Add ca_atoms_centroid site evaluation center method with tests

src/main/groovy/cz/siret/prank/domain/Ligand.groovy

@@ -1,6 +1,7 @@
 package cz.siret.prank.domain
 
 import cz.siret.prank.geom.Atoms
+import cz.siret.prank.geom.Struct
 import cz.siret.prank.program.params.Parametrized
 import cz.siret.prank.utils.PdbUtils
 import groovy.transform.CompileStatic
@@ -106,6 +107,12 @@ class Ligand implements BindingSite, Parametrized {
                 return atoms.centerOfMass
             case SiteCentroidMethod.sas_points_centroid:
                 return getSasPoints().centroid
+            case SiteCentroidMethod.ca_atoms_centroid:
+                // Select contact residues and compute geometric centroid of their CA atoms
+                List<Residue> contactResidues = protein.residues.getDistinctForAtoms(
+                    protein.proteinAtoms.cutoutShell(atoms, params.ligand_protein_contact_distance)
+                )
+                return Struct.calcCaCentroid(contactResidues)
             default:
                 throw new IllegalArgumentException("Unsupported site_eval_center_method: '${method}'")
         }

src/main/groovy/cz/siret/prank/domain/ResidueSite.groovy

@@ -1,6 +1,7 @@
 package cz.siret.prank.domain
 
 import cz.siret.prank.geom.Atoms
+import cz.siret.prank.geom.Struct
 import cz.siret.prank.program.params.Parametrized
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
@@ -68,6 +69,8 @@ class ResidueSite implements BindingSite, Parametrized {
                 return getSasPoints().centroid
             case SiteCentroidMethod.atoms_center_of_mass:
                 return getAtoms().centerOfMass
+            case SiteCentroidMethod.ca_atoms_centroid:
+                return Struct.calcCaCentroid(residues)
             default:
                 throw new IllegalArgumentException("Unsupported site_eval_center_method: '${method}'")
         }

src/main/groovy/cz/siret/prank/domain/SiteCentroidMethod.groovy

@@ -15,7 +15,10 @@ enum SiteCentroidMethod {
     atoms_center_of_mass(true, true),
 
     /** Centroid of SAS points around site atoms */
-    sas_points_centroid(true, true)
+    sas_points_centroid(true, true),
+
+    /** Geometric centroid of CA atoms of contact residues */
+    ca_atoms_centroid(true, true)
 
     /** Supported for ligand-defined sites */
     final boolean supportedForLigandSites

src/main/groovy/cz/siret/prank/geom/Struct.groovy

@@ -203,6 +203,29 @@ class Struct {
         return getGroups(struc).findAll{ isHetGroup(it) }.asList()
     }
 
+    /**
+     * Calculate geometric centroid of CA atoms from the given residues.
+     * Residues without CA atoms (e.g. non-standard residues) are skipped.
+     * @return centroid atom or null if no CA atoms found
+     */
+    @Nullable
+    static Atom calcCaCentroid(List<Residue> residues) {
+        List<Atom> caAtoms = new ArrayList<>()
+        for (Residue res : residues) {
+            AminoAcid aa = res.aminoAcid
+            if (aa != null) {
+                Atom ca = aa.getCA()
+                if (ca != null) {
+                    caAtoms.add(ca)
+                }
+            }
+        }
+        if (caAtoms.isEmpty()) {
+            return null
+        }
+        return new Atoms(caAtoms).centroid
+    }
+
     /**
      * single linkage clustering
      * @param clusters

src/main/groovy/cz/siret/prank/program/params/Params.groovy

@@ -829,11 +829,15 @@ class Params {
     boolean vis_highlight_ligands = false
 
     /**
-     * Method for computing binding site center for evaluation (DCC criterion).
-     * Values: explicit, atoms_center_of_mass, sas_points_centroid
+     * Method for computing binding site center of observed pocket for evaluation (used by DCC criterion).
+     * Observed pocket can be defined by ligand or can be explicit (set of residues defined in the dataset).
+     * Values: explicit, atoms_center_of_mass, sas_points_centroid, ca_atoms_centroid
      *
      * Note: atoms_center_of_mass uses mass-weighted center of ligand/residue atoms for both site types.
      * explicit is only supported for explicitly defined sites (not ligand-defined).
+     * ca_atoms_centroid uses geometric centroid of CA atoms of contact residues
+     * (for ligand sites: contact residues within ligand_protein_contact_distance;
+     *  for explicit sites: the defined residues directly).
      *
      * @see cz.siret.prank.domain.SiteCentroidMethod
      */

