molcraft 0.1.0a18__py3-none-any.whl → 0.1.0a20__py3-none-any.whl

molcraft/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.1.0a18'
+__version__ = '0.1.0a20'
 
 import os
 os.environ["TF_CPP_MIN_LOG_LEVEL"] = "3"

molcraft/applications/proteomics.py

@@ -165,18 +165,8 @@ class ResidueEmbedding(keras.layers.Layer):
         residues = {**default_residues, **residues}
         self._residues = {}
         for residue, smiles in residues.items():
-            permuted_smiles = permute_residue_smiles(smiles)
-            # Returned smiles should begin with the amino group.
-            # It seems that the returned smiles ends with carboxyl group,
-            # though we do another check just in case. 
-            if not has_c_terminal_mod(residue):
-                carboxyl_group = 'C(=O)O'
-                if not permuted_smiles.endswith(carboxyl_group):
-                    raise ValueError(
-                        f'Unsupported permutation of {residue!r} smiles: {permuted_smiles!r}.'
-                    )
-            self._residues[residue] = permuted_smiles
-            self._residues[residue + '*'] = permuted_smiles.rstrip('O')
+            self._residues[residue] = smiles
+            self._residues[residue + '*'] = smiles.rstrip('O')
 
         residue_keys = sorted(self._residues.keys())
         residue_values = range(len(residue_keys))

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,

molcraft/layers.py

@@ -279,7 +279,7 @@ class GraphConv(GraphLayer):
         use_bias (bool):
             Whether bias should be used in the dense layers. Default to `True`.
         normalize (bool, str):
-            Whether normalization should be applied to the final output. Default to `False`.
+            Whether a normalization layer should be obtain by `get_norm()`. Default to `False`.
         skip_connect (bool):
             Whether node feature input should be added to the node feature output. Default to `True`.
         kernel_initializer (keras.initializers.Initializer, str):
@@ -366,6 +366,7 @@ class GraphConv(GraphLayer):
         has_overridden_message = self.__class__.message != GraphConv.message 
         if not has_overridden_message:
             self._message_intermediate_dense = self.get_dense(self.units)
+            self._message_norm = self.get_norm()
             self._message_intermediate_activation = self.activation
             self._message_final_dense = self.get_dense(self.units)
 
@@ -376,19 +377,10 @@ class GraphConv(GraphLayer):
         has_overridden_update = self.__class__.update != GraphConv.update 
         if not has_overridden_update:
             self._update_intermediate_dense = self.get_dense(self.units)
+            self._update_norm = self.get_norm()
             self._update_intermediate_activation = self.activation
             self._update_final_dense = self.get_dense(self.units)
 
-        if not self._normalize:
-            self._message_norm = keras.layers.Identity()
-            self._update_norm = keras.layers.Identity()
-        elif str(self._normalize).lower().startswith('layer'):
-            self._message_norm = keras.layers.LayerNormalization()
-            self._update_norm = keras.layers.LayerNormalization()
-        else:
-            self._message_norm = keras.layers.BatchNormalization()
-            self._update_norm = keras.layers.BatchNormalization()
-
     def propagate(self, tensor: tensors.GraphTensor) -> tensors.GraphTensor:
         """Forward pass.
 
@@ -533,6 +525,14 @@ class GraphConv(GraphLayer):
             }
         )
 
+    def get_norm(self, **kwargs):
+        if not self._normalize:
+            return keras.layers.Identity()
+        elif str(self._normalize).lower().startswith('layer'):
+            return keras.layers.LayerNormalization(**kwargs)
+        else:
+            return keras.layers.BatchNormalization(**kwargs)
+        
     def get_config(self) -> dict:
         config = super().get_config()
         config.update({

