1 /* Copyright (C) 2001-2007  The Chemistry Development Kit (CDK) Project
2  *
3  *  Contact: cdk-devel@lists.sourceforge.net
4  *
5  *  This program is free software; you can redistribute it and/or
6  *  modify it under the terms of the GNU Lesser General Public License
7  *  as published by the Free Software Foundation; either version 2.1
8  *  of the License, or (at your option) any later version.
9  *  All we ask is that proper credit is given for our work, which includes
10  *  - but is not limited to - adding the above copyright notice to the beginning
11  *  of your source code files, and to any copyright notice that you may distribute
12  *  with programs based on this work.
13  *
14  *  This program is distributed in the hope that it will be useful,
15  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
16  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
17  *  GNU Lesser General Public License for more details.
18  *
19  *  You should have received a copy of the GNU Lesser General Public License
20  *  along with this program; if not, write to the Free Software
21  *  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
22  *
23  */
24 package org.openscience.cdk.aromaticity;
25 
26 import org.openscience.cdk.CDKConstants;
27 import org.openscience.cdk.interfaces.IAtom;
28 import org.openscience.cdk.interfaces.IAtomContainer;
29 import org.openscience.cdk.interfaces.IBond;
30 import org.openscience.cdk.interfaces.IRing;
31 
32 /**
33  * @cdk.module standard
34  * @cdk.githash
35  *
36  * @author Oliver Horlacher <oliver.horlacher@therastrat.com>
37  * @cdk.created    2002-03-14
38  *
39  * @cdk.keyword aromaticity detector
40  * @deprecated use {@link Aromaticity}
41  */
42 @Deprecated
43 public class AromaticityCalculator {
44 
45     /**
46      *  Tests the <code>ring</code> in the <code>molecule</code> for aromaticity. Uses the
47      *  H&uuml;ckel rule (4n + 2) pie electrons. sp<sup>2</sup> hybridized C contibute 1 electron non
48      *  sp<sup>2</sup> hybridized heteroatoms contribute 2 electrons (N and O should never be sp in
49      *  or anything else in a ring and d electron elements get to complicated)
50      *  sp<sup>2</sup> hybridized heteroatoms contribute 1 electron hybridization is worked out by
51      *  counting the number of bonds with order 2. Therefore sp<sup>2</sup> hybridization is assumed
52      *  if there is one bond of order 2. Otherwise sp<sup>3</sup> hybridization is assumed.
53      *
54      * @param  ring      the ring to test
55      * @param  atomContainer  the AtomContainer the ring is in
56      * @return           true if the ring is aromatic false otherwise.
57      */
isAromatic(IRing ring, IAtomContainer atomContainer)58     public static boolean isAromatic(IRing ring, IAtomContainer atomContainer) {
59 
60         java.util.Iterator<IAtom> ringAtoms = ring.atoms().iterator();
61         int eCount = 0;
62         java.util.List<IBond> conectedBonds;
63         int numDoubleBond = 0;
64         boolean allConnectedBondsSingle;
65 
66         while (ringAtoms.hasNext()) {
67             IAtom atom = ringAtoms.next();
68             numDoubleBond = 0;
69             allConnectedBondsSingle = true;
70             conectedBonds = atomContainer.getConnectedBondsList(atom);
71             for (IBond conectedBond : conectedBonds) {
72                 if (conectedBond.getOrder() == IBond.Order.DOUBLE && ring.contains(conectedBond)) {
73                     numDoubleBond++;
74                 }
75 
76                 // Count the Electron if bond order = 1.5
77                 else if (conectedBond.getFlag(CDKConstants.ISAROMATIC) && ring.contains(conectedBond)) {
78                     numDoubleBond = 1;
79                 }
80 
81                 if (conectedBond.getOrder() != IBond.Order.SINGLE) {
82                     allConnectedBondsSingle = false;
83                 }
84             }
85             if (numDoubleBond == 1) {
86                 //C or heteroatoms both contibute 1 electron in sp2 hybridized form
87                 eCount++;
88             } else if (!atom.getSymbol().equals("C")) {
89                 //Heteroatom probably in sp3 hybrid therefore 2 electrons contributed.
90                 eCount = eCount + 2;
91             } else if (atom.getFlag(CDKConstants.ISAROMATIC)) {
92                 eCount++;
93             } else if (allConnectedBondsSingle && atom.getSymbol().equals("C") && atom.getFormalCharge() == 1.0) {
94                 // This is for tropylium and kinds.
95                 // Dependence on hybridisation would be better:
96                 // empty p-orbital is needed
97                 continue;
98             } else {
99                 return false;
100             }
101         }
102         return eCount - 2 != 0 && (eCount - 2) % 4 == 0;
103     }
104 }
105