Tests for pocket-grid-point descriptors + extract DescriptorListValidator

Adds focused regression tests for the new framework: 11 tests in three
new files plus 4 added to PocketGridRowsTest.

  PocketGridRowsTest +4
    - descriptor schema uses "{name}.{col}" prefix for multi-col
    - getRow appends descriptor values after the base 4 columns
    - unknown descriptor name throws at construction
    - scalar descriptor emits bare name() with no prefix (uses an
      inline ScalarTestDescriptor registered via the now-public
      registry hook — none of the shipped descriptors are scalar so
      the branch was untested)
  VolsiteGridPointDescriptorTest (new, 4 tests)
    - covers indicator aggregation + radius cutoff
  VolsiteSmoothGridPointDescriptorTest (new, 4 tests)
    - covers Gaussian kernel arithmetic + 4σ cutoff
  PocketGridPointDescriptorRegistryTest (new, 2 tests)
    - shipped names resolve, unknown name throws helpful error
  DescriptorListValidatorTest (new, 8 tests)
    - null/empty/valid/unknown/duplicate/null-entry/blank/dash-prefix

Refactors Main.validateDescriptorList out to a self-contained Java
utility (DescriptorListValidator) under predict/output/. The two call
sites in Main.validatePocketGridParams now invoke the static helper;
the private helper in Main is removed (-37 lines).

PocketGridPointDescriptorRegistry.register is promoted from private to
public so tests (and future external descriptor plugins) can add
descriptors without touching the registry's static initializer. The
shipped registrations still happen at class-load.

src/main/groovy/cz/siret/prank/program/Main.groovy

@@ -235,13 +235,8 @@ class Main implements Parametrized, Writable {
                     "Known: ${knownAssigners}")
         }
 
-        // Every name in -pocket_descriptors must be registered. null/blank entries are
-        // rejected (rather than skipped) so a malformed config file fails fast instead
-        // of slipping through to the consumers (which would otherwise hit
-        // PocketDescriptorRegistry.get('') with a less useful error). Duplicates are
-        // rejected too — accepting them would produce a CSV with duplicate header cells
-        // and break Parquet's schema builder.
-        validateDescriptorList(params.pocket_descriptors,
+        cz.siret.prank.program.routines.predict.output.DescriptorListValidator.validate(
+                params.pocket_descriptors,
                 cz.siret.prank.program.routines.predict.output.descriptors.PocketDescriptorRegistry.knownNames(),
                 "pocket_descriptors")
 
@@ -285,7 +280,8 @@ class Main implements Parametrized, Writable {
                     "-vis_pocket_grid_gaussian_iso must be > 0 (got ${params.vis_pocket_grid_gaussian_iso}).")
         }
 
-        validateDescriptorList(params.pocket_grid_point_descriptors,
+        cz.siret.prank.program.routines.predict.output.DescriptorListValidator.validate(
+                params.pocket_grid_point_descriptors,
                 cz.siret.prank.program.routines.predict.output.grid.descriptors.PocketGridPointDescriptorRegistry.knownNames(),
                 "pocket_grid_point_descriptors")
         if (params.pocket_grid_volsite_radius <= 0d) {
@@ -305,31 +301,6 @@ class Main implements Parametrized, Writable {
         }
     }
 
-    /**
-     * Shared shape for validating a name-list param against a registry: rejects
-     * null/blank entries, unknown names, and duplicates. {@code paramName} is the
-     * Params property name (without the {@code -} prefix) used in error messages.
-     */
-    private static void validateDescriptorList(List<String> names, Set<String> known, String paramName) {
-        if (names == null) return
-        Set<String> seen = new HashSet<>()
-        for (String name : names) {
-            if (name == null || name.trim().isEmpty()) {
-                throw new PrankException(
-                        "-${paramName} contains an empty/null entry. Known: ${known}")
-            }
-            if (!known.contains(name)) {
-                throw new PrankException(
-                        "Unknown name in -${paramName}: '${name}'. Known: ${known}")
-            }
-            if (!seen.add(name)) {
-                throw new PrankException(
-                        "-${paramName} contains duplicate name '${name}'. " +
-                        "Each descriptor may be listed at most once.")
-            }
-        }
-    }
-
     String evalDirParam(String dirParam, String relativePrefixDir) {
         if (dirParam == null) {
             dirParam = "."