molcraft/tensors.py

@@ -16,13 +16,15 @@ class GraphTensorBatchEncoder(tf.experimental.ExtensionTypeBatchEncoder):
             if isinstance(f, tf.TensorSpec):
                 return tf.TensorSpec(
                     shape=[None] + f.shape[1:],
-                    dtype=f.dtype)
+                    dtype=f.dtype
+                )
             elif isinstance(f, tf.RaggedTensorSpec):
                 return tf.RaggedTensorSpec(
                     shape=[batch_size, None] + f.shape[1:],
                     dtype=f.dtype,
                     ragged_rank=1,
-                    row_splits_dtype=f.row_splits_dtype)
+                    row_splits_dtype=f.row_splits_dtype
+                )
             elif isinstance(f, tf.TypeSpec):
                 return f.__batch_encoder__.batch(f, batch_size)
             return f
@@ -33,7 +35,8 @@ class GraphTensorBatchEncoder(tf.experimental.ExtensionTypeBatchEncoder):
         batched_spec = object.__new__(type(spec))
         batched_context_fields = tf.nest.map_structure(
             lambda spec: tf.TensorSpec([batch_size] + spec.shape, spec.dtype), 
-            context_fields)
+            context_fields
+        )
         batched_spec.__dict__.update({'context': batched_context_fields})
         batched_spec.__dict__.update(batched_fields)
         return batched_spec
@@ -46,13 +49,15 @@ class GraphTensorBatchEncoder(tf.experimental.ExtensionTypeBatchEncoder):
             if isinstance(f, tf.TensorSpec):
                 return tf.TensorSpec(
                     shape=[None] + f.shape[1:],
-                    dtype=f.dtype)
+                    dtype=f.dtype
+                )
             elif isinstance(f, tf.RaggedTensorSpec):
                 return tf.RaggedTensorSpec(
                     shape=[None] + f.shape[2:],
                     dtype=f.dtype,
                     ragged_rank=0,
-                    row_splits_dtype=f.row_splits_dtype)
+                    row_splits_dtype=f.row_splits_dtype
+                )
             elif isinstance(f, tf.TypeSpec):
                 return f.__batch_encoder__.unbatch(f)
             return f
@@ -62,7 +67,8 @@ class GraphTensorBatchEncoder(tf.experimental.ExtensionTypeBatchEncoder):
         unbatched_fields = tf.nest.map_structure(unbatch_field, fields)
         unbatched_context_fields = tf.nest.map_structure(
             lambda spec: tf.TensorSpec(spec.shape[1:], spec.dtype), 
-            context_fields)
+            context_fields
+        )
         unbatched_spec = object.__new__(type(spec))
         unbatched_spec.__dict__.update({'context': unbatched_context_fields})
         unbatched_spec.__dict__.update(unbatched_fields)
@@ -91,7 +97,8 @@ class GraphTensorBatchEncoder(tf.experimental.ExtensionTypeBatchEncoder):
                     shape=([None] if scalar else [None, None]) + f.shape[1:], 
                     dtype=f.dtype, 
                     ragged_rank=(0 if scalar else 1),
-                    row_splits_dtype=spec.context['size'].dtype)
+                    row_splits_dtype=spec.context['size'].dtype
+                )
             return f
         fields = dict(spec.__dict__)
         context_fields = fields.pop('context')
@@ -99,7 +106,7 @@ class GraphTensorBatchEncoder(tf.experimental.ExtensionTypeBatchEncoder):
         encoded_fields = {**{'context': context_fields}, **encoded_fields}
         spec_components = tuple(encoded_fields.values())
         spec_components = tuple(
-            x for x in tf.nest.flatten(spec_components) 
+            x for x in tf.nest.flatten(spec_components)
             if isinstance(x, tf.TypeSpec)
         )
         return spec_components
@@ -117,7 +124,6 @@ class GraphTensorBatchEncoder(tf.experimental.ExtensionTypeBatchEncoder):
         fields = dict(zip(spec.__dict__.keys(), value_tuple))
         value = object.__new__(spec.value_type)
         value.__dict__.update(fields)
-
         flatten = is_ragged(value) and not is_ragged(spec)
         if flatten:
             value = value.flatten()
@@ -125,7 +131,7 @@ class GraphTensorBatchEncoder(tf.experimental.ExtensionTypeBatchEncoder):
     
 
 class GraphTensor(tf.experimental.BatchableExtensionType):
-    context: typing.Mapping[str, typing.Union[tf.Tensor, tf.RaggedTensor]]
+    context: typing.Mapping[str, tf.Tensor]
     node: typing.Mapping[str, typing.Union[tf.Tensor, tf.RaggedTensor]]
     edge: typing.Mapping[str, typing.Union[tf.Tensor, tf.RaggedTensor]]
 

{molcraft-0.1.0a18.dist-info → molcraft-0.1.0a20.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: molcraft
-Version: 0.1.0a18
+Version: 0.1.0a20
 Summary: Graph Neural Networks for Molecular Machine Learning
 Author-email: Alexander Kensert <alexander.kensert@gmail.com>
 License: MIT License

