smilesgenerator.java

化学图形处理软件

			return;
		}
		if (atomContainer.getBond(a1, a2) == null)
		{
			return;
		}
		int type = 0;
		type = (int) atomContainer.getBond(a1, a2).getOrder();
		if (type == 1)
		{
		} else if (type == 2)
		{
			line.append("=");

		} else if (type == 3)
		{
			line.append("#");
		} else
		{
			// //logger.debug("Unknown bond type");
		}
	}


	/**
	 *  Generates the SMILES string for the atom
	 *
	 *@param  a                        the atom to generate the SMILES for.
	 *@param  buffer                   the string buffer that the atom is to be
	 *      apended to.
	 *@param  container                the AtomContainer to analyze.
	 *@param  chiral                   is a chiral smiles wished?
	 *@param  parent                   the atom we came from.
	 *@param  atomsInOrderOfSmiles     a vector containing the atoms in the order
	 *      they are in the smiles.
	 *@param  currentChain             The chain we currently deal with.
   	 *@param useAromaticity				true=aromaticity or sp2 will trigger lower case letters, wrong=only sp2
	 */
	private void parseAtom(IAtom a, StringBuffer buffer, IAtomContainer container, boolean chiral, boolean[] doubleBondConfiguration, IAtom parent, Vector atomsInOrderOfSmiles, Vector currentChain, boolean useAromaticity)
	{
		String symbol = a.getSymbol();
		boolean stereo = BondTools.isStereo(container, a);
		boolean brackets = symbol.equals("B") || symbol.equals("C") || symbol.equals("N") || symbol.equals("O") || symbol.equals("P") || symbol.equals("S") || symbol.equals("F") || symbol.equals("Br") || symbol.equals("I") || symbol.equals("Cl");
		brackets = !brackets;
		//logger.debug("in parseAtom()");
		//Deal with the start of a double bond configuration
		if (isStartOfDoubleBond(container, a, parent, doubleBondConfiguration))
		{
			buffer.append('/');
		}

		if (a instanceof IPseudoAtom)
		{
			buffer.append("[*]");
		} else
		{
			String mass = generateMassString(a);
			brackets = brackets | !mass.equals("");

			String charge = generateChargeString(a);
			brackets = brackets | !charge.equals("");

			if (chiral && stereo && (BondTools.isTrigonalBipyramidalOrOctahedral(container, a)!=0 || BondTools.isSquarePlanar(container, a) || BondTools.isTetrahedral(container, a,false) != 0 || BondTools.isSquarePlanar(container, a)))
			{
				brackets = true;
			}
			if (brackets)
			{
				buffer.append('[');
			}
			buffer.append(mass);
			if ((useAromaticity && a.getFlag(CDKConstants.ISAROMATIC)) || (a.getHybridization() != CDKConstants.UNSET && a.getHybridization() == CDKConstants.HYBRIDIZATION_SP2))
			{
				buffer.append(a.getSymbol().toLowerCase());
			} else
			{
				buffer.append(symbol);
			}
			if (a.getProperty(RING_CONFIG) != null && a.getProperty(RING_CONFIG).equals(UP))
			{
				buffer.append('/');
			}
			if (a.getProperty(RING_CONFIG) != null && a.getProperty(RING_CONFIG).equals(DOWN))
			{
				buffer.append('\\');
			}
			if (chiral && stereo && (BondTools.isTrigonalBipyramidalOrOctahedral(container, a)!=0 || BondTools.isSquarePlanar(container, a) || BondTools.isTetrahedral(container, a,false) != 0))
			{
				buffer.append('@');
			}
			if (chiral && stereo && BondTools.isSquarePlanar(container, a))
			{
				buffer.append("SP1");
			}
			//chiral
			//hcount
			buffer.append(charge);
			if (brackets)
			{
				buffer.append(']');
			}
		}
		//logger.debug("in parseAtom() after dealing with Pseudoatom or not");
		//Deal with the end of a double bond configuration
		if (isEndOfDoubleBond(container, a, parent, doubleBondConfiguration))
		{
			IAtom viewFrom = null;
			for (int i = 0; i < currentChain.size(); i++)
			{
				if (currentChain.get(i) == parent)
				{
					int k = i - 1;
					while (k > -1)
					{
						if (currentChain.get(k) instanceof IAtom)
						{
							viewFrom = (IAtom) currentChain.get(k);
							break;
						}
						k--;
					}
				}
			}
			if (viewFrom == null)
			{
				for (int i = 0; i < atomsInOrderOfSmiles.size(); i++)
				{
					if (atomsInOrderOfSmiles.get(i) == parent)
					{
						viewFrom = (IAtom) atomsInOrderOfSmiles.get(i - 1);
					}
				}
			}
			boolean afterThisAtom = false;
			IAtom viewTo = null;
			for (int i = 0; i < currentChain.size(); i++)
			{
				if (afterThisAtom && currentChain.get(i) instanceof IAtom)
				{
					viewTo = (IAtom) currentChain.get(i);
					break;
				}
				if (afterThisAtom && currentChain.get(i) instanceof Vector)
				{
					viewTo = (IAtom) ((Vector) currentChain.get(i)).get(0);
					break;
				}
				if (a == currentChain.get(i))
				{
					afterThisAtom = true;
				}
			}
      try{
        if (BondTools.isCisTrans(viewFrom,a,parent,viewTo,container))
        {
          buffer.append('\\');
        } else
        {
          buffer.append('/');
        }
      }catch(CDKException ex){
        //If the user wants a double bond configuration, where there is none, we ignore this.
      }
		}
		Vector v = new Vector();
		Iterator it = getRingOpenings(a, v).iterator();
		Iterator it2 = v.iterator();
		//logger.debug("in parseAtom() after checking for Ring openings");
		while (it.hasNext())
		{
			Integer integer = (Integer) it.next();
			IAtom a2=(IAtom) it2.next();
			IBond b = container.getBond(a2, a);
			int type = (int) b.getOrder();
			if (!(useAromaticity && a.getFlag(CDKConstants.ISAROMATIC) && a2.getFlag(CDKConstants.ISAROMATIC))){
				if (type == 2) {
					buffer.append("=");
				} else if (type == 3) {
					buffer.append("#");
				}
			}
			buffer.append(integer);
		}
		atomsInOrderOfSmiles.add(a);
		//logger.debug("End of parseAtom()");
	}


