temporarily disable rotations and bring back java 11 support

rdk · Jun 25, 2024 · afa71a3 · afa71a3
1 parent 48c3da9
commit afa71a3
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Showing 6 changed files with 95 additions and 86 deletions.
diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml
@@ -15,7 +15,7 @@ jobs:
     strategy:
       matrix:
         os: [ ubuntu-latest, windows-latest, macos-latest ]
-        java-version: [ '17', '20', '21', '22' ]
+        java-version: [ '11', '17', '20', '21', '22' ]
 
     steps:
     - uses: actions/checkout@v4

diff --git a/build.gradle b/build.gradle
@@ -179,7 +179,7 @@ dependencies {
     implementation 'org.tukaani:xz:1.9'
     implementation 'com.github.luben:zstd-jni:1.5.6-3'
     implementation 'com.github.dpaukov:combinatoricslib3:3.4.0'
-    implementation 'us.ihmc:euclid:0.21.0'
+    //implementation 'us.ihmc:euclid:0.21.0'
 
     implementation 'org.slf4j:slf4j-api:1.7.36'
     implementation 'org.apache.logging.log4j:log4j-slf4j-impl:2.23.1'

diff --git a/src/main/groovy/cz/siret/prank/geom/transform/Rotation.groovy b/src/main/groovy/cz/siret/prank/geom/transform/Rotation.groovy
@@ -4,25 +4,33 @@ package cz.siret.prank.geom.transform
 import groovy.transform.CompileStatic
 import org.biojava.nbio.structure.Atom
 import org.biojava.nbio.structure.Calc
-import us.ihmc.euclid.matrix.RotationMatrix
+//import us.ihmc.euclid.matrix.RotationMatrix
 
 /**
  *
  */
 @CompileStatic
 class Rotation extends GeometricTransformation {
 
-    private double[][] matrix
-
-    Rotation(String name, RotationMatrix rotMatrix) {
+//    private double[][] matrix
+//
+//    Rotation(String name, RotationMatrix rotMatrix) {
+//        super(name)
+//
+//        this.matrix = Rotations.rotationMatrixToArrays(rotMatrix)
+//    }
+//
+//    @Override
+//    void transformAtom(Atom atom) {
+//        Calc.rotate(atom, matrix)
+//    }
+
+    Rotation(String name) {
         super(name)
-
-        this.matrix = Rotations.rotationMatrixToArrays(rotMatrix)
     }
 
     @Override
     void transformAtom(Atom atom) {
-        Calc.rotate(atom, matrix)
-    }
 
+    }
 }
diff --git a/src/main/groovy/cz/siret/prank/geom/transform/Rotations.java b/src/main/groovy/cz/siret/prank/geom/transform/Rotations.java
@@ -3,8 +3,8 @@
 import org.biojava.nbio.structure.Calc;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
-import us.ihmc.euclid.matrix.RotationMatrix;
-import us.ihmc.euclid.tools.EuclidCoreRandomTools;
+//import us.ihmc.euclid.matrix.RotationMatrix;
+//import us.ihmc.euclid.tools.EuclidCoreRandomTools;
 
 import java.util.Random;
 
@@ -13,36 +13,36 @@
  */
 public class Rotations {
 
-    /**
-     * see https://msl.cs.uiuc.edu/planning/node198.html
-     */
-    public static RotationMatrix generateRandomRotation(Random rand) {
-        return EuclidCoreRandomTools.nextRotationMatrix(rand);
-    }
-
-    public static double[][] rotationMatrixToArrays(RotationMatrix mat) {
-        double[] aux = new double[9];
-        mat.get(aux); // fill in
-
-        double[][] res = new double[3][];
-
-        res[0] = new double[] { aux[0], aux[1], aux[2] };
-        res[1] = new double[] { aux[3], aux[4], aux[5] };
-        res[2] = new double[] { aux[6], aux[7], aux[8] };
-
-        return res;
-    }
-
-    public static void rotateStructureInplace(Structure structure, double[][] rotationMatrix3D) {
-        try {
-            Calc.rotate(structure, rotationMatrix3D);
-        } catch (StructureException e) {
-            throw new RuntimeException("Failed to rotate the structure.", e);
-        }
-    }
-
-    public static void rotateStructureInplace(Structure structure, RotationMatrix rotationMatrix3D) {
-        rotateStructureInplace(structure, rotationMatrixToArrays(rotationMatrix3D));
-    }
+//    /**
+//     * see https://msl.cs.uiuc.edu/planning/node198.html
+//     */
+//    public static RotationMatrix generateRandomRotation(Random rand) {
+//        return EuclidCoreRandomTools.nextRotationMatrix(rand);
+//    }
+//
+//    public static double[][] rotationMatrixToArrays(RotationMatrix mat) {
+//        double[] aux = new double[9];
+//        mat.get(aux); // fill in
+//
+//        double[][] res = new double[3][];
+//
+//        res[0] = new double[] { aux[0], aux[1], aux[2] };
+//        res[1] = new double[] { aux[3], aux[4], aux[5] };
+//        res[2] = new double[] { aux[6], aux[7], aux[8] };
+//
+//        return res;
+//    }
+//
+//    public static void rotateStructureInplace(Structure structure, double[][] rotationMatrix3D) {
+//        try {
+//            Calc.rotate(structure, rotationMatrix3D);
+//        } catch (StructureException e) {
+//            throw new RuntimeException("Failed to rotate the structure.", e);
+//        }
+//    }
+//
+//    public static void rotateStructureInplace(Structure structure, RotationMatrix rotationMatrix3D) {
+//        rotateStructureInplace(structure, rotationMatrixToArrays(rotationMatrix3D));
+//    }
 
