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Bump biojava to 7.2.5 (biojava-structure 7.2.5-rdk.1)

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Vendor the 7.2.5-rdk.1 fork under lib/local-mvn-repo the same way as
the previous 7.2.4-rdk.1, and align biojava-core / biojava-alignment.
This commit is contained in:
rdk
2026-05-20 11:39:09 +02:00
parent 550ab9e1a0
commit 84148eb95b
4 changed files with 196 additions and 3 deletions
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6
build.gradle
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@@ -214,9 +214,9 @@ dependencies {
implementation 'org.apache.logging.log4j:log4j-core:2.26.0'
implementation 'org.apache.logging.log4j:log4j-slf4j2-impl:2.26.0'
implementation 'org.biojava:biojava-core:7.2.4'
implementation 'org.biojava:biojava-alignment:7.2.4'
implementation 'org.biojava:biojava-structure:7.2.4-rdk.1' // forked version with new parseSites param
implementation 'org.biojava:biojava-core:7.2.5'
implementation 'org.biojava:biojava-alignment:7.2.5'
implementation 'org.biojava:biojava-structure:7.2.5-rdk.1' // forked version with new parseSites param
implementation 'org.openscience.cdk:cdk-qsarmolecular:2.12' // for NumericalSurface class
implementation 'org.openscience.cdk:cdk-silent:2.12' // for Atom class

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lib/local-mvn-repo/org/biojava/biojava-structure/7.2.5-rdk.1/_remote.repositories Normal file
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@@ -0,0 +1,4 @@
#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
#Wed May 20 11:34:49 CEST 2026
biojava-structure-7.2.5-rdk.1.jar>=
biojava-structure-7.2.5-rdk.1.pom>=

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lib/local-mvn-repo/org/biojava/biojava-structure/7.2.5-rdk.1/biojava-structure-7.2.5-rdk.1.pom Normal file
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@@ -0,0 +1,189 @@
<?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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<artifactId>biojava</artifactId>
<groupId>org.biojava</groupId>
<version>7.2.5</version>
</parent>
<artifactId>biojava-structure</artifactId>
<name>biojava-structure</name>
<version>7.2.5-rdk.1</version>
<description>The protein structure modules of BioJava.</description>
<licenses>
<license>
<name>GNU LGPL v2</name>
<url>http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt</url>
<distribution>repo</distribution>
</license>
</licenses>
<dependencies>
<dependency>
<groupId>org.rcsb</groupId>
<artifactId>${ciftools.artifact}</artifactId>
<version>${ciftools.version}</version>
</dependency>
<dependency>
<groupId>org.rcsb</groupId>
<artifactId>mmtf-api</artifactId>
<version>${mmtf.version}</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.rcsb</groupId>
<artifactId>mmtf-serialization</artifactId>
<version>${mmtf.version}</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.rcsb</groupId>
<artifactId>mmtf-codec</artifactId>
<version>${mmtf.version}</version>
<scope>compile</scope>
<exclusions>
<!-- This is needed because mmtf uses slf4j 1.7 and the log4j2 slf4j1 binding, somehow clashing with slf4j2 in this repo -->
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-alignment</artifactId>
<version>7.2.5</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
<version>7.2.5</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>java3d</groupId>
<artifactId>vecmath</artifactId>
<version>1.3.1</version>
</dependency>
<dependency>
<groupId>org.jgrapht</groupId>
<artifactId>jgrapht-core</artifactId>
<!-- Pin! Java 8 requires 1.4.0 -->
<version>1.4.0</version>
</dependency>
<dependency>
<groupId>jakarta.xml.bind</groupId>
<artifactId>jakarta.xml.bind-api</artifactId>
</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
</dependency>
<!-- Used for json deserialization in PDBStatus -->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.13.4.2</version>
</dependency>
<!-- logging dependencies (managed by parent pom, don't set versions or
scopes here) -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</dependency>
<!-- binding for log4j2, scope=runTime set in parent pom -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j2-impl</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
</dependency>
<!-- Testing related dependencies -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>xmlunit</groupId>
<artifactId>xmlunit</artifactId>
<version>1.6</version>
<scope>test</scope>
</dependency>
<!-- Junit5 dependencies, defined in parent pom. -->
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-params</artifactId>
</dependency>
<dependency>
<groupId>org.junit.vintage</groupId>
<artifactId>junit-vintage-engine</artifactId>
</dependency>
</dependencies>
<properties>
<maven.build.timestamp.format>yyyyMMdd-HHmm</maven.build.timestamp.format>
<timestamp>${maven.build.timestamp}</timestamp>
</properties>
<build>
<plugins>
<!-- Excluding demo package is required for avoiding namespace clashes
(demo package is in all modules) for signing the jar. See issue #387 -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<excludes>
<exclude>demo/**</exclude>
</excludes>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
</plugin>
</plugins>
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
<includes>
<include>**/*.properties</include>
</includes>
</resource>
<resource>
<directory>src/main/resources</directory>
<filtering>false</filtering>
<includes>
<include>**/*.cif.gz</include>
<include>**/*.pdb.gz</include>
<include>**/*.mat</include>
<include>**/*.xml</include>
</includes>
</resource>
</resources>
</build>
</project>