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<?xml version="1.0" encoding="UTF-8"?>
<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">
    <modelVersion>4.0.0</modelVersion>

    <groupId>org.example</groupId>
    <artifactId>bio_java_maven_hello_world</artifactId>
    <version>1.0-SNAPSHOT</version>

    <properties>
        <maven.compiler.source>17</maven.compiler.source>
        <maven.compiler.target>17</maven.compiler.target>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    </properties>

    <dependencies>
        <dependency>
            <groupId>org.biojava</groupId>
            <artifactId>biojava-core</artifactId>
            <version>5.4.0</version>
        </dependency>
        <dependency>
            <groupId>org.biojava</groupId>
            <artifactId>biojava-structure</artifactId>
            <version>5.4.0</version>
        </dependency>
    </dependencies>
</project>

package org.example;

import org.biojava.nbio.structure.*;
import org.biojava.nbio.structure.io.LocalPDBDirectory;
import org.biojava.nbio.structure.io.PDBFileReader;

public class BioJavaPDBHelloWorld {
    public static void main(String[] args) {
        try {
            PDBFileReader pdbReader = new PDBFileReader();

            // Set the path to the local PDB file directory
            pdbReader.setPath("C:\PDB files");
            pdbReader.setFetchBehavior(LocalPDBDirectory.FetchBehavior.LOCAL_ONLY);

            // Reading a structure by PDB code
            Structure structure = pdbReader.getStructureById("1LVZ"); // Example PDB code

            // Print the PDB ID
            System.out.println("PDB ID: " + structure.getPDBCode());

            // Print the title of the structure
            System.out.println("Title: " + structure.getPDBHeader().getTitle());

            // Print number of atoms in the structure
            System.out.println("ID : " + structure.getId());

