LICENSE
NOTICES.md
README.md
pyproject.toml
licenses/LICENSE.BOLTZ-MIT
licenses/LICENSE.GEOSTD
licenses/LICENSE.GPL-3.0
licenses/LICENSE.LGPL-3.0
licenses/LICENSE.NVIDIA-FOLD-CP-MIT
licenses/LICENSE.PYTORCH3D-BSD
licenses/LICENSE.TORCH-SCATTER-MIT
src/bioemu2/__init__.py
src/bioemu2/checkpoints.py
src/bioemu2/cli.py
src/bioemu2/cp.py
src/bioemu2/embedding_cache.py
src/bioemu2/inference.py
src/bioemu2/model.py
src/bioemu2/paths.py
src/bioemu2/physicality.py
src/bioemu2/precision.py
src/bioemu2/propagation.py
src/bioemu2/rng.py
src/bioemu2/sampling.py
src/bioemu2/shortcuts.py
src/bioemu2/trajectory_io.py
src/bioemu2/visualization.py
src/bioemu2.egg-info/PKG-INFO
src/bioemu2.egg-info/SOURCES.txt
src/bioemu2.egg-info/dependency_links.txt
src/bioemu2.egg-info/entry_points.txt
src/bioemu2.egg-info/requires.txt
src/bioemu2.egg-info/top_level.txt
src/bioemu2/assets/polymer_templates.pt
src/bioemu2/assets/stereo_chemistry.yaml
src/bioemu2/assets/examples/systems/ake.yaml
src/bioemu2/assets/examples/systems/chignolin.yaml
src/bioemu2/assets/examples/systems/meteorin_like_7tlw.yaml
src/bioemu2/assets/examples/systems/myoglobin_101m.yaml
src/bioemu2/assets/examples/systems/shp2_3tkz.yaml
src/bioemu2/biomoa/__init__.py
src/bioemu2/biomoa/models/__init__.py
src/bioemu2/biomoa/models/base.py
src/bioemu2/biomoa/models/edm_schedule.py
src/bioemu2/biomoa/models/score_model.py
src/bioemu2/biomoa/modules/__init__.py
src/bioemu2/biomoa/modules/conditioning.py
src/bioemu2/biomoa/modules/diffusion.py
src/bioemu2/biomoa/modules/embedders.py
src/bioemu2/biomoa/modules/encoders.py
src/bioemu2/biomoa/modules/pairmixer.py
src/bioemu2/biomoa/modules/relative_position_encoder.py
src/bioemu2/biomoa/modules/time.py
src/bioemu2/biomoa/modules/transformer.py
src/bioemu2/biomoa/ops/__init__.py
src/bioemu2/biomoa/ops/atom_token_ops.py
src/bioemu2/biomoa/ops/attention_pair_bias.py
src/bioemu2/biomoa/ops/dropout.py
src/bioemu2/biomoa/ops/outer_product_mean.py
src/bioemu2/biomoa/ops/pair_weighted_averaging.py
src/bioemu2/biomoa/ops/transition.py
src/bioemu2/biomoa/ops/triangle_multiplication.py
src/bioemu2/biomoa/ops/triton/__init__.py
src/bioemu2/biomoa/ops/triton/opm.py
src/bioemu2/biomoa/utils/__init__.py
src/bioemu2/biomoa/utils/feature_converter.py
src/bioemu2/biomoa/utils/precision.py
src/bioemu2/biomoa/utils/strategy.py
src/bioemu2/biomoa/utils/tiling.py
src/bioemu2/biomoa/utils/warnings.py
src/bioemu2/conditioning/__init__.py
src/bioemu2/conditioning/contact.py
src/bioemu2/conditioning/method.py
src/bioemu2/context_parallel/__init__.py
src/bioemu2/context_parallel/api.py
src/bioemu2/context_parallel/diagnostics.py
src/bioemu2/context_parallel/features.py
src/bioemu2/context_parallel/diffusion/__init__.py
src/bioemu2/context_parallel/distributed/__init__.py
src/bioemu2/context_parallel/distributed/comm.py
src/bioemu2/context_parallel/distributed/manager.py
src/bioemu2/context_parallel/distributed/utils.py
src/bioemu2/context_parallel/layers/__init__.py
src/bioemu2/context_parallel/layers/relative_position_encoder.py
src/bioemu2/context_parallel/layers/transformer_layers.py
src/bioemu2/context_parallel/models/__init__.py
src/bioemu2/context_parallel/models/score_model.py
src/bioemu2/context_parallel/modules/__init__.py
src/bioemu2/context_parallel/modules/conditioning.py
src/bioemu2/context_parallel/modules/diffusion.py
src/bioemu2/context_parallel/modules/embedders.py
src/bioemu2/context_parallel/modules/encoders.py
src/bioemu2/context_parallel/modules/pairmixer.py
src/bioemu2/context_parallel/ops/__init__.py
src/bioemu2/context_parallel/ops/atom_token_ops.py
src/bioemu2/context_parallel/ops/attention.py
src/bioemu2/context_parallel/ops/attention_impl.py
src/bioemu2/context_parallel/ops/cat_and_chunk.py
