smilesgenerator.java

化学图形处理软件

						}
						if (container.getBond(parent, atom).getStereo() == CDKConstants.STEREO_BOND_UNDEFINED || container.getBond(parent, atom).getStereo() == CDKConstants.STEREO_BOND_NONE)
						{
							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() == CDKConstants.STEREO_BOND_UP)
									{
										sorted[1] = (IAtom) chiralNeighbours.get(i);
									}
								}
							}
						}
					}
					if (BondTools.isTetrahedral(container, atom,false) == 6)
					{
						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_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_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 && 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 && !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() == 0)
									{
										sorted[1] = (IAtom) chiralNeighbours.get(i);
									}
								}
							}
						}
						if (container.getBond(parent, atom).getStereo() == CDKConstants.STEREO_BOND_UNDEFINED || container.getBond(parent, atom).getStereo() == CDKConstants.STEREO_BOND_NONE)
						{
							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 && 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 && !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)
									{
										sorted[1] = (IAtom) chiralNeighbours.get(i);
									}
								}
							}
						}
					}
					if (BondTools.isSquarePlanar(container, atom))
					{
						sorted = new IAtom[3];
						//This produces a U=SP1 order in every case
						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 = 0; i < ohere.length; i++)
						{
							sorted[i] = ((IAtom) chiralNeighbours.get(((Integer) ohere[i]).intValue()));
						}
					}
					if (BondTools.isTrigonalBipyramidalOrOctahedral(container, atom)!=0)
					{
						sorted = new IAtom[container.getConnectedAtomsCount(atom) - 1];
						TreeMap hm = new TreeMap();
						if (container.getBond(parent, atom).getStereo() == CDKConstants.STEREO_BOND_UP)
						{
							for (int i = 0; i < chiralNeighbours.size(); i++)
							{
								if (container.getBond(atom, (IAtom) chiralNeighbours.get(i)).getStereo() == 0)
								{
									hm.put(new Double(BondTools.giveAngle(atom, parent, ((IAtom) chiralNeighbours.get(i)))), new Integer(i));
								}
								if (container.getBond(atom, (IAtom) chiralNeighbours.get(i)).getStereo() == CDKConstants.STEREO_BOND_DOWN)
								{
									sorted[sorted.length - 1] = (IAtom) chiralNeighbours.get(i);
								}
							}
							Object[] ohere = hm.values().toArray();
							for (int i = 0; i < ohere.length; i++)
							{
								sorted[i] = ((IAtom) chiralNeighbours.get(((Integer) ohere[i]).intValue()));
							}
						}
						if (container.getBond(parent, atom).getStereo() == CDKConstants.STEREO_BOND_DOWN)
						{
							for (int i = 0; i < chiralNeighbours.size(); i++)
							{
								if (container.getBond(atom, (IAtom) chiralNeighbours.get(i)).getStereo() == 0)
								{
									hm.put(new Double(BondTools.giveAngle(atom, parent, ((IAtom) chiralNeighbours.get(i)))), new Integer(i));
								}
								if (container.getBond(atom, (IAtom) chiralNeighbours.get(i)).getStereo() == CDKConstants.STEREO_BOND_UP)
								{
									sorted[sorted.length - 1] = (IAtom) chiralNeighbours.get(i);
								}
							}
							Object[] ohere = hm.values().toArray();
							for (int i = 0; i < ohere.length; i++)
							{
								sorted[i] = ((IAtom) chiralNeighbours.get(((Integer) ohere[i]).intValue()));
							}
						}
						if (container.getBond(parent, atom).getStereo() == 0)
						{
							for (int i = 0; i < chiralNeighbours.size(); i++)
							{
								if (chiralNeighbours.get(i) != parent)
								{
									if (container.getBond(atom, (IAtom) chiralNeighbours.get(i)).getStereo() == 0)
									{
										hm.put(new Double((BondTools.giveAngleFromMiddle(atom, parent, ((IAtom) chiralNeighbours.get(i))))), new Integer(i));
									}
									if (container.getBond(atom, (IAtom) chiralNeighbours.get(i)).getStereo() == CDKConstants.STEREO_BOND_UP)
									{
										sorted[0] = (IAtom) chiralNeighbours.get(i);
									}
									if (container.getBond(atom, (IAtom) chiralNeighbours.get(i)).getStereo() == CDKConstants.STEREO_BOND_DOWN)
									{
										sorted[sorted.length - 2] = (IAtom) chiralNeighbours.get(i);
									}
								}
							}
							Object[] ohere = hm.values().toArray();
							sorted[sorted.length - 1] = ((IAtom) chiralNeighbours.get(((Integer) ohere[ohere.length - 1]).intValue()));
							if (ohere.length == 2)
							{
								sorted[sorted.length - 3] = ((IAtom) chiralNeighbours.get(((Integer) ohere[0]).intValue()));
								if (BondTools.giveAngleFromMiddle(atom, parent, ((IAtom) chiralNeighbours.get(((Integer) ohere[1]).intValue()))) < 0)
								{
									IAtom dummy = sorted[sorted.length - 2];
									sorted[sorted.length - 2] = sorted[0];
									sorted[0] = dummy;
								}
							}
							if (ohere.length == 3)
							{
								sorted[sorted.length - 3] = sorted[sorted.length - 2];
								sorted[sorted.length - 2] = ((IAtom) chiralNeighbours.get(((Integer) ohere[ohere.length - 2]).intValue()));
								sorted[sorted.length - 4] = ((IAtom) chiralNeighbours.get(((Integer) ohere[ohere.length - 3]).intValue()));
							}
						}
					}
					//This builds an onew[] containing the objects after the center of the chirality in the order given by sorted[]
