BioJava – Could not read dir from system property PDB_DIR or environment variable PDB_DIR, using system’s temp directory
C:WINDOWSsystem32>mvn -v Apache Maven 3.9.6 (bc0240f3c744dd6b6ec2920b3cd08dcc295161ae) Maven home: C:ProgramDatachocolateylibmavenapache-maven-3.9.6 Java version: 11.0.22, vendor: Microsoft, runtime: C:Program FilesMicrosoftjdk-11.0.22.7-hotspot Default locale: en_US, platform encoding: Cp1252 OS name: “windows 10”, version: “10.0”, arch: “amd64”, family: “windows” C:WindowsSystem32>cd C:>echo %PDB_DIR% C:pdb C:> <?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>11</maven.compiler.source> <maven.compiler.target>11</maven.compiler.target> <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> </properties> […]
BioJava – java.io.IOException: Structure 1LVZ not found in “C:PDB files” and configured not to download
<?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(); […]
BioJava – java.net.ConnectException: Connection timed out: no further information
Why am I seeing the error?