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alternate methods to breaking the symmetry of uniform hashed atom env…
…ironments. Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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src/main/org/openscience/cdk/hash/equivalent/AllEquivalentCyclicSet.java
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| /* | ||
| * Copyright (c) 2013. John May <jwmay@users.sf.net> | ||
| * | ||
| * Contact: cdk-devel@lists.sourceforge.net | ||
| * | ||
| * This program is free software; you can redistribute it and/or | ||
| * modify it under the terms of the GNU Lesser General Public License | ||
| * as published by the Free Software Foundation; either version 2.1 | ||
| * of the License, or (at your option) any later version. | ||
| * All we ask is that proper credit is given for our work, which includes | ||
| * - but is not limited to - adding the above copyright notice to the beginning | ||
| * of your source code files, and to any copyright notice that you may distribute | ||
| * with programs based on this work. | ||
| * | ||
| * This program is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU Lesser General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU Lesser General Public License | ||
| * along with this program; if not, write to the Free Software | ||
| * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U | ||
| */ | ||
|
|
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| package org.openscience.cdk.hash.equivalent; | ||
|
|
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| import org.openscience.cdk.annotations.TestClass; | ||
| import org.openscience.cdk.annotations.TestMethod; | ||
| import org.openscience.cdk.interfaces.IAtomContainer; | ||
| import org.openscience.cdk.ringsearch.RingSearch; | ||
|
|
||
| import java.util.HashSet; | ||
| import java.util.Map; | ||
| import java.util.Set; | ||
| import java.util.TreeMap; | ||
| import java.util.TreeSet; | ||
|
|
||
| /** | ||
| * Finds the set of equivalent values are members of a ring. This class is | ||
| * intended to drive the systematic perturbation of the {@link | ||
| * org.openscience.cdk.hash.PerturbedAtomHashGenerator}. This {@link | ||
| * EquivalentSetFinder} provides the highest probability of avoid collisions due | ||
| * to uniform atom environments but is much more demanding then the simpler | ||
| * {@link MinimumEquivalentCyclicSet}. | ||
| * | ||
| * <p/><br/> The easiest way to use this class is with the {@link | ||
| * org.openscience.cdk.hash.HashGeneratorMaker}. | ||
| * <blockquote><pre> | ||
| * MoleculeHashGenerator generator = | ||
| * new HashGeneratorMaker().depth(6) | ||
| * .elemental() | ||
| * .perturbWith(new AllEquivalentCyclicSet()) | ||
| * .molecular(); | ||
| * </pre></blockquote> | ||
| * | ||
| * @author John May | ||
| * @cdk.module hash | ||
| * @see org.openscience.cdk.hash.PerturbedAtomHashGenerator | ||
| * @see MinimumEquivalentCyclicSet | ||
| * @see MinimumEquivalentCyclicSetUnion | ||
| */ | ||
| @TestClass("org.openscience.cdk.hash.equivalent.AllEquivalentCyclicSetTest") | ||
| public final class AllEquivalentCyclicSet implements EquivalentSetFinder { | ||
|
|
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| /** | ||
| * @inheritDoc | ||
| */ | ||
| @Override | ||
| @TestMethod("testFind,testFind_Distinct,testScenario") | ||
| public Set<Integer> find(long[] invariants, IAtomContainer container, int[][] graph) { | ||
|
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| int n = invariants.length; | ||
|
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| // find cyclic vertices using DFS | ||
| RingSearch ringSearch = new RingSearch(container, graph); | ||
|
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| // ordered map of the set of vertices for each value | ||
| Map<Long, Set<Integer>> equivalent = new TreeMap<Long, Set<Integer>>(); | ||
|
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| // divide the invariants into equivalent indexed and ordered sets | ||
| for (int i = 0; i < invariants.length; i++) { | ||
|
|
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| Long invariant = invariants[i]; | ||
| Set<Integer> set = equivalent.get(invariant); | ||
|
|
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| if (set == null) { | ||
| if (ringSearch.cyclic(i)) { | ||
| set = new HashSet<Integer>(n / 2); | ||
| set.add(i); | ||
| equivalent.put(invariant, set); | ||
| } | ||
| } else { | ||
| set.add(i); | ||
| } | ||
| } | ||
|
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| // find the smallest set of equivalent cyclic vertices | ||
| Set<Integer> set = new TreeSet<Integer>(); | ||
| for (Map.Entry<Long, Set<Integer>> e : equivalent.entrySet()) { | ||
| Set<Integer> vertices = e.getValue(); | ||
| if (vertices.size() > 1) { | ||
| set.addAll(vertices); | ||
| } | ||
| } | ||
|
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||
| return set; | ||
| } | ||
| } |