src/main/groovy/cz/siret/prank/program/routines/predict/output/DescriptorListValidator.java

@@ -0,0 +1,58 @@
+package cz.siret.prank.program.routines.predict.output;
+
+import cz.siret.prank.program.PrankException;
+
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+/**
+ * Validates a name-list param (e.g. {@code -pocket_descriptors},
+ * {@code -pocket_grid_point_descriptors}) against the names registered in a
+ * descriptor registry. Rejects:
+ *
+ * <ul>
+ *   <li>null or blank entries — a malformed config file should fail fast rather than
+ *       slip through and hit {@code Registry.get('')} with a less useful error.</li>
+ *   <li>unknown names — names not registered in the registry.</li>
+ *   <li>duplicates — would produce duplicate output columns and break Parquet's
+ *       schema builder.</li>
+ * </ul>
+ *
+ * <p>A {@code null} list is treated as "no entries selected" and accepted without
+ * change — matches the existing Params convention where a missing list means
+ * "no extra columns".
+ */
+public final class DescriptorListValidator {
+
+    private DescriptorListValidator() {}
+
+    /**
+     * @param names      values passed on the CLI / from a config file. A {@code null}
+     *                   list is treated as empty and accepted.
+     * @param known      the registry's known-names set (from {@code Registry.knownNames()}).
+     * @param paramName  the Params property name, used to format error messages
+     *                   (the leading {@code -} is added by the validator).
+     */
+    public static void validate(List<String> names, Set<String> known, String paramName)
+            throws PrankException {
+        if (names == null) return;
+        Set<String> seen = new HashSet<>();
+        for (String name : names) {
+            if (name == null || name.trim().isEmpty()) {
+                throw new PrankException(
+                        "-" + paramName + " contains an empty/null entry. Known: " + known);
+            }
+            if (!known.contains(name)) {
+                throw new PrankException(
+                        "Unknown name in -" + paramName + ": '" + name + "'. Known: " + known);
+            }
+            if (!seen.add(name)) {
+                throw new PrankException(
+                        "-" + paramName + " contains duplicate name '" + name + "'. " +
+                        "Each descriptor may be listed at most once.");
+            }
+        }
+    }
+
+}

src/main/groovy/cz/siret/prank/program/routines/predict/output/grid/descriptors/PocketGridPointDescriptorRegistry.java

@@ -29,7 +29,14 @@ public final class PocketGridPointDescriptorRegistry {
 
     private PocketGridPointDescriptorRegistry() {}
 
-    private static void register(PocketGridPointDescriptor d) {
+    /**
+     * Add a descriptor to the registry. Called from the static initializer for
+     * the shipped descriptors; also exposed for tests that need to register a
+     * fixture descriptor and for future external descriptor plugins. The
+     * registry has no remove/clear — a registered descriptor lives for the JVM's
+     * lifetime, which is intentional (CLI selection by name must be deterministic).
+     */
+    public static void register(PocketGridPointDescriptor d) {
         List<String> cols = d.columnNames();
         if (cols.size() > 1 && new HashSet<>(cols).size() != cols.size()) {
             throw new IllegalStateException(

src/test/groovy/cz/siret/prank/program/routines/predict/output/DescriptorListValidatorTest.groovy