	/**
	 *  Creates a string for the charge of atom <code>a</code>. If the charge is 1
	 *  + is returned if it is -1 - is returned. The positive values all have + in
	 *  front of them.
	 *
	 *@return    string representing the charge on <code>a</code>
	 */
	private String generateChargeString(IAtom a)
	{
		int charge = a.getFormalCharge();
		StringBuffer buffer = new StringBuffer(3);
		if (charge > 0)
		{
			//Positive
			buffer.append('+');
			if (charge > 1)
			{
				buffer.append(charge);
			}
		} else if (charge < 0)
		{
			//Negative
			if (charge == -1)
			{
				buffer.append('-');
			} else
			{
				buffer.append(charge);
			}
		}
		return buffer.toString();
	}


	/**
	 *  Creates a string containing the mass of the atom <code>a</code>. If the
	 *  mass is the same as the majour isotope an empty string is returned.
	 *
	 *@param  a  the atom to create the mass
	 */
	private String generateMassString(IAtom a)
	{
		if (isotopeFactory == null) setupIsotopeFactory(a.getBuilder());

        if (a instanceof IPseudoAtom) return Integer.toString(a.getMassNumber());

        IIsotope majorIsotope = isotopeFactory.getMajorIsotope(a.getSymbol());
		if (majorIsotope.getMassNumber() == a.getMassNumber())
		{
			return "";
		} else if (a.getMassNumber() == 0)
		{
			return "";
		} else
		{
			return Integer.toString(a.getMassNumber());
		}
	}


	private void setupIsotopeFactory(IChemObjectBuilder builder) {
		try {
			isotopeFactory = IsotopeFactory.getInstance(builder);
		} catch (IOException e) {
			e.printStackTrace();
		}
    }


	class BrokenBond
	{

		/**
		 *  The atoms which close the ring
		 */
		private org.openscience.cdk.interfaces.IAtom a1, a2;

		/**
		 *  The number of the marker
		 */
		private int marker;


		/**
		 *  Construct a BrokenBond between <code>a1</code> and <code>a2</code> with
		 *  the marker <code>marker</code>.
		 *
		 *@param  marker  the ring closure marker. (Great comment!)
		 */
		BrokenBond(org.openscience.cdk.interfaces.IAtom a1, org.openscience.cdk.interfaces.IAtom a2, int marker)
		{
			this.a1 = a1;
			this.a2 = a2;
			this.marker = marker;
		}


		/**
		 *  Getter method for a1 property
		 *
		 *@return    The a1 value
		 */
		public org.openscience.cdk.interfaces.IAtom getA1()
		{
			return a1;
		}


		/**
		 *  Getter method for a2 property
		 *
		 *@return    The a2 value
		 */
		public org.openscience.cdk.interfaces.IAtom getA2()
		{
			return a2;
		}


		/**
		 *  Getter method for marker property
		 *
		 *@return    The marker value
		 */
		public int getMarker()
		{
			return marker;
		}


		public String toString()
		{
			return Integer.toString(marker);
		}


		public boolean equals(Object o)
		{
			if (!(o instanceof BrokenBond))
			{
				return false;
			}
			BrokenBond bond = (BrokenBond) o;
			return (a1.equals(bond.getA1()) && a2.equals(bond.getA2())) || (a1.equals(bond.getA2()) && a2.equals(bond.getA1()));
		}
	}


	/**
	 *  Returns the current AllRingsFinder instance
	 *
	 *@return   the current AllRingsFinder instance
	 */
	public AllRingsFinder getRingFinder()
	{
		return ringFinder;
	}


	/**
	 *  Sets the current AllRingsFinder instance
	 * Use this if you want to customize the timeout for 
	 * the AllRingsFinder. AllRingsFinder is stopping its 
	 * quest to find all rings after a default of 5 seconds.
	 *
	 * @see org.openscience.cdk.ringsearch.AllRingsFinder
	 * 
	 * @param  ringFinder  The value to assign ringFinder.
	 */
	public void setRingFinder(AllRingsFinder ringFinder)
	{
		this.ringFinder = ringFinder;
	}

	/**
	 * @param false=only SP2-hybridized atoms will be lower case (default), true=SP2 or aromaticity trigger lower case 
	 */
	public void setUseAromaticityFlag(boolean useAromaticityFlag) {
		this.useAromaticityFlag = useAromaticityFlag;
	}

}