bondtools.java

化学图形处理软件

			}
			return 0;
		}
		if (up == 1 && down == 0 && !strict)
		{
			return 3;
		}
		if (down == 1 && up == 0 && !strict)
		{
			return 4;
		}
		if (down == 2 && up == 1 && !strict)
		{
			return 5;
		}
		if (down == 1 && up == 2 && !strict)
		{
			return 6;
		}
		return 0;
	}


	/**
	 *  Says if an atom as a center of a trigonal-bipyramidal or actahedral
	 *  chirality
	 *
	 *@param  a          The atom which is the center
	 *@param  container  The atomContainer the atom is in
	 *@return            true=is square planar, false=is not
	 */
	public static int isTrigonalBipyramidalOrOctahedral(IAtomContainer container, IAtom a)
	{
		java.util.List atoms = container.getConnectedAtomsList(a);
		if (atoms.size() < 5 || atoms.size() > 6)
		{
			return (0);
		}
		java.util.List bonds = container.getConnectedBondsList(a);
        int up = 0;
		int down = 0;
		for (int i = 0; i < bonds.size(); i++)
		{
			IBond bond = (IBond)bonds.get(i);
			if (bond.getStereo() == CDKConstants.STEREO_BOND_UNDEFINED || bond.getStereo() == CDKConstants.STEREO_BOND_NONE)
			{
            }
			if (bond.getStereo() == CDKConstants.STEREO_BOND_UP)
			{
				up++;
			}
			if (bond.getStereo() == CDKConstants.STEREO_BOND_DOWN)
			{
				down++;
			}
		}
		if (up == 1 && down == 1)
		{
			if(atoms.size()==5)
				return 1;
			else
				return 2;
		}
		return 0;
	}


	/**
	 *  Says if an atom as a center of any valid stereo configuration or not
	 *
	 *@param  a          The atom which is the center
	 *@param  container  The atomContainer the atom is in
	 *@return            true=is a stereo atom, false=is not
	 */
	public static boolean isStereo(IAtomContainer container, IAtom a)
	{
		java.util.List atoms = container.getConnectedAtomsList(a);
		if (atoms.size() < 4 || atoms.size() > 6)
		{
			return (false);
		}
		java.util.List bonds = container.getConnectedBondsList(a);
		int stereo = 0;
		for (int i = 0; i < bonds.size(); i++)
		{
			if (((IBond)bonds.get(i)).getStereo() != 0)
			{
				stereo++;
			}
		}
		if (stereo == 0)
		{
			return false;
		}
		int differentAtoms = 0;
		for (int i = 0; i < atoms.size(); i++)
		{
			boolean isDifferent = true;
			for (int k = 0; k < i; k++)
			{
				if (((IAtom)atoms.get(i)).getSymbol().equals(((IAtom)atoms.get(i)).getSymbol()))
				{
					isDifferent = false;
					break;
				}
			}
			if (isDifferent)
			{
				differentAtoms++;
			}
		}
		if (differentAtoms != atoms.size())
		{
			int[] morgannumbers = MorganNumbersTools.getMorganNumbers(container);
			Vector differentSymbols = new Vector();
			for (int i = 0; i < atoms.size(); i++)
			{
				IAtom atom = (IAtom)atoms.get(i);
				if (!differentSymbols.contains(atom.getSymbol()))
				{
					differentSymbols.add(atom.getSymbol());
				}
			}
			int[] onlyRelevantIfTwo = new int[2];
			if (differentSymbols.size() == 2)
			{
				for (int i = 0; i < atoms.size(); i++)
				{
					IAtom atom = (IAtom)atoms.get(i);
					if (differentSymbols.indexOf(atom.getSymbol()) == 0)
					{
						onlyRelevantIfTwo[0]++;
					} else
					{
						onlyRelevantIfTwo[1]++;
					}
				}
			}
			boolean[] symbolsWithDifferentMorganNumbers = new boolean[differentSymbols.size()];
			Vector[] symbolsMorganNumbers = new Vector[differentSymbols.size()];
			for (int i = 0; i < symbolsWithDifferentMorganNumbers.length; i++)
			{
				symbolsWithDifferentMorganNumbers[i] = true;
				symbolsMorganNumbers[i] = new Vector();
			}
			for (int k = 0; k < atoms.size(); k++)
			{
				IAtom atom = (IAtom)atoms.get(k);
				int elementNumber = differentSymbols.indexOf(atom.getSymbol());
				if (symbolsMorganNumbers[elementNumber].contains(new Integer(morgannumbers[container.getAtomNumber(atom)])))
				{
					symbolsWithDifferentMorganNumbers[elementNumber] = false;
				} else
				{
					symbolsMorganNumbers[elementNumber].add(new Integer(morgannumbers[container.getAtomNumber(atom)]));
				}
			}
			int numberOfSymbolsWithDifferentMorganNumbers = 0;
			for (int i = 0; i < symbolsWithDifferentMorganNumbers.length; i++)
			{
				if (symbolsWithDifferentMorganNumbers[i] == true)
				{
					numberOfSymbolsWithDifferentMorganNumbers++;
				}
			}
			if (numberOfSymbolsWithDifferentMorganNumbers != differentSymbols.size())
			{
				if ((atoms.size() == 5 || atoms.size() == 6) && (numberOfSymbolsWithDifferentMorganNumbers + differentAtoms > 2 || (differentAtoms == 2 && onlyRelevantIfTwo[0] > 1 && onlyRelevantIfTwo[1] > 1)))
				{
					return (true);
				}
				if (isSquarePlanar(container, a) && (numberOfSymbolsWithDifferentMorganNumbers + differentAtoms > 2 || (differentAtoms == 2 && onlyRelevantIfTwo[0] > 1 && onlyRelevantIfTwo[1] > 1)))
				{
					return (true);
				}
				return false;
			}
		}
		return (true);
	}


