Drop pose-variant absolute coordinates from native-3d descriptors

CHANGELOG.md

@@ -9,6 +9,18 @@ API changes; these are called out under **Changed** where they occur.
 
 ## [Unreleased]
 
+### Changed
+
+- **Breaking:** the ``native-3d`` descriptor preset no longer emits the six
+  absolute-coordinate columns ``centroid_x/y/z`` and ``center_of_mass_x/y/z``
+  (preset width drops from 80 to 74). These recorded where a structure happened
+  to sit in its input file's coordinate frame, so they were translation- and
+  rotation-variant: two identical molecules placed differently produced different
+  features, letting a model learn the arbitrary input frame. Size and shape are
+  already captured frame-independently by ``radius_of_gyration``, ``dim_x/y/z``,
+  ``principal_moments`` and the gyration-tensor shape scalars. The ``native-basic``
+  and ``rdkit-basic`` presets are unaffected.
+
 ## [0.15.0] - 2026-06-07
 
 ### Added

molscope/descriptors.py

@@ -97,15 +97,7 @@ def descriptors(
         return _apply_preset(desc, preset, elements_to_count, distance_bins, rdkit_prefix)
 
     dims = molecule.dimensions
-    centroid = molecule.centroid
-    center_of_mass = molecule.center_of_mass
     desc.update({
-        "centroid_x": float(centroid[0]),
-        "centroid_y": float(centroid[1]),
-        "centroid_z": float(centroid[2]),
-        "center_of_mass_x": float(center_of_mass[0]),
-        "center_of_mass_y": float(center_of_mass[1]),
-        "center_of_mass_z": float(center_of_mass[2]),
         "radius_of_gyration": molecule.radius_of_gyration,
         "dim_x": float(dims[0]),
         "dim_y": float(dims[1]),
@@ -462,12 +454,6 @@ def flatten_descriptors(desc: dict) -> dict[str, float]:
 
 def _empty_descriptors(desc: dict, distance_bins: int) -> dict:
     desc.update({
-        "centroid_x": 0.0,
-        "centroid_y": 0.0,
-        "centroid_z": 0.0,
-        "center_of_mass_x": 0.0,
-        "center_of_mass_y": 0.0,
-        "center_of_mass_z": 0.0,
         "radius_of_gyration": 0.0,
         "dim_x": 0.0,
         "dim_y": 0.0,
@@ -674,12 +660,6 @@ def _preset_scalar_names(preset: str, elements_to_count, rdkit_prefix: str) -> l
     ]
     if preset == "native-3d":
         names += [
-            "centroid_x",
-            "centroid_y",
-            "centroid_z",
-            "center_of_mass_x",
-            "center_of_mass_y",
-            "center_of_mass_z",
             "shape_anisotropy",
             "asphericity",
             "acylindricity",

tests/test_descriptors.py

@@ -108,6 +108,20 @@ def test_native_3d_preset_includes_shape_descriptors():
     assert "asphericity" not in water().descriptors(preset="native-basic")
 
 
+def test_native_3d_omits_pose_variant_absolute_coordinates():
+    # Absolute centroid / centre-of-mass coordinates are translation- and
+    # rotation-variant, so they were dropped from the ML feature table.
+    desc = water().descriptors(preset="native-3d")
+    abs_cols = {
+        "centroid_x", "centroid_y", "centroid_z",
+        "center_of_mass_x", "center_of_mass_y", "center_of_mass_z",
+    }
+    assert abs_cols.isdisjoint(desc)
+    assert abs_cols.isdisjoint(descriptor_feature_names("native-3d"))
+    # The default (preset=None) output drops them too, not just the named preset.
+    assert abs_cols.isdisjoint(water().descriptors())
+
+
 def test_flatten_descriptors_expands_vector_features():
     flat = flatten_descriptors({"n_atoms": 3.0, "principal_moments": [1.0, 2.0, 3.0]})
     assert flat == {