Lazy-init EnergyCalculator and LJEnergyCalculator in energy features

src/main/groovy/cz/siret/prank/features/implementation/energy/MethylEnergyCloudSF.groovy

@@ -27,14 +27,6 @@ class MethylEnergyCloudSF extends SasFeatureCalculator implements Parametrized {
     // Immutable calculator instance
     private LJEnergyCalculator calculator
 
-    MethylEnergyCloudSF() {
-        // TODO re-init with new params before each run
-        initializeCalculator()
-    }
-
-    /**
-     * Initialize the feature with the energy calculator
-     */
     @Override
     void preProcessProtein(Protein protein, ProcessedItemContext itemContext) {
         initializeCalculator()

src/main/groovy/cz/siret/prank/features/implementation/energy/MethylEnergyCloudX2FullSF.groovy

@@ -29,14 +29,6 @@ class MethylEnergyCloudX2FullSF extends SasFeatureCalculator implements Parametr
     // Immutable calculator instance
     private LJEnergyCalculator calculator
 
-    MethylEnergyCloudX2FullSF() {
-        // TODO re-init with new params before each run
-        initializeCalculator()
-    }
-
-    /**
-     * Initialize the feature with the energy calculator
-     */
     @Override
     void preProcessProtein(Protein protein, ProcessedItemContext itemContext) {
         initializeCalculator()

src/main/groovy/cz/siret/prank/features/implementation/energy/MethylEnergyCloudX2SF.groovy

@@ -29,14 +29,6 @@ class MethylEnergyCloudX2SF extends SasFeatureCalculator implements Parametrized
     // Immutable calculator instance
     private LJEnergyCalculator calculator
 
-    MethylEnergyCloudX2SF() {
-        // TODO re-init with new params before each run
-        initializeCalculator()
-    }
-
-    /**
-     * Initialize the feature with the energy calculator
-     */
     @Override
     void preProcessProtein(Protein protein, ProcessedItemContext itemContext) {
         initializeCalculator()

src/main/groovy/cz/siret/prank/features/implementation/energy/MethylEnergyCloudXFullSF.groovy

@@ -29,14 +29,6 @@ class MethylEnergyCloudXFullSF extends SasFeatureCalculator implements Parametri
     // Immutable calculator instance
     private LJEnergyCalculator calculator
 
-    MethylEnergyCloudXFullSF() {
-        // TODO re-init with new params before each run
-        initializeCalculator()
-    }
-
-    /**
-     * Initialize the feature with the energy calculator
-     */
     @Override
     void preProcessProtein(Protein protein, ProcessedItemContext itemContext) {
         initializeCalculator()

src/main/groovy/cz/siret/prank/features/implementation/energy/MethylEnergyCloudXSF.groovy

@@ -29,14 +29,6 @@ class MethylEnergyCloudXSF extends SasFeatureCalculator implements Parametrized
     // Immutable calculator instance
     private LJEnergyCalculator calculator
 
-    MethylEnergyCloudXSF() {
-        // TODO re-init with new params before each run
-        initializeCalculator()
-    }
-
-    /**
-     * Initialize the feature with the energy calculator
-     */
     @Override
     void preProcessProtein(Protein protein, ProcessedItemContext itemContext) {
         initializeCalculator()

src/main/groovy/cz/siret/prank/features/implementation/energy/MethylEnergyFeature.groovy

@@ -22,25 +22,11 @@ class MethylEnergyFeature extends SasFeatureCalculator implements Parametrized {
     // Immutable calculator instance
     private LJEnergyCalculator calculator
 
-    MethylEnergyFeature() {
-        // TODO re-init with new params before each run
-        initializeCalculator()
-    }
-
-//    /**
-//     * Initialize the feature with the energy calculator
-//     */
-//    @Override
-//    void preProcessProtein(Protein protein, ProcessedItemContext itemContext) {
-//        initializeCalculator()
-//    }
-
-
-
     /**
-     * Initialize the energy calculator with current parameters
+     * Initialize the energy calculator with current parameters (lazy, called on first use per protein).
      */
-    private void initializeCalculator() {
+    private void ensureCalculatorInitialized() {
+        if (calculator != null) return
         calculator = new LJEnergyCalculator(
             params.energy_probe_sigma,
             params.energy_probe_epsilon,
@@ -63,8 +49,8 @@ class MethylEnergyFeature extends SasFeatureCalculator implements Parametrized {
      */
     @Override
     double[] calculateForSasPoint(Atom sasPoint, SasFeatureCalculationContext context) {
+            ensureCalculatorInitialized()
 
-//        try {
             // Get neighbor atoms around the SAS point
             //Atoms neighbourAtoms = context.extractor.deepLayer.cutoutSphere(sasPoint, params.energy_rc)
             Atoms neighbourAtoms = context.neighbourhoodAtoms

src/main/groovy/cz/siret/prank/features/implementation/energy2/AbstractProbeEnergyFeature.groovy

@@ -27,14 +27,9 @@ import static cz.siret.prank.utils.MathUtils.nanToZero
 @CompileStatic
 abstract class AbstractProbeEnergyFeature extends SasFeatureCalculator implements Parametrized {
 
-    // Immutable calculator instance
     protected EnergyCalculator calculator
     protected EnergyCalculatorConfig config
 
-    AbstractProbeEnergyFeature() {
-        initializeCalculator()
-    }
-
     /**
      * Get the probe type that this feature calculates
      */
@@ -46,7 +41,8 @@ abstract class AbstractProbeEnergyFeature extends SasFeatureCalculator implement
     abstract String getSecondaryDataKey()
 
     /**
-     * Initialize the energy calculator with current parameters and specific probe selection
+     * Initialize the energy calculator with current parameters and specific probe selection.
+     * Called lazily from preProcessProtein before first use.
      */
     protected void initializeCalculator() {
         // Create config with only the specific probe type selected