smilesgenerator.java

化学图形处理软件

								{
									allrings.getAtom(k).setProperty(RING_CONFIG, UP);
								} else
								{
									allrings.getAtom(k).setProperty(RING_CONFIG, DOWN);
								}
							}
						}
					}
				}
			}
		}

		StringBuffer l = new StringBuffer();
		createSMILES(start, l, molecule, chiral, doubleBondConfiguration,useAromaticityFlag);
		rings = null;
		
		// remove all CanonicalLable/InvariancePair props
		for (int k = 0; k < molecule.getAtomCount(); k++) {
			molecule.getAtom(k).removeProperty("CanonicalLable");
			molecule.getAtom(k).removeProperty("InvariancePair");
		}
		
		return l.toString();
	}

	private org.openscience.cdk.interfaces.IAtom hasWedges(IAtomContainer ac, org.openscience.cdk.interfaces.IAtom a)
	{
		List atoms = ac.getConnectedAtomsList(a);
		IAtom atomi = null;
//		for (int i = 0; i < atoms.size(); i++)
//		{
//			atomi = (IAtom)atoms.get(i);
//			if (ac.getBond(a, atomi).getStereo() != CDKConstants.STEREO_BOND_NONE && !atomi.getSymbol().equals("H"))
//			{
//				return (atomi);
//			}
//		}
		for (int i = 0; i < atoms.size(); i++)
		{
			atomi = (IAtom)atoms.get(i);
			if (ac.getBond(a, atomi).getStereo() != CDKConstants.STEREO_BOND_NONE)
			{
				return (atomi);
			}
		}
		return (null);
	}


	/**
	 *  Says if an atom is the end of a double bond configuration
	 *
	 *@param  atom                     The atom which is the end of configuration
	 *@param  container                The atomContainer the atom is in
	 *@param  parent                   The atom we came from
	 *@param  doubleBondConfiguration  The array indicating where double bond
	 *      configurations are specified (this method ensures that there is
	 *      actually the possibility of a double bond configuration)
	 *@return                          false=is not end of configuration, true=is
	 */
	private boolean isEndOfDoubleBond(IAtomContainer container, org.openscience.cdk.interfaces.IAtom atom, org.openscience.cdk.interfaces.IAtom parent, boolean[] doubleBondConfiguration)
	{
		if (container.getBondNumber(atom, parent) == -1 || doubleBondConfiguration.length <= container.getBondNumber(atom, parent) || !doubleBondConfiguration[container.getBondNumber(atom, parent)])
		{
			return false;
		}
		// TO-DO: We make the silent assumption of unset hydrogen count equals zero hydrogen count here.
		int lengthAtom = container.getConnectedAtomsCount(atom) + ((atom.getHydrogenCount() == CDKConstants.UNSET) ? 0 : atom.getHydrogenCount());
		// TO-DO: We make the silent assumption of unset hydrogen count equals zero hydrogen count here.
		int lengthParent = container.getConnectedAtomsCount(parent) + ((parent.getHydrogenCount() == CDKConstants.UNSET) ? 0 : parent.getHydrogenCount());
		if (container.getBond(atom, parent) != null)
		{
			if (container.getBond(atom, parent).getOrder() == CDKConstants.BONDORDER_DOUBLE && (lengthAtom == 3 || (lengthAtom == 2 && atom.getSymbol().equals("N"))) && (lengthParent == 3 || (lengthParent == 2 && parent.getSymbol().equals("N"))))
			{
				List atoms = container.getConnectedAtomsList(atom);
				org.openscience.cdk.interfaces.IAtom one = null;
				org.openscience.cdk.interfaces.IAtom two = null;
				IAtom atomi = null;
				for (int i = 0; i < atoms.size(); i++)
				{
					atomi = (IAtom)container.getAtom(i);
					if (atomi != parent && one == null)
					{
						one = atomi;
					} else if (atomi != parent && one != null)
					{
						two = atomi;
					}
				}
				String[] morgannumbers = MorganNumbersTools.getMorganNumbersWithElementSymbol(container);
				if ((one != null && two == null && atom.getSymbol().equals("N") && Math.abs(BondTools.giveAngleBothMethods(parent, atom, one, true)) > Math.PI / 10) || (!atom.getSymbol().equals("N") && one != null && two != null && !morgannumbers[container.getAtomNumber(one)].equals(morgannumbers[container.getAtomNumber(two)])))
				{
					return (true);
				} else
				{
					return (false);
				}
			}
		}
		return (false);
	}


