molcraft 0.1.0a1__tar.gz → 0.1.0a2__tar.gz

{molcraft-0.1.0a1 → molcraft-0.1.0a2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: molcraft
-Version: 0.1.0a1
+Version: 0.1.0a2
 Summary: Graph Neural Networks for Molecular Machine Learning
 Author-email: Alexander Kensert <alexander.kensert@gmail.com>
 License: MIT License
@@ -56,3 +56,70 @@ Dynamic: license-file
 - Modular graph **layers**
 - Serializable graph **featurizers** and **models**
 - Flexible **GraphTensor**
+
+## Examples 
+
+```python
+from molcraft import features
+from molcraft import descriptors
+from molcraft import featurizers 
+from molcraft import layers
+from molcraft import models 
+import keras
+
+featurizer = featurizers.MolGraphFeaturizer(
+    atom_features=[
+        features.AtomType(),
+        features.TotalNumHs(),
+        features.Degree(),
+    ],
+    bond_features=[
+        features.BondType(),
+        features.IsRotatable(),
+    ],
+    super_atom=True,
+    self_loops=False,
+)
+
+graph = featurizer([('N[C@@H](C)C(=O)O', 2.0), ('N[C@@H](CS)C(=O)O', 1.0)])
+print(graph)
+
+model = models.GraphModel.from_layers(
+    [
+        layers.Input(graph.spec),
+        layers.NodeEmbedding(dim=128),
+        layers.EdgeEmbedding(dim=128),
+        layers.GraphTransformer(units=128),
+        layers.GraphTransformer(units=128),
+        layers.GraphTransformer(units=128),
+        layers.GraphTransformer(units=128),
+        layers.Readout(mode='mean'),
+        keras.layers.Dense(units=1024, activation='relu'),
+        keras.layers.Dense(units=1024, activation='relu'),
+        keras.layers.Dense(1)
+    ]
+)
+
+pred = model(graph)
+print(pred)
+
+# featurizers.save_featurizer(featurizer, '/tmp/featurizer.json')
+# models.save_model(model, '/tmp/model.keras')
+
+# featurizers.load_featurizer('/tmp/featurizer.json')
+# models.load_model('/tmp/model.keras')
+```
+
+## Installation
+
+Install the pre-release of molcraft via pip:
+
+```bash
+pip install molcraft --pre
+```
+
+with GPU support:
+
+```bash
+pip install molcraft[gpu] --pre
+```

molcraft-0.1.0a2/README.md

@@ -0,0 +1,81 @@
+<img src="https://github.com/akensert/molcraft/blob/main/docs/_static/molcraft-logo.png" alt="molcraft-logo">
+
+**Deep Learning on Molecules**: A Minimalistic GNN package for Molecular ML. 
+
+> [!NOTE]  
+> In progress/Unfinished.
+
+## Highlights
+- Compatible with **Keras 3**
+- Simplified API
+- Fast featurization
+- Modular graph **layers**
+- Serializable graph **featurizers** and **models**
+- Flexible **GraphTensor**
+
+## Examples 
+
+```python
+from molcraft import features
+from molcraft import descriptors
+from molcraft import featurizers 
+from molcraft import layers
+from molcraft import models 
+import keras
+
+featurizer = featurizers.MolGraphFeaturizer(
+    atom_features=[
+        features.AtomType(),
+        features.TotalNumHs(),
+        features.Degree(),
+    ],
+    bond_features=[
+        features.BondType(),
+        features.IsRotatable(),
+    ],
+    super_atom=True,
+    self_loops=False,
+)
+
+graph = featurizer([('N[C@@H](C)C(=O)O', 2.0), ('N[C@@H](CS)C(=O)O', 1.0)])
+print(graph)
+
+model = models.GraphModel.from_layers(
+    [
+        layers.Input(graph.spec),
+        layers.NodeEmbedding(dim=128),
+        layers.EdgeEmbedding(dim=128),
+        layers.GraphTransformer(units=128),
+        layers.GraphTransformer(units=128),
+        layers.GraphTransformer(units=128),
+        layers.GraphTransformer(units=128),
+        layers.Readout(mode='mean'),
+        keras.layers.Dense(units=1024, activation='relu'),
+        keras.layers.Dense(units=1024, activation='relu'),
+        keras.layers.Dense(1)
+    ]
+)
+
+pred = model(graph)
+print(pred)
+
+# featurizers.save_featurizer(featurizer, '/tmp/featurizer.json')
+# models.save_model(model, '/tmp/model.keras')
+
+# featurizers.load_featurizer('/tmp/featurizer.json')
+# models.load_model('/tmp/model.keras')
+```
+
+## Installation
+
+Install the pre-release of molcraft via pip:
+
+```bash
+pip install molcraft --pre
+```
+
+with GPU support:
+
+```bash
+pip install molcraft[gpu] --pre
+```

