public static void setAtomProperties(IAtomContainerSet set, Object propKey, Object propVal) { if (set != null) { for (int i = 0; i < set.getAtomContainerCount(); i++) { AtomContainerManipulator.setAtomProperties(set.getAtomContainer(i), propKey, propVal); } } }
public static IAtomContainerSet getAllAgents(IReaction reaction) { IAtomContainerSet moleculeSet = reaction.getBuilder().newInstance(IAtomContainerSet.class); IAtomContainerSet agents = reaction.getAgents(); for (int i = 0; i < agents.getAtomContainerCount(); i++) { moleculeSet.addAtomContainer(agents.getAtomContainer(i)); } return moleculeSet; }
/** * Returns all the AtomContainer's of a MoleculeSet. * * @param set The collection of IAtomContainer objects * @return A list of individual IAtomContainer's */ public static List<IAtomContainer> getAllAtomContainers(IAtomContainerSet set) { List<IAtomContainer> atomContainerList = new ArrayList<IAtomContainer>(); for (IAtomContainer atomContainer : set.atomContainers()) { atomContainerList.add(atomContainer); } return atomContainerList; }
/** * @param set The collection of IAtomContainer objects * @return The summed charges of all atoms in this set. */ public static double getTotalCharge(IAtomContainerSet set) { double charge = 0; for (int i = 0; i < set.getAtomContainerCount(); i++) { int thisCharge = AtomContainerManipulator.getTotalFormalCharge(set.getAtomContainer(i)); double stoich = set.getMultiplier(i); charge += stoich * thisCharge; } return charge; }
public static List<String> getAllIDs(IAtomContainerSet set) { List<String> idList = new ArrayList<String>(); if (set != null) { if (set.getID() != null) idList.add(set.getID()); for (int i = 0; i < set.getAtomContainerCount(); i++) { idList.addAll(AtomContainerManipulator.getAllIDs(set.getAtomContainer(i))); } } return idList; }
@Test public void testBug2679343() { IAtomContainerSet som = (IAtomContainerSet) newChemObject(); IAtomContainer ac1 = som.getBuilder().newInstance(IAtomContainer.class); IAtomContainer ac2 = som.getBuilder().newInstance(IAtomContainer.class); som.addAtomContainer(ac1); som.addAtomContainer(ac2); som.addAtomContainer(ac2); Assert.assertEquals(3, som.getAtomContainerCount()); som.removeAtomContainer(ac2); Assert.assertEquals(1, som.getAtomContainerCount()); }
/** * Test to recognize if this IAtomContainer_1 matches correctly into the CDKAtomTypes. */ @Test public void testAtomTypesAtomContainer1() throws Exception { IAtomContainer moleculeTest = getExampleReactants().getAtomContainer(0); makeSureAtomTypesAreRecognized(moleculeTest); }
/** * Returns the number of reactants in this reaction. * * @return The number of reactants in this reaction */ @Override public int getReactantCount() { return reactants.getAtomContainerCount(); }
public static double calculateAverageBondLength(IAtomContainerSet moleculeSet) { double averageBondModelLength = 0.0; for (IAtomContainer atomContainer : moleculeSet.atomContainers()) { averageBondModelLength += GeometryTools.getBondLengthAverage(atomContainer); } return averageBondModelLength / moleculeSet.getAtomContainerCount(); }
/** * Adds a reactant to this reaction with a stoichiometry coefficient. * * @param reactant Molecule added as reactant to this reaction * @param coefficient Stoichiometry coefficient for this molecule * @see #getReactants */ @Override public void addReactant(IAtomContainer reactant, Double coefficient) { reactants.addAtomContainer(reactant, coefficient); }
@Test public void testAdd_IAtomContainerSet() { IAtomContainerSet som = (IAtomContainerSet) newChemObject(); som.addAtomContainer(som.getBuilder().newInstance(IAtomContainer.class)); som.addAtomContainer(som.getBuilder().newInstance(IAtomContainer.class)); som.addAtomContainer(som.getBuilder().newInstance(IAtomContainer.class)); IAtomContainerSet tested = som.getBuilder().newInstance(IAtomContainerSet.class); Assert.assertEquals(0, tested.getAtomContainerCount()); tested.add(som); Assert.assertEquals(3, tested.getAtomContainerCount()); }