	/**
	 *  Says if an atom as a center of a square planar chirality
	 *
	 *@param  a          The atom which is the center
	 *@param  container  The atomContainer the atom is in
	 *@return            true=is square planar, false=is not
	 */
	public static boolean isSquarePlanar(IAtomContainer container, IAtom a)
	{
		java.util.List atoms = container.getConnectedAtomsList(a);
		if (atoms.size() != 4)
		{
			return (false);
		}
		java.util.List bonds = container.getConnectedBondsList(a);
        int up = 0;
		int down = 0;
		for (int i = 0; i < bonds.size(); i++)
		{
			IBond bond = (IBond)bonds.get(i);
			if (bond.getStereo() == CDKConstants.STEREO_BOND_UNDEFINED || bond.getStereo() == CDKConstants.STEREO_BOND_NONE)
			{
            }
			if (bond.getStereo() == CDKConstants.STEREO_BOND_UP)
			{
				up++;
			}
			if (bond.getStereo() == CDKConstants.STEREO_BOND_DOWN)
			{
				down++;
			}
		}
		if (up == 2 && down == 2 && !stereosAreOpposite(container, a))
		{
			return true;
		}
		return false;
	}


	/**
	 *  Says if of four atoms connected two one atom the up and down bonds are
	 *  opposite or not, i. e.if it's tetrehedral or square planar. The method
	 *  doesnot check if there are four atoms and if two or up and two are down
	 *
	 *@param  a          The atom which is the center
	 *@param  container  The atomContainer the atom is in
	 *@return            true=are opposite, false=are not
	 */
	public static boolean stereosAreOpposite(IAtomContainer container, IAtom a)
	{
		List atoms = container.getConnectedAtomsList(a);
		TreeMap hm = new TreeMap();
		for (int i = 1; i < atoms.size(); i++)
		{
			hm.put(new Double(giveAngle(a, (IAtom) atoms.get(0), ((IAtom) atoms.get(i)))), new Integer(i));
		}
		Object[] ohere = hm.values().toArray();
		int stereoOne = container.getBond(a, (IAtom) atoms.get(0)).getStereo();
		int stereoOpposite = container.getBond(a, (IAtom) atoms.get((((Integer) ohere[1])).intValue())).getStereo();
		if (stereoOpposite == stereoOne)
		{
			return true;
		} else
		{
			return false;
		}
	}


	/**
	 *  Calls giveAngleBothMethods with bool = true
	 *
	 *@param  from  the atom to view from
	 *@param  to1   first direction to look in
	 *@param  to2   second direction to look in
	 *@return       The angle in rad from 0 to 2*PI
	 */
	public static double giveAngle(IAtom from, IAtom to1, IAtom to2)
	{
		return (giveAngleBothMethods(from, to1, to2, true));
	}


	/**
	 *  Calls giveAngleBothMethods with bool = false
	 *
	 *@param  from  the atom to view from
	 *@param  to1   first direction to look in
	 *@param  to2   second direction to look in
	 *@return       The angle in rad from -PI to PI
	 */
	public static double giveAngleFromMiddle(IAtom from, IAtom to1, IAtom to2)
	{
		return (giveAngleBothMethods(from, to1, to2, false));
	}
	
	public static void  makeUpDownBonds(IAtomContainer container){
	    for (int i = 0; i < container.getAtomCount(); i++) {
	        IAtom a = container.getAtom(i);
	        if (container.getConnectedAtomsList(a).size() == 4) {
	          int up = 0;
	          int down = 0;
	          int hs = 0;
	          IAtom h = null;
	          for (int k = 0; k < 4; k++) {
	        	  IAtom conAtom = (IAtom)container.getConnectedAtomsList(a).get(k);
	        	  int stereo = container.getBond(a,conAtom).getStereo();
	        	  if (stereo  == CDKConstants.STEREO_BOND_UP) {
	        		  up++;
	        	  }
	        	  else if (stereo == CDKConstants.STEREO_BOND_DOWN) {
	        		  down++;
	        	  }
	        	  else if (stereo == CDKConstants.STEREO_BOND_NONE && conAtom.getSymbol().equals("H")) {
	        		  h = conAtom;
	        		  hs++;
	        	  } else {
	        		  h = null;
	        	  }
	          }
	          if (up == 0 && down == 1 && h != null && hs == 1) {
	            container.getBond(a, h).setStereo(CDKConstants.STEREO_BOND_UP);
	          }
	          if (up == 1 && down == 0 && h != null && hs == 1) {
	            container.getBond(a, h).setStereo(CDKConstants.STEREO_BOND_DOWN);
	          }
	        }
	      }
	}
}