src/bioemu2/context_parallel/ops/outer_product_mean.py
src/bioemu2/context_parallel/ops/pair_averaging.py
src/bioemu2/context_parallel/ops/pair_weighted_averaging.py
src/bioemu2/context_parallel/ops/readout_superposition.py
src/bioemu2/context_parallel/ops/scatter.py
src/bioemu2/context_parallel/ops/tiled_params_replicated.py
src/bioemu2/context_parallel/ops/transition.py
src/bioemu2/context_parallel/ops/triangle_multiplication.py
src/bioemu2/context_parallel/ops/triangular_mult_impl.py
src/bioemu2/context_parallel/ops/distributed_primitives/__init__.py
src/bioemu2/context_parallel/ops/distributed_primitives/dtensor_metadata_tools.py
src/bioemu2/context_parallel/ops/distributed_primitives/elementwise_op.py
src/bioemu2/context_parallel/ops/distributed_primitives/flatten_and_unflatten.py
src/bioemu2/context_parallel/ops/distributed_primitives/gather.py
src/bioemu2/context_parallel/ops/distributed_primitives/layernorm.py
src/bioemu2/context_parallel/ops/distributed_primitives/linear.py
src/bioemu2/context_parallel/ops/distributed_primitives/modules_utils.py
src/bioemu2/context_parallel/ops/distributed_primitives/outer_gather.py
src/bioemu2/context_parallel/ops/distributed_primitives/redistribute_transpose.py
src/bioemu2/context_parallel/ops/distributed_primitives/sigmoid_gate.py
src/bioemu2/context_parallel/ops/distributed_primitives/utils.py
src/bioemu2/context_parallel/ops/triton/__init__.py
src/bioemu2/context_parallel/ops/triton/flash_attn.py
src/bioemu2/context_parallel/ops/triton/flash_attn_impl.py
src/bioemu2/context_parallel/ops/triton/opm.py
src/bioemu2/context_parallel/scripts/cp_env.sh
src/bioemu2/context_parallel/utils/__init__.py
src/bioemu2/context_parallel/utils/dtensor.py
src/bioemu2/context_parallel/utils/mesh.py
src/bioemu2/context_parallel/utils/padding.py
src/bioemu2/context_parallel/utils/rng.py
src/bioemu2/context_parallel/utils/session.py
src/bioemu2/data_interface/__init__.py
src/bioemu2/data_interface/boltz.py
src/bioemu2/data_interface/bond_reference.py
src/bioemu2/data_interface/cif.py
src/bioemu2/data_interface/const.py
src/bioemu2/data_interface/ligand_validators.py
src/bioemu2/data_interface/structure_hierarchy.py
src/bioemu2/data_interface/system.py
src/bioemu2/denoising/__init__.py
src/bioemu2/denoising/augmentation.py
src/bioemu2/denoising/cp_sync.py
src/bioemu2/denoising/edm.py
src/bioemu2/denoising/rigid_align.py
src/bioemu2/denoising/samplers.py
src/bioemu2/denoising/steering/__init__.py
src/bioemu2/denoising/steering/conditioning.py
src/bioemu2/denoising/steering/edm_fkc.py
src/bioemu2/denoising/steering/edm_steered.py
src/bioemu2/denoising/steering/feats.py
src/bioemu2/denoising/steering/geometry_topology.py
src/bioemu2/denoising/steering/potentials.py
src/bioemu2/denoising/steering/rdkit_constraints.py
src/bioemu2/msa/__init__.py
src/bioemu2/msa/alignment.py
src/bioemu2/msa/arrays.py
src/bioemu2/msa/colabfold.py
src/bioemu2/msa/features.py
src/bioemu2/patches/__init__.py
src/bioemu2/patches/mdtraj_patcher.py
src/bioemu2/patches/openmm_patches.py
src/bioemu2/structure/__init__.py
src/bioemu2/structure/all_atom_structure.py
src/bioemu2/structure/batch.py
src/bioemu2/structure/builder.py
src/bioemu2/structure/cif.py
src/bioemu2/structure/inference_inputs.py
src/bioemu2/structure/polymer_builder.py
src/bioemu2/structure/preparation.py
src/bioemu2/structure/ref_struct.py
src/bioemu2/structure/scatter.py
src/bioemu2/structure/templates.py
tests/test_convert_boltz.py
tests/test_import.py
tests/test_physicality.py
tests/test_propagation.py
tests/test_release_contract.py
tests/test_rng.py
tests/test_sample_protein_protein_constraints.py
tests/test_sampling.py
tests/test_trajectory_io.py
tests/test_visualization.py