molcraft 0.1.0a19__tar.gz → 0.1.0a21__tar.gz

{molcraft-0.1.0a19 → molcraft-0.1.0a21}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: molcraft
-Version: 0.1.0a19
+Version: 0.1.0a21
 Summary: Graph Neural Networks for Molecular Machine Learning
 Author-email: Alexander Kensert <alexander.kensert@gmail.com>
 License: MIT License

{molcraft-0.1.0a19 → molcraft-0.1.0a21}/molcraft/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.1.0a19'
+__version__ = '0.1.0a21'
 
 import os
 os.environ["TF_CPP_MIN_LOG_LEVEL"] = "3"

{molcraft-0.1.0a19 → molcraft-0.1.0a21}/molcraft/chem.py

@@ -427,11 +427,9 @@ def embed_conformers(
             f'{num_conformers - num_successes} conformer(s) using different embedding methods.',
             stacklevel=2
         )
-        max_attempts = (20 * mol.num_atoms) # increasing it from 10xN to 20xN
         for fallback_method in [method, 'ETDG', 'KDG']:
             fallback_embedding_method = available_embedding_methods[fallback_method]
             fallback_embedding_method.useRandomCoords = True
-            fallback_embedding_method.maxAttempts = max_attempts
             fallback_embedding_method.clearConfs = False
             if random_seed is not None:
                 fallback_embedding_method.randomSeed = random_seed
@@ -463,14 +461,14 @@ def optimize_conformers(
             f'Could not find `method` {method!r}. Specify either of: '
             '`UFF`, `MMFF`, `MMFF94` or `MMFF94s`.'
         )
-    mol = Mol(mol)
+    mol_optimized = Mol(mol)
     try:
         if method.startswith('MMFF'):
             variant = method 
             if variant == 'MMFF':
                 variant += '94'
             _, _ = _mmff_optimize_conformers(
-                mol, 
+                mol_optimized, 
                 num_threads=num_threads, 
                 max_iter=max_iter, 
                 variant=variant,
@@ -478,7 +476,7 @@ def optimize_conformers(
             )
         else:
             _, _ = _uff_optimize_conformers(
-                mol,
+                mol_optimized,
                 num_threads=num_threads,
                 max_iter=max_iter,
                 vdw_threshold=vdw_threshold,
@@ -486,11 +484,11 @@ def optimize_conformers(
             )
     except RuntimeError as e:
         warnings.warn(
-            f'{method} force field minimization raised {e}. '
-            '\nProceeding without force field minimization.',
+            f'{method} force field minimization did not succeed. Proceeding without it.',
             stacklevel=2
         )
-    return mol
+        return mol
+    return mol_optimized
 
 def prune_conformers(
     mol: Mol,

{molcraft-0.1.0a19 → molcraft-0.1.0a21}/molcraft/featurizers.py

@@ -323,7 +323,9 @@ class MolGraphFeaturizer3D(MolGraphFeaturizer):
         include_hydrogens: bool = False,
         radius: int | float | None = 6.0,
         random_seed: int | None = None,
+        **kwargs,
     ) -> None:
+        kwargs.pop('bond_features', None)
         super().__init__(
             atom_features=atom_features,
             bond_features=None,
@@ -413,7 +415,6 @@ class MolGraphFeaturizer3D(MolGraphFeaturizer):
 
     def get_config(self):
         config = super().get_config()
-        config.pop('bond_features', None)
         config['radius'] = self._radius
         config['pair_features'] = keras.saving.serialize_keras_object(
             self._pair_features

{molcraft-0.1.0a19 → molcraft-0.1.0a21}/molcraft.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: molcraft
-Version: 0.1.0a19
+Version: 0.1.0a21
 Summary: Graph Neural Networks for Molecular Machine Learning
 Author-email: Alexander Kensert <alexander.kensert@gmail.com>
 License: MIT License

{molcraft-0.1.0a19 → molcraft-0.1.0a21}/tests/test_featurizers.py

@@ -1,4 +1,6 @@
 import unittest 
+import tempfile
+import shutil
 
 from molcraft import features
 from molcraft import featurizers
@@ -42,6 +44,12 @@ class TestFeaturizer(unittest.TestCase):
             include_hydrogens=False, 
         ) 
 
+        tmp_dir = tempfile.mkdtemp()
+        tmp_file = tmp_dir + '/featurizer.json'
+        featurizers.save_featurizer(featurizer, tmp_file)
+        _ = featurizers.load_featurizer(tmp_file)
+        shutil.rmtree(tmp_dir)
+        
         node_dim = 9
         edge_dim = 4
 
@@ -127,6 +135,12 @@ class TestFeaturizer(unittest.TestCase):
             radius=5.0, 
         ) 
 
+        tmp_dir = tempfile.mkdtemp()
+        tmp_file = tmp_dir + '/featurizer.json'
+        featurizers.save_featurizer(featurizer, tmp_file)
+        _ = featurizers.load_featurizer(tmp_file)
+        shutil.rmtree(tmp_dir)
+
         node_dim = 10
         edge_dim = 22