/** * Adds an atomContainer to this container. * * @param atomContainer The atomContainer to be added to this container */ @Override public void addAtomContainer(IAtomContainer atomContainer) { addAtomContainer(atomContainer, 1.0); /* * notifyChanged is called below */ }
/** * Clones this <code>RingSet</code> including the Rings. * * @return The cloned object */ @Override public Object clone() throws CloneNotSupportedException { return super.clone(); }
/** * Adds an atomContainer to this container with the given * multiplier. * * @param atomContainer The atomContainer to be added to this container * @param multiplier The multiplier of this atomContainer */ @Override public void addAtomContainer(IAtomContainer atomContainer, double multiplier) { if (atomContainerCount + 1 >= atomContainers.length) { growAtomContainerArray(); } atomContainers[atomContainerCount] = atomContainer; multipliers[atomContainerCount] = multiplier; atomContainerCount++; }
@Override public IChemObject newTestObject() { return new AtomContainerSet(); } });
/** * Clones this AtomContainerSet and its content. * * @return the cloned Object */ @Override public Object clone() throws CloneNotSupportedException { AtomContainerSet clone = (AtomContainerSet) super.clone(); clone.atomContainers = new IAtomContainer[atomContainerCount]; clone.atomContainerCount = 0; for (int i = 0; i < atomContainerCount; i++) { clone.addAtomContainer((IAtomContainer) atomContainers[i].clone()); clone.setMultiplier(i, getMultiplier(i)); } return clone; }
@Override public void remove() { removeAtomContainer(--pointer); } }
/** * Returns the String representation of this AtomContainerSet. * * @return The String representation of this AtomContainerSet */ @Override public String toString() { StringBuffer buffer = new StringBuffer(32); buffer.append("AtomContainerSet("); buffer.append(this.hashCode()); if (getAtomContainerCount() > 0) { buffer.append(", M=").append(getAtomContainerCount()); for (int i = 0; i < atomContainerCount; i++) { buffer.append(", ").append(atomContainers[i].toString()); } } buffer.append(')'); return buffer.toString(); }
@BeforeClass public static void setUp() { setTestObjectBuilder(new ITestObjectBuilder() { @Override public IChemObject newTestObject() { return new AtomContainerSet(); } }); }
/** * Clones this AtomContainerSet and its content. * * @return the cloned Object */ @Override public Object clone() throws CloneNotSupportedException { AtomContainerSet clone = (AtomContainerSet) super.clone(); clone.atomContainers = new IAtomContainer[atomContainerCount]; clone.atomContainerCount = 0; for (int i = 0; i < atomContainerCount; i++) { clone.addAtomContainer((IAtomContainer) atomContainers[i].clone()); clone.setMultiplier(i, getMultiplier(i)); } return clone; }
/** * Removes an AtomContainer from this container. * * @param atomContainer The atomContainer to be removed from this container */ @Override public void removeAtomContainer(IAtomContainer atomContainer) { for (int i = atomContainerCount - 1; i >= 0; i--) { if (atomContainers[i] == atomContainer) removeAtomContainer(i); } }
/** * Returns the String representation of this AtomContainerSet. * * @return The String representation of this AtomContainerSet */ @Override public String toString() { StringBuffer buffer = new StringBuffer(32); buffer.append("AtomContainerSet("); buffer.append(this.hashCode()); if (getAtomContainerCount() > 0) { buffer.append(", M=").append(getAtomContainerCount()); for (int i = 0; i < atomContainerCount; i++) { buffer.append(", ").append(atomContainers[i].toString()); } } buffer.append(')'); return buffer.toString(); }
@Test public void testAtomContainerSet() { IAtomContainerSet som = new AtomContainerSet(); Assert.assertNotNull(som); Assert.assertEquals(0, som.getAtomContainerCount()); }
/** * Removes an AtomContainer from this container. * * @param atomContainer The atomContainer to be removed from this container */ @Override public void removeAtomContainer(IAtomContainer atomContainer) { for (int i = atomContainerCount - 1; i >= 0; i--) { if (atomContainers[i] == atomContainer) removeAtomContainer(i); } }
/** * Adds an atomContainer to this container. * * @param atomContainer The atomContainer to be added to this container */ @Override public void addAtomContainer(IAtomContainer atomContainer) { addAtomContainer(atomContainer, 1.0); /* * notifyChanged is called below */ }
/** * Clones this <code>RingSet</code> including the Rings. * * @return The cloned object */ @Override public Object clone() throws CloneNotSupportedException { return super.clone(); }
/** * Adds an atomContainer to this container with the given * multiplier. * * @param atomContainer The atomContainer to be added to this container * @param multiplier The multiplier of this atomContainer */ @Override public void addAtomContainer(IAtomContainer atomContainer, double multiplier) { if (atomContainerCount + 1 >= atomContainers.length) { growAtomContainerArray(); } atomContainers[atomContainerCount] = atomContainer; multipliers[atomContainerCount] = multiplier; atomContainerCount++; }
@Test public void testMoleculeSetID() throws Exception { StringWriter writer = new StringWriter(); IAtomContainerSet moleculeSet = new AtomContainerSet(); moleculeSet.setID("ms0"); CMLWriter cmlWriter = new CMLWriter(writer); cmlWriter.write(moleculeSet); cmlWriter.close(); String cmlContent = writer.toString(); logger.debug("****************************** testReactionCustomization()"); logger.debug(cmlContent); logger.debug("******************************"); Assert.assertTrue(cmlContent.indexOf("<moleculeList convention=\"cdk:moleculeSet\" id=\"ms0") != -1); }
@Override public void remove() { removeAtomContainer(--pointer); } }
/** * Adds all atomContainers in the AtomContainerSet to this container. * * @param atomContainerSet The AtomContainerSet */ @Override public void add(IAtomContainerSet atomContainerSet) { for (IAtomContainer iter : atomContainerSet.atomContainers()) { addAtomContainer(iter); } /* * notifyChanged() is called by addAtomContainer() */ }
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); SMILESReader reader = new SMILESReader(ins); IAtomContainerSet som = reader.read(new AtomContainerSet()); Assert.assertEquals("We must have read 99 structures", 99, som.getAtomContainerCount()); CrossoverMachine cm = new CrossoverMachine();