 }
diff --git a/src/main/groovy/cz/siret/prank/program/params/Params.groovy b/src/main/groovy/cz/siret/prank/program/params/Params.groovy
@@ -1289,11 +1289,11 @@ class Params {
     int loaded_pockets_limit = 0
 
 
-    /**
-     * Add random rotations of each protein (from training dataset) to the training dataset
-     */
-    @RuntimeParam // training
-    int train_random_rotated_copies = 0
+//    /**
+//     * Add random rotations of each protein (from training dataset) to the training dataset
+//     */
+//    @RuntimeParam // training
+//    int train_random_rotated_copies = 0
 
 //===========================================================================================================//
 // Derived parameters

diff --git a/src/main/groovy/cz/siret/prank/program/routines/traineval/CollectVectorsRoutine.groovy b/src/main/groovy/cz/siret/prank/program/routines/traineval/CollectVectorsRoutine.groovy
@@ -17,7 +17,7 @@ import cz.siret.prank.utils.PerfUtils
 import cz.siret.prank.utils.WekaUtils
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
-import us.ihmc.euclid.matrix.RotationMatrix
+//import us.ihmc.euclid.matrix.RotationMatrix
 import weka.core.Instance
 import weka.core.Instances
 
@@ -49,13 +49,13 @@ class CollectVectorsRoutine extends Routine {
             dataset = dataset.randomSubset(params.train_protein_limit, params.seed)
         }
 
-        // add random rotations
-        // TODO move to TrainEvalRoutine to make use of dataset caching
-        if (params.train_random_rotated_copies > 0) {
-            dataset = expandDatasetWithRandomRotations(dataset, params.train_random_rotated_copies)
-
-            // savePdbsToDir(dataset, outdir + "/train_pdbs")   // TODO remove
-        }
+//        // add random rotations
+//        // TODO move to TrainEvalRoutine to make use of dataset caching
+//        if (params.train_random_rotated_copies > 0) {
+//            dataset = expandDatasetWithRandomRotations(dataset, params.train_random_rotated_copies)
+//
+//            // savePdbsToDir(dataset, outdir + "/train_pdbs")   // TODO remove
+//        }
 
         return dataset
     }
@@ -69,36 +69,37 @@ class CollectVectorsRoutine extends Routine {
     }
 
     private Dataset expandDatasetWithRandomRotations(Dataset dataset, int numRotations) {
-        log.info "Extending training dataset with {} random rotations of each protein", numRotations
-
-        Random rand = new Random(params.seed)
-
-        List<Dataset.Item> newItems = new ArrayList<>()
-
-        newItems.addAll( dataset.items.collect { it.copy() } )
-
-        for (int i=1; i<=numRotations; ++i) {
-            String nameSuffix = "rotation." + i
-
-            RotationMatrix matrix = Rotations.generateRandomRotation(rand)
-            Rotation rotation = new Rotation(nameSuffix, matrix)
-
-            //matrix.setIdentity() // TODO xxx temp
-            matrix.normalize()
-
-            log.info "Random rotation $i: " + matrix
-
-            List<Dataset.Item> rotItems = dataset.items.collect { it.cleanCopy() }
-            for (Dataset.Item item : rotItems) {
-                item.label += nameSuffix
-                item.transformation = rotation
-                // TODO conditionally rotate predictions (pockets of other methods)
-            }
-
-            newItems.addAll(rotItems)
-        }
-
-        return dataset.copyWithNewItems(newItems, dataset.name + "-with-rotations")
+        throw new UnsupportedOperationException("Rotations are not supported in this version")
+//        log.info "Extending training dataset with {} random rotations of each protein", numRotations
+//
+//        Random rand = new Random(params.seed)
+//
+//        List<Dataset.Item> newItems = new ArrayList<>()
+//
+//        newItems.addAll( dataset.items.collect { it.copy() } )
+//
+//        for (int i=1; i<=numRotations; ++i) {
+//            String nameSuffix = "rotation." + i
+//
+//            RotationMatrix matrix = Rotations.generateRandomRotation(rand)
+//            Rotation rotation = new Rotation(nameSuffix, matrix)
+//
+//            //matrix.setIdentity() // TODO xxx temp
+//            matrix.normalize()
+//
+//            log.info "Random rotation $i: " + matrix
+//
+//            List<Dataset.Item> rotItems = dataset.items.collect { it.cleanCopy() }
+//            for (Dataset.Item item : rotItems) {
+//                item.label += nameSuffix
+//                item.transformation = rotation
+//                // TODO conditionally rotate predictions (pockets of other methods)
+//            }
+//
+//            newItems.addAll(rotItems)
+//        }
+//
+//        return dataset.copyWithNewItems(newItems, dataset.name + "-with-rotations")
     }
 
     /**