Remove not tested scorer

src/kartograf/atom_mapping_scorer.py

@@ -2,9 +2,6 @@
 # For details, see https://github.com/OpenFreeEnergy/kartograf
 
 import logging
-import numpy as np
-
-from gufe.mapping import AtomMapping
 
 from .mapping_metrics import MappingRMSDScorer
 from .mapping_metrics import (
@@ -13,55 +10,4 @@
 )
 from .mapping_metrics import MappingVolumeRatioScorer
 
-from .mapping_metrics._abstract_scorer import _AbstractAtomMappingScorer
-
 logger = logging.getLogger(__name__)
-
-
-class DefaultKartografScorer(_AbstractAtomMappingScorer):
-    """
-    Warning this is highly experimental!
-    """
-
-    def __init__(self):
-        """ Mapping Scorer
-        this could be a future scorer using the here defined metrics?
-
-        don't use ;)
-        """
-        self.scorers = [
-            MappingVolumeRatioScorer(),
-            MappingShapeOverlapScorer(),
-            MappingShapeMismatchScorer(),
-            MappingRMSDScorer(),
-        ]
-
-        self.weights = np.array([1, 3, 3, 3])
-        self.weights = self.weights / np.sum(self.weights)
-
-    def get_score(self, mapping: AtomMapping) -> float:
-        """ Calculate a Score
-
-            Under Development
-
-        Parameters
-        ----------
-        mapping : AtomMapping
-            AtomMapping to be scored
-
-        Returns
-        -------
-        float
-            normalized score
-        """
-        logger.info("Kartograf Score:")
-        scores = []
-        for weight, scorer in zip(self.weights, self.scorers):
-            s = scorer.get_score(mapping)
-            logger.info(f"\t{scorer.__class__.__name__}\t{s}\tweight{weight}")
-            scores.append(s)
-
-        score = np.round(np.average(scores, weights=self.weights), 2)
-        score = score if (score > 0) else 0.0
-        logger.info(f"Result: {score}")
-        return score

src/kartograf/filters/__init__.py

@@ -1,4 +1,4 @@
-from .element_change import (
+from .atom_changes import (
     filter_atoms_h_only_h_mapped,
     filter_element_changes,
     filter_hybridization_changes,

src/kartograf/tests/test_atom_mapping_scorer.py

@@ -2,14 +2,12 @@
 # For details, see https://github.com/OpenFreeEnergy/kartograf
 
 import pytest
-from kartograf.atom_mapping_scorer import DefaultKartografScorer
 from kartograf.mapping_metrics import (
     MappingRMSDScorer,
     MappingShapeMismatchScorer,
     MappingShapeOverlapScorer,
     MappingVolumeRatioScorer,
     MappingRatioMappedAtomsScorer,
-
 )
 
 from kartograf.mapping_metrics.metric_shape_difference import (
@@ -35,6 +33,7 @@ def test_score_norm_mapping_rmsd(stereo_chem_mapping):
     score = scorer.get_rmsd_p(stereo_chem_mapping)
     print(score)
 
+
 def test_score_mapping_volume_ratio(stereo_chem_mapping):
     """
     Currently a smoke test
@@ -52,6 +51,7 @@ def test_score_shape_dist(stereo_chem_mapping):
     score = scorer(stereo_chem_mapping)
     print(score)
 
+
 def test_score_shape_overlap(stereo_chem_mapping):
     """
     Currently a smoke test
@@ -60,6 +60,7 @@ def test_score_shape_overlap(stereo_chem_mapping):
     score = scorer(stereo_chem_mapping)
     print(score)
 
+
 def test_score_shape_mismatch(stereo_chem_mapping):
     """
     Currently a smoke test
@@ -69,13 +70,13 @@ def test_score_shape_mismatch(stereo_chem_mapping):
     print(score)
 
 
-@pytest.mark.parametrize("scorer_class", [ MappingRMSDScorer,
-    _MappingShapeDistanceScorer,
-    MappingShapeMismatchScorer,
-    MappingShapeOverlapScorer,
-    MappingVolumeRatioScorer,
-    MappingRatioMappedAtomsScorer,
-    DefaultKartografScorer])
+@pytest.mark.parametrize("scorer_class", [MappingRMSDScorer,
+                                          _MappingShapeDistanceScorer,
+                                          MappingShapeMismatchScorer,
+                                          MappingShapeOverlapScorer,
+                                          MappingVolumeRatioScorer,
+                                          MappingRatioMappedAtomsScorer,
+                                          ])
 def test_scorer_identical_molecules(scorer_class, benzene_benzene_mapping):
     """
     Currently a smoke test
@@ -92,25 +93,26 @@ def test_scorer_identical_molecules(scorer_class, benzene_benzene_mapping):
                                                (MappingShapeMismatchScorer, 0),
                                                (MappingShapeOverlapScorer, 0),
                                                (MappingRatioMappedAtomsScorer, 0)])
-def test_scorer_empty_mapping(scorer_class, exp:float, benzene_benzene_empty_mapping):
+def test_scorer_empty_mapping(scorer_class, exp: float, benzene_benzene_empty_mapping):
     """
     Currently a smoke test
     """
     scorer = scorer_class()
     score = scorer(benzene_benzene_empty_mapping)
 
     assert isinstance(score, float)
-    assert score == exp, "Score of non-Mapping should be "+str(exp)+" for "+str(scorer_class.__name__)+" but is: "+str(score)
+    assert score == exp, "Score of non-Mapping should be " + str(exp) + " for " + str(
+        scorer_class.__name__) + " but is: " + str(score)
 
 
 @pytest.mark.parametrize("scorer_class, exp", [(MappingVolumeRatioScorer, 1),
-                                               (DefaultKartografScorer,1)])
-def test_scorer_empty_mapping_err(scorer_class, exp:float, benzene_benzene_empty_mapping):
+                                               ])
+def test_scorer_empty_mapping_err(scorer_class, exp: float, benzene_benzene_empty_mapping):
     """
     Currently a smoke test
     """
     with pytest.raises(ValueError) as exc:
         scorer = scorer_class()
         score = scorer(benzene_benzene_empty_mapping)
 
-    assert "Mapping is too small to calculate convex hull" in str(exc.value)
+    assert "Mapping is too small to calculate convex hull" in str(exc.value)