smilesgenerator.java

化学图形处理软件

			{
				//Found ring closure between next and a
				//logger.debug("found ringclosure in DFTTreeCreation");
				ringMarker++;
				BrokenBond bond = new BrokenBond(a, next, ringMarker);
				if (!brokenBonds.contains(bond))
				{
					brokenBonds.add(bond);
				} else
				{
					ringMarker--;
				}
			}
		}
	}


	/**
	 *  Parse a branch
	 */
	private void parseChain(Vector v, StringBuffer buffer, IAtomContainer container, IAtom parent, boolean chiral, boolean[] doubleBondConfiguration, Vector atomsInOrderOfSmiles, boolean useAromaticity)
	{
		int positionInVector = 0;
		IAtom atom;
		//logger.debug("in parse chain. Size of tree: " + v.size());
		for (int h = 0; h < v.size(); h++)
		{
			Object o = v.get(h);
			if (o instanceof IAtom)
			{
				atom = (IAtom) o;
				if (parent != null)
				{
					parseBond(buffer, atom, parent, container, useAromaticity);
				} else
				{
					if (chiral && BondTools.isStereo(container, atom))
					{
						parent = (IAtom) ((Vector) v.get(1)).get(0);
					}
				}
				parseAtom(atom, buffer, container, chiral, doubleBondConfiguration, parent, atomsInOrderOfSmiles, v, useAromaticity);
				//logger.debug("in parseChain after parseAtom()");
				/*
				 *  The principle of making chiral smiles is quite simple, although the code is
				 *  pretty uggly. The Atoms connected to the chiral center are put in sorted[] in the
				 *  order they have to appear in the smiles. Then the Vector v is rearranged according
				 *  to sorted[]
				 */
				if (chiral && BondTools.isStereo(container, atom) && container.getBond(parent, atom) != null)
				{
					//logger.debug("in parseChain in isChiral");
					IAtom[] sorted = null;
					List chiralNeighbours = container.getConnectedAtomsList(atom);
					if (BondTools.isTetrahedral(container, atom,false) > 0)
					{
						sorted = new IAtom[3];
					}
					if (BondTools.isTetrahedral(container, atom,false) == 1)
					{
						if (container.getBond(parent, atom).getStereo() == CDKConstants.STEREO_BOND_DOWN)
						{
							for (int i = 0; i < chiralNeighbours.size(); i++)
							{
								if (chiralNeighbours.get(i) != parent)
								{
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == 0 && BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom))
									{
										sorted[2] = (IAtom) chiralNeighbours.get(i);
									}
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == 0 && !BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom))
									{
										sorted[1] = (IAtom) chiralNeighbours.get(i);
									}
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == CDKConstants.STEREO_BOND_UP && !isBondBroken((IAtom) chiralNeighbours.get(i), atom))
									{
										sorted[0] = (IAtom) chiralNeighbours.get(i);
									}
								}
							}
						}
						if (container.getBond(parent, atom).getStereo() == CDKConstants.STEREO_BOND_UP)
						{
							for (int i = 0; i < chiralNeighbours.size(); i++)
							{
								if (chiralNeighbours.get(i) != parent)
								{
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == 0 && BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom))
									{
										sorted[1] = (IAtom) chiralNeighbours.get(i);
									}
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == 0 && !BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom))
									{
										sorted[2] = (IAtom) chiralNeighbours.get(i);
									}
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == CDKConstants.STEREO_BOND_DOWN && !isBondBroken((IAtom) chiralNeighbours.get(i), atom))
									{
										sorted[0] = (IAtom) chiralNeighbours.get(i);
									}
								}
							}
						}
						if (container.getBond(parent, atom).getStereo() == CDKConstants.STEREO_BOND_UNDEFINED || container.getBond(parent, atom).getStereo() == CDKConstants.STEREO_BOND_NONE)
						{
							boolean normalBindingIsLeft = false;
							for (int i = 0; i < chiralNeighbours.size(); i++)
							{
								if (chiralNeighbours.get(i) != parent)
								{
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == 0)
									{
										if (BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom))
										{
											normalBindingIsLeft = true;
											break;
										}
									}
								}
							}
							for (int i = 0; i < chiralNeighbours.size(); i++)
							{
								if (chiralNeighbours.get(i) != parent)
								{
									if (normalBindingIsLeft)
									{