{molcraft-0.1.0a1 → molcraft-0.1.0a2}/molcraft/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.1.0a1'
+__version__ = '0.1.0a2'
 
 import os
 os.environ["TF_CPP_MIN_LOG_LEVEL"] = "3"

molcraft-0.1.0a2/molcraft/datasets.py

@@ -0,0 +1,123 @@
+import numpy as np
+import pandas as pd
+
+
+def split(
+    data: pd.DataFrame | np.ndarray,
+    train_size: float | None = None,
+    validation_size: float | None = None, 
+    test_size: float = 0.1,
+    shuffle: bool = False, 
+    random_state: int | None = None,
+) -> pd.DataFrame | np.ndarray:
+    """Splits dataset into subsets.
+
+    Args:
+        data: 
+            A pd.DataFrame or np.ndarray object.
+        train_size:
+            Optional train size, as a fraction (`float`) or size (`int`).
+        validation_size:
+            Optional validation size, as a fraction (`float`) or size (`int`).
+        test_size:
+            Required test size, as a fraction (`float`) or size (`int`).
+        shuffle:
+            Whether the dataset should be shuffled prior to splitting.
+        random_state:
+            The random state (or seed). Only applicable if shuffling.
+    """
+
+    if not isinstance(data, (pd.DataFrame, np.ndarray, list)):
+        raise ValueError(
+            '`data` needs to be a pd.DataFrame, np.ndarray or a list. '
+            f'Found {type(data)}.'
+        )
+    
+    size = len(data)
+    
+    if test_size is None:
+        raise ValueError('`test_size` is required.')
+    elif test_size <= 0:
+        raise ValueError(
+            f'Test size needs to be positive. Found: {test_size}. '
+            'Either specify a positive `float` (fraction) or '
+            'a positive `int` (size).'
+        )
+    if train_size is not None and train_size <= 0:
+        raise ValueError(
+            f'Train size needs to be None or positive. Found: {train_size}. '
+            'Either specify `None`, a positive `float` (fraction) or '
+            'a positive `int` (size).'
+        )
+    if validation_size is not None and validation_size <= 0:
+        raise ValueError(
+            f'Validation size needs to be None or positive. Found: {validation_size}. '
+            'Either specify `None`, a positive `float` (fraction) or '
+            'a positive `int` (size).'
+        )
+    
+    if isinstance(test_size, float):
+        test_size = int(size * test_size)
+    if validation_size and isinstance(validation_size, float):
+        validation_size = int(size * validation_size)
+    elif not validation_size:
+        validation_size = 0
+
+    if train_size and isinstance(train_size, float):
+        train_size = int(size * train_size)
+    elif not train_size:
+        train_size = 0
+
+    if not train_size:
+        train_size = size - test_size
+        if not validation_size:
+            train_size -= validation_size
+
+    remainder = size - (train_size + validation_size + test_size)
+
+    if remainder < 0:
+        raise ValueError(
+            'Sizes of data subsets add up to more than the size of the original data set: '
+            f'{size} < ({train_size} + {validation_size} + {test_size})'
+        )
+    if test_size <= 0:
+        raise ValueError(
+            f'Test size needs to be greater than 0. Found: {test_size}.'
+        )
+    if train_size <= 0:
+        raise ValueError(
+            f'Train size needs to be greater than 0. Found: {train_size}.'
+        )
+    
+    train_size += remainder
+
+    if isinstance(data, pd.DataFrame):
+        if shuffle:
+            data = data.sample(
+                frac=1.0, replace=False, random_state=random_state
+            )
+        train_data = data.iloc[:train_size]
+        test_data = data.iloc[-test_size:]
+        if not validation_size:
+            return train_data, test_data 
+        validation_data = data.iloc[train_size:-test_size]
+        return train_data, validation_data, test_data
+    
+    if not isinstance(data, np.ndarray):
+        data = np.asarray(data)
+
+    np.random.seed(random_state)
+
+    random_indices = np.arange(size)
+    np.random.shuffle(random_indices)
+    data = data[random_indices]
+
+    train_data = data[:train_size]
+    test_data = data[-test_size:]
+    if not validation_size:
+        return train_data, test_data 
+    validation_data = data[train_size:-test_size]
+    return train_data, validation_data, test_data
+    
+
+    

{molcraft-0.1.0a1 → molcraft-0.1.0a2}/molcraft/experimental/peptides.py

@@ -9,75 +9,36 @@ from molcraft import chem
 from molcraft import features 
 from molcraft import featurizers
 from molcraft import tensors
+from molcraft import descriptors
 