{molcraft-0.1.0a18.dist-info → molcraft-0.1.0a20.dist-info}/RECORD

@@ -1,21 +1,21 @@
-molcraft/__init__.py,sha256=nK5aO2tHHpVmGxS0I5gz7gDmmf3yyyggcGCAKBAjdyU,477
+molcraft/__init__.py,sha256=Wyi1uJsnW3jzksFRcgtcyHJXNHczxn5ClKBLUUC2-rA,477
 molcraft/callbacks.py,sha256=x5HnkZhqcFRrW6xdApt_jZ4X08A-0fxcnFKfdmRKa0c,3571
 molcraft/chem.py,sha256=e56qBDuqh8rq_4-UMyp6LCQNxxSx8hZ7gzuz-87DHgw,21652
 molcraft/datasets.py,sha256=Nd2lw5USUZE52vvAiNr-q-n03Y3--NlZlK0NzqHgp-E,4145
 molcraft/descriptors.py,sha256=Cl3KnBPsTST7XLgRLktkX5LwY9MV0P_lUlrt8iPV5no,3508
 molcraft/features.py,sha256=s0WeV8eZcDEypPgC1m37f4s9QkvWIlVgn-L43Cdsa14,13525
-molcraft/featurizers.py,sha256=bD3RFY9eg89-O-Nxgy6gote1zS4cyjOgzdSiSJZJdJE,17664
-molcraft/layers.py,sha256=FanfJGsB4FxHe_uzNw-0RRJMLtgkf_eH5WMIEm3JwfM,64616
+molcraft/featurizers.py,sha256=b9b8XUGqMku3EwwQcjeE2rsaMQ0T_XovupUXjX0Awug,17724
+molcraft/layers.py,sha256=H7XZru4XGJA6gbRO9V1BsGqh1mIrMdhzNCKS5o6oNok,64544
 molcraft/losses.py,sha256=qnS2yC5g-O3n_zVea9MR6TNiFraW2yqRgePOisoUP4A,1065
 molcraft/models.py,sha256=2Pc1htT9fCukGd8ZxrvE0rzEHsPBm0pluHw4FZXaUE4,21963
 molcraft/ops.py,sha256=bQbdFDt9waxVCzF5-dkTB6vlpj9eoSt8I4Qg7ZGXbsU,6178
 molcraft/records.py,sha256=0j4EWP55sfnkoQIH5trdaAIevPfVbAtPLrygTRmLyFw,5686
-molcraft/tensors.py,sha256=EOUKx496KUZsjA1zA2ABc7tU_TW3Jv7AXDsug_QsLbA,22407
+molcraft/tensors.py,sha256=vk-W8zZu-re1g18YevDEEoVQRxT4AdIiMdI-4EvtJI4,22477
 molcraft/applications/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 molcraft/applications/chromatography.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-molcraft/applications/proteomics.py,sha256=qy6KTUrpu0MGOgAsbh0mw4ibtZbYQZa1GLlGA6g1ivg,8991
-molcraft-0.1.0a18.dist-info/licenses/LICENSE,sha256=sbVeqlrtZ0V63uYhZGL5dCxUm8rBAOqe2avyA1zIQNk,1074
-molcraft-0.1.0a18.dist-info/METADATA,sha256=glSAlKMG_kYkWKy4slJ7srY9-CVnc4VPcw-J_lh4osM,3930
-molcraft-0.1.0a18.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-molcraft-0.1.0a18.dist-info/top_level.txt,sha256=dENV6MfOceshM6MQCgJlcN1ojZkiCL9B4F7XyUge3QM,9
-molcraft-0.1.0a18.dist-info/RECORD,,
+molcraft/applications/proteomics.py,sha256=BL3EtW-q-0j79pLYO7npC67mA2ApRhH-XI4rOaP8_wc,8407
+molcraft-0.1.0a20.dist-info/licenses/LICENSE,sha256=sbVeqlrtZ0V63uYhZGL5dCxUm8rBAOqe2avyA1zIQNk,1074
+molcraft-0.1.0a20.dist-info/METADATA,sha256=YntROeUGzofMiRKkfjtpIWFXHzJ6Jo5FG1t1dNraUTE,3930
+molcraft-0.1.0a20.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+molcraft-0.1.0a20.dist-info/top_level.txt,sha256=dENV6MfOceshM6MQCgJlcN1ojZkiCL9B4F7XyUge3QM,9
+molcraft-0.1.0a20.dist-info/RECORD,,