										if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == 0)
										{
											sorted[0] = (IAtom) chiralNeighbours.get(i);
										}
										if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == CDKConstants.STEREO_BOND_UP)
										{
											sorted[2] = (IAtom) chiralNeighbours.get(i);
										}
										if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == CDKConstants.STEREO_BOND_DOWN)
										{
											sorted[1] = (IAtom) chiralNeighbours.get(i);
										}
									} else
									{
										if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == CDKConstants.STEREO_BOND_UP)
										{
											sorted[1] = (IAtom) chiralNeighbours.get(i);
										}
										if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == 0)
										{
											sorted[0] = (IAtom) chiralNeighbours.get(i);
										}
										if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == CDKConstants.STEREO_BOND_DOWN)
										{
											sorted[2] = (IAtom) chiralNeighbours.get(i);
										}
									}
								}
							}
						}
					}
					if (BondTools.isTetrahedral(container, atom,false) == 2)
					{
						if (container.getBond(parent, atom).getStereo() == CDKConstants.STEREO_BOND_UP)
						{
							for (int i = 0; i < chiralNeighbours.size(); i++)
							{
								if (chiralNeighbours.get(i) != parent)
								{
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == CDKConstants.STEREO_BOND_DOWN && BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom))
									{
										sorted[1] = (IAtom) chiralNeighbours.get(i);
									}
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == CDKConstants.STEREO_BOND_DOWN && !BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom))
									{
										sorted[2] = (IAtom) chiralNeighbours.get(i);
									}
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == CDKConstants.STEREO_BOND_UP && !isBondBroken((IAtom) chiralNeighbours.get(i), atom))
									{
										sorted[0] = (IAtom) chiralNeighbours.get(i);
									}
								}
							}
						}
						if (container.getBond(parent, atom).getStereo() == CDKConstants.STEREO_BOND_DOWN)
						{
							double angle1 = 0;
							double angle2 = 0;
							IAtom atom1 = null;
							IAtom atom2 = null;
							for (int i = 0; i < chiralNeighbours.size(); i++)
							{
								if (chiralNeighbours.get(i) != parent)
								{
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == CDKConstants.STEREO_BOND_UP && !isBondBroken((IAtom) chiralNeighbours.get(i), atom))
									{
										if (angle1 == 0)
										{
											angle1 = BondTools.giveAngle(atom, parent, (IAtom) chiralNeighbours.get(i));
											atom1 = (IAtom) chiralNeighbours.get(i);
										} else
										{
											angle2 = BondTools.giveAngle(atom, parent, (IAtom) chiralNeighbours.get(i));
											atom2 = (IAtom) chiralNeighbours.get(i);
										}
									}
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == CDKConstants.STEREO_BOND_DOWN && !isBondBroken((IAtom) chiralNeighbours.get(i), atom))
									{
										sorted[1] = (IAtom) chiralNeighbours.get(i);
									}
								}
							}
							if (angle1 < angle2)
							{
								sorted[0] = atom2;
								sorted[2] = atom1;
							} else
							{
								sorted[0] = atom1;
								sorted[2] = atom2;
							}
						}
					}
					if (BondTools.isTetrahedral(container, atom,false) == 3)
					{
						if (container.getBond(parent, atom).getStereo() == CDKConstants.STEREO_BOND_UP)
						{
							TreeMap hm = new TreeMap();
							for (int i = 0; i < chiralNeighbours.size(); i++)
							{
								if (chiralNeighbours.get(i) != parent && !isBondBroken((IAtom) chiralNeighbours.get(i), atom))
								{
									hm.put(new Double(BondTools.giveAngle(atom, parent, ((IAtom) chiralNeighbours.get(i)))), new Integer(i));
								}
							}
							Object[] ohere = hm.values().toArray();
							for (int i = ohere.length - 1; i > -1; i--)
							{
								sorted[i] = ((IAtom) chiralNeighbours.get(((Integer) ohere[i]).intValue()));
							}
						}
						if (container.getBond(parent, atom).getStereo() == 0)
						{
							double angle1 = 0;
							double angle2 = 0;
							IAtom atom1 = null;
							IAtom atom2 = null;
							for (int i = 0; i < chiralNeighbours.size(); i++)
							{
								if (chiralNeighbours.get(i) != parent)
								{
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == 0 && !isBondBroken((IAtom) chiralNeighbours.get(i), atom))
