atomplacer3d.java

化学图形处理软件

	 * @param  id2            Description of the Parameter
	 * @param  id3            Description of the Parameter
	 * @return                The angleKey value
	 * @exception  Exception  Description of the Exception
	 */
	public double getAngleValue(String id1, String id2, String id3) throws Exception {
		String akey = "";
		if (pSet.containsKey(("angle" + id1 + ";" + id2 + ";" + id3))) {
			akey = "angle" + id1 + ";" + id2 + ";" + id3;
		} else if (pSet.containsKey(("angle" + id3 + ";" + id2 + ";" + id1))) {
			akey = "angle" + id3 + ";" + id2 + ";" + id1;
		} else if (pSet.containsKey(("angle" + id2 + ";" + id1 + ";" + id3))) {
			akey = "angle" + id2 + ";" + id1 + ";" + id3;
		} else if (pSet.containsKey(("angle" + id1 + ";" + id3 + ";" + id2))) {
			akey = "angle" + id1 + ";" + id3 + ";" + id2;
		} else if (pSet.containsKey(("angle" + id3 + ";" + id1 + ";" + id2))) {
			akey = "angle" + id3 + ";" + id1 + ";" + id2;
		} else if (pSet.containsKey(("angle" + id2 + ";" + id3 + ";" + id1))) {
			akey = "angle" + id2 + ";" + id3 + ";" + id1;
		} else {
			//logger.debug("KEYErrorAngle:Unknown angle key in pSet: " +id2 + " ; " + id3 + " ; " + id1+" take default angle:"+DEFAULT_ANGLE);
			return -1;
		}
		return ((Double) (((Vector) pSet.get(akey)).get(0))).doubleValue();
	}


	/**
	 *  Gets the nextUnplacedHeavyAtomWithAliphaticPlacedNeighbour from an atom container or molecule
	 *
	 * @return    The nextUnplacedHeavyAtomWithAliphaticPlacedNeighbour value
	 * author:    steinbeck,cho
	 */
	public IAtom getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(IAtomContainer molecule) {
        Iterator bonds = molecule.bonds();
        while (bonds.hasNext()) {
            IBond bond = (IBond) bonds.next();
			if (bond.getAtom(0).getFlag(CDKConstants.ISPLACED) & !(bond.getAtom(1).getFlag(CDKConstants.ISPLACED))) {
				if (bond.getAtom(1).getFlag(CDKConstants.ISALIPHATIC) & !bond.getAtom(1).getSymbol().equals("H")) {
					return bond.getAtom(1);
				}
			}
			if (bond.getAtom(1).getFlag(CDKConstants.ISPLACED) & !(bond.getAtom(0).getFlag(CDKConstants.ISPLACED))) {
				if (bond.getAtom(0).getFlag(CDKConstants.ISALIPHATIC) & !bond.getAtom(0).getSymbol().equals("H")) {
					return bond.getAtom(0);
				}
			}
		}
		return null;
	}

	/**
	 *  Gets the nextPlacedHeavyAtomWithAliphaticPlacedNeigbor from an atom container or molecule
	 *
	 * @return    The nextUnplacedHeavyAtomWithUnplacedAliphaticNeigbor
	 * author: steinbeck,cho
	 */
	public IAtom getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(IAtomContainer molecule) {
        Iterator bonds = molecule.bonds();
        while (bonds.hasNext()) {
            IBond bond = (IBond) bonds.next();
			IAtom atom0 = bond.getAtom(0);
			IAtom atom1 = bond.getAtom(1);
			if (atom0.getFlag(CDKConstants.ISPLACED) & !(atom1.getFlag(CDKConstants.ISPLACED))) {
				if (atom1.getFlag(CDKConstants.ISALIPHATIC) & !atom0.getSymbol().equals("H") & !atom1.getSymbol().equals("H")) {
					return atom0;
				}
			}
			if (atom1.getFlag(CDKConstants.ISPLACED) & !(atom0.getFlag(CDKConstants.ISPLACED))) {
				if (atom0.getFlag(CDKConstants.ISALIPHATIC) & !atom1.getSymbol().equals("H") & !atom0.getSymbol().equals("H")) {
					return atom1;
				}
			}
		}
		return null;
	}

