/** *{@inheritDoc} */ @Override public IRing clone() throws CloneNotSupportedException { return (IRing) super.clone(); }
/** *{@inheritDoc} */ @Override public IMonomer clone() throws CloneNotSupportedException { return (IMonomer) super.clone(); }
/** *{@inheritDoc} */ @Override public IRing clone() throws CloneNotSupportedException { return (IRing) super.clone(); }
/** *{@inheritDoc} */ @Override public IMonomer clone() throws CloneNotSupportedException { return (IMonomer) super.clone(); }
/** * {@inheritDoc} */ @Override public IAtomContainer clone() throws CloneNotSupportedException { IAtomContainer clone = null; try { clone = super.clone(); } catch (Exception exception) { logger.error("Could not clone DebugAtomContainer: " + exception.getMessage(), exception); logger.debug(exception); } return clone; }
@Override public IStrand clone() throws CloneNotSupportedException { Strand clone = (Strand) super.clone(); clone.monomers.clear(); for (Iterator<String> iter = clone.getMonomerNames().iterator(); iter.hasNext();) { Monomer monomerClone = (Monomer) (clone.getMonomer(iter.next().toString()).clone()); Iterator<IAtom> atoms = monomerClone.atoms().iterator(); while (atoms.hasNext()) { clone.addAtom(atoms.next(), monomerClone); } } return clone; } }
@Override public IStrand clone() throws CloneNotSupportedException { Strand clone = (Strand) super.clone(); clone.monomers.clear(); for (Iterator<String> iter = clone.getMonomerNames().iterator(); iter.hasNext();) { Monomer monomerClone = (Monomer) (clone.getMonomer(iter.next().toString()).clone()); Iterator<IAtom> atoms = monomerClone.atoms().iterator(); while (atoms.hasNext()) { clone.addAtom(atoms.next(), monomerClone); } } return clone; } }
/** * Makes a clone of this crystal. * * @return The cloned crystal. */ @Override public ICrystal clone() throws CloneNotSupportedException { Crystal clone = (Crystal) super.clone(); // clone the axes clone.setA(new Vector3d(this.aAxis)); clone.setB(new Vector3d(this.bAxis)); clone.setC(new Vector3d(this.cAxis)); return clone; }
/** * Makes a clone of this crystal. * * @return The cloned crystal. */ @Override public ICrystal clone() throws CloneNotSupportedException { Crystal clone = (Crystal) super.clone(); // clone the axes clone.setA(new Vector3d(this.aAxis)); clone.setB(new Vector3d(this.bAxis)); clone.setC(new Vector3d(this.cAxis)); return clone; }
/** * Returns deep copy of the molecule * * @param container * @return deep copy of the mol * @throws CloneNotSupportedException */ public static IAtomContainer cloneWithIDs(IAtomContainer container) throws CloneNotSupportedException { IAtomContainer ac = new AtomContainer(container).clone(); ac.setProperties(container.getProperties()); ac.setFlags(container.getFlags()); ac.setID(container.getID()); ac.notifyChanged(); return ac; }
@Override public IPolymer clone() throws CloneNotSupportedException { Polymer clone = (Polymer) super.clone(); clone.removeAllElements(); clone.monomers = new Hashtable<String, IMonomer>();
@Override public IPolymer clone() throws CloneNotSupportedException { Polymer clone = (Polymer) super.clone(); clone.removeAllElements(); clone.monomers = new Hashtable<String, IMonomer>();
/** * Returns deep copy of the molecule * * @param container * @return deep copy of the mol * @throws CloneNotSupportedException */ public static IAtomContainer cloneWithIDs(IAtomContainer container) throws CloneNotSupportedException { //setNullHCountToZero(container); IAtomContainer ac = new AtomContainer(container).clone();/*Set IDs as CDK clone doesn't*/ for (int i = 0; i < ac.getAtomCount(); i++) { ac.getAtom(i).setID(container.getAtom(i).getID()); if (ac.getAtom(i).getProperties() == null) { ac.getAtom(i).setProperties(new HashMap<>()); } } for (int i = 0; i < ac.getBondCount(); i++) { if (ac.getBond(i).getProperties() == null) { ac.getBond(i).setProperties(new HashMap<>()); } } ac.setProperties(container.getProperties()); ac.setFlags(container.getFlags()); ac.setID(container.getID()); ac.notifyChanged(); return ac; }
IAtomContainer ac = new AtomContainer(container).clone();/*Set IDs as CDK clone doesn't*/ for (int i = 0; i < ac.getAtomCount(); i++) { ac.getAtom(i).setID(container.getAtom(i).getID());