									{
										if (angle1 == 0)
										{
											angle1 = BondTools.giveAngle(atom, parent, (IAtom) chiralNeighbours.get(i));
											atom1 = (IAtom) chiralNeighbours.get(i);
										} else
										{
											angle2 = BondTools.giveAngle(atom, parent, (IAtom) chiralNeighbours.get(i));
											atom2 = (IAtom) chiralNeighbours.get(i);
										}
									}
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == CDKConstants.STEREO_BOND_UP && !isBondBroken((IAtom) chiralNeighbours.get(i), atom))
									{
										sorted[0] = (IAtom) chiralNeighbours.get(i);
									}
								}
							}
							if (angle1 < angle2)
							{
								sorted[1] = atom2;
								sorted[2] = atom1;
							} else
							{
								sorted[1] = atom1;
								sorted[2] = atom2;
							}
						}
					}
					if (BondTools.isTetrahedral(container, atom,false) == 4)
					{
						if (container.getBond(parent, atom).getStereo() == CDKConstants.STEREO_BOND_DOWN)
						{
							TreeMap hm = new TreeMap();
							for (int i = 0; i < chiralNeighbours.size(); i++)
							{
								if (chiralNeighbours.get(i) != parent && !isBondBroken((IAtom) chiralNeighbours.get(i), atom))
								{
									hm.put(new Double(BondTools.giveAngle(atom, parent, ((IAtom) chiralNeighbours.get(i)))), new Integer(i));
								}
							}
							Object[] ohere = hm.values().toArray();
							for (int i = ohere.length - 1; i > -1; i--)
							{
								sorted[i] = ((IAtom) chiralNeighbours.get(((Integer) ohere[i]).intValue()));
							}
						}
						if (container.getBond(parent, atom).getStereo() == 0)
						{
							double angle1 = 0;
							double angle2 = 0;
							IAtom atom1 = null;
							IAtom atom2 = null;
							for (int i = 0; i < chiralNeighbours.size(); i++)
							{
								if (chiralNeighbours.get(i) != parent)
								{
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == 0 && !isBondBroken((IAtom) chiralNeighbours.get(i), atom))
									{
										if (angle1 == 0)
										{
											angle1 = BondTools.giveAngle(atom, parent, (IAtom) chiralNeighbours.get(i));
											atom1 = (IAtom) chiralNeighbours.get(i);
										} else
										{
											angle2 = BondTools.giveAngle(atom, parent, (IAtom) chiralNeighbours.get(i));
											atom2 = (IAtom) chiralNeighbours.get(i);
										}
									}
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == CDKConstants.STEREO_BOND_DOWN && !isBondBroken((IAtom) chiralNeighbours.get(i), atom))
									{
										sorted[2] = (IAtom) chiralNeighbours.get(i);
									}
								}
							}
							if (angle1 < angle2)
							{
								sorted[1] = atom2;
								sorted[0] = atom1;
							} else
							{
								sorted[1] = atom1;
								sorted[0] = atom2;
							}
						}
					}
					if (BondTools.isTetrahedral(container, atom,false) == 5)
					{
						if (container.getBond(parent, atom).getStereo() == CDKConstants.STEREO_BOND_DOWN)
						{
							for (int i = 0; i < chiralNeighbours.size(); i++)
							{
								if (chiralNeighbours.get(i) != parent)
								{
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == CDKConstants.STEREO_BOND_UP)
									{
										sorted[0] = (IAtom) chiralNeighbours.get(i);
									}
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == 0)
									{
										sorted[2] = (IAtom) chiralNeighbours.get(i);
									}
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == CDKConstants.STEREO_BOND_DOWN)
									{
										sorted[1] = (IAtom) chiralNeighbours.get(i);
									}
								}
							}
						}
						if (container.getBond(parent, atom).getStereo() == CDKConstants.STEREO_BOND_UP)
						{
							for (int i = 0; i < chiralNeighbours.size(); i++)
							{
								if (chiralNeighbours.get(i) != parent)
								{
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == CDKConstants.STEREO_BOND_DOWN && BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom))
									{
										sorted[0] = (IAtom) chiralNeighbours.get(i);
									}
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == CDKConstants.STEREO_BOND_DOWN && !BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom))
									{
										sorted[2] = (IAtom) chiralNeighbours.get(i);
									}
									if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == 0)
									{
										sorted[1] = (IAtom) chiralNeighbours.get(i);
									}
								}
							}