src/test/groovy/cz/siret/prank/domain/SiteMetricsTest.groovy

@@ -1,8 +1,10 @@
 package cz.siret.prank.domain
 
 import cz.siret.prank.geom.Atoms
+import cz.siret.prank.geom.Struct
 import cz.siret.prank.prediction.pockets.PrankPocket
 import cz.siret.prank.prediction.pockets.criteria.DCA
+import cz.siret.prank.program.params.Params
 import cz.siret.prank.program.routines.results.EvalContext
 import cz.siret.prank.program.routines.results.Evaluation
 import groovy.transform.CompileStatic
@@ -243,6 +245,51 @@ class SiteMetricsTest {
     // TODO: test evaluation getStats() with site-based results
     // TODO: test with sites that are far from any pocket (unidentified case)
 
+//===========================================================================================================//
+// ca_atoms_centroid tests
+//===========================================================================================================//
+
+    @Test
+    void caCentroidMethodWorksForResidueSite() {
+        List<Residue> residues = protein.residues.toList().subList(0, 10)
+        ResidueSite site = makeSite("ca_test", residues)
+
+        String savedMethod = Params.inst.site_eval_center_method
+        try {
+            Params.inst.site_eval_center_method = "ca_atoms_centroid"
+
+            def result = site.getCenterForEval()
+            def expected = Struct.calcCaCentroid(residues)
+
+            assertNotNull(result)
+            assertEquals(expected.x, result.x, 0.001)
+            assertEquals(expected.y, result.y, 0.001)
+            assertEquals(expected.z, result.z, 0.001)
+        } finally {
+            Params.inst.site_eval_center_method = savedMethod
+        }
+    }
+
+    @Test
+    void caCentroidMethodWorksForLigand() {
+        Ligand ligand = protein.ligands.relevantLigands[0]
+        assertNotNull(ligand, "Test protein should have at least one relevant ligand")
+
+        String savedMethod = Params.inst.site_eval_center_method
+        try {
+            Params.inst.site_eval_center_method = "ca_atoms_centroid"
+
+            def result = ligand.getCenterForEval()
+            assertNotNull(result, "ca_atoms_centroid should return non-null for a ligand with nearby protein residues")
+
+            // Result should be within reasonable distance of the ligand
+            double dist = protein.proteinAtoms.dist(result)
+            assertTrue(dist < 20.0, "CA centroid should be near the protein surface")
+        } finally {
+            Params.inst.site_eval_center_method = savedMethod
+        }
+    }
+
 //===========================================================================================================//
 // Helpers
 //===========================================================================================================//

src/test/groovy/cz/siret/prank/geom/StructTest.groovy

@@ -1,11 +1,14 @@
 package cz.siret.prank.geom
 
 import cz.siret.prank.domain.Protein
+import cz.siret.prank.domain.Residue
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
+import org.biojava.nbio.structure.AminoAcid
+import org.biojava.nbio.structure.Atom
 import org.junit.jupiter.api.Test
 
-import static org.junit.jupiter.api.Assertions.assertEquals
+import static org.junit.jupiter.api.Assertions.*
 
 /**
  *
@@ -38,4 +41,33 @@ class StructTest {
         // TODo add test for chain with phosphorylated residue
     }
 
+    @Test
+    void calcCaCentroidReturnsGeometricCenterOfCaAtoms() {
+        Protein p = Protein.load("$dataDir/2nbr.pdb.gz")
+        List<Residue> residues = p.residues.toList().subList(0, 5)
+
+        Atom result = Struct.calcCaCentroid(residues)
+        assertNotNull(result)
+
+        // Manually compute expected centroid from CA atoms
+        List<Atom> caAtoms = []
+        for (Residue res : residues) {
+            AminoAcid aa = res.aminoAcid
+            if (aa != null) {
+                Atom ca = aa.getCA()
+                if (ca != null) caAtoms.add(ca)
+            }
+        }
+        Atom expected = new Atoms(caAtoms).centroid
+
+        assertEquals(expected.x, result.x, 0.001)
+        assertEquals(expected.y, result.y, 0.001)
+        assertEquals(expected.z, result.z, 0.001)
+    }
+
+    @Test
+    void calcCaCentroidReturnsNullForEmptyList() {
+        assertNull(Struct.calcCaCentroid([]))
+    }
+
 }