hydrogenadder.java

化学图形处理软件

    	IAtomContainer intermediateContainer= null;
    	for (int k = 0; k < moleculeSet.getAtomContainerCount(); k++) {
    		IMolecule molPart = moleculeSet.getMolecule(k);
    		java.util.Iterator atoms = molPart.atoms();
    		while (atoms.hasNext()) {
    			intermediateContainer = addHydrogensToSatisfyValency(molPart, (IAtom)atoms.next(), molecule);
    			changedAtomsAndBonds.add(intermediateContainer);
    		}

    	}
    	logger.debug("End of addExplicitHydrogensToSatisfyValency");
    	return changedAtomsAndBonds;
    }

    /**
     * Method that saturates an atom in a molecule by adding explicit hydrogens.
     * In order to get coordinates for these Hydrogens, you need to 
     * remember the average bondlength of you molecule (coordinates for 
     * all atoms should be available) by using
     * double bondLength = GeometryTools.getBondLengthAverage(atomContainer);
     * and then use this method here and then use
     * org.openscience.cdk.HydrogenPlacer(atomContainer, bondLength);
     *
     * @param  atom      Atom to saturate
     * @param  container AtomContainer containing the atom
     * @param  totalContainer In case you have a container containing multiple structures, this is the total container, whereas container is a partial structure
     *
     * @cdk.keyword          hydrogen, adding
     * @cdk.keyword          explicit hydrogen
     *
     * @deprecated
     */
    public IAtomContainer addHydrogensToSatisfyValency(IAtomContainer container, IAtom atom, IAtomContainer totalContainer) 
        throws IOException, ClassNotFoundException, CDKException
    {
	logger.debug("Start of addHydrogensToSatisfyValency(AtomContainer container, Atom atom)");
    IAtomContainer changedAtomsAndBonds = addExplicitHydrogensToSatisfyValency(container, atom, totalContainer);
	logger.debug("End of addHydrogensToSatisfyValency(AtomContainer container, Atom atom)");
    return changedAtomsAndBonds;
    }

    /**
     * Method that saturates an atom in a molecule by adding explicit hydrogens.
     * In order to get coordinates for these Hydrogens, you need to
     * remember the average bondlength of you molecule (coordinates for
     * all atoms should be available) by using
     * double bondLength = GeometryTools.getBondLengthAverage(atomContainer);
     * and then use this method here and then use
     * org.openscience.cdk.HydrogenPlacer(atomContainer, bondLength);
     *
     * @param  atom      Atom to saturate
     * @param  container AtomContainer containing the atom
     *
     * @cdk.keyword hydrogen, adding
     * @cdk.keyword explicit hydrogen
     */
    public IAtomContainer addExplicitHydrogensToSatisfyValency(IAtomContainer container, IAtom atom)
            throws IOException, ClassNotFoundException, CDKException {
        // set number of implicit hydrogens to zero
        // add explicit hydrogens
        logger.debug("Start of addExplicitHydrogensToSatisfyValency(AtomContainer container, Atom atom)");
        int missingHydrogens = calculateNumberOfImplicitHydrogens(container, atom);
        logger.debug("According to valencyChecker, " + missingHydrogens + " are missing");
        IAtomContainer changedAtomsAndBonds = addExplicitHydrogensToSatisfyValency(container, atom, missingHydrogens, container);
        logger.debug("End of addExplicitHydrogensToSatisfyValency(AtomContainer container, Atom atom)");
        return changedAtomsAndBonds;
    }


    /**
     * Method that saturates an atom in a molecule by adding explicit hydrogens.
     * In order to get coordinates for these Hydrogens, you need to 
     * remember the average bondlength of you molecule (coordinates for 
     * all atoms should be available) by using
     * double bondLength = GeometryTools.getBondLengthAverage(atomContainer);
     * and then use this method here and then use
     * org.openscience.cdk.HydrogenPlacer(atomContainer, bondLength);
     *
     * @param  atom      Atom to saturate
     * @param  container AtomContainer containing the atom
     * @param  totalContainer In case you have a container containing multiple structures, this is the total container, whereas container is a partial structure
     *
     * @cdk.keyword          hydrogen, adding
     * @cdk.keyword          explicit hydrogen
     */
    public IAtomContainer addExplicitHydrogensToSatisfyValency(IAtomContainer container, IAtom atom, IAtomContainer totalContainer) 
        throws IOException, ClassNotFoundException, CDKException
    {
        // set number of implicit hydrogens to zero
        // add explicit hydrogens
	logger.debug("Start of addExplicitHydrogensToSatisfyValency(AtomContainer container, Atom atom)");
        int missingHydrogens = calculateNumberOfImplicitHydrogens(container, atom);
  logger.debug("According to valencyChecker, " + missingHydrogens + " are missing");
        IAtomContainer changedAtomsAndBonds = addExplicitHydrogensToSatisfyValency(container, atom, missingHydrogens, totalContainer);
	logger.debug("End of addExplicitHydrogensToSatisfyValency(AtomContainer container, Atom atom)");
    return changedAtomsAndBonds;
    }
    
