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Migrate namespace uk.ac.ebi → com.bioinceptionlabs
Complete package namespace migration from legacy EBI to BioInception: - Moved 321 source files + 6 test files to com/bioinceptionlabs/ - Updated all package declarations and import statements - Updated groupId: uk.ac.ebi.rdt → com.bioinceptionlabs.rdt - Updated mainClass references in pom.xml and pom-local.xml - Updated README.md API examples with new imports - Added migration guide section to README.md for v2.x users - Preserved org.openscience.smsd/cdk namespaces (external library) All 40 tests pass. API is unchanged — only package names moved. Author: Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>
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‎README.md‎

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@@ -41,9 +41,9 @@ import org.openscience.cdk.silent.SilentChemObjectBuilder;
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import org.openscience.cdk.smiles.SmiFlavor;
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import org.openscience.cdk.smiles.SmilesGenerator;
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import org.openscience.cdk.smiles.SmilesParser;
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import uk.ac.ebi.reactionblast.mechanism.MappingSolution;
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import uk.ac.ebi.reactionblast.mechanism.ReactionMechanismTool;
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import uk.ac.ebi.reactionblast.tools.StandardizeReaction;
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import com.bioinceptionlabs.reactionblast.mechanism.MappingSolution;
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import com.bioinceptionlabs.reactionblast.mechanism.ReactionMechanismTool;
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import com.bioinceptionlabs.reactionblast.tools.StandardizeReaction;
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public class Example {
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public static void main(String[] args) throws Exception {
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```
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Migrating from v2.x
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====================
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The package namespace has changed from `uk.ac.ebi` to `com.bioinceptionlabs` in v3.0.0.
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**Maven dependency**
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```xml
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<!-- Old (v2.x) -->
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<groupId>uk.ac.ebi.rdt</groupId>
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<!-- New (v3.0.0) -->
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<groupId>com.bioinceptionlabs.rdt</groupId>
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```
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**Import changes**
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Replace imports in your code:
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| Old (v2.x) | New (v3.0.0) |
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|-------------|--------------|
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| `uk.ac.ebi.aamtool.*` | `com.bioinceptionlabs.aamtool.*` |
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| `uk.ac.ebi.reactionblast.*` | `com.bioinceptionlabs.reactionblast.*` |
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| `uk.ac.ebi.centres.*` | `com.bioinceptionlabs.centres.*` |
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A simple find-and-replace of `uk.ac.ebi` with `com.bioinceptionlabs` in your import statements is sufficient. The API itself is unchanged.
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License
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=======
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‎pom-local.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<groupId>uk.ac.ebi.rdt</groupId>
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<groupId>com.bioinceptionlabs.rdt</groupId>
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<artifactId>rdt</artifactId>
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<description>Reaction Decoder Tool</description>
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<version>3.0.0</version>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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<maven.compiler.source>11</maven.compiler.source>
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<maven.compiler.target>11</maven.compiler.target>
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<mainClass>uk.ac.ebi.aamtool.ReactionDecoder</mainClass>
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<mainClass>com.bioinceptionlabs.aamtool.ReactionDecoder</mainClass>
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</properties>
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<licenses>
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</descriptorRefs>
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<archive>
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<manifest>
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<mainClass>uk.ac.ebi.aamtool.ReactionDecoder</mainClass>
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<mainClass>com.bioinceptionlabs.aamtool.ReactionDecoder</mainClass>
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</manifest>
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</archive>
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</configuration>

‎pom.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<groupId>uk.ac.ebi.rdt</groupId>
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<groupId>com.bioinceptionlabs.rdt</groupId>
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<artifactId>rdt</artifactId>
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<description>Reaction Decoder Tool</description>
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<version>3.0.0</version>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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<maven.compiler.source>11</maven.compiler.source>
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<maven.compiler.target>11</maven.compiler.target>
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<mainClass>uk.ac.ebi.aamtool.ReactionDecoder</mainClass>
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<mainClass>com.bioinceptionlabs.aamtool.ReactionDecoder</mainClass>
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</properties>
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<scm>
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</descriptorRefs>
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<archive>
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<manifest>
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<mainClass>uk.ac.ebi.aamtool.ReactionDecoder</mainClass>
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<mainClass>com.bioinceptionlabs.aamtool.ReactionDecoder</mainClass>
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</manifest>
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</archive>
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</configuration>

src/main/java/uk/ac/ebi/aamtool/Annotator.java renamed to src/main/java/com/bioinceptionlabs/aamtool/Annotator.java

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* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
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* MA 02110-1301 USA
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*/
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package uk.ac.ebi.aamtool;
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package com.bioinceptionlabs.aamtool;
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import java.io.BufferedWriter;
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import java.io.File;
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import org.w3c.dom.Attr;
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import org.w3c.dom.Document;
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import org.w3c.dom.Element;
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import uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter;
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import uk.ac.ebi.reactionblast.fingerprints.ReactionFingerprinter;
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import uk.ac.ebi.reactionblast.fingerprints.interfaces.IPatternFingerprinter;
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import uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator;
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import uk.ac.ebi.reactionblast.mechanism.MappingSolution;
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import uk.ac.ebi.reactionblast.mechanism.ReactionMechanismTool;
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import uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair;
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import static uk.ac.ebi.reactionblast.tools.ReactionSimilarityTool.getSimilarity;
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import uk.ac.ebi.reactionblast.tools.StandardizeReaction;
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import com.bioinceptionlabs.reactionblast.fingerprints.PatternFingerprinter;
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import com.bioinceptionlabs.reactionblast.fingerprints.ReactionFingerprinter;
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import com.bioinceptionlabs.reactionblast.fingerprints.interfaces.IPatternFingerprinter;
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import com.bioinceptionlabs.reactionblast.mechanism.BondChangeCalculator;
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import com.bioinceptionlabs.reactionblast.mechanism.MappingSolution;
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import com.bioinceptionlabs.reactionblast.mechanism.ReactionMechanismTool;
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import com.bioinceptionlabs.reactionblast.mechanism.helper.MoleculeMoleculePair;
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import static com.bioinceptionlabs.reactionblast.tools.ReactionSimilarityTool.getSimilarity;
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import com.bioinceptionlabs.reactionblast.tools.StandardizeReaction;
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/**
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* @contact Syed Asad Rahman, BioInception.