	/**
	 *  Says if an atom is the start of a double bond configuration
	 *
	 *@param  a                        The atom which is the start of configuration
	 *@param  container                The atomContainer the atom is in
	 *@param  parent                   The atom we came from
	 *@param  doubleBondConfiguration  The array indicating where double bond
	 *      configurations are specified (this method ensures that there is
	 *      actually the possibility of a double bond configuration)
	 *@return                          false=is not start of configuration, true=is
	 */
	private boolean isStartOfDoubleBond(IAtomContainer container, org.openscience.cdk.interfaces.IAtom a, org.openscience.cdk.interfaces.IAtom parent, boolean[] doubleBondConfiguration)
	{
		// TO-DO: We make the silent assumption of unset hydrogen count equals zero hydrogen count here.
		int lengthAtom = container.getConnectedAtomsCount(a) + ((a.getHydrogenCount() == CDKConstants.UNSET) ? 0 : a.getHydrogenCount());
		if (lengthAtom != 3 && (lengthAtom != 2 && a.getSymbol() != ("N")))
		{
			return (false);
		}
		List atoms = container.getConnectedAtomsList(a);
		org.openscience.cdk.interfaces.IAtom one = null;
		org.openscience.cdk.interfaces.IAtom two = null;
		boolean doubleBond = false;
		org.openscience.cdk.interfaces.IAtom nextAtom = null;
		IAtom atomi = null;
		for (int i = 0; i < atoms.size(); i++)
		{
			atomi = (IAtom)atoms.get(i);
			if (atomi != parent && container.getBond(atomi, a).getOrder() == CDKConstants.BONDORDER_DOUBLE && isEndOfDoubleBond(container, atomi, a, doubleBondConfiguration))
			{
				doubleBond = true;
				nextAtom = atomi;
			}
			if (atomi != nextAtom && one == null)
			{
				one = atomi;
			} else if (atomi != nextAtom && one != null)
			{
				two = atomi;
			}
		}
		String[] morgannumbers = MorganNumbersTools.getMorganNumbersWithElementSymbol(container);
		if (one != null && ((!a.getSymbol().equals("N") && two != null && !morgannumbers[container.getAtomNumber(one)].equals(morgannumbers[container.getAtomNumber(two)]) && doubleBond && doubleBondConfiguration[container.getBondNumber(a, nextAtom)]) || (doubleBond && a.getSymbol().equals("N") && Math.abs(BondTools.giveAngleBothMethods(nextAtom, a, parent, true)) > Math.PI / 10)))
		{
			return (true);
		} else
		{
			return (false);
		}
	}


	/**
	 *  Gets the bondBroken attribute of the SmilesGenerator object
	 */
	private boolean isBondBroken(IAtom a1, IAtom a2)
	{
		Iterator it = brokenBonds.iterator();
		while (it.hasNext())
		{
			BrokenBond bond = ((BrokenBond) it.next());
			if ((bond.getA1().equals(a1) || bond.getA1().equals(a2)) && (bond.getA2().equals(a1) || bond.getA2().equals(a2)))
			{
				return (true);
			}
		}
		return false;
	}


	/**
	 *  Determines if the atom <code>a</code> is a atom with a ring marker.
	 *
	 *@param  a  the atom to test
	 *@return    true if the atom participates in a bond that was broken in the
	 *      first pass.
	 */
//	private boolean isRingOpening(IAtom a)
//	{
//		Iterator it = brokenBonds.iterator();
//		while (it.hasNext())
//		{
//			BrokenBond bond = (BrokenBond) it.next();
//			if (bond.getA1().equals(a) || bond.getA2().equals(a))
//			{
//				return true;
//			}
//		}
//		return false;
//	}


	/**
	 *  Determines if the atom <code>a</code> is a atom with a ring marker.
     *
	 *@return     true if the atom participates in a bond that was broken in the
	 *      first pass.
	 */
	private boolean isRingOpening(IAtom a1, Vector v)
	{
		Iterator it = brokenBonds.iterator();
		while (it.hasNext())
		{
			BrokenBond bond = (BrokenBond) it.next();
			for (int i = 0; i < v.size(); i++)
			{
				if ((bond.getA1().equals(a1) && bond.getA2().equals((IAtom) v.get(i))) || (bond.getA1().equals((IAtom) v.get(i)) && bond.getA2().equals(a1)))
				{
					return true;
				}
			}
		}
		return false;
	}


	/**
	 *  Return the neighbours of atom <code>a</code> in canonical order with the
	 *  atoms that have high bond order at the front.
	 *
	 *@param  a          the atom whose neighbours are to be found.
	 *@param  container  the AtomContainer that is being parsed.
	 *@return            Vector of atoms in canonical oreder.
	 */
	private List getCanNeigh(final org.openscience.cdk.interfaces.IAtom a, final IAtomContainer container)
	{
		List v = container.getConnectedAtomsList(a);
		if (v.size() > 1)
		{
			Collections.sort(v,
				new Comparator()
				{
					public int compare(Object o1, Object o2)
					{
						return (int) (((Long) ((IAtom) o1).getProperty("CanonicalLable")).longValue() - ((Long) ((IAtom) o2).getProperty("CanonicalLable")).longValue());
					}
				});
		}
		return v;
	}


