Merge pull request #283 from mjo22/update-to-assembly-stuff

get rid of AbstractStructualEnsembleBatcher

src/cryojax/simulator/__init__.py

@@ -59,7 +59,6 @@
 from ._structural_ensemble import (
     AbstractConformationalVariable as AbstractConformationalVariable,
     AbstractStructuralEnsemble as AbstractStructuralEnsemble,
-    AbstractStructuralEnsembleBatcher as AbstractStructuralEnsembleBatcher,
     DiscreteConformationalVariable as DiscreteConformationalVariable,
     DiscreteStructuralEnsemble as DiscreteStructuralEnsemble,
     SingleStructureEnsemble as SingleStructureEnsemble,

src/cryojax/simulator/_assembly/assembly.py

@@ -6,7 +6,6 @@
 from abc import abstractmethod
 from functools import cached_property
 from typing import Optional
-from typing_extensions import override
 
 import equinox as eqx
 import jax
@@ -18,11 +17,10 @@
 from .._structural_ensemble import (
     AbstractConformationalVariable,
     AbstractStructuralEnsemble,
-    AbstractStructuralEnsembleBatcher,
 )
 
 
-class AbstractAssembly(AbstractStructuralEnsembleBatcher, strict=True):
+class AbstractAssembly(eqx.Module, strict=True):
     """Abstraction of a biological assembly.
 
     To subclass an `AbstractAssembly`,
@@ -103,7 +101,3 @@ def subunits(self) -> AbstractStructuralEnsemble:
         else:
             where = lambda s: s.pose
             return eqx.tree_at(where, self.subunit, self.poses)
-
-    @override
-    def get_batched_structural_ensemble(self) -> AbstractStructuralEnsemble:
-        return self.subunits

src/cryojax/simulator/_scattering_theory/weak_phase_scattering_theory.py

@@ -7,14 +7,14 @@
 import jax.numpy as jnp
 from jaxtyping import Array, Complex, PRNGKeyArray
 
+from .._assembly import AbstractAssembly
 from .._instrument_config import InstrumentConfig
 from .._pose import AbstractPose
 from .._potential_integrator import AbstractPotentialIntegrator
 from .._solvent import AbstractIce
 from .._structural_ensemble import (
     AbstractConformationalVariable,
     AbstractStructuralEnsemble,
-    AbstractStructuralEnsembleBatcher,
 )
 from .._transfer_theory import ContrastTransferTheory
 from .base_scattering_theory import AbstractScatteringTheory
@@ -123,12 +123,12 @@ def compute_fourier_contrast_at_detector_plane(
 
 
 class LinearSuperpositionScatteringTheory(AbstractWeakPhaseScatteringTheory, strict=True):
-    """Compute the superposition of images of the structural ensemble batch returned by
-    the `AbstractStructuralEnsembleBatcher`. This must operate in the weak phase
+    """Compute the superposition of images over a batch of poses and potentials
+    parameterized by an `AbstractAssembly`. This must operate in the weak phase
     approximation.
     """
 
-    structural_ensemble_batcher: AbstractStructuralEnsembleBatcher
+    assembly: AbstractAssembly
     potential_integrator: AbstractPotentialIntegrator
     transfer_theory: ContrastTransferTheory
     solvent: Optional[AbstractIce] = None
@@ -163,9 +163,7 @@ def compute_image_superposition(
             )
 
         # Get the batch
-        ensemble_batch = (
-            self.structural_ensemble_batcher.get_batched_structural_ensemble()
-        )
+        ensemble_batch = self.assembly.subunits
         # Setup vmap over the pose and conformation
         is_mapped = lambda x: isinstance(
             x, (AbstractPose, AbstractConformationalVariable)
@@ -222,9 +220,7 @@ def compute_image_superposition(
             )
 
         # Get the batch
-        ensemble_batch = (
-            self.structural_ensemble_batcher.get_batched_structural_ensemble()
-        )
+        ensemble_batch = self.assembly.subunits
         # Setup vmap over the pose and conformation
         is_mapped = lambda x: isinstance(
             x, (AbstractPose, AbstractConformationalVariable)
@@ -254,9 +250,9 @@ def compute_image_superposition(
 
 LinearSuperpositionScatteringTheory.__init__.__doc__ = """**Arguments:**
 
-- `structural_ensemble_batcher`: The batcher that computes the states that over which to
-                                 compute a superposition of images. Most commonly, this
-                                 would be an `AbstractAssembly` concrete class.
+- `assembly`: An concrete class of an `AbstractAssembly`. This is used to
+              output a batch of states over which to
+              compute a superposition of images.
 - `potential_integrator`: The method for integrating the specimen potential.
 - `transfer_theory`: The contrast transfer theory.
 - `solvent`: The model for the solvent.

src/cryojax/simulator/_structural_ensemble/__init__.py

@@ -9,6 +9,3 @@
     DiscreteConformationalVariable as DiscreteConformationalVariable,
     DiscreteStructuralEnsemble as DiscreteStructuralEnsemble,
 )
-from .ensemble_batcher import (
-    AbstractStructuralEnsembleBatcher as AbstractStructuralEnsembleBatcher,
-)

tests/test_helix.py

@@ -108,7 +108,7 @@ def test_c6_rotation(
     @eqx.filter_jit
     def compute_rotated_image(pipeline, pose):
         pipeline = eqx.tree_at(
-            lambda m: m.scattering_theory.structural_ensemble_batcher.pose,
+            lambda m: m.scattering_theory.assembly.pose,
             pipeline,
             pose,
         )
@@ -154,7 +154,7 @@ def compute_rotated_image_with_helix(
         pipeline: cs.ContrastImagingPipeline, pose: cs.AbstractPose
     ):
         pipeline = eqx.tree_at(
-            lambda m: m.scattering_theory.structural_ensemble_batcher.pose,
+            lambda m: m.scattering_theory.assembly.pose,
             pipeline,
             pose,
         )