refactor name?

lilyminium · Mar 21, 2022 · 54bec35 · 54bec35
1 parent 1608727
commit 54bec35
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Showing 4 changed files with 10 additions and 8 deletions.
diff --git a/rdkit_utilities/Utils.py → rdkit_utilities/_utils.py b/rdkit_utilities/Utils.py → rdkit_utilities/_utils.py
diff --git a/rdkit_utilities/rdDistGeom.py b/rdkit_utilities/rdDistGeom.py
@@ -229,7 +229,7 @@ def SelectDiverseConformers(
     """
     from .rdMolAlign import GetBestConformerRMS
     from .rdmolops import KeepConformerIds
-    from .utils import get_maximally_diverse_indices
+    from ._utils import get_maximally_diverse_indices
 
     rms_matrix = GetBestConformerRMS(mol, heavyAtomsOnly=True)
     diverse_indices = get_maximally_diverse_indices(
@@ -335,13 +335,13 @@ def CalculateElectrostaticEnergy(
     forcefield: Literal["MMFF94", "MMFF94s"] = "MMFF94",
 ) -> np.ndarray:
     """Calculate electrostatic energy of all conformers using force field
-    
+
     Returns
     -------
     energies: numpy.ndarray
         Array of energies, one for each conformer
     """
-    from .utils import compute_atom_distance_matrix
+    from ._utils import compute_atom_distance_matrix
 
     conformers = np.array([c.GetPositions() for c in mol.GetConformers()])
     distances = compute_atom_distance_matrix(conformers)
@@ -381,7 +381,7 @@ def RemoveConformersOutsideEnergyWindow(
     ffIgnoreInterfragInteractions: bool = True,
 ) -> int:
     """Remove conformers outside energy window using force field, in-place
-    
+
     The window covers an energy range from the conformer with the lowest
     energy. The molecule also has its conformers sorted by force field
     energy.

diff --git a/rdkit_utilities/tests/conftest.py b/rdkit_utilities/tests/conftest.py
@@ -41,3 +41,5 @@ def ethane():
     rdChem.SanitizeMol(mol)
     AllChem.EmbedMolecule(mol)
     return mol
+
+
diff --git a/rdkit_utilities/tests/test_utils.py b/rdkit_utilities/tests/test_utils.py
@@ -5,9 +5,9 @@
 
 
 def test_compute_distance_matrix():
-    from rdkit_utilities import utils
+    from rdkit_utilities import _utils
     arr = np.arange(24).reshape((2, 4, 3))
-    rms = utils.compute_atom_distance_matrix(arr)
+    rms = _utils.compute_atom_distance_matrix(arr)
     assert rms.shape == (2, 4, 4)
 
     first_row = [0, 5.19615242, 10.39230485, 15.58845727]
@@ -27,14 +27,14 @@ def test_compute_distance_matrix():
     (5.4, 4, [0, 3, 1]),
 ])
 def test_get_maximally_diverse_indices(threshold, n_indices, indices):
-    from rdkit_utilities import utils
+    from rdkit_utilities import _utils
     arr = np.array([
         [ 0.         , 5.49615242 ,10.39230485 ,15.58845727],
         [ 5.49615242 , 0.         , 5.19615242 ,10.39230485],
         [10.39230485 , 5.19615242 , 0.         , 5.19615242],
         [15.58845727 ,10.39230485 , 5.19615242 , 0.        ],
     ])
-    computed = utils.get_maximally_diverse_indices(
+    computed = _utils.get_maximally_diverse_indices(
         arr,
         distance_threshold=threshold,
         n_indices=n_indices,