@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; }
/** * 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(); } atomContainer.addListener(this); atomContainers[atomContainerCount] = atomContainer; multipliers[atomContainerCount] = multiplier; atomContainerCount++; notifyChanged(); }
/** * Called by objects to which this object has * registered as a listener. * * @param event A change event pointing to the source of the change */ @Override public void stateChanged(IChemObjectChangeEvent event) { notifyChanged(event); }
/** {@inheritDoc} */ @Override public void addAtomContainer(IAtomContainer atomContainer, double multiplier) { logger.debug("Adding atom container with multiplier: ", "" + multiplier, atomContainer); super.addAtomContainer(atomContainer, multiplier); }
/** {@inheritDoc} */ @Override public int getAtomContainerCount() { logger.debug("Getting atom container count: ", super.getAtomContainerCount()); return super.getAtomContainerCount(); }
/** {@inheritDoc} */ @Override public Double getMultiplier(int number) { logger.debug("Getting multiplier at: ", number); return super.getMultiplier(number); }
/** * Called by objects to which this object has * registered as a listener. * * @param event A change event pointing to the source of the change */ @Override public void stateChanged(IChemObjectChangeEvent event) { notifyChanged(event); }
/** {@inheritDoc} */ @Override public void addAtomContainer(IAtomContainer atomContainer, double multiplier) { logger.debug("Adding atom container with multiplier: ", "" + multiplier, atomContainer); super.addAtomContainer(atomContainer, multiplier); }
/** * 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(); } atomContainer.addListener(this); atomContainers[atomContainerCount] = atomContainer; multipliers[atomContainerCount] = multiplier; atomContainerCount++; notifyChanged(); }
/** {@inheritDoc} */ @Override public int getAtomContainerCount() { logger.debug("Getting atom container count: ", super.getAtomContainerCount()); return super.getAtomContainerCount(); }
/** {@inheritDoc} */ @Override public Double getMultiplier(int number) { logger.debug("Getting multiplier at: ", number); return super.getMultiplier(number); }
/** * Load an IChemModel from an InChI. * * @param url location * @return InChI instance * @throws CDKException InChI could not be generated */ public static IChemModel readInChI(URL url) throws CDKException { IChemModel chemModel = new ChemModel(); try { IAtomContainerSet moleculeSet = new AtomContainerSet(); chemModel.setMoleculeSet(moleculeSet); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); String line; while ((line = in.readLine()) != null) { if (line.toLowerCase().startsWith("inchi=")) { moleculeSet.addAtomContainer(parseInChI(line)); } } in.close(); } catch (Exception e) { e.printStackTrace(); throw new CDKException(e.getMessage()); } return chemModel; } }
/** * 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; }
/** * Sets the coefficient of a AtomContainer to a given value. * * @param position The position of the AtomContainer for which the multiplier is * set in [0,..] * @param multiplier The new multiplier for the AtomContatiner at * <code>position</code> * @see #getMultiplier(int) */ @Override public void setMultiplier(int position, Double multiplier) { multipliers[position] = multiplier; notifyChanged(); }
/** {@inheritDoc} */ @Override public void addAtomContainer(IAtomContainer atomContainer) { logger.debug("Adding atom container: ", atomContainer); super.addAtomContainer(atomContainer); }
/** * Clones this <code>RingSet</code> including the Rings. * * @return The cloned object */ @Override public Object clone() throws CloneNotSupportedException { return super.clone(); }
/** * 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(); }
/** {@inheritDoc} */ @Override public Double getMultiplier(IAtomContainer container) { logger.debug("Getting multiplier for atom container: ", container); return super.getMultiplier(container); }