2Bond2 = ringset.getBuilder().newInstance(IBond.class, sharedAtom1, ring2Atom1); IBond ring2Bond3 = ringset.getBuilder().newInstance(IBond.class, sharedAtom2, ring2Atom2); IRing ring1 = ringset.getBuilder().newInstance(IRing.class); ring1.addAtom(ring1Atom1); ring1.addAtom(ring1Atom2); ring1.addBond(ring1Bond3); ring1.addBond(sharedBond); IRing ring2 = ringset.getBuilder().newInstance(IRing.class); ring2.addAtom(ring2Atom1); ring2.addAtom(ring2Atom2);
IRingSet ringset = (IRingSet) newChemObject(); IAtom ring1Atom1 = ringset.getBuilder().newInstance(IAtom.class, "C"); // rather artificial molecule IAtom ring1Atom2 = ringset.getBuilder().newInstance(IAtom.class, "C"); IAtom sharedAtom1 = ringset.getBuilder().newInstance(IAtom.class, "C"); IAtom sharedAtom2 = ringset.getBuilder().newInstance(IAtom.class, "C"); IAtom ring2Atom1 = ringset.getBuilder().newInstance(IAtom.class, "C"); IAtom ring2Atom2 = ringset.getBuilder().newInstance(IAtom.class, "C"); IBond ring1Bond1 = ringset.getBuilder().newInstance(IBond.class, ring1Atom1, ring1Atom2); IBond ring1Bond2 = ringset.getBuilder().newInstance(IBond.class, sharedAtom1, ring1Atom1); IBond ring1Bond3 = ringset.getBuilder().newInstance(IBond.class, sharedAtom2, ring1Atom2); IBond sharedBond = ringset.getBuilder().newInstance(IBond.class, sharedAtom1, sharedAtom2); IBond ring2Bond1 = ringset.getBuilder().newInstance(IBond.class, ring2Atom1, ring2Atom2); IBond ring2Bond2 = ringset.getBuilder().newInstance(IBond.class, sharedAtom1, ring2Atom1); IBond ring2Bond3 = ringset.getBuilder().newInstance(IBond.class, sharedAtom2, ring2Atom2); IRing ring1 = ringset.getBuilder().newInstance(IRing.class); ring1.addAtom(ring1Atom1); ring1.addAtom(ring1Atom2); ring1.addBond(ring1Bond3); ring1.addBond(sharedBond); IRing ring2 = ringset.getBuilder().newInstance(IRing.class); ring2.addAtom(ring2Atom1); ring2.addAtom(ring2Atom2);
@Test public void testAdd_IRingSet() { IRingSet rs = (IRingSet) newChemObject(); IRing r1 = rs.getBuilder().newInstance(IRing.class, 5, "C"); IRing r2 = rs.getBuilder().newInstance(IRing.class, 3, "C"); rs.addAtomContainer(r1); IRingSet rs2 = (IRingSet) newChemObject(); rs2.addAtomContainer(r2); rs2.add(rs); Assert.assertEquals(1, rs.getAtomContainerCount()); Assert.assertEquals(2, rs2.getAtomContainerCount()); }
IRingSet ringset = (IRingSet) newChemObject(); IAtom ring1Atom1 = ringset.getBuilder().newInstance(IAtom.class, "C"); // rather artificial molecule IAtom ring1Atom2 = ringset.getBuilder().newInstance(IAtom.class, "C"); IAtom sharedAtom1 = ringset.getBuilder().newInstance(IAtom.class, "C"); IAtom sharedAtom2 = ringset.getBuilder().newInstance(IAtom.class, "C"); IAtom ring2Atom1 = ringset.getBuilder().newInstance(IAtom.class, "C"); IAtom ring2Atom2 = ringset.getBuilder().newInstance(IAtom.class, "C"); IBond ring1Bond1 = ringset.getBuilder().newInstance(IBond.class, ring1Atom1, ring1Atom2); IBond ring1Bond2 = ringset.getBuilder().newInstance(IBond.class, sharedAtom1, ring1Atom1); IBond ring1Bond3 = ringset.getBuilder().newInstance(IBond.class, sharedAtom2, ring1Atom2); IBond sharedBond = ringset.getBuilder().newInstance(IBond.class, sharedAtom1, sharedAtom2); IBond ring2Bond1 = ringset.getBuilder().newInstance(IBond.class, ring2Atom1, ring2Atom2); IBond ring2Bond2 = ringset.getBuilder().newInstance(IBond.class, sharedAtom1, ring2Atom1); IBond ring2Bond3 = ringset.getBuilder().newInstance(IBond.class, sharedAtom2, ring2Atom2); IRing ring1 = ringset.getBuilder().newInstance(IRing.class); ring1.addAtom(ring1Atom1); ring1.addAtom(ring1Atom2); ring1.addBond(ring1Bond3); ring1.addBond(sharedBond); IRing ring2 = ringset.getBuilder().newInstance(IRing.class); ring2.addAtom(ring2Atom1); ring2.addAtom(ring2Atom2);
