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Biohub/esm

14.2 Moderate pattern signal View on GitHub

Maintenance and Governance Review

This report summarizes scanner evidence for Biohub/esm, a Jupyter Notebook project with 2,986 GitHub stars. SynthScan examined 131,766 lines of code across 221 source files, recording 1149 pattern matches distributed across 19 syntactic categories. The legacy adjusted pattern signal is 14.2 (Moderate pattern signal); it is not an authorship estimate.

Use the findings to ask whether maintainers can explain intent, verify dependencies, simplify unnecessary scaffolding, and focus review effort. Risk Payload v1 adds ownership, supply-chain, over-engineering, and review-effort vectors when available. These are prompts for human verification, not probabilities, security findings, or measured maintenance costs.

14.2
Adjusted Signal
14.2
Raw Pattern Score
100%
Time Factor
2026-09-16
Last Push
3.0K
Stars
Jupyter Notebook
Language
131.8K
Lines of Code
221
Files
1.1K
Pattern Hits
2026-10-12
Scan Date
0.06
HC Hit Rate

Risk Review · v3

Use each vector to guide manual verification of the underlying findings.

Cognitive Ownership Risk 22.6/100 · LOW

Can maintainers explain intent, assumptions, and trade-offs? 663 finding(s).

Hallucinated Dependency & Supply Chain Risk 4.0/100 · LOW

Are imports declared and package/API names verified? 98 finding(s).

Agent Over-Engineering Ratio 44.6/100 · MEDIUM

Are wrappers, guards, and repeated structures necessary? 884 finding(s).

PR Review Velocity Impact 49.9/100 · MEDIUM

Which changes need focused human review? 1149 finding(s).

What These Metrics Mean

Adjusted Signal
Legacy pattern score normalized per 1,000 scanned lines and multiplied by the repository-level time factor. It is not an estimate of AI authorship.
Raw Pattern Score
Sum of severity- and context-weighted pattern findings before applying the time factor.
Time Factor
A coarse multiplier based on repository last-push metadata. It does not identify when individual code was written.
Pattern Hits
Count of configured pattern findings. Review each location and surrounding code before acting.
HC Hit Rate
High- and critical-severity findings per scanned file. Severity is a configured detector weight, not proof of a vulnerability or authorship.
Lines / Files
Scan coverage denominators used by the legacy normalized score.

Pattern-Signal History

This chart tracks the legacy adjusted pattern score across scan runs. Changes can reflect source changes, scan coverage, or detector/scoring versions; they do not measure AI adoption or prove that a team refactored code. Compare runs only when their scoring versions are compatible. The dashed line tracks the raw pattern-hit count.

Severity Breakdown

Groups findings by configured severity weight. Severity is not a confidence estimate, security rating, or proof that a package is missing. Verify imports against the project's manifests and inspect each finding in its local design context.

CRITICAL 0HIGH 14MEDIUM 300LOW 835

Directory Score Breakdown

This horizontal bar chart shows where configured pattern scores accumulate across directories. Treat the bars as locations to inspect, not as evidence of authorship or code quality. Use the file-level findings to decide whether a directory needs a focused ownership, dependency, complexity, or review check.

Pattern Findings

The scanner identified 1149 distinct pattern matches across 19 syntactic categories. Each entry below represents a discrete location in the source code where the engine recorded a detector match to inspect in context. Expand any category row to inspect the individual file paths, line numbers, code snippets, and the lexical context (CODE, COMMENT, or STRING) in which each match was detected.

Reading the findings table: The Severity column indicates the configured finding weight (CRITICAL / HIGH / MEDIUM / LOW). The Context column identifies whether the match occurred inside executable code, an inline comment, or a string literal — legacy comment-context matches receive a ×1.5 score weight. The ⚡ bolt icon marks clustered matches: three or more patterns within a 10-line window, each receiving an additional ×1.5 density multiplier under the legacy scoring model.

Decorative Section Separators284 hits · 948 pts
SeverityFileLineSnippetContext
MEDIUMesm/models/esmfold2/config.py35# ---------------------------------------------------------------------------COMMENT
MEDIUMesm/models/esmfold2/config.py37# ---------------------------------------------------------------------------COMMENT
MEDIUMesm/models/esmfold2/config.py345# ---------------------------------------------------------------------------COMMENT
MEDIUMesm/models/esmfold2/config.py347# ---------------------------------------------------------------------------COMMENT
MEDIUM⚡esm/models/esmfold2/experimental.py130 # ------------------------------------------------------------------COMMENT
MEDIUM⚡esm/models/esmfold2/experimental.py132 # ------------------------------------------------------------------COMMENT
MEDIUM⚡esm/models/esmfold2/experimental.py140 # ------------------------------------------------------------------COMMENT
MEDIUM⚡esm/models/esmfold2/experimental.py142 # ------------------------------------------------------------------COMMENT
MEDIUM⚡esm/models/esmfold2/experimental.py525# ===========================================================================COMMENT
MEDIUM⚡esm/models/esmfold2/experimental.py527# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/experimental.py69# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/experimental.py71# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/experimental.py157 # ------------------------------------------------------------------COMMENT
MEDIUMesm/models/esmfold2/experimental.py159 # ------------------------------------------------------------------COMMENT
MEDIUMesm/models/esmfold2/experimental.py346# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/experimental.py348# ===========================================================================COMMENT
MEDIUM⚡esm/models/esmfold2/constants.py6# =============================================================================COMMENT
MEDIUM⚡esm/models/esmfold2/constants.py8# =============================================================================COMMENT
MEDIUM⚡esm/models/esmfold2/constants.py15# =============================================================================COMMENT
MEDIUM⚡esm/models/esmfold2/constants.py17# =============================================================================COMMENT
MEDIUMesm/models/esmfold2/constants.py55# =============================================================================COMMENT
MEDIUMesm/models/esmfold2/constants.py57# =============================================================================COMMENT
MEDIUMesm/models/esmfold2/constants.py164# =============================================================================COMMENT
MEDIUMesm/models/esmfold2/constants.py166# =============================================================================COMMENT
MEDIUMesm/models/esmfold2/constants.py201# =============================================================================COMMENT
MEDIUMesm/models/esmfold2/constants.py203# =============================================================================COMMENT
MEDIUMesm/models/esmfold2/constants.py302# =