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A structure pattern filter for atom-atom maps.
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tool/smarts/src/main/java/org/openscience/cdk/smiles/smarts/SmartsAtomAtomMapFilter.java
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| /* | ||
| * Copyright (c) 2016 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.smiles.smarts; | ||
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|
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| import com.google.common.base.Predicate; | ||
| import com.google.common.collect.ArrayListMultimap; | ||
| import com.google.common.collect.Multimap; | ||
| import com.google.common.primitives.Ints; | ||
| import org.openscience.cdk.CDKConstants; | ||
| import org.openscience.cdk.ReactionRole; | ||
| import org.openscience.cdk.interfaces.IAtom; | ||
| import org.openscience.cdk.interfaces.IAtomContainer; | ||
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|
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| import java.util.ArrayList; | ||
| import java.util.Arrays; | ||
| import java.util.Collection; | ||
| import java.util.HashSet; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
| import java.util.Set; | ||
|
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| /** | ||
| * A filter for substructure matches implementing the logic for Atom-Atom Mapping matching. The following | ||
| * table from the Daylight theory manual summarises the expected functionality: | ||
| * | ||
| * <pre> | ||
| * C>>C CC>>CC 4 hits No maps, normal match. | ||
| * C>>C [CH3:7][CH3:8]>>[CH3:7][CH3:8] 4 hits No maps in query, maps in target are ignored. | ||
| * [C:1]>>C [CH3:7][CH3:8]>>[CH3:7][CH3:8] 4 hits Unpaired map in query ignored. | ||
| * [C:1]>>[C:1] CC>>CC 0 hits No maps in target, hence no matches. | ||
| * [C:?1]>>[C:?1] CC>>CC 4 hits Query says mapped as shown or not present. | ||
| * [C:1]>>[C:1] [CH3:7][CH3:8]>>[CH3:7][CH3:8] 2 hits Matches for target 7,7 and 8,8 atom pairs. | ||
| * [C:1]>>[C:2] [CH3:7][CH3:8]>>[CH3:7][CH3:8] 4 hits When a query class is not found on both sides of the | ||
| * query, it is ignored; this query does NOT say that the | ||
| * atoms are in different classes. | ||
| * [C:1][C:1]>>[C:1] [CH3:7][CH3:7]>>[CH3:7][CH3:7] 4 hits Atom maps match with "or" logic. All atoms get bound to | ||
| * class 7. | ||
| * [C:1][C:1]>>[C:1] [CH3:7][CH3:8]>>[CH3:7][CH3:8] 4 hits The reactant atoms are bound to classes 7 and 8. Note that | ||
| * having the first query atom bound to class 7 does not | ||
| * preclude binding the second atom. Next, the product | ||
| * atom can bind to classes 7 or 8. | ||
| * [C:1][C:1]>>[C:1] [CH3:7][CH3:7]>>[CH3:7][CH3:8] 2 hits The reactants are bound to class 7. The product atom can | ||
| * bind to class 7 only. | ||
| * </pre> | ||
| * | ||
| * @see <a href="http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html">Daylight Theory Manual</a> | ||
| */ | ||
| final class SmartsAtomAtomMapFilter implements Predicate<int[]> { | ||
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| private final List<MappedPairs> mapped = new ArrayList<>(); | ||
| private final IAtomContainer target; | ||
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| SmartsAtomAtomMapFilter(IAtomContainer query, IAtomContainer target) { | ||
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| Multimap<Integer,Integer> reactInvMap = null; | ||
| Multimap<Integer,Integer> prodInvMap = null; | ||
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| this.target = target; | ||
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| // transform query maps in to matchable data-structure | ||
| final int numAtoms = query.getAtomCount(); | ||
| for (int idx = 0; idx < numAtoms; idx++) { | ||
| IAtom atom = query.getAtom(idx); | ||
| final int mapidx = mapidx(atom); | ||
| if (mapidx == 0) continue; | ||
| switch (role(atom)) { | ||
| case Reactant: | ||
