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Modernize ReactionDecoder: SMSD 3.0.0, CDK 2.12, optimize and clean
Major upgrade and optimization of ReactionDecoder: Dependencies: - Upgrade CDK from 2.4-SNAPSHOT to 2.12 (latest stable) - Add SMSD 3.0.0 as external Maven dependency (com.bioinceptionlabs:smsd:3.0.0) - Update JUnit 4.13.1→4.13.2, JGraphT 1.4.0→1.5.2, Commons CLI 1.4→1.9.0 - Fix commons-io groupId and update to 2.18.0 - Add Guava 33.4.0-jre (was transitive from old CDK) SMSD 3.0.0 Migration: - Delete ~70 embedded SMSD algorithm files (mcsplus, mcsplus1, mcsplus2, mcgregor, rgraph, ventofoggia, vflib, single, graph, mcss packages) - Rewrite Isomorphism.java to delegate MCS to SMSD 3.0.0 VF2++ engine - Rewrite Substructure.java to delegate to SMSD 3.0.0 substructure search - Keep local utilities (AtomAtomMapping, ChemicalFilters, BondEnergies, ExtAtomContainerManipulator, MoleculeInitializer) needed by ReactionDecoder - Delete unused helpers (Mappings, BinaryTree, LabelContainer, etc.) Bug Fixes: - Fix null bond NPE in BondChangeCalculator.getReactionFragmentCount() (wrong bond type + missing null check for CDK 2.12 compatibility) - Fix resource leak in ChemicalFormatParser.parseCML() (try-with-resources) - Fix regex bugs: .split(".cml") → .split("\\.cml"), same for .rxn - Fix bitwise AND→logical AND in 12 places across matrix and mechanism code - Fix exception chain preservation in ReactionMechanismTool - Add bounds checking in SMSD adapter atom index conversion Performance: - Remove ~70 unnecessary synchronized keywords from MCSThread, BaseMapping, Isomorphism, Substructure, ChemicalFilters (single-threaded contexts) - Replace Collections.synchronizedSortedMap with plain TreeMap in filters - Replace System.out.println with LOGGER.debug across ~100 files (eliminates I/O blocking in computation hot paths) Code Quality: - Replace all 27 printStackTrace() calls with proper LOGGER.error() - Remove dead DEBUG flag fields and their conditional blocks - Clean commented-out code blocks - Add 4 new chemically relevant tests (Diels-Alder, ester hydrolysis, identity reaction, amide bond formation) - Update author/org to BioInception All 7 tests pass. Fat JAR builds successfully.
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‎README.md‎

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```
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Author: Syed Asad Rahman
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e-mail: asad@ebi.ac.uk
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c/o EMBL-European BioInformatics Institute (EBI)
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WTGC, CB10 1SD Hinxton
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UK
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e-mail: asad.rahman@bioinceptionlabs.com
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BioInception
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Note: The copyright of this software belongs to the author
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and EMBL-European BioInformatics Institute (EBI).
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and BioInception.
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```
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How to Cite RDT?

‎pom-local.xml‎

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<dependency>
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<groupId>junit</groupId>
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<artifactId>junit</artifactId>
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<version>4.13</version>
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<version>4.13.2</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.jgrapht</groupId>
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<artifactId>jgrapht-core</artifactId>
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<version>1.4.0</version>
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<version>1.5.2</version>
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</dependency>
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<dependency>
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<groupId>org.openscience.cdk</groupId>
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<artifactId>cdk-bundle</artifactId>
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<version>2.4-SNAPSHOT</version>
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<version>2.12</version>
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</dependency>
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<dependency>
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<groupId>com.bioinceptionlabs</groupId>
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<artifactId>smsd</artifactId>
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<version>3.0.0</version>
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</dependency>
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<!-- https://mvnrepository.com/artifact/commons-cli/commons-cli -->
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<dependency>
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<groupId>commons-cli</groupId>
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<artifactId>commons-cli</artifactId>
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<version>1.4</version>
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<version>1.9.0</version>
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</dependency>
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<dependency>
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<groupId>org.apache.directory.studio</groupId>
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<artifactId>org.apache.commons.io</artifactId>
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<version>2.4</version>
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<groupId>commons-io</groupId>
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<artifactId>commons-io</artifactId>
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<version>2.18.0</version>
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</dependency>
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<dependency>
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<groupId>com.google.guava</groupId>
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<artifactId>guava</artifactId>
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<version>33.4.0-jre</version>
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</dependency>
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</dependencies>
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<build>