src/main/java/uk/ac/ebi/aamtool/ChemicalFormatParser.java renamed to src/main/java/com/bioinceptionlabs/aamtool/ChemicalFormatParser.java

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* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
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* MA 02110-1301 USA
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*/
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package uk.ac.ebi.aamtool;
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package com.bioinceptionlabs.aamtool;
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import java.io.File;
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import java.io.FileInputStream;
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import org.openscience.cdk.tools.ILoggingTool;
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import org.openscience.cdk.tools.LoggingToolFactory;
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import org.openscience.smsd.tools.ExtAtomContainerManipulator;
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import uk.ac.ebi.reactionblast.tools.rxnfile.MDLRXNV2000Reader;
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import com.bioinceptionlabs.reactionblast.tools.rxnfile.MDLRXNV2000Reader;
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/**
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* @contact Syed Asad Rahman, BioInception.

src/main/java/uk/ac/ebi/aamtool/CommandLineOptions.java renamed to src/main/java/com/bioinceptionlabs/aamtool/CommandLineOptions.java

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* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
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* MA 02110-1301 USA
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*/
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package uk.ac.ebi.aamtool;
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package com.bioinceptionlabs.aamtool;
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import org.apache.commons.cli.Options;
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import org.openscience.cdk.tools.ILoggingTool;

src/main/java/uk/ac/ebi/aamtool/Helper.java renamed to src/main/java/com/bioinceptionlabs/aamtool/Helper.java

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* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
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* MA 02110-1301 USA
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*/
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package uk.ac.ebi.aamtool;
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package com.bioinceptionlabs.aamtool;
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import java.io.File;
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import static java.io.File.separator;
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import org.openscience.cdk.interfaces.IReaction;
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import org.openscience.cdk.tools.ILoggingTool;
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import org.openscience.cdk.tools.LoggingToolFactory;
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import uk.ac.ebi.reactionblast.tools.ImageGenerator;
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import uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000RXNWriter;
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import com.bioinceptionlabs.reactionblast.tools.ImageGenerator;
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import com.bioinceptionlabs.reactionblast.tools.rxnfile.MDLV2000RXNWriter;
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/**
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* @contact Syed Asad Rahman, BioInception.

src/main/java/uk/ac/ebi/aamtool/ReactionDecoder.java renamed to src/main/java/com/bioinceptionlabs/aamtool/ReactionDecoder.java

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* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
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* MA 02110-1301 USA
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*/
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package uk.ac.ebi.aamtool;
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package com.bioinceptionlabs.aamtool;
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import java.io.File;
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import java.io.FileNotFoundException;
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import org.openscience.cdk.tools.LoggingToolFactory;
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import org.w3c.dom.DOMException;
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import org.w3c.dom.Document;
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import static uk.ac.ebi.aamtool.Annotator.getReactionMechanismTool;
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import static uk.ac.ebi.aamtool.ChemicalFormatParser.parseRXN;
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import static uk.ac.ebi.aamtool.Helper.displayBlankLines;
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import static uk.ac.ebi.aamtool.Helper.getHeader;
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import static uk.ac.ebi.aamtool.Helper.printHelp;
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import uk.ac.ebi.reactionblast.mechanism.ReactionMechanismTool;
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import static com.bioinceptionlabs.aamtool.Annotator.getReactionMechanismTool;
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import static com.bioinceptionlabs.aamtool.ChemicalFormatParser.parseRXN;
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import static com.bioinceptionlabs.aamtool.Helper.displayBlankLines;
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import static com.bioinceptionlabs.aamtool.Helper.getHeader;
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import static com.bioinceptionlabs.aamtool.Helper.printHelp;
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import com.bioinceptionlabs.reactionblast.mechanism.ReactionMechanismTool;
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/**
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* @contact Syed Asad Rahman, BioInception.

src/main/java/uk/ac/ebi/aamtool/SimilarityResult.java renamed to src/main/java/com/bioinceptionlabs/aamtool/SimilarityResult.java

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* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
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* MA 02110-1301 USA
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*/
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package uk.ac.ebi.aamtool;
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package com.bioinceptionlabs.aamtool;
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import java.util.Map;
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import org.openscience.cdk.tools.ILoggingTool;

src/main/java/uk/ac/ebi/aamtool/rgroup/ECRgroupFrequency.java renamed to src/main/java/com/bioinceptionlabs/aamtool/rgroup/ECRgroupFrequency.java

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* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
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* MA 02110-1301 USA
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*/
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package uk.ac.ebi.aamtool.rgroup;
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package com.bioinceptionlabs.aamtool.rgroup;
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import java.io.File;
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import java.io.FileNotFoundException;
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import org.openscience.cdk.exception.CDKException;
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import org.openscience.cdk.tools.ILoggingTool;
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import org.openscience.cdk.tools.LoggingToolFactory;
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import uk.ac.ebi.reactionblast.tools.rxnfile.MDLRXNV2000Reader;
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import com.bioinceptionlabs.reactionblast.tools.rxnfile.MDLRXNV2000Reader;
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/**
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* @contact Syed Asad Rahman, BioInception.

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