    /**
     * Method that saturates an atom in a molecule by adding explicit hydrogens.
     *
     * @param  atom      Atom to saturate
     * @param  container AtomContainer containing the atom
     * @param  count     Number of hydrogens to add
     * @param  totalContainer In case you have a container containing multiple structures, this is the total container, whereas container is a partial structure
     *
     * @cdk.keyword          hydrogen, adding
     * @cdk.keyword          explicit hydrogen
     */
    public IAtomContainer addExplicitHydrogensToSatisfyValency(IAtomContainer container, IAtom atom, int count, IAtomContainer totalContainer) 
        throws IOException, ClassNotFoundException
    {
        //boolean create2DCoordinates = GeometryTools.has2DCoordinates(container);
        
        IIsotope isotope = IsotopeFactory.getInstance(container.getBuilder()).getMajorIsotope("H");
        atom.setHydrogenCount(0);
        IAtomContainer changedAtomsAndBonds = container.getBuilder().newAtomContainer();
        for (int i = 1; i <= count; i++) {
            IAtom hydrogen = container.getBuilder().newAtom("H");
            IsotopeFactory.getInstance(container.getBuilder()).configure(hydrogen, isotope);
            totalContainer.addAtom(hydrogen);
            IBond newBond = container.getBuilder().newBond((IAtom)atom, hydrogen, 1.0);
            totalContainer.addBond(newBond);
            changedAtomsAndBonds.addAtom(hydrogen);
            changedAtomsAndBonds.addBond(newBond);
        }
        return changedAtomsAndBonds;
    }
    
    /**
     * Method that saturates a molecule by adding implicit hydrogens.
     *
     *@param  container  Molecule to saturate
     *@cdk.keyword          hydrogen, adding
     *@cdk.keyword          implicit hydrogen
     */
    public HashMap addImplicitHydrogensToSatisfyValency(IAtomContainer container) throws CDKException {
      IMoleculeSet moleculeSet = ConnectivityChecker.partitionIntoMolecules(container);
      HashMap hydrogenAtomMap = new HashMap();
      for (int k = 0; k < moleculeSet.getAtomContainerCount(); k++) {
    	IMolecule molPart = moleculeSet.getMolecule(k);
        java.util.Iterator atoms = molPart.atoms();
        while (atoms.hasNext()) {
        	IAtom atom = (IAtom)atoms.next();
            int[] hydrogens = addImplicitHydrogensToSatisfyValency(molPart, atom);
            hydrogenAtomMap.put(atom, hydrogens);
        }
      }
      return hydrogenAtomMap;
    }
    
    /**
     * Method that saturates an atom in a molecule by adding implicit hydrogens.
     *
     * @param  container  Molecule to saturate
     * @param  atom      Atom to satureate.
     * @cdk.keyword          hydrogen, adding
     * @cdk.keyword          implicit hydrogen
     */
    public int[] addImplicitHydrogensToSatisfyValency(IAtomContainer container, IAtom atom) throws CDKException
    {
        int formerHydrogens = atom.getHydrogenCount();
        int missingHydrogens = calculateNumberOfImplicitHydrogens(container, atom);
        atom.setHydrogenCount(missingHydrogens);
        int[] hydrogens = new int[2];
        hydrogens[0] = formerHydrogens;
        hydrogens[1] = missingHydrogens;
        return hydrogens;
    }

    private int calculateNumberOfImplicitHydrogens(IAtomContainer container, IAtom atom) throws CDKException {
    	return valencyChecker.calculateNumberOfImplicitHydrogens(atom, container);
    }
}