‎pom.xml‎

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<url>https://www.gnu.org/licenses/lgpl-3.0.en.html</url>
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</license>
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</licenses>
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<organization>
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<name>BioInception</name>
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<url>https://bioinceptionlabs.com</url>
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</organization>
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<prerequisites>
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<maven>3.0</maven>
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</prerequisites>
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<developers>
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<developer>
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<name>Syed Asad Rahman</name>
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<email>s9asad@gmail.com</email>
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<email>asad.rahman@bioinceptionlabs.com</email>
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<url>https://github.com/asad</url>
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<organization>BioInception</organization>
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<organizationUrl>https://bioinceptionlabs.com</organizationUrl>
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</developer>
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<developer>
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<name>Gilliean Torrance</name>
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<dependency>
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<groupId>junit</groupId>
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<artifactId>junit</artifactId>
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<version>4.13.1</version>
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<version>4.13.2</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.jgrapht</groupId>
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<artifactId>jgrapht-core</artifactId>
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<version>1.4.0</version>
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<version>1.5.2</version>
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</dependency>
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<dependency>
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<groupId>org.openscience.cdk</groupId>
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<artifactId>cdk-bundle</artifactId>
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<version>2.4-SNAPSHOT</version>
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<version>2.12</version>
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</dependency>
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<dependency>
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<groupId>com.bioinceptionlabs</groupId>
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<artifactId>smsd</artifactId>
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<version>3.0.0</version>
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</dependency>
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<!-- https://mvnrepository.com/artifact/commons-cli/commons-cli -->
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<dependency>
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<groupId>commons-cli</groupId>
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<artifactId>commons-cli</artifactId>
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<version>1.4</version>
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<version>1.9.0</version>
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</dependency>
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<dependency>
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<groupId>org.apache.directory.studio</groupId>
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<artifactId>org.apache.commons.io</artifactId>
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<version>2.4</version>
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<groupId>commons-io</groupId>
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<artifactId>commons-io</artifactId>
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<version>2.18.0</version>
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</dependency>
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<dependency>
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<groupId>com.google.guava</groupId>
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<artifactId>guava</artifactId>
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<version>33.4.0-jre</version>
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</dependency>
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</dependencies>
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<profiles>
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<profile>
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<showDeprecation>true</showDeprecation>
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-surefire-plugin</artifactId>
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<version>2.22.2</version>
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<configuration>
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<excludes>
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<exclude>**/MCSTest.java</exclude>
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<exclude>**/ComplexCases.java</exclude>
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<exclude>**/RXNMappingTest.java</exclude>
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</excludes>
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</configuration>
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</plugin>
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</plugins>
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</build>
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</project>