     
-class PeptideGraphFeaturizer(featurizers.MolGraphFeaturizer):
-    
-    def __init__(
-        self,
-        atom_features: list[features.Feature] | str | None = None,
-        bond_features: list[features.Feature] | str | None = None,
-        super_atom_feature: features.Feature | bool = None,
-        radius: int | float | None = None,
-        self_loops: bool = False,
-        include_hs: bool = False,
-        feature_dtype: str = 'float32',
-        index_dtype: str = 'int32',
-    ) -> None:
-        if super_atom_feature is None:
-            super_atom_feature = AminoAcidType()
-        super().__init__(
-            atom_features=atom_features,
-            bond_features=bond_features,
-            super_atom_feature=super_atom_feature,
-            radius=radius,
-            self_loops=self_loops,
-            include_hs=include_hs,
-            feature_dtype=feature_dtype,
-            index_dtype=index_dtype
-        )
+def Graph(
+    inputs,
+    atom_features: list[features.Feature] | str | None = 'auto',
+    bond_features: list[features.Feature] | str | None = 'auto',
+    super_atom: bool = True,
+    radius: int | float | None = None,
+    self_loops: bool = False,
+    include_hs: bool = False,
+    **kwargs,
+):
+    featurizer = featurizers.MolGraphFeaturizer(
+        atom_features=atom_features,
+        bond_features=bond_features,
+        molecule_features=[AminoAcidType()],
+        super_atom=super_atom,
+        radius=radius,
+        self_loops=self_loops,
+        include_hs=include_hs,
+        **kwargs,
+    )
 
-    def to_index(self, sequence: str):
-        pass
-
-    def static(self, inputs):
-        # TODO: Make sure it is an ordered sequence
-        inputs = [
-            features.residues[x] for x in ['G'] + inputs
-        ]
-        mols = [
-            chem.Mol.from_encoding(x, explicit_hs=self.include_hs) for x in inputs
-        ]
-        mols = [
-            mol for mol in mols if mol is not None
-        ]
-        if not mols:
-            return None 
-        tensor_list: list[tensors.GraphTensor] = [super().call(mol) for mol in mols]
-        tensor: tensors.GraphTensor = tf.stack(tensor_list, axis=0)
-        return tensor 
-    
-    def call(self, inputs: str | tuple) -> tensors.GraphTensor:
-        args = []
-        if isinstance(inputs, (list, tuple, np.ndarray)):
-            inputs, *args = inputs
-        inputs = [
-            features.residues[x] for x in chem.sequence_split(inputs)
-        ]
-        tensor_list: list[tensors.GraphTensor] = [super().call(x) for x in inputs]
-        tensor: tensors.GraphTensor = tf.stack(tensor_list, axis=0)
-        tensor = tensor._merge()
-        context = {
-            k: v for (k, v) in zip(['label', 'weight'], args)
-        }
-        tensor = tensor.update(
-            {
-                'context': context
-            }
-        )
+    inputs = [
+        residues[x] for x in ['G'] + inputs
+    ]
+    tensor_list = [featurizer(x) for x in inputs]
+    return tf.stack(tensor_list, axis=0)
 
-        return tensor
-    
 
 def GraphLookup(graph: tensors.GraphTensor) -> 'GraphLookupLayer':
     lookup = GraphLookupLayer()
@@ -203,7 +164,7 @@ class Gather(keras.layers.Layer):
     
 
 @keras.saving.register_keras_serializable(package='molcraft')
-class AminoAcidType(features.Feature):
+class AminoAcidType(descriptors.Descriptor):
 
     def __init__(self, vocab=None, **kwargs):
         vocab = [
@@ -217,7 +178,7 @@ class AminoAcidType(features.Feature):
         if not residue:
             raise KeyError(f'Could not find {mol.canonical_smiles} in `residues_reverse`.')
         mol = chem.remove_hs(mol)
-        return [_extract_residue_type(residues_reverse[mol.canonical_smiles])]
+        return _extract_residue_type(residues_reverse[mol.canonical_smiles])
     
 def sequence_split(sequence: str):
     patterns = [

{molcraft-0.1.0a1 → molcraft-0.1.0a2}/molcraft/featurizers.py

@@ -200,12 +200,13 @@ class MolGraphFeaturizer(Featurizer):
         self.feature_dtype = 'float32'
         self.index_dtype = 'int32'
 
-    def call(self, x: str | typing.Tuple) -> tensors.GraphTensor:
-
-        if isinstance(x, (tuple, list, np.ndarray)):
-            x, *args = x
+    def call(self, inputs: str | tuple) -> tensors.GraphTensor:
+        if isinstance(inputs, (tuple, list, np.ndarray)):
+            x, *context = inputs
+            if len(context) and isinstance(context[0], dict):
+                context = copy.deepcopy(context[0])
         else:
-            args = []
+            x, context = inputs, None
 
         mol = chem.Mol.from_encoding(x, explicit_hs=self.include_hs)
 
