molcraft 0.1.0a15__py3-none-any.whl → 0.1.0a17__py3-none-any.whl

molcraft/apps/qsrr.py

@@ -1,47 +0,0 @@
-import molcraft
-import keras
-
-@keras.saving.register_keras_serializable(package='molcraft')
-class AuxiliaryFeatureInjection(molcraft.layers.GraphLayer):
-
-    def __init__(
-        self,
-        field: str = 'auxiliary_feature',
-        depth: int = 2,
-        drop: bool = True,
-        activation: str | None = None,
-        **kwargs,
-    ) -> None:
-        super().__init__(**kwargs)
-        self.field = field 
-        self.depth = depth 
-        self.drop = drop
-        self.activation = keras.activations.get(activation)
-
-    def build(self, spec: molcraft.tensors.GraphTensor.Spec) -> None:
-        units = spec.node['feature'].shape[1]
-        for i in range(self.depth):
-            setattr(
-                self, f'dense_{i}', self.get_dense(units, activation=self.activation)
-            )
-
-    def propagate(self, tensor: molcraft.tensors.GraphTensor) -> None:
-        x = tensor.context[self.field] 
-        if self.drop:
-            tensor = tensor.update({'context': {self.field: None}})
-        for i in range(self.depth):
-            x = getattr(self, f'dense_{i}')(x)
-        node_feature = molcraft.ops.scatter_add(
-            tensor.node['feature'], tensor.node['super'], x
-        )
-        return tensor.update({'node': {'feature': node_feature}})
-    
-    def get_config(self) -> dict:
-        config = super().get_config()
-        config.update({
-            'field': self.field,
-            'depth': self.depth,
-            'drop': self.drop,
-            'activation': keras.activations.serialize(self.activation)
-        })
-        return config

molcraft/conformers.py

@@ -1,151 +0,0 @@
-import keras
-
-from molcraft import chem
-
-
-@keras.saving.register_keras_serializable(package="molcraft")
-class ConformerProcessor:
-
-    def get_config(self) -> dict:
-        return {}
-
-    @classmethod
-    def from_config(cls, config: dict):
-        return cls(**config)
-
-    def __call__(self, mol: chem.Mol) -> chem.Mol:
-        raise NotImplementedError
-
-
-@keras.saving.register_keras_serializable(package="molcraft")
-class ConformerEmbedder(ConformerProcessor):
-
-    def __init__(
-        self, 
-        method: str = 'ETKDGv3',
-        num_conformers: int = 5, 
-        **kwargs,
-    ) -> None:
-        self.method = method 
-        self.num_conformers = num_conformers 
-        self.kwargs = kwargs 
-
-    def get_config(self) -> dict:
-        config = {
-            'method': self.method, 
-            'num_conformers': self.num_conformers, 
-        }
-        config.update({
-            k: v for (k, v) in self.kwargs.items()
-        })
-        return config
-    
-    def __call__(self, mol: chem.Mol) -> chem.Mol:
-        return chem.embed_conformers(
-            mol, 
-            method=self.method,
-            num_conformers=self.num_conformers,
-            **self.kwargs,
-        )
-
-
-@keras.saving.register_keras_serializable(package="molcraft")
-class ConformerOptimizer(ConformerProcessor):
-
-    def __init__(
-        self, 
-        method: str = 'UFF',
-        max_iter: int = 200, 
-        ignore_interfragment_interactions: bool = True,
-        vdw_threshold: float = 10.0,
-        **kwargs,
-    ) -> None:
-        self.method = method 
-        self.max_iter = max_iter 
-        self.ignore_interfragment_interactions = ignore_interfragment_interactions
-        self.vdw_threshold = vdw_threshold 
-        self.kwargs = kwargs
-
-    def get_config(self) -> dict:
-        config = {
-            'method': self.method,
-            'max_iter': self.max_iter,
-            'ignore_interfragment_interactions': self.ignore_interfragment_interactions,
-            'vdw_threshold': self.vdw_threshold,
-        }
-        config.update({
-            k: v for (k, v) in self.kwargs.items()
-        })
-        return config
-    
-    def __call__(self, mol: chem.Mol) -> chem.Mol:
-        return chem.optimize_conformers(
-            mol,
-            method=self.method,
-            max_iter=self.max_iter,
-            ignore_interfragment_interactions=self.ignore_interfragment_interactions,
-            vdw_threshold=self.vdw_threshold,
-            **self.kwargs,
-        )
-
-
-@keras.saving.register_keras_serializable(package="molcraft")
-class ConformerPruner(ConformerProcessor):
-    def __init__(
-        self,
-        keep: int = 1,
-        threshold: float = 0.0,
-        energy_force_field: str = 'UFF',
-        **kwargs,
-    ) -> None:
-        self.keep = keep
-        self.threshold = threshold
-        self.energy_force_field = energy_force_field
-        self.kwargs = kwargs
-
-    def get_config(self) -> dict:
-        config = {
-            'keep': self.keep,
-            'threshold': self.threshold,
-            'energy_force_field': self.energy_force_field,
-        }
-        config.update({
-            k: v for (k, v) in self.kwargs.items()
-        })
-        return config
-    
-    def __call__(self, mol: chem.Mol) -> chem.Mol:
-        return chem.prune_conformers(
-            mol,
-            keep=self.keep,
-            threshold=self.threshold,
-            energy_force_field=self.energy_force_field,
-            **self.kwargs,
-        )
-
-
-@keras.saving.register_keras_serializable(package='molcraft')
-class ConformerGenerator(ConformerProcessor):
-
-    def __init__(self, steps: list[ConformerProcessor]) -> None:
-        self.steps = steps
-
-    def get_config(self) -> dict:
-        return {
-            "steps": [
-                keras.saving.serialize_keras_object(step) for step in self.steps
-            ]
-        }
-
-    @classmethod
-    def from_config(cls, config: dict) -> 'ConformerGenerator':
-        steps = [
-            keras.saving.deserialize_keras_object(obj) 
-            for obj in config["steps"]
-        ]
-        return cls(steps)
-
-    def __call__(self, mol: chem.Mol) -> chem.Mol:
-        for step in self.steps:
-            mol = step(mol)
-        return mol