	/**
	 *  Gets the nextPlacedHeavyAtomWithUnplacedRingNeighbour attribute of the AtomPlacer3D object
	 *
	 * @return    The nextPlacedHeavyAtomWithUnplacedRingNeighbour value
	 */
	public IAtom getNextPlacedHeavyAtomWithUnplacedRingNeighbour(IAtomContainer molecule) {
//		IBond[] bonds = molecule.getBonds();
        Iterator bonds = molecule.bonds();
        while (bonds.hasNext()) {
            IBond bond = (IBond) bonds.next();
			IAtom atom0 = bond.getAtom(0);
			IAtom atom1 = bond.getAtom(1);
			if (atom0.getFlag(CDKConstants.ISPLACED) & !(atom1.getFlag(CDKConstants.ISPLACED))) {
				if (atom1.getFlag(CDKConstants.ISINRING) & !atom0.getSymbol().equals("H") & !atom1.getSymbol().equals("H")) {
					return atom0;
				}
			}
			if (atom1.getFlag(CDKConstants.ISPLACED) & !(atom0.getFlag(CDKConstants.ISPLACED))) {
				if (atom0.getFlag(CDKConstants.ISINRING) & !atom1.getSymbol().equals("H") & !atom0.getSymbol().equals("H")) {
					return atom1;
				}
			}
		}
		return null;
	}

	/**
	 *  Gets the farthestAtom attribute of the AtomPlacer3D object
	 *
	 * @param  refAtomPoint  Description of the Parameter
	 * @param  ac            Description of the Parameter
	 * @return               The farthestAtom value
	 */
	public IAtom getFarthestAtom(Point3d refAtomPoint, IAtomContainer ac) {
		double distance = 0;
		IAtom atom = null;
		for (int i = 0; i < ac.getAtomCount(); i++) {
			if (ac.getAtom(i).getPoint3d() != null) {
				if (Math.abs(refAtomPoint.distance(ac.getAtom(i).getPoint3d())) > distance) {
					atom = ac.getAtom(i);
					distance = Math.abs(refAtomPoint.distance(ac.getAtom(i).getPoint3d()));
				}
			}
		}
		return atom;
	}

	/**
	 *  Gets the unplacedRingHeavyAtom attribute of the AtomPlacer3D object
	 *
	 * @param  atom  Description of the Parameter
	 * @return       The unplacedRingHeavyAtom value
	 */
	public IAtom getUnplacedRingHeavyAtom(IAtomContainer molecule, IAtom atom) {

		java.util.List bonds = molecule.getConnectedBondsList(atom);
		IAtom connectedAtom = null;
		for (int i = 0; i < bonds.size(); i++) {
			connectedAtom = ((IBond)bonds.get(i)).getConnectedAtom(atom);
			if (!connectedAtom.getFlag(CDKConstants.ISPLACED) && !connectedAtom.getSymbol().equals("H") && connectedAtom.getFlag(CDKConstants.ISINRING)) {
				return connectedAtom;
			}
		}
		return connectedAtom;
	}

	/**
	 *  Calculates the geometric center of all placed atoms in the atomcontainer
	 *
	 * @return    Point3d the geometric center
	 */
	public Point3d geometricCenterAllPlacedAtoms(IAtomContainer molecule) {
		IAtomContainer allPlacedAtoms = getAllPlacedAtoms(molecule);
		return GeometryToolsInternalCoordinates.get3DCenter(allPlacedAtoms);
	}

	/**
	 *  Returns an unplaced atom connected to a given atom
	 *
	 * @param  atom  The Atom whose unplaced bonding partners are to be returned
	 * @return       an unplaced heavy atom connected to a given atom
	 * author:      steinbeck,cho
	 */
	public IAtom getUnplacedHeavyAtom(IAtomContainer molecule, IAtom atom) {

		java.util.List bonds = molecule.getConnectedBondsList(atom);
		IAtom connectedAtom = null;
		for (int i = 0; i < bonds.size(); i++) {
			connectedAtom = ((IBond)bonds.get(i)).getConnectedAtom(atom);
			if (!connectedAtom.getFlag(CDKConstants.ISPLACED) & !connectedAtom.getSymbol().equals("H")) {
				return connectedAtom;
			}
		}
		return connectedAtom;
	}

	/**
	 *  Returns a placed atom connected to a given atom
	 *
	 * @param  atom  The Atom whose placed bonding partners are to be returned
	 * @return       a placed heavy atom connected to a given atom
	 * author:      steinbeck
	 */
	public IAtom getPlacedHeavyAtom(IAtomContainer molecule, IAtom atom) {

		java.util.List bonds = molecule.getConnectedBondsList(atom);
		IAtom connectedAtom = null;
		for (int i = 0; i < bonds.size(); i++) {
			connectedAtom = ((IBond)bonds.get(i)).getConnectedAtom(atom);
			if (connectedAtom.getFlag(CDKConstants.ISPLACED) & !connectedAtom.getSymbol().equals("H")) {
				return connectedAtom;
			}
		}
		return connectedAtom;
	}

	/**
	 *  Gets the placedAtom attribute of the AtomPlacer3D object
	 *
	 * @param  atomA  Description of the Parameter
	 * @param  atomB  Description of the Parameter
	 * @return        The placedAtom value
	 */
	public IAtom getPlacedAtom(IAtomContainer molecule, IAtom atomA, IAtom atomB) {

		java.util.List bonds = molecule.getConnectedBondsList(atomA);
		IAtom connectedAtom = null;
		for (int i = 0; i < bonds.size(); i++) {
			connectedAtom = ((IBond)bonds.get(i)).getConnectedAtom(atomA);
			if (connectedAtom.getFlag(CDKConstants.ISPLACED) && connectedAtom != atomB) {
				return connectedAtom;
			}
		}
		return connectedAtom;
	}