	/**
	 *  Gets the ringOpenings attribute of the SmilesGenerator object
	 */
	private Vector getRingOpenings(IAtom a, Vector vbonds)
	{
		Iterator it = brokenBonds.iterator();
		Vector v = new Vector(10);
		while (it.hasNext())
		{
			BrokenBond bond = (BrokenBond) it.next();
			if (bond.getA1().equals(a) || bond.getA2().equals(a))
			{
				v.add(new Integer(bond.getMarker()));
				if (vbonds != null)
				{
					vbonds.add(bond.getA1().equals(a) ? bond.getA2() : bond.getA1());
				}
			}
		}
		Collections.sort(v);
		return v;
	}


	/**
	 *  Returns true if the <code>atom</code> in the <code>container</code> has
	 *  been marked as a chiral center by the user.
	 */
//	private boolean isChiralCenter(IAtom atom, IAtomContainer container)
//	{
//		IBond[] bonds = container.getConnectedBonds(atom);
//		for (int i = 0; i < bonds.length; i++)
//		{
//			IBond bond = bonds[i];
//			int stereo = bond.getStereo();
//			if (stereo == CDKConstants.STEREO_BOND_DOWN ||
//					stereo == CDKConstants.STEREO_BOND_UP)
//			{
//				return true;
//			}
//		}
//		return false;
//	}


	/**
	 *  Gets the last atom object (not Vector) in a Vector as created by
	 *  createDSFTree.
	 *
	 *@param  v       The Vector
	 *@param  result  The feature to be added to the Atoms attribute
	 */
	private void addAtoms(Vector v, Vector result)
	{
		for (int i = 0; i < v.size(); i++)
		{
			if (v.get(i) instanceof IAtom)
			{
				result.add((IAtom) v.get(i));
			} else
			{
				addAtoms((Vector) v.get(i), result);
			}
		}
	}
	
	/**
	 *  Performes a DFS search on the <code>atomContainer</code>. Then parses the
	 *  resulting tree to create the SMILES string.
	 *
	 *@param  a                        the atom to start the search at.
	 *@param  line                     the StringBuffer that the SMILES is to be
	 *      appended to.
	 *@param  chiral                   true=SMILES will be chiral, false=SMILES
	 *      will not be chiral.
	 *@param  atomContainer            the AtomContainer that the SMILES string is
	 *      generated for.
	 *@param useAromaticity				true=aromaticity or sp2 will trigger lower case letters, wrong=only sp2
	 */
	private void createSMILES(org.openscience.cdk.interfaces.IAtom a, StringBuffer line, IAtomContainer atomContainer, boolean chiral, boolean[] doubleBondConfiguration, boolean useAromaticity)
	{
		Vector tree = new Vector();
		
		// set all ISVISITED labels to FALSE
		Iterator atoms = atomContainer.atoms();
		while (atoms.hasNext()) ((IAtom)atoms.next()).setFlag(CDKConstants.VISITED, false);
		
		createDFSTree(a, tree, null, atomContainer);
		//logger.debug("Done with tree");
		
		parseChain(tree, line, atomContainer, null, chiral, doubleBondConfiguration, new Vector(), useAromaticity);
	}


	/**
	 *  Recursively perform a DFS search on the <code>container</code> placing
	 *  atoms and branches in the vector <code>tree</code>.
	 *
	 *@param  a          the atom being visited.
	 *@param  tree       vector holding the tree.
	 *@param  parent     the atom we came from.
	 *@param  container  the AtomContainer that we are parsing.
	 */
	private void createDFSTree(org.openscience.cdk.interfaces.IAtom a, Vector tree, org.openscience.cdk.interfaces.IAtom parent, IAtomContainer container)
	{
		tree.add(a);
		List neighbours = getCanNeigh(a, container);
		neighbours.remove(parent);
		IAtom next;
		a.setFlag(CDKConstants.VISITED, true);
		//logger.debug("Starting with DFSTree and AtomContainer of size " + container.getAtomCount());
		//logger.debug("Current Atom has " + neighbours.size() + " neighbours");
		Iterator iter = neighbours.iterator();
		while (iter.hasNext()) {
			next = (IAtom)iter.next();
			if (!next.getFlag(CDKConstants.VISITED))
			{
				if (!iter.hasNext())
				{
					//Last neighbour therefore in this chain
					createDFSTree(next, tree, a, container);
				} else
				{
					Vector branch = new Vector();
					tree.add(branch);
					//logger.debug("adding branch");
					createDFSTree(next, branch, a, container);
				}
			} else