        } catch (Exception e) {
            e.printStackTrace();
        }
    }
}

"C:Program FilesJavajdk-17.0.2binjava.exe" "-javaagent:C:Program FilesJetBrainsIntelliJ IDEA 2023.1.6libidea_rt.jar=54171:C:Program FilesJetBrainsIntelliJ IDEA 2023.1.6bin" -Dfile.encoding=UTF-8 -classpath C:gitbio_java_maven_hello_worldtargetclasses;C:Userspc.m2repositoryorgbiojavabiojava-core5.4.0biojava-core-5.4.0.jar;C:Userspc.m2repositoryorgslf4jslf4j-api1.7.30slf4j-api-1.7.30.jar;C:Userspc.m2repositoryorgapachelogginglog4jlog4j-slf4j-impl2.13.1log4j-slf4j-impl-2.13.1.jar;C:Userspc.m2repositoryorgapachelogginglog4jlog4j-api2.13.1log4j-api-2.13.1.jar;C:Userspc.m2repositoryorgapachelogginglog4jlog4j-core2.13.1log4j-core-2.13.1.jar;C:Userspc.m2repositoryorgbiojavabiojava-structure5.4.0biojava-structure-5.4.0.jar;C:Userspc.m2repositoryorgrcsbciftools-java.7.1ciftools-java-0.7.1.jar;C:Userspc.m2repositoryjavaxannotationjavax.annotation-api1.3.2javax.annotation-api-1.3.2.jar;C:Userspc.m2repositorycomgooglecodegsongson2.8.5gson-2.8.5.jar;C:Userspc.m2repositoryorgrcsbmmtf-api1.0.9mmtf-api-1.0.9.jar;C:Userspc.m2repositoryorgrcsbmmtf-serialization1.0.9mmtf-serialization-1.0.9.jar;C:Userspc.m2repositoryorgmsgpackjackson-dataformat-msgpack.8.18jackson-dataformat-msgpack-0.8.18.jar;C:Userspc.m2repositoryorgmsgpackmsgpack-core.8.18msgpack-core-0.8.18.jar;C:Userspc.m2repositorycomfasterxmljacksoncorejackson-databind2.9.9.3jackson-databind-2.9.9.3.jar;C:Userspc.m2repositorycomfasterxmljacksoncorejackson-annotations2.9.0jackson-annotations-2.9.0.jar;C:Userspc.m2repositorycomfasterxmljacksoncorejackson-core2.9.9jackson-core-2.9.9.jar;C:Userspc.m2repositoryorgrcsbmmtf-codec1.0.9mmtf-codec-1.0.9.jar;C:Userspc.m2repositorycommons-langcommons-lang2.4commons-lang-2.4.jar;C:Userspc.m2repositoryorgbiojavabiojava-alignment5.4.0biojava-alignment-5.4.0.jar;C:Userspc.m2repositoryorgbiojavathirdpartyforester1.038forester-1.038.jar;C:Userspc.m2repositoryjava3dvecmath1.3.1vecmath-1.3.1.jar;C:Userspc.m2repositoryorgjgraphtjgrapht-core1.1.0jgrapht-core-1.1.0.jar;C:Userspc.m2repositoryjavaxxmlbindjaxb-api2.3.0jaxb-api-2.3.0.jar;C:Userspc.m2repositorycomsunxmlbindjaxb-core2.3.0jaxb-core-2.3.0.jar;C:Userspc.m2repositorycomsunxmlbindjaxb-impl2.3.0jaxb-impl-2.3.0.jar;C:Userspc.m2repositoryjavaxactivationactivation1.1.1activation-1.1.1.jar org.example.BioJavaPDBHelloWorld
20:43:37 [main] WARN  org.biojava.nbio.structure.align.util.UserConfiguration - Could not read dir from system property PDB_DIR or environment variable PDB_DIR, using system's temp directory C:UserspcAppDataLocalTemp
java.io.IOException: Structure 1LVZ not found in C:PDB files and configured not to download.
    at org.biojava.nbio.structure.io.LocalPDBDirectory.downloadStructure(LocalPDBDirectory.java:447)
    at org.biojava.nbio.structure.io.LocalPDBDirectory.getInputStream(LocalPDBDirectory.java:353)
    at org.biojava.nbio.structure.io.LocalPDBDirectory.getStructureById(LocalPDBDirectory.java:327)
    at org.example.BioJavaPDBHelloWorld.main(BioJavaPDBHelloWorld.java:17)

Process finished with exit code 0

I have the file in the given location.

C:PDB files>dir
 Volume in drive C has no label.
 Volume Serial Number is DEFD-2FA5

 Directory of C:PDB files

24-Apr-24  08:42 PM    <DIR>          .
24-Apr-24  08:42 PM    <DIR>          ..
12-Apr-24  03:30 PM           309,420 1aqg.pdb
12-Apr-24  02:49 PM           124,335 1ejg.pdb
12-Apr-24  03:31 PM            27,378 1lb0.pdb
12-Apr-24  03:30 PM           316,872 1lvz.pdb
12-Apr-24  03:31 PM           229,311 1m23.pdb
12-Apr-24  03:32 PM            31,104 1niz.pdb
12-Apr-24  03:30 PM            78,165 1tor.pdb
12-Apr-24  03:30 PM            49,329 1tos.pdb
12-Apr-24  02:47 PM           130,491 1trz.pdb
12-Apr-24  03:33 PM            34,506 3cmh.pdb
12-Apr-24  03:35 PM           658,206 3ifn.pdb
12-Apr-24  02:36 PM            38,475 5awl.pdb
12-Apr-24  02:58 PM           439,344 6a5j.pdb
12-Apr-24  02:57 PM           118,098 7ur8.pdb
24-Apr-24  08:18 PM    <DIR>          data
              14 File(s)      2,585,034 bytes
               3 Dir(s)  31,268,425,728 bytes free

C:PDB files>

So, why is BioJava not finding the file?

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Danh mục

BioJava – java.io.IOException: Structure 1LVZ not found in “C:PDB files” and configured not to download