@@ -0,0 +1,81 @@
+package cz.siret.prank.program.routines.predict.output
+
+import cz.siret.prank.program.PrankException
+import groovy.transform.CompileStatic
+import org.junit.jupiter.api.Test
+
+import static org.junit.jupiter.api.Assertions.*
+
+@CompileStatic
+class DescriptorListValidatorTest {
+
+    private static final Set<String> KNOWN = ['volume', 'sphericity', 'num_residues'] as Set
+    private static final String PARAM = 'pocket_descriptors'
+
+    @Test
+    void nullListIsAcceptedAsEmpty() {
+        // A missing list should be a no-op so a default-empty Params field doesn't
+        // require the caller to special-case it. Failure mode = any thrown exception.
+        DescriptorListValidator.validate(null, KNOWN, PARAM)
+    }
+
+    @Test
+    void emptyListIsAccepted() {
+        DescriptorListValidator.validate([], KNOWN, PARAM)
+    }
+
+    @Test
+    void validNamesAreAccepted() {
+        DescriptorListValidator.validate(['volume', 'sphericity'], KNOWN, PARAM)
+    }
+
+    @Test
+    void unknownNameThrowsAndNamesTheOffender() {
+        // The error message MUST include the typo so the user can locate it in their
+        // config, and MUST include the known list so they can correct it.
+        PrankException e = assertThrows(PrankException.class) {
+            DescriptorListValidator.validate(['volume', 'sphericty'], KNOWN, PARAM)
+        } as PrankException
+        assertTrue(e.message.contains("'sphericty'"), "missing typo: ${e.message}")
+        assertTrue(e.message.contains('-pocket_descriptors'), "missing param: ${e.message}")
+        assertTrue(e.message.contains('volume'), "missing known list: ${e.message}")
+    }
+
+    @Test
+    void duplicateNameThrows() {
+        PrankException e = assertThrows(PrankException.class) {
+            DescriptorListValidator.validate(['volume', 'volume'], KNOWN, PARAM)
+        } as PrankException
+        assertTrue(e.message.contains("'volume'"), "missing dup name: ${e.message}")
+        assertTrue(e.message.toLowerCase().contains('duplicate'), "missing 'duplicate': ${e.message}")
+    }
+
+    @Test
+    void nullEntryThrows() {
+        // Distinguishes "list of one valid name" from "list with a null inside" —
+        // catches malformed Groovy config files (e.g. trailing comma in a list literal).
+        PrankException e = assertThrows(PrankException.class) {
+            DescriptorListValidator.validate([null] as List<String>, KNOWN, PARAM)
+        } as PrankException
+        assertTrue(e.message.toLowerCase().contains('empty/null'), e.message)
+    }
+
+    @Test
+    void blankEntryThrows() {
+        PrankException e = assertThrows(PrankException.class) {
+            DescriptorListValidator.validate(['volume', '  '], KNOWN, PARAM)
+        } as PrankException
+        assertTrue(e.message.toLowerCase().contains('empty/null'), e.message)
+    }
+
+    @Test
+    void paramNameIsRenderedWithDashPrefix() {
+        // We don't want the validator to be inconsistent about CLI-flag formatting.
+        PrankException e = assertThrows(PrankException.class) {
+            DescriptorListValidator.validate(['xx'], KNOWN, 'some_param')
+        } as PrankException
+        assertTrue(e.message.contains('-some_param'),
+                "expected leading dash on param name, got: ${e.message}")
+    }
+
+}

src/test/groovy/cz/siret/prank/program/routines/predict/output/PocketGridRowsTest.groovy

@@ -1,11 +1,18 @@
 package cz.siret.prank.program.routines.predict.output
 
 import com.carrotsearch.hppc.LongIntHashMap
+import cz.siret.prank.domain.Pocket
+import cz.siret.prank.domain.Protein
 import cz.siret.prank.geom.Atoms
 import cz.siret.prank.geom.Point
+import cz.siret.prank.program.PrankException
 import cz.siret.prank.program.routines.predict.output.grid.PocketGrid
+import cz.siret.prank.program.routines.predict.output.grid.descriptors.PocketGridPointContext
+import cz.siret.prank.program.routines.predict.output.grid.descriptors.PocketGridPointDescriptor
+import cz.siret.prank.program.routines.predict.output.grid.descriptors.PocketGridPointDescriptorRegistry
 import groovy.transform.CompileStatic
 import org.biojava.nbio.structure.Atom
+import org.junit.jupiter.api.BeforeAll
 import org.junit.jupiter.api.Test
 
 import static org.junit.jupiter.api.Assertions.*
@@ -80,4 +87,83 @@ class PocketGridRowsTest {
         assertEquals(TableData.ColumnType.INT, data.getColumnType(3))
     }
 