	/**
	 *  Gets the placedHeavyAtom attribute of the AtomPlacer3D object
	 *
	 * @param  atomA  Description of the Parameter
	 * @param  atomB  Description of the Parameter
	 * @return        The placedHeavyAtom value
	 */
	public IAtom getPlacedHeavyAtom(IAtomContainer molecule, IAtom atomA, IAtom atomB) {
		java.util.List bonds = molecule.getConnectedBondsList(atomA);
		IAtom connectedAtom = null;
		for (int i = 0; i < bonds.size(); i++) {
			connectedAtom = ((IBond)bonds.get(i)).getConnectedAtom(atomA);
			if (connectedAtom.getFlag(CDKConstants.ISPLACED) && !connectedAtom.getSymbol().equals("H")
					 && connectedAtom != atomB) {
				return connectedAtom;
			}
		}
		return connectedAtom;
	}

	/**
	 *  Gets the placedHeavyAtoms attribute of the AtomPlacer3D object
	 *
	 * @param  atom  Description of the Parameter
	 * @return       The placedHeavyAtoms value
	 */
	public IAtomContainer getPlacedHeavyAtoms(IAtomContainer molecule, IAtom atom) {

		java.util.List bonds = molecule.getConnectedBondsList(atom);
		IAtomContainer connectedAtoms = new org.openscience.cdk.AtomContainer();
		IAtom connectedAtom = null;
		for (int i = 0; i < bonds.size(); i++) {
			connectedAtom = ((IBond)bonds.get(i)).getConnectedAtom(atom);
			if (connectedAtom.getFlag(CDKConstants.ISPLACED) & !(connectedAtom.getSymbol().equals("H"))) {
				connectedAtoms.addAtom(connectedAtom);
			}
		}
		return connectedAtoms;
	}

	/**
	 *  Gets all unplacedAtoms around a atom
	 *
	 * @param  molecule AtomContainer
	 * @param  atom  atom: center of search
	 * @return       AtomContainer of unplaced atoms
	 */
	public IAtomContainer getUnplacedAtoms(IAtomContainer molecule, IAtom atom) {

		java.util.List bonds = molecule.getConnectedBondsList(atom);
		IAtomContainer connectedAtoms = new org.openscience.cdk.AtomContainer();
		IAtom connectedAtom = null;
		for (int i = 0; i < bonds.size(); i++) {
			connectedAtom = ((IBond)bonds.get(i)).getConnectedAtom(atom);
			if (!connectedAtom.getFlag(CDKConstants.ISPLACED)) {
				connectedAtoms.addAtom(connectedAtom);
			}
		}
		return connectedAtoms;
	}
	
	/**
	 *  Gets numberOfUnplacedHeavyAtoms (no Flag ISPLACED, no Hydrogens)
	 *
	 * @param  ac AtomContainer
	 * @return int #UnplacedAtoms 
	 */
	public int numberOfUnplacedHeavyAtoms(IAtomContainer ac) {
		int nUnplacedHeavyAtoms=0;
		for (int i = 0; i < ac.getAtomCount(); i++) {
			if (!ac.getAtom(i).getFlag(CDKConstants.ISPLACED) && !ac.getAtom(i).equals("H")) {
				nUnplacedHeavyAtoms+=1;
			}
		}
		return nUnplacedHeavyAtoms;
	}
	
	/**
	 *  Gets the allPlacedAtoms attribute of the AtomPlacer3D object
	 *
	 * @return    The allPlacedAtoms value
	 */
	public IAtomContainer getAllPlacedAtoms(IAtomContainer molecule) {
		IAtomContainer placedAtoms = new org.openscience.cdk.AtomContainer();
		for (int i = 0; i < molecule.getAtomCount(); i++) {
			if (molecule.getAtom(i).getFlag(CDKConstants.ISPLACED)) {
				placedAtoms.addAtom(molecule.getAtom(i));
			}
		}
		return placedAtoms;
	}

	/**
	 *  True is all the atoms in the given AtomContainer have been placed
	 *
	 * @param  ac  The AtomContainer to be searched
	 * @return     True is all the atoms in the given AtomContainer have been placed
	 */
	public boolean allHeavyAtomsPlaced(IAtomContainer ac) {
		for (int i = 0; i < ac.getAtomCount(); i++) {
			if (!ac.getAtom(i).getFlag(CDKConstants.ISPLACED) & !(ac.getAtom(i).getSymbol().equals("H"))) {
				return false;
			}
		}
		return true;
	}
}