1 /* Copyright (C) 2004-2007 The Chemistry Development Kit (CDK) project 2 * 2013 European Bioinformatics Institute 3 * John May 4 * 5 * This library is free software; you can redistribute it and/or 6 * modify it under the terms of the GNU Lesser General Public 7 * License as published by the Free Software Foundation; either 8 * version 2.1 of the License, or (at your option) any later version. 9 * 10 * This library is distributed in the hope that it will be useful, 11 * but WITHOUT ANY WARRANTY; without even the implied warranty of 12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 * Lesser General Public License for more details. 14 * 15 * You should have received a copy of the GNU Lesser General Public 16 * License along with this library; if not, write to the Free Software 17 * Foundation, 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. 18 * (or see http://www.gnu.org/copyleft/lesser.html) 19 */ 20 package org.openscience.cdk.isomorphism.matchers.smarts; 21 22 import org.openscience.cdk.interfaces.IAtom; 23 import org.openscience.cdk.interfaces.IChemObjectBuilder; 24 25 /** 26 * Match an atom with the defined degree. The degree is also referred to as the 27 * explicit connectivity and is encoded in smarts using {@code D<NUMBER>}. 28 * 29 * @cdk.module smarts 30 * @cdk.keyword SMARTS 31 * @cdk.githash 32 */ 33 @Deprecated 34 public final class ExplicitConnectionAtom extends SMARTSAtom { 35 36 /** Number of explicit connections. */ 37 private int degree; 38 39 /** 40 * Create a query atom for matching the degree of an atom. The degree is the 41 * number connected atoms. 42 */ ExplicitConnectionAtom(int degree, IChemObjectBuilder builder)43 public ExplicitConnectionAtom(int degree, IChemObjectBuilder builder) { 44 super(builder); 45 this.degree = degree; 46 } 47 48 /**{@inheritDoc} */ 49 @Override matches(IAtom atom)50 public boolean matches(IAtom atom) { 51 // XXX: this is incorrect but bug 824 expects this behaviour. The reason 52 // Daylight matches is because the explicit hydrogens are 53 // suppressed by default turning on explicit hydrogens in depict 54 // match shows correct functionality. Discussion needed to revert 55 // but because other invariants aren't adjusted (implicit h) we 56 // can't really do this and the correct option is to enable/disable 57 // hydrogen suppression (removal of explicit H atoms) as a prepossessing 58 // step 59 return invariants(atom).connectivity() - invariants(atom).totalHydrogenCount() == degree; 60 } 61 } 62