pub_soft/p2rank
3
0
Fork 0
mirror of https://github.com/rdk/p2rank.git synced 2026-06-04 12:44:24 +08:00
Code Issues Packages Projects Releases Wiki Activity

add custom biojava build biojava-structure-7.2.2-rdk.1.jar

Browse Source
This commit is contained in:
rdk
2025-08-07 18:40:31 +02:00
parent e065350dd6
commit 4b723fd1d3
7 changed files with 11 additions and 195 deletions
Download Patch File Download Diff File Expand all files Collapse all files

8
build.gradle
View File

@@ -22,11 +22,7 @@ apply plugin: "com.github.ben-manes.versions" // ./gradlew dependencyUpdates
group = 'cz.siret'
<<<<<<< HEAD
version = '2.5.1-rc.1'
=======
version = '2.5.1-dev.3-parsFix'
>>>>>>> 2e40ef0e (fix pdbe's updated cifs parsing problem using forked biojava with new parseSites parsing param)
version = '2.5.1-rc.2'
description = 'Ligand binding site prediction based on machine learning.'
@@ -195,7 +191,7 @@ dependencies {
implementation 'org.biojava:biojava-core:7.2.2'
implementation 'org.biojava:biojava-alignment:7.2.2'
implementation 'org.biojava:biojava-structure:7.2.2'
implementation 'org.biojava:biojava-structure:7.2.2-rdk.1' // forked version with new parseSites param
implementation 'org.openscience.cdk:cdk-qsarmolecular:2.11' // for NumericalSurface class
implementation 'org.openscience.cdk:cdk-silent:2.11' // for Atom class

BIN
lib/local-mvn-repo/org/biojava/biojava-structure/7.0.2-rdk1/biojava-structure-7.0.2-rdk1.jar
View File

Binary file not shown.

184
lib/local-mvn-repo/org/biojava/biojava-structure/7.0.2-rdk1/biojava-structure-7.0.2-rdk1.pom
View File

@@ -1,184 +0,0 @@
<?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>7.0.2</version>
</parent>
<artifactId>biojava-structure</artifactId>
<name>biojava-structure</name>
<version>7.0.2-rdk1</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>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-alignment</artifactId>
<version>7.0.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
<version>7.0.2</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>
<!-- JAXb explicit dependency is needed since Java 9. See https://stackoverflow.com/questions/43574426/how-to-resolve-java-lang-noclassdeffounderror-javax-xml-bind-jaxbexception-in-j
Note versions are set in parent pom in dependency management section -->
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-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-slf4j-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>

4
lib/local-mvn-repo/org/biojava/biojava-structure/7.2.2-rdk.1/_remote.repositories Normal file
View File

@@ -0,0 +1,4 @@
#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
#Thu Aug 07 18:37:47 CEST 2025
biojava-structure-7.2.2-rdk.1.jar>=
biojava-structure-7.2.2-rdk.1.pom>=

BIN
lib/local-mvn-repo/org/biojava/biojava-structure/7.1.5-SNAP-rdk.1/biojava-structure-7.1.5-SNAP-rdk.1.jar → lib/local-mvn-repo/org/biojava/biojava-structure/7.2.2-rdk.1/biojava-structure-7.2.2-rdk.1.jar
View File

Binary file not shown.

8
lib/local-mvn-repo/org/biojava/biojava-structure/7.1.5-SNAP-rdk.1/biojava-structure-7.1.5-SNAP-rdk.1.pom → lib/local-mvn-repo/org/biojava/biojava-structure/7.2.2-rdk.1/biojava-structure-7.2.2-rdk.1.pom
View File

@@ -4,11 +4,11 @@
<parent>
<artifactId>biojava</artifactId>
<groupId>org.biojava</groupId>
<version>7.1.5-SNAPSHOT</version>
<version>7.2.2</version>
</parent>
<artifactId>biojava-structure</artifactId>
<name>biojava-structure</name>
<version>7.1.5-SNAP-rdk.1</version>
<version>7.2.2-rdk.1</version>
<description>The protein structure modules of BioJava.</description>
<licenses>
<license>
@@ -52,13 +52,13 @@
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-alignment</artifactId>
<version>7.1.5-SNAPSHOT</version>
<version>7.2.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
<version>7.1.5-SNAPSHOT</version>
<version>7.2.2</version>
<scope>compile</scope>
</dependency>

2
src/test/groovy/cz/siret/prank/domain/ProteinParsingTest.groovy
View File

@@ -18,7 +18,7 @@ class ProteinParsingTest {
/**
* Test parsing PDBe specific "updates cifs"
*/
@Disabled // until solved in BioJava
//@Disabled // until solved in BioJava
@Test
void testParsePdbeUpdatedCif() {
Protein protein = Protein.load("$DIR/4gqq.cif")