+    private static Protein emptyProtein() {
+        Protein p = new Protein()
+        p.proteinAtoms = new Atoms()
+        return p
+    }
+
+    @Test
+    void descriptorColumnsPrefixedWithDescriptorName() {
+        // Multi-column descriptor (volsite, 6 cols) must produce 6 prefixed
+        // headers; the prefix rule is documented contract for the export.
+        PocketGridRows data = new PocketGridRows(buildTwoPocketGrid(), false,
+                emptyProtein(), [] as List<Pocket>, ['volsite'])
+        assertEquals(['x', 'y', 'z', 'pocket',
+                      'volsite.vsAromatic', 'volsite.vsCation', 'volsite.vsAnion',
+                      'volsite.vsHydrophobic', 'volsite.vsAcceptor', 'volsite.vsDonor'],
+                data.header)
+    }
+
+    @Test
+    void getRowAppendsDescriptorValuesAfterBaseColumns() {
+        // Empty protein → cutoutSphere is empty → all 6 indicator columns are 0.
+        // The point of the test is the row LAYOUT (base 4 then 6 descriptor cols),
+        // not the descriptor's numeric semantics — that's covered in
+        // VolsiteGridPointDescriptorTest.
+        PocketGridRows data = new PocketGridRows(buildTwoPocketGrid(), false,
+                emptyProtein(), [] as List<Pocket>, ['volsite'])
+        double[] row = data.getRow(0)
+        assertEquals(10, row.length)
+        // base columns intact
+        assertEquals(1.0d, row[0], 0d); assertEquals(0d, row[1], 0d); assertEquals(0d, row[2], 0d)
+        assertEquals(1, (int) row[3])
+        // descriptor columns all zero (no atoms to classify)
+        for (int i = 4; i < row.length; i++) assertEquals(0d, row[i], 0d)
+    }
+
+    @Test
+    void unknownDescriptorNameThrowsAtConstruction() {
+        PocketGrid grid = buildTwoPocketGrid()
+        PrankException e = assertThrows(PrankException.class) {
+            new PocketGridRows(grid, false, emptyProtein(), [] as List<Pocket>, ['no_such_descriptor'])
+        } as PrankException
+        // The message must name the typo so the user can fix it.
+        assertTrue(e.message.contains('no_such_descriptor'),
+                "expected message to mention typo, got: ${e.message}")
+    }
+
+    /** Fixture: a 1-column descriptor that exercises the scalar branch of the header rule. */
+    @CompileStatic
+    private static final class ScalarTestDescriptor implements PocketGridPointDescriptor {
+        @Override String name() { return TEST_SCALAR_NAME }
+        @Override List<String> columnNames() { return ['ignored'] }
+        @Override List<TableData.ColumnType> columnTypes() { return [TableData.ColumnType.DOUBLE] }
+        @Override double[] compute(PocketGridPointContext ctx) { return [42.0d] as double[] }
+    }
+    private static final String TEST_SCALAR_NAME = '__test_scalar_descriptor__'
+
+    @BeforeAll
+    static void registerScalarFixture() {
+        // Idempotent: register() overwrites by name, so re-running tests in the same JVM
+        // is safe. Name is namespaced with underscores so it can't collide with any
+        // user-facing CLI name.
+        PocketGridPointDescriptorRegistry.register(new ScalarTestDescriptor())
+    }
+
+    @Test
+    void scalarDescriptorEmitsBareNameWithNoPrefix() {
+        // The "{name}.{col}" prefix rule applies ONLY when a descriptor has more than
+        // one column. A single-column descriptor's header is exactly name() — sub-name
+        // is ignored. None of the shipped descriptors are scalar, so this branch
+        // exists for future descriptors and the registered fixture exercises it.
+        PocketGridRows data = new PocketGridRows(buildTwoPocketGrid(), false,
+                emptyProtein(), [] as List<Pocket>, [TEST_SCALAR_NAME])
+        assertEquals(['x', 'y', 'z', 'pocket', TEST_SCALAR_NAME], data.header)
+        // The value 42 from compute() must land in the trailing descriptor column.
+        double[] row = data.getRow(0)
+        assertEquals(5, row.length)
+        assertEquals(42.0d, row[4], 0d)
+    }
+
 }