@Test public void testAddAtomContainer_IAtomContainer_double() { IAtomContainerSet som = (IAtomContainerSet) newChemObject(); som.addAtomContainer(som.getBuilder().newInstance(IAtomContainer.class), 2.0); Assert.assertEquals(1, som.getAtomContainerCount()); Assert.assertEquals(2.0, som.getMultiplier(0), 0.00001); }
@Test public void testRemoveAllAtomContainers() { IAtomContainerSet som = (IAtomContainerSet) newChemObject(); IAtomContainer ac1 = som.getBuilder().newInstance(IAtomContainer.class); IAtomContainer ac2 = som.getBuilder().newInstance(IAtomContainer.class); som.addAtomContainer(ac1); som.addAtomContainer(ac2); Assert.assertEquals(2, som.getAtomContainerCount()); som.removeAllAtomContainers(); Assert.assertEquals(0, som.getAtomContainerCount()); }
private int getfragmentCount(IAtomContainer molecule) { boolean fragmentFlag = true; IAtomContainerSet fragmentMolSet = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainerSet.class); int countFrag = 0; if (molecule.getAtomCount() > 0) { fragmentFlag = ConnectivityChecker.isConnected(molecule); if (!fragmentFlag) { fragmentMolSet.add(ConnectivityChecker.partitionIntoMolecules(molecule)); } else { fragmentMolSet.addAtomContainer(molecule); } countFrag = fragmentMolSet.getAtomContainerCount(); } return countFrag; }
@Test public void testReplaceAtomContainer_int_IAtomContainer() { IAtomContainerSet som = (IAtomContainerSet) newChemObject(); IAtomContainer ac1 = som.getBuilder().newInstance(IAtomContainer.class); IAtomContainer ac2 = som.getBuilder().newInstance(IAtomContainer.class); IAtomContainer ac3 = som.getBuilder().newInstance(IAtomContainer.class); som.addAtomContainer(ac1); som.addAtomContainer(ac2); Assert.assertEquals(ac2, som.getAtomContainer(1)); som.replaceAtomContainer(1, ac3); Assert.assertEquals(ac3, som.getAtomContainer(1)); }
@Test public void testGetAtomContainerCount() { IAtomContainerSet som = (IAtomContainerSet) newChemObject(); som.addAtomContainer(som.getBuilder().newInstance(IAtomContainer.class)); som.addAtomContainer(som.getBuilder().newInstance(IAtomContainer.class)); som.addAtomContainer(som.getBuilder().newInstance(IAtomContainer.class)); Assert.assertEquals(3, som.getAtomContainerCount()); }
@Test public void testGetAtomContainer_int() { IAtomContainerSet som = (IAtomContainerSet) newChemObject(); som.addAtomContainer(som.getBuilder().newInstance(IAtomContainer.class)); som.addAtomContainer(som.getBuilder().newInstance(IAtomContainer.class)); som.addAtomContainer(som.getBuilder().newInstance(IAtomContainer.class)); Assert.assertNotNull(som.getAtomContainer(2)); // third molecule should exist Assert.assertNull(som.getAtomContainer(3)); // fourth molecule must not exist }
@Test public void testSetMultiplier_int_Double() { IAtomContainerSet som = (IAtomContainerSet) newChemObject(); som.addAtomContainer(som.getBuilder().newInstance(IAtomContainer.class)); Assert.assertEquals(1.0, som.getMultiplier(0), 0.00001); som.setMultiplier(0, 2.0); Assert.assertEquals(2.0, som.getMultiplier(0), 0.00001); }
@Test public void testGetMultiplier_IAtomContainer() { IAtomContainerSet som = (IAtomContainerSet) newChemObject(); som.addAtomContainer(som.getBuilder().newInstance(IAtomContainer.class)); Assert.assertEquals(-1.0, som.getMultiplier(som.getBuilder().newInstance(IAtomContainer.class)), 0.00001); }
@Test public void testSetMultipliers_arrayDouble() { IAtomContainerSet som = (IAtomContainerSet) newChemObject(); IAtomContainer container = som.getBuilder().newInstance(IAtomContainer.class); som.addAtomContainer(container); IAtomContainer container2 = som.getBuilder().newInstance(IAtomContainer.class); som.addAtomContainer(container2); Assert.assertEquals(1.0, som.getMultiplier(0), 0.00001); Assert.assertEquals(1.0, som.getMultiplier(1), 0.00001); Double[] multipliers = new Double[2]; multipliers[0] = 2.0; multipliers[1] = 3.0; som.setMultipliers(multipliers); Assert.assertEquals(2.0, som.getMultiplier(0), 0.00001); Assert.assertEquals(3.0, som.getMultiplier(1), 0.00001); }