| if (reactInvMap == null) reactInvMap = ArrayListMultimap.create(); | ||
| reactInvMap.put(mapidx, idx); | ||
| break; | ||
| case Product: | ||
| if (prodInvMap == null) prodInvMap = ArrayListMultimap.create(); | ||
| prodInvMap.put(mapidx, idx); | ||
| break; | ||
| } | ||
| } | ||
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| if (reactInvMap != null && prodInvMap != null) { | ||
| for (Map.Entry<Integer, Collection<Integer>> e : reactInvMap.asMap().entrySet()) { | ||
| int[] reacMaps = Ints.toArray(e.getValue()); | ||
| int[] prodMaps = Ints.toArray(prodInvMap.get(e.getKey())); | ||
| if (prodMaps.length == 0) | ||
| continue; // unpaired | ||
| mapped.add(new MappedPairs(reacMaps, prodMaps)); | ||
| } | ||
| } | ||
| } | ||
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| /** | ||
| * Safely access the mapidx of an atom, returns 0 if null. | ||
| * | ||
| * @param atom atom | ||
| * @return mapidx, 0 if undefined | ||
| */ | ||
| private int mapidx(IAtom atom) { | ||
| Integer mapidx = atom.getProperty(CDKConstants.ATOM_ATOM_MAPPING); | ||
| if (mapidx != null) | ||
| return mapidx; | ||
| return 0; | ||
| } | ||
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| /** | ||
| * Safely access the reaction role of an atom, returns {@link ReactionRole#None} if null. | ||
| * | ||
| * @param atom atom | ||
| * @return mapidx, None if undefined | ||
| */ | ||
| private ReactionRole role(IAtom atom) { | ||
| ReactionRole role = atom.getProperty(CDKConstants.REACTION_ROLE); | ||
| if (role != null) | ||
| return role; | ||
| return ReactionRole.None; | ||
| } | ||
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| /** | ||
| * Filters a structure match (described as an index permutation query -> target) for | ||
| * those where the atom-atom maps are acceptable. | ||
| * | ||
| * @param perm permuation | ||
| * @return whether the match should be accepted | ||
| */ | ||
| @Override | ||
| public boolean apply(int[] perm) { | ||
| for (MappedPairs mpair : mapped) { | ||
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| // possibly 'or' of query maps, need to use a set | ||
| if (mpair.rIdxs.length > 1) { | ||
| // bind target reactant maps | ||
| final Set<Integer> bound = new HashSet<>(); | ||
| for (int rIdx : mpair.rIdxs) { | ||
| int refidx = mapidx(target.getAtom(perm[rIdx])); | ||
| if (refidx == 0) return false; // unmapped in target | ||
| bound.add(refidx); | ||
| } | ||
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| // check product maps | ||
| for (int pIdx : mpair.pIdxs) { | ||
| if (!bound.contains(mapidx(target.getAtom(perm[pIdx])))) | ||
| return false; | ||
| } | ||
| } | ||
| // no 'or' of query atom map (more common case) | ||
| else { | ||
| final int refidx = mapidx(target.getAtom(perm[mpair.rIdxs[0]])); | ||
| if (refidx == 0) return false; // unmapped in target | ||
| // pairwise mismatch | ||
| if (refidx != mapidx(target.getAtom(perm[mpair.pIdxs[0]]))) | ||
| return false; | ||
| for (int i = 1; i < mpair.pIdxs.length; i++) { | ||
| if (refidx != mapidx(target.getAtom(perm[mpair.pIdxs[i]]))) | ||
| return false; | ||
| } | ||
| } | ||
|
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|
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| } | ||
| return true; | ||
| } | ||
|
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| /** | ||
| * Helper class list all reactant atom indices (rIdxs) and product | ||
| * atom indices (pIdxs) that are in the same Atom-Atom-Mapping class. | ||
| */ | ||
| private final class MappedPairs { | ||
| final int[] rIdxs, pIdxs; | ||
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| private MappedPairs(int[] rIdxs, int[] pIdxs) { | ||
| this.rIdxs = rIdxs; | ||
| this.pIdxs = pIdxs; | ||
| } | ||
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| @Override | ||
| public String toString() { | ||
| return "{" + Arrays.toString(rIdxs) + "=>" + Arrays.toString(pIdxs) + "}"; | ||
| } | ||
| } | ||
| } |
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