src/test/groovy/cz/siret/prank/program/routines/predict/output/grid/descriptors/PocketGridPointDescriptorRegistryTest.groovy

@@ -0,0 +1,32 @@
+package cz.siret.prank.program.routines.predict.output.grid.descriptors
+
+import cz.siret.prank.program.PrankException
+import groovy.transform.CompileStatic
+import org.junit.jupiter.api.Test
+
+import static org.junit.jupiter.api.Assertions.*
+
+@CompileStatic
+class PocketGridPointDescriptorRegistryTest {
+
+    @Test
+    void shippedDescriptorsAreRegistered() {
+        // If someone removes one of the shipped descriptors, the CLI -pocket_grid_point_descriptors
+        // default no longer resolves and existing user config files start to fail. This test
+        // pins both shipped names.
+        assertNotNull(PocketGridPointDescriptorRegistry.get('volsite'))
+        assertNotNull(PocketGridPointDescriptorRegistry.get('volsite_smooth'))
+    }
+
+    @Test
+    void unknownNameThrowsWithKnownList() {
+        PrankException e = assertThrows(PrankException.class) {
+            PocketGridPointDescriptorRegistry.get('does_not_exist')
+        } as PrankException
+        // The error message must name the typo AND list the known names so the
+        // user can see the correct spelling.
+        assertTrue(e.message.contains('does_not_exist'), "missing typo in: ${e.message}")
+        assertTrue(e.message.contains('volsite'), "missing 'volsite' in known list: ${e.message}")
+    }
+
+}

src/test/groovy/cz/siret/prank/program/routines/predict/output/grid/descriptors/VolsiteGridPointDescriptorTest.groovy