@@ -220,14 +221,30 @@ class MolGraphFeaturizer(Featurizer):
         bond_feature = self.bond_features(mol)
         context_feature = self.context_feature(mol)
         molecule_size = self.num_atoms(mol)
-
-        context, node, edge = {}, {}, {}
-        for field, value in zip(['size', 'label', 'weight'], [molecule_size] + args):
-            context[field] = value
+        
+        if isinstance(context, dict):
+            if 'x' in context:
+                context['feature'] = context.pop('x')
+            if 'y' in context:
+                context['label'] = context.pop('y')
+            if 'sample_weight' in context:
+                context['weight'] = context.pop('sample_weight')
+            context = {
+                **{'size': molecule_size}, 
+                **context
+            }
+        elif isinstance(context, list):
+            context = {
+                **{'size': molecule_size}, 
+                **{key: value for (key, value) in zip(['label', 'weight'], context)}
+            }
+        else:
+            context = {'size': molecule_size}
 
         if context_feature is not None:
             context['feature'] = context_feature
 
+        node = {}
         node['feature'] = atom_feature
 
         if bond_feature is not None and (self.radius > 1 or self.self_loops):
@@ -239,6 +256,7 @@ class MolGraphFeaturizer(Featurizer):
                 [bond_feature, zero_bond_feature], axis=0
             )    
         
+        edge = {}
         if self.radius == 1:
             edge['source'], edge['target'] = mol.adjacency(
                 fill='full', sparse=True, self_loops=self.self_loops, dtype=self.index_dtype
@@ -494,19 +512,25 @@ class MolGraphFeaturizer3D(MolGraphFeaturizer):
         self.embed_conformer = self.conformer_generator is not None
         self.radius = float(radius) if radius else None
         
-    def call(self, x: str | typing.Tuple) -> tensors.GraphTensor:
+    def call(self, inputs: str | tuple) -> tensors.GraphTensor:
 
-        if isinstance(x, (tuple, list, np.ndarray)):
-            x, *args = x
+        if isinstance(inputs, (tuple, list, np.ndarray)):
+            x, *context = inputs
+            if len(context) and isinstance(context[0], dict):
+                context = copy.deepcopy(context[0])
         else:
-            args = []
+            x, context = inputs, None
 
         explicit_hs = (self.include_hs or self.embed_conformer)
         mol = chem.Mol.from_encoding(x, explicit_hs=explicit_hs)
-
+        
         if mol is None:
+            warn(
+                f'Could not obtain `chem.Mol` from {x}. '
+                'Proceeding without it.'
+            )
             return None
-        
+
         if self.embed_conformer:
             mol = self.conformer_generator(mol)
             if not self.include_hs:
@@ -519,21 +543,38 @@ class MolGraphFeaturizer3D(MolGraphFeaturizer):
                 'of the `Featurizer` or input a 3D representation of the molecule. '
             )
 
-        context, node, edge = {}, {}, {}
-
-        context['size'] = self.num_atoms(mol) + int(self.super_atom)
-        for field, value in zip(['label', 'weight'], args):
-            context[field] = value
+        context_feature = self.context_feature(mol)
+        molecule_size = self.num_atoms(mol) + int(self.super_atom)
+
+        if isinstance(context, dict):
+            if 'x' in context:
+                context['feature'] = context.pop('x')
+            if 'y' in context:
+                context['label'] = context.pop('y')
+            if 'sample_weight' in context:
+                context['weight'] = context.pop('sample_weight')
+            context = {
+                **{'size': molecule_size}, 
+                **context
+            }
+        elif isinstance(context, list):
+            context = {
+                **{'size': molecule_size}, 
+                **{key: value for (key, value) in zip(['label', 'weight'], context)}
+            }
+        else:
+            context = {'size': molecule_size}
 
+        if context_feature is not None:
+            context['feature'] = context_feature
+            
+        node = {}
         node['feature'] = self.atom_features(mol)
 
         if self._bond_features:
             edge_feature = self.bond_features(mol)
 
-        context_feature = self.context_feature(mol)
-        if context_feature is not None:
-            context['feature'] = context_feature
-
+        edge = {}
         mols = chem._split_mol_by_confs(mol)
         tensor_list = []
         for i, mol in enumerate(mols):
@@ -563,11 +604,10 @@ class MolGraphFeaturizer3D(MolGraphFeaturizer):
                 node_conformer['coordinate'] = np.concatenate(
                     [node_conformer['coordinate'], conformer.centroid[None]], axis=0
                 )
-
             tensor_list.append(
                 tensors.GraphTensor(context, node_conformer, edge_conformer)
             )
-
+            
         return tensor_list
     
     def stack(self, outputs):