molcraft-0.1.0a15.dist-info/RECORD

@@ -1,22 +0,0 @@
-molcraft/__init__.py,sha256=4yc0HLuOki-T3c1zX4_5III8vUIhGS4T8AfmIVvb0bw,464
-molcraft/callbacks.py,sha256=x5HnkZhqcFRrW6xdApt_jZ4X08A-0fxcnFKfdmRKa0c,3571
-molcraft/chem.py,sha256=--4AdZV0TCj_cf5i-TRidNJGSFyab1ksUEMjmDi7zaM,21837
-molcraft/conformers.py,sha256=K6ZtiSUNDN_fwqGP9JrPcwALLFFvlMlF_XejEJH3Sr4,4205
-molcraft/datasets.py,sha256=QKHi9SUBKvJvdkRFmRQNowhrnu35pQqtujuLatOK8bE,4151
-molcraft/descriptors.py,sha256=jJpT0XWu3Tx_bxnwk1rENySRkaM8cMDMaDIjG8KKvtg,3097
-molcraft/features.py,sha256=GwOecLCNUIuGfbIVzsAJH4LikkzWMKj5IT7zSgGTttU,13846
-molcraft/featurizers.py,sha256=8Jmd2yguYmVRyh5wkn6sRzzEENkJ0TqHSlR8qgC4zNY,27131
-molcraft/layers.py,sha256=cUpo9dqqNEnc7rNf-Dze8adFhOkTV5F9IhHOKs13OUI,60134
-molcraft/losses.py,sha256=qnS2yC5g-O3n_zVea9MR6TNiFraW2yqRgePOisoUP4A,1065
-molcraft/models.py,sha256=hKYSV8z65ohRKfPyjjzxZeVjipm064BWeUBGZE0tpyU,21882
-molcraft/ops.py,sha256=bQbdFDt9waxVCzF5-dkTB6vlpj9eoSt8I4Qg7ZGXbsU,6178
-molcraft/records.py,sha256=MbvYkcCunbAmpy_MWXmQ9WBGi2WvwxFUlwQSPKPvSSk,5534
-molcraft/tensors.py,sha256=EOUKx496KUZsjA1zA2ABc7tU_TW3Jv7AXDsug_QsLbA,22407
-molcraft/apps/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-molcraft/apps/peptides.py,sha256=N5wJDGDIDRbmOmxin_dTY-odLqb0avAX9FU22U6x6c0,14576
-molcraft/apps/qsrr.py,sha256=HhsJzTUuSSvHcl5fmPrI7VtzAUP711yesQ_pAc9hNhU,1572
-molcraft-0.1.0a15.dist-info/licenses/LICENSE,sha256=sbVeqlrtZ0V63uYhZGL5dCxUm8rBAOqe2avyA1zIQNk,1074
-molcraft-0.1.0a15.dist-info/METADATA,sha256=hOAPpbo8vhG-9Jr0WzA8NgugAm0d46Um0R3IhtZpeZU,3893
-molcraft-0.1.0a15.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-molcraft-0.1.0a15.dist-info/top_level.txt,sha256=dENV6MfOceshM6MQCgJlcN1ojZkiCL9B4F7XyUge3QM,9
-molcraft-0.1.0a15.dist-info/RECORD,,