@@ -0,0 +1,97 @@
+package cz.siret.prank.program.routines.predict.output.grid.descriptors
+
+import cz.siret.prank.domain.Protein
+import cz.siret.prank.geom.Atoms
+import cz.siret.prank.geom.Point
+import groovy.transform.CompileStatic
+import org.biojava.nbio.structure.Atom
+import org.biojava.nbio.structure.AtomImpl
+import org.biojava.nbio.structure.Element
+import org.biojava.nbio.structure.Group
+import org.biojava.nbio.structure.AminoAcidImpl
+import org.junit.jupiter.api.Test
+
+import static org.junit.jupiter.api.Assertions.*
+
+/**
+ * Behavioural tests for the indicator volsite descriptor. We don't test every
+ * pharmacophore branch (that's {@code VolSitePharmacophore}'s domain) — we
+ * verify that the descriptor correctly aggregates per-atom flags into the
+ * 6-column row and honors the cutoff radius.
+ *
+ * <p>Column order (matches {@code VolSitePharmacophore.COLUMN_NAMES}):
+ * aromatic, cation, anion, hydrophobic, acceptor, donor.
+ */
+@CompileStatic
+class VolsiteGridPointDescriptorTest {
+
+    private static final int AROMATIC = 0, CATION = 1, ANION = 2,
+                             HYDROPHOBIC = 3, ACCEPTOR = 4, DONOR = 5
+
+    private static Atom atomAt(String element, String resName, String atomName,
+                                double x, double y, double z) {
+        AtomImpl a = new AtomImpl()
+        a.element = Element.valueOfIgnoreCase(element)
+        a.name = atomName
+        a.x = x; a.y = y; a.z = z
+        Group g = new AminoAcidImpl()
+        g.setPDBName(resName)
+        a.setGroup(g)
+        return a
+    }
+
+    private static PocketGridPointContext ctxAt(double x, double y, double z, Atoms proteinAtoms) {
+        Protein p = new Protein()
+        p.proteinAtoms = proteinAtoms
+        return new PocketGridPointContext(0, new Point(x, y, z), 0, null, p, null)
+    }
+
+    @Test
+    void singleHydrophobicAtomNearbySetsOnlyHydrophobic() {
+        // Atom name "C" + any residue → hydrophobic (first branch in VolSitePharmacophore).
+        Atom c = atomAt("C", "ALA", "C", 1d, 0d, 0d)  // 1 Å from grid point — well inside default 4 Å
+        double[] out = new VolsiteGridPointDescriptor().compute(
+                ctxAt(0d, 0d, 0d, new Atoms([c])))
+
+        assertEquals(1d, out[HYDROPHOBIC])
+        for (int i = 0; i < 6; i++) if (i != HYDROPHOBIC) assertEquals(0d, out[i], 0d, "col $i")
+    }
+
+    @Test
+    void atomOutsideRadiusContributesNothing() {
+        // Default -pocket_grid_volsite_radius is 4.0; place a hydrophobic atom at 5 Å.
+        Atom c = atomAt("C", "ALA", "C", 5d, 0d, 0d)
+        double[] out = new VolsiteGridPointDescriptor().compute(
+                ctxAt(0d, 0d, 0d, new Atoms([c])))
+
+        for (int i = 0; i < 6; i++) assertEquals(0d, out[i], 0d, "col $i")
+    }
+
+    @Test
+    void mixedNearbyAtomsSetMultipleIndependentFlags() {
+        // One donor (N backbone) + one anion (OD1 in ASP) + one cation (ZN — name-only rule).
+        // All within 4 Å of origin. Three indicators should fire; the other three should not.
+        Atoms protein = new Atoms([
+                atomAt("N", "ALA", "N",   1d, 0d, 0d),
+                atomAt("O", "ASP", "OD1", 0d, 1d, 0d),
+                atomAt("ZN", "ZN", "ZN",  0d, 0d, 1d),
+        ])
+        double[] out = new VolsiteGridPointDescriptor().compute(
+                ctxAt(0d, 0d, 0d, protein))
+
+        assertEquals(1d, out[DONOR])
+        assertEquals(1d, out[ANION])
+        assertEquals(1d, out[CATION])
+        assertEquals(0d, out[AROMATIC])
+        assertEquals(0d, out[HYDROPHOBIC])
+        assertEquals(0d, out[ACCEPTOR])
+    }
+
+    @Test
+    void emptyNeighborhoodAllZeros() {
+        double[] out = new VolsiteGridPointDescriptor().compute(
+                ctxAt(0d, 0d, 0d, new Atoms()))
+        for (int i = 0; i < 6; i++) assertEquals(0d, out[i], 0d)
+    }
+
+}

src/test/groovy/cz/siret/prank/program/routines/predict/output/grid/descriptors/VolsiteSmoothGridPointDescriptorTest.groovy