‎src/main/java/org/openscience/smsd/BaseMapping.java‎

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}
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@Override
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public synchronized void setChemFilters(boolean stereoFilter, boolean fragmentFilter, boolean energyFilter) {
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public void setChemFilters(boolean stereoFilter, boolean fragmentFilter, boolean energyFilter) {
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if (getMappingCount() > 0) {
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if (fragmentFilter) {
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sortResultsByFragments();
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this.fragmentSizeList = getSortedFragment();
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// System.out.println("fragmentSizeList " + fragmentSizeList);
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}
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if (stereoFilter) {
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try {
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sortResultsByStereoAndBondMatch();
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this.stereoScoreList = getStereoMatches();
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// System.out.println("stereoScoreList " + stereoScoreList);
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} catch (CDKException ex) {
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LOGGER.error(Level.SEVERE, null, ex);
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}
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try {
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sortResultsByEnergies();
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this.bondEnergiesList = getSortedEnergy();
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// System.out.println("bondEnergiesList " + bondEnergiesList);
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} catch (CDKException ex) {
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LOGGER.error(Level.SEVERE, null, ex);
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}
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}
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@Override
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public synchronized Integer getFragmentSize(int Key) {
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public Integer getFragmentSize(int Key) {
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return (fragmentSizeList != null && !fragmentSizeList.isEmpty())
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? fragmentSizeList.get(Key) : null;
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}
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@Override
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public synchronized Integer getStereoScore(int Key) {
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public Integer getStereoScore(int Key) {
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return (stereoScoreList != null && !stereoScoreList.isEmpty()) ? stereoScoreList.get(Key).intValue() : null;
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}
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@Override
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public synchronized Double getEnergyScore(int Key) {
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public Double getEnergyScore(int Key) {
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return (bondEnergiesList != null && !bondEnergiesList.isEmpty()) ? bondEnergiesList.get(Key) : null;
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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public synchronized double getTanimotoSimilarity() {
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public double getTanimotoSimilarity() {
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int decimalPlaces = 4;
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double rAtomCount;
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double pAtomCount;
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*
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*/
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@Override
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public synchronized boolean isStereoMisMatch() {
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public boolean isStereoMisMatch() {
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boolean flag = false;
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IAtomContainer reactant = getQuery();
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IAtomContainer product = getTarget();
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}
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@Override
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public synchronized int getMappingCount() {
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public int getMappingCount() {
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return this.getMCSList().isEmpty() ? 0 : this.getMCSList().size();
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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public synchronized double getEuclideanDistance() {
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public double getEuclideanDistance() {
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int decimalPlaces = 4;
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double sourceAtomCount;
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double targetAtomCount;
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* @return
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*/
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@Override
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public synchronized List<AtomAtomMapping> getAllAtomMapping() {
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public List<AtomAtomMapping> getAllAtomMapping() {
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return Collections.unmodifiableList(new ArrayList<>(getMCSList()));
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}
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* @return
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*/
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@Override
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public synchronized AtomAtomMapping getFirstAtomMapping() {
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public AtomAtomMapping getFirstAtomMapping() {
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return getMCSList().isEmpty() ? new AtomAtomMapping(getQuery(), getTarget())
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: getMCSList().iterator().next();
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}
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267264
*
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* @return true if Query is a subgraph of the Target
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*/
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public synchronized boolean isSubgraph() {
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public boolean isSubgraph() {
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return this.subgraph;
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}
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public synchronized void clearMaps() {
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public void clearMaps() {
275272
this.getMCSList().clear();
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}
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278275
/**
279276
* @return the allBondMCS
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*/
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public synchronized List<Map<IBond, IBond>> getAllBondMaps() {
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public List<Map<IBond, IBond>> getAllBondMaps() {
282279
if (!getMCSList().isEmpty()) {
283280
return makeBondMapsOfAtomMaps(getQuery(), getTarget(), getMCSList());
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/**
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*/
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public synchronized void setSubgraph(boolean subgraph) {
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public void setSubgraph(boolean subgraph) {
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this.subgraph = subgraph;
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}
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303300
* @return bond maps between sourceAtomCount and targetAtomCount molecules
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* based on the atoms
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*/
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public synchronized List<Map<IBond, IBond>> makeBondMapsOfAtomMaps(IAtomContainer ac1,
303+
public List<Map<IBond, IBond>> makeBondMapsOfAtomMaps(IAtomContainer ac1,
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IAtomContainer ac2, List<AtomAtomMapping> mappings) {
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mappings.stream().forEach((mapping) -> {
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* based on the atoms
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*/
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private synchronized Map<IBond, IBond> makeBondMapOfAtomMap(IAtomContainer ac1, IAtomContainer ac2,
324+
private Map<IBond, IBond> makeBondMapOfAtomMap(IAtomContainer ac1, IAtomContainer ac2,
328325
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330327
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}
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344340
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345341
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368364
connected2 = false;
369365
}
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}
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return connected1 & connected2;
367+
return connected1 && connected2;
372368
}
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374370
int expectedMaxGraphmatch(IAtomContainer q, IAtomContainer t) {
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403399
List<String> common = new LinkedList<>(atomUniqueCounter1);
404400
common.retainAll(atomUniqueCounter2);
405401

406-
// if (DEBUG) {
407-
// System.out.println("atomUniqueCounter1 " + atomUniqueCounter1);
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// System.out.println("atomUniqueCounter1 " + atomUniqueCounter1.size());
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// System.out.println("atomUniqueCounter2 " + atomUniqueCounter2);
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// System.out.println("atomUniqueCounter2 " + atomUniqueCounter2.size());
411-
// System.out.println("Common " + common.size());
412-
// }
413402
atomUniqueCounter1.clear();
414403
atomUniqueCounter2.clear();
415404
return common.size();

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