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upgrade FasterForest to 2.6.0 and fix GString compilation errors
Replace flat jar with local Maven repo dependency at correct path (groupId/artifactId/version/). Fix GString-to-String type errors in AnalyzeRoutine that broke compilation with @CompileStatic.
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@@ -22,7 +22,7 @@ apply plugin: "com.github.ben-manes.versions" // ./gradlew dependencyUpdates
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group = 'cz.siret'
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version = '2.5.2-dev.6'
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version = '2.5.2-dev.8'
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description = 'Ligand binding site prediction based on machine learning.'
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@@ -215,6 +215,7 @@ dependencies {
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implementation 'org.openscience.cdk:cdk-silent:2.11' // for Atom class
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implementation 'cz.cuni.cusbg:faster-molecular-surface:1.0'
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implementation 'cz.siret.prank:FasterForest:2.6.0'
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implementation 'nz.ac.waikato.cms.weka:weka-dev:3.9.6'
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@@ -0,0 +1,33 @@
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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 https://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
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<!-- This module was also published with a richer model, Gradle metadata, -->
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<!-- which should be used instead. Do not delete the following line which -->
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<!-- is to indicate to Gradle or any Gradle module metadata file consumer -->
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<!-- that they should prefer consuming it instead. -->
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<!-- do_not_remove: published-with-gradle-metadata -->
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<modelVersion>4.0.0</modelVersion>
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<groupId>cz.siret.prank</groupId>
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<artifactId>FasterForest</artifactId>
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<version>2.6.0</version>
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<dependencies>
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-lang3</artifactId>
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<version>3.18.0</version>
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<scope>runtime</scope>
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</dependency>
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<dependency>
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<groupId>nz.ac.waikato.cms.weka</groupId>
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<artifactId>weka-dev</artifactId>
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<version>3.9.6</version>
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<scope>runtime</scope>
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</dependency>
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<dependency>
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<groupId>com.carrotsearch</groupId>
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<artifactId>hppc</artifactId>
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<version>0.10.0</version>
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<scope>runtime</scope>
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</dependency>
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</dependencies>
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</project>
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@@ -181,7 +181,7 @@ class AnalyzeRoutine extends Routine {
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String mmcifId = it.mmcifId
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int nres = it.length
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String chars = it.biojavaCodeCharString
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csvRows.add("${item.label}, $nchains, $chainId, $mmcifId, $nres, $chars ")
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csvRows.add("${item.label}, $nchains, $chainId, $mmcifId, $nres, $chars " as String)
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}
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}
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String csv = "protein, n_chains, chain_id, mmcif_id, n_residues, residue_string\n" +
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@@ -290,7 +290,7 @@ class AnalyzeRoutine extends Routine {
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String chainIds = p.residueChains.collect { it.authorId }.join(" ")
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int nres = p.residues.size()
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int nlabres = s.total
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csvRows.add("${item.label}, $nchains, $chainIds, $nres, $nlabres, ${s.positives}, ${s.negatives}, ${s.unlabeled}")
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csvRows.add("${item.label}, $nchains, $chainIds, $nres, $nlabres, ${s.positives}, ${s.negatives}, ${s.unlabeled}" as String)
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if (params.visualizations) {
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new NewPymolRenderer("$outdir/visualizations", new RenderingModel(
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