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src/main/org/openscience/cdk/hash/equivalent/MinimumEquivalentCyclicSetUnion.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,110 @@ | ||
| package org.openscience.cdk.hash.equivalent; | ||
|
|
||
| import org.openscience.cdk.annotations.TestClass; | ||
| import org.openscience.cdk.annotations.TestMethod; | ||
| import org.openscience.cdk.interfaces.IAtomContainer; | ||
| import org.openscience.cdk.ringsearch.RingSearch; | ||
|
|
||
| import java.util.Collections; | ||
| import java.util.HashSet; | ||
| import java.util.Map; | ||
| import java.util.Set; | ||
| import java.util.TreeMap; | ||
|
|
||
| /** | ||
| * The union of all the smallest set of equivalent values are members of a ring. | ||
| * This class is intended to drive the systematic perturbation of the {@link | ||
| * org.openscience.cdk.hash.PerturbedAtomHashGenerator}. The method is more | ||
| * comprehensive then a single {@link MinimumEquivalentCyclicSet} and not as | ||
| * computationally demanding as {@link AllEquivalentCyclicSet}. In reality one | ||
| * should choose either use the fast (but good) heuristic {@link | ||
| * MinimumEquivalentCyclicSet} or the exact {@link AllEquivalentCyclicSet}. This | ||
| * method is provided for demonstration only. | ||
| * | ||
| * As with the {@link MinimumEquivalentCyclicSet} perturbation, this method does | ||
| * not guarantee that all molecules will be distinguished. At the time of | ||
| * writing (Feb 2013) there are only 8 structure in PubChem-Compound which need | ||
| * the more comprehensive perturbation method ({@link AllEquivalentCyclicSet}), | ||
| * these are listed below. | ||
| * | ||
| * <table><tr><td>CID <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=144432">144432</a> | ||
| * and CID <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=15584856">15584856</a></td></tr> | ||
| * <tr><td>CID <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=138898">138898</a> | ||
| * and CID <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=241107">241107</a></td></tr> | ||
| * <tr><td>CID <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=9990759">9990759</a> | ||
| * and CID <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=10899923">10899923</a></td></tr> | ||
| * <tr><td>CID <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5460768">5460768</a> | ||
| * and CID <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=20673269">20673269</a></td></tr> | ||
| * </table> | ||
| * | ||
| * <p/><br/> The easiest way to use this class is with the {@link | ||
| * org.openscience.cdk.hash.HashGeneratorMaker}. | ||
| * <blockquote><pre> | ||
| * MoleculeHashGenerator generator = | ||
| * new HashGeneratorMaker().depth(6) | ||
| * .elemental() | ||
| * .perturbWith(new MinimumEquivalentCyclicSetUnion()) | ||
| * .molecular(); | ||
| * </pre></blockquote> | ||
| * | ||
| * @author John May | ||
| * @cdk.module hash | ||
| * @see org.openscience.cdk.hash.PerturbedAtomHashGenerator | ||
| * @see MinimumEquivalentCyclicSet | ||
| * @see AllEquivalentCyclicSet | ||
| * @deprecated provided for to demonstrate a relatively robust but ultimately | ||
| * incomplete approach | ||
| */ | ||
| @Deprecated | ||
| @TestClass("org.openscience.cdk.hash.equivalent.MinimumEquivalentCyclicSetUnionTest") | ||
| public final class MinimumEquivalentCyclicSetUnion | ||
| implements EquivalentSetFinder { | ||
|
|
||
| /** | ||
| * @inheritDoc | ||
| */ | ||
| @TestMethod("testFind,testFind_Distinct,testScenario") | ||
| @Override | ||
| public Set<Integer> find(long[] invariants, IAtomContainer container, int[][] graph) { | ||
|
|
||
| int n = invariants.length; | ||
|
|
||
| // find cyclic vertices using DFS | ||
| RingSearch ringSearch = new RingSearch(container, graph); | ||
|
|
||
| // ordered map of the set of vertices for each value | ||
| Map<Long, Set<Integer>> equivalent = new TreeMap<Long, Set<Integer>>(); | ||
|
|
||
| // divide the invariants into equivalent indexed and ordered sets | ||
| for (int i = 0; i < invariants.length; i++) { | ||
|
|
||
| Long invariant = invariants[i]; | ||
| Set<Integer> set = equivalent.get(invariant); | ||
|
|
||
| if (set == null) { | ||
| if (ringSearch.cyclic(i)) { | ||
| set = new HashSet<Integer>(n / 2); | ||
| set.add(i); | ||
| equivalent.put(invariant, set); | ||
| } | ||
| } else { | ||
| set.add(i); | ||
| } | ||
| } | ||
|
|
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| // find the smallest set of equivalent cyclic vertices | ||
| int minSize = Integer.MAX_VALUE; | ||
| Set<Integer> min = Collections.emptySet(); | ||
| for (Map.Entry<Long, Set<Integer>> e : equivalent.entrySet()) { | ||
| Set<Integer> vertices = e.getValue(); | ||
| if (vertices.size() < minSize && vertices.size() > 1) { | ||
| min = vertices; | ||
| minSize = vertices.size(); | ||
| } else if (vertices.size() == minSize) { | ||
| min.addAll(vertices); | ||
| } | ||
| } | ||
|
|
||
| return min; | ||
| } | ||
| } |
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