IRingSet ringset = (IRingSet) newChemObject(); IAtom ring1Atom1 = ringset.getBuilder().newInstance(IAtom.class, "C"); // rather artificial molecule IAtom ring1Atom2 = ringset.getBuilder().newInstance(IAtom.class, "C"); IAtom sharedAtom1 = ringset.getBuilder().newInstance(IAtom.class, "C"); IAtom sharedAtom2 = ringset.getBuilder().newInstance(IAtom.class, "C"); IAtom ring2Atom1 = ringset.getBuilder().newInstance(IAtom.class, "C"); IAtom ring2Atom2 = ringset.getBuilder().newInstance(IAtom.class, "C"); IBond ring1Bond1 = ringset.getBuilder().newInstance(IBond.class, ring1Atom1, ring1Atom2); IBond ring1Bond2 = ringset.getBuilder().newInstance(IBond.class, sharedAtom1, ring1Atom1); IBond ring1Bond3 = ringset.getBuilder().newInstance(IBond.class, sharedAtom2, ring1Atom2); IBond sharedBond = ringset.getBuilder().newInstance(IBond.class, sharedAtom1, sharedAtom2); IBond ring2Bond1 = ringset.getBuilder().newInstance(IBond.class, ring2Atom1, ring2Atom2); IBond ring2Bond2 = ringset.getBuilder().newInstance(IBond.class, sharedAtom1, ring2Atom1); IBond ring2Bond3 = ringset.getBuilder().newInstance(IBond.class, sharedAtom2, ring2Atom2); IRing ring1 = ringset.getBuilder().newInstance(IRing.class); ring1.addAtom(ring1Atom1); ring1.addAtom(ring1Atom2); ring1.addBond(ring1Bond3); ring1.addBond(sharedBond); IRing ring2 = ringset.getBuilder().newInstance(IRing.class); ring2.addAtom(ring2Atom1); ring2.addAtom(ring2Atom2);
IRing leftCyclohexane = ringSet.getBuilder().newInstance(IRing.class, 6, "C"); IRing rightCyclopentane = ringSet.getBuilder().newInstance(IRing.class, 5, "C"); IRing leftCyclopentane = ringSet.getBuilder().newInstance(IRing.class); IBond leftCyclohexane0RightCyclopentane4 = ringSet.getBuilder().newInstance(IBond.class, leftCyclohexane.getAtom(0), rightCyclopentane.getAtom(4)); IBond leftCyclohexane1RightCyclopentane2 = ringSet.getBuilder().newInstance(IBond.class, leftCyclohexane.getAtom(1), rightCyclopentane.getAtom(2)); leftCyclopentane.addAtom(leftCyclohexane.getAtom(0)); leftCyclopentane.addBond(leftCyclohexane0RightCyclopentane4); IRing rightCyclohexane = ringSet.getBuilder().newInstance(IRing.class); IAtom rightCyclohexaneAtom0 = ringSet.getBuilder().newInstance(IAtom.class, "C"); IAtom rightCyclohexaneAtom1 = ringSet.getBuilder().newInstance(IAtom.class, "C"); IAtom rightCyclohexaneAtom2 = ringSet.getBuilder().newInstance(IAtom.class, "C"); IAtom rightCyclohexaneAtom5 = ringSet.getBuilder().newInstance(IAtom.class, "C"); IBond rightCyclohexaneAtom0Atom1 = ringSet.getBuilder().newInstance(IBond.class, rightCyclohexaneAtom0, rightCyclohexaneAtom1); IBond rightCyclohexaneAtom1Atom2 = ringSet.getBuilder().newInstance(IBond.class, rightCyclohexaneAtom1, rightCyclohexaneAtom2); IBond rightCyclohexane2rightCyclopentane1 = ringSet.getBuilder().newInstance(IBond.class, rightCyclohexaneAtom2, rightCyclopentane.getAtom(1)); IBond rightCyclohexane5rightCyclopentane0 = ringSet.getBuilder().newInstance(IBond.class, rightCyclohexaneAtom5, rightCyclopentane.getAtom(0)); IBond rightCyclohexaneAtom0Atom5 = ringSet.getBuilder().newInstance(IBond.class, rightCyclohexaneAtom0, rightCyclohexaneAtom5); rightCyclohexane.addAtom(rightCyclohexaneAtom0);
Iterator<IAtomContainer> containers = RingSetManipulator.getAllAtomContainers(atomRingSet) .iterator(); atomRingSet = rs.getBuilder().newInstance(IRingSet.class); while (containers.hasNext()) {
Iterator<IAtomContainer> containers = RingSetManipulator.getAllAtomContainers(atomRingSet) .iterator(); atomRingSet = rs.getBuilder().newInstance(IRingSet.class); while (containers.hasNext()) {
@Test @Override public void testClone() throws CloneNotSupportedException { IRingSet ringset = (IRingSet) newChemObject(); IRing ring = ringset.getBuilder().newInstance(IRing.class); ringset.addAtomContainer(ring); IRingSet clone = (IRingSet) ringset.clone(); Assert.assertNotNull(clone); Assert.assertTrue(clone instanceof IRingSet); Assert.assertEquals(1, clone.getAtomContainerCount()); Assert.assertNotSame(ring, clone.getAtomContainer(0)); }