					if (sorted != null)
					{
						int numberOfAtoms = 3;
						if (BondTools.isTrigonalBipyramidalOrOctahedral(container, atom)!=0)
						{
							numberOfAtoms = container.getConnectedAtomsCount(atom) - 1;
						}
						Object[] omy = new Object[numberOfAtoms];
						Object[] onew = new Object[numberOfAtoms];
						for (int k = getRingOpenings(atom, null).size(); k < numberOfAtoms; k++)
						{
							if (positionInVector + 1 + k - getRingOpenings(atom, null).size() < v.size())
							{
								omy[k] = v.get(positionInVector + 1 + k - getRingOpenings(atom, null).size());
							}
						}
						for (int k = 0; k < sorted.length; k++)
						{
							if (sorted[k] != null)
							{
								for (int m = 0; m < omy.length; m++)
								{
									if (omy[m] instanceof IAtom)
									{
										if (omy[m] == sorted[k])
										{
											onew[k] = omy[m];
										}
									} else
									{
										if (omy[m] == null)
										{
											onew[k] = null;
										} else
										{
											if (((Vector) omy[m]).get(0) == sorted[k])
											{
												onew[k] = omy[m];
											}
										}
									}
								}
							} else
							{
								onew[k] = null;
							}
						}
						//This is a workaround for 3624.MOL.2 I don't have a better solution currently
						boolean doubleentry = false;
						for (int m = 0; m < onew.length; m++)
						{
							for (int k = 0; k < onew.length; k++)
							{
								if (m != k && onew[k] == onew[m])
								{
									doubleentry = true;
								}
							}
						}
						if (!doubleentry)
						{
							//Make sure that the first atom in onew is the first one in the original smiles order. This is important to have a canonical smiles.
							if (positionInVector + 1 < v.size())
							{
								Object atomAfterCenterInOriginalSmiles = v.get(positionInVector + 1);
								int l = 0;
								while (onew[0] != atomAfterCenterInOriginalSmiles)
								{
									Object placeholder = onew[onew.length - 1];
									for (int k = onew.length - 2; k > -1; k--)
									{
										onew[k + 1] = onew[k];
									}
									onew[0] = placeholder;
									l++;
									if (l > onew.length)
									{
										break;
									}
								}
							}
							//This cares about ring openings. Here the ring closure (represendted by a figure) must be the first atom. In onew the closure is null.
							if (getRingOpenings(atom, null).size() > 0)
							{
								int l = 0;
								while (onew[0] != null)
								{
									Object placeholder = onew[0];
									for (int k = 1; k < onew.length; k++)
									{
										onew[k - 1] = onew[k];
									}
									onew[onew.length - 1] = placeholder;
									l++;
									if (l > onew.length)
									{
										break;
									}
								}
							}
							//The last in onew is a vector: This means we need to exchange the rest of the original smiles with the rest of this vector.
							if (onew[numberOfAtoms - 1] instanceof Vector)
							{
								for (int i = 0; i < numberOfAtoms; i++)
								{
									if (onew[i] instanceof IAtom)
									{
										Vector vtemp = new Vector();
										vtemp.add(onew[i]);
										for (int k = positionInVector + 1 + numberOfAtoms; k < v.size(); k++)
										{
											vtemp.add(v.get(k));
										}
										onew[i] = vtemp;
										for (int k = v.size() - 1; k > positionInVector + 1 + numberOfAtoms - 1; k--)
										{
											v.remove(k);
										}
										for (int k = 1; k < ((Vector) onew[numberOfAtoms - 1]).size(); k++)
										{
											v.add(((Vector) onew[numberOfAtoms - 1]).get(k));
										}
										onew[numberOfAtoms - 1] = ((Vector) onew[numberOfAtoms - 1]).get(0);
										break;
									}
								}
							}
							//Put the onew objects in the original Vector
							int k = 0;
							for (int m = 0; m < onew.length; m++)
							{
								if (onew[m] != null)
								{
									v.set(positionInVector + 1 + k, onew[m]);
									k++;
								}
							}
						}
					}
				}
				parent = atom;
			} else
			{
				//Have Vector
				//logger.debug("in parseChain after else");
				boolean brackets = true;
				Vector result = new Vector();
				addAtoms((Vector) o, result);
				if (isRingOpening(parent, result) && container.getConnectedBondsCount(parent) < 4)
				{
					brackets = false;
				}
				if (brackets)
				{
					buffer.append('(');
				}
				parseChain((Vector) o, buffer, container, parent, chiral, doubleBondConfiguration, atomsInOrderOfSmiles, useAromaticity);
				if (brackets)
				{
					buffer.append(')');
				}
			}

			positionInVector++;
			//logger.debug("in parseChain after positionVector++");
		}
	}


	/**
	 *  Append the symbol for the bond order between <code>a1</code> and <code>a2</code>
	 *  to the <code>line</code>.
	 *
	 *@param  line           the StringBuffer that the bond symbol is appended to.
	 *@param  a1             Atom participating in the bond.
	 *@param  a2             Atom participating in the bond.
	 *@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 parseBond(StringBuffer line, IAtom a1, IAtom a2, IAtomContainer atomContainer, boolean useAromaticity)
	{
		//logger.debug("in parseBond()");
		if (useAromaticity && a1.getFlag(CDKConstants.ISAROMATIC) && a2.getFlag(CDKConstants.ISAROMATIC))
		{