@@ -0,0 +1,90 @@
+package cz.siret.prank.program.routines.predict.output.grid.descriptors
+
+import cz.siret.prank.domain.Protein
+import cz.siret.prank.geom.Atoms
+import cz.siret.prank.geom.Point
+import cz.siret.prank.program.params.Params
+import groovy.transform.CompileStatic
+import org.biojava.nbio.structure.Atom
+import org.biojava.nbio.structure.AtomImpl
+import org.biojava.nbio.structure.Element
+import org.biojava.nbio.structure.Group
+import org.biojava.nbio.structure.AminoAcidImpl
+import org.junit.jupiter.api.Test
+
+import static org.junit.jupiter.api.Assertions.*
+
+/**
+ * Tests the Gaussian weighting math: kernel value at known distances, summing
+ * across atoms, and the 4σ cutoff. These are the numeric facts that, if broken,
+ * silently produce wrong scores — exactly what unit tests should catch.
+ */
+@CompileStatic
+class VolsiteSmoothGridPointDescriptorTest {
+
+    private static final double DELTA = 1e-9
+
+    private static final int AROMATIC = 0, CATION = 1, ANION = 2,
+                             HYDROPHOBIC = 3, ACCEPTOR = 4, DONOR = 5
+
+    private static Atom atomAt(String atomName, String resName, double x, double y, double z) {
+        AtomImpl a = new AtomImpl()
+        a.element = Element.C
+        a.name = atomName
+        a.x = x; a.y = y; a.z = z
+        Group g = new AminoAcidImpl()
+        g.setPDBName(resName)
+        a.setGroup(g)
+        return a
+    }
+
+    private static PocketGridPointContext ctxAt(double x, double y, double z, Atoms proteinAtoms) {
+        Protein p = new Protein()
+        p.proteinAtoms = proteinAtoms
+        return new PocketGridPointContext(0, new Point(x, y, z), 0, null, p, null)
+    }
+
+    @Test
+    void weightAtZeroDistanceIsOne() {
+        // exp(0) = 1.0 exactly. Atom name "C" is hydrophobic.
+        Atom c = atomAt("C", "ALA", 0d, 0d, 0d)
+        double[] out = new VolsiteSmoothGridPointDescriptor().compute(
+                ctxAt(0d, 0d, 0d, new Atoms([c])))
+        assertEquals(1.0d, out[HYDROPHOBIC], DELTA)
+    }
+
+    @Test
+    void weightAtSigmaMatchesGaussianFormula() {
+        // At distance r = σ, weight = exp(-r²/(2σ²)) = exp(-1/2) ≈ 0.6065.
+        double sigma = Params.inst.pocket_grid_volsite_sigma
+        Atom c = atomAt("C", "ALA", sigma, 0d, 0d)
+        double[] out = new VolsiteSmoothGridPointDescriptor().compute(
+                ctxAt(0d, 0d, 0d, new Atoms([c])))
+        assertEquals(Math.exp(-0.5d), out[HYDROPHOBIC], DELTA)
+    }
+
+    @Test
+    void weightsFromMultipleAtomsOfSameTypeSum() {
+        // Two hydrophobic atoms at distance σ each → sum = 2 × exp(-0.5).
+        double sigma = Params.inst.pocket_grid_volsite_sigma
+        Atoms protein = new Atoms([
+                atomAt("C", "ALA", sigma, 0d, 0d),
+                atomAt("C", "ALA", 0d, sigma, 0d),
+        ])
+        double[] out = new VolsiteSmoothGridPointDescriptor().compute(
+                ctxAt(0d, 0d, 0d, protein))
+        assertEquals(2d * Math.exp(-0.5d), out[HYDROPHOBIC], DELTA)
+    }
+
+    @Test
+    void atomBeyondCutoffContributesZero() {
+        // 4σ is the hard cutoff (cutoutSphere is the gate). At 5σ the atom isn't even
+        // in the kdtree result. Zero contribution.
+        double sigma = Params.inst.pocket_grid_volsite_sigma
+        Atom c = atomAt("C", "ALA", 5d * sigma, 0d, 0d)
+        double[] out = new VolsiteSmoothGridPointDescriptor().compute(
+                ctxAt(0d, 0d, 0d, new Atoms([c])))
+        assertEquals(0d, out[HYDROPHOBIC], DELTA)
+    }
+
+}