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Added extended-connectivity fingerprints example [skip ci]
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‎README.md‎

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@@ -39,6 +39,7 @@ Or check out some examples:
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- [Binary embeddings](examples/cohere/src/main/java/com/example/Example.java) with Cohere
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- [Sentence embeddings](examples/djl/src/main/java/com/example/Example.java) with Deep Java Library
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- [Hybrid search](examples/hybrid/src/main/java/com/example/Example.java) with Deep Java Library (Reciprocal Rank Fusion)
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- [Extended-connectivity fingerprints](examples/cdk/src/main/java/com/example/Example.java) with the Chemistry Development Kit
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- [Horizontal scaling](examples/citus/src/main/java/com/example/Example.java) with Citus
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- [Bulk loading](examples/loading/src/main/java/com/example/Example.java) with `COPY`
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‎examples/cdk/pom.xml‎

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<?xml version='1.0' encoding='UTF-8'?>
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<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0">
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<modelVersion>4.0.0</modelVersion>
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<groupId>com.example</groupId>
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<artifactId>example</artifactId>
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<version>1</version>
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<properties>
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<maven.compiler.release>11</maven.compiler.release>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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</properties>
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<dependencies>
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<dependency>
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<groupId>org.postgresql</groupId>
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<artifactId>postgresql</artifactId>
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<version>42.7.3</version>
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</dependency>
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<dependency>
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<groupId>com.pgvector</groupId>
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<artifactId>pgvector</artifactId>
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<version>0.1.6</version>
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</dependency>
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<dependency>
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<artifactId>cdk-fingerprint</artifactId>
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<groupId>org.openscience.cdk</groupId>
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<version>2.9</version>
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</dependency>
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<dependency>
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<artifactId>cdk-silent</artifactId>
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<groupId>org.openscience.cdk</groupId>
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<version>2.9</version>
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</dependency>
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<dependency>
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<artifactId>cdk-smiles</artifactId>
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<groupId>org.openscience.cdk</groupId>
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<version>2.9</version>
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</dependency>
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</dependencies>
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<build>
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<plugins>
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<plugin>
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<artifactId>maven-assembly-plugin</artifactId>
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<version>3.7.1</version>
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<configuration>
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<descriptorRefs>
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<descriptorRef>jar-with-dependencies</descriptorRef>
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</descriptorRefs>
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<archive>
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<manifest>
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<mainClass>com.example.Example</mainClass>
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</manifest>
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</archive>
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<finalName>example</finalName>
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</configuration>
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<executions>
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<execution>
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<id>make-assembly</id>
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<phase>package</phase>
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<goals>
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<goal>single</goal>
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</goals>
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</execution>
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</executions>
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</plugin>
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</plugins>
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</build>
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</project>

‎examples/cdk/src/main/java/com/example/Example.java‎

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package com.example;
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import java.sql.Connection;
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import java.sql.DriverManager;
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import java.sql.PreparedStatement;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.sql.Statement;
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import com.pgvector.PGbit;
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import org.openscience.cdk.exception.CDKException;
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import org.openscience.cdk.exception.InvalidSmilesException;
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import org.openscience.cdk.fingerprint.CircularFingerprinter;
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import org.openscience.cdk.fingerprint.IBitFingerprint;
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import org.openscience.cdk.interfaces.IAtomContainer;
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import org.openscience.cdk.silent.SilentChemObjectBuilder;
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import org.openscience.cdk.smiles.SmilesParser;
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public class Example {
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public static void main(String[] args) throws CDKException, InvalidSmilesException, SQLException {
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Connection conn = DriverManager.getConnection("jdbc:postgresql://localhost:5432/pgvector_example");
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Statement setupStmt = conn.createStatement();
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setupStmt.executeUpdate("CREATE EXTENSION IF NOT EXISTS vector");
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setupStmt.executeUpdate("DROP TABLE IF EXISTS molecules");
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Statement createStmt = conn.createStatement();
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createStmt.executeUpdate("CREATE TABLE molecules (id text PRIMARY KEY, fingerprint bit(2048))");
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String[] molecules = {
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"Cc1ccccc1",
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"Cc1ncccc1",
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"c1ccccn1"
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};
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for (String molecule : molecules) {
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PreparedStatement insertStmt = conn.prepareStatement("INSERT INTO molecules (id, fingerprint) VALUES (?, ?)");
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insertStmt.setString(1, molecule);
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insertStmt.setObject(2, new PGbit(generateFingerprint(molecule)));
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insertStmt.executeUpdate();
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}
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String queryMolecule = "c1ccco1";
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PreparedStatement queryStmt = conn.prepareStatement("SELECT id, fingerprint <%> ? AS distance FROM molecules ORDER BY distance LIMIT 5");
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queryStmt.setObject(1, new PGbit(generateFingerprint(queryMolecule)));
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ResultSet rs = queryStmt.executeQuery();
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while (rs.next()) {
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System.out.println(String.format("%s: %f", rs.getString("id"), rs.getDouble("distance")));
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}
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conn.close();
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}
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private static boolean[] generateFingerprint(String molecule) throws CDKException, InvalidSmilesException {
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SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());
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IAtomContainer m = sp.parseSmiles(molecule);
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CircularFingerprinter fingerprinter = new CircularFingerprinter(CircularFingerprinter.CLASS_ECFP6, 2048);
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IBitFingerprint fp = fingerprinter.getBitFingerprint(m);
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boolean[] ba = new boolean[(int) fp.size()];
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for (int i : fp.getSetbits()) {
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ba[i] = true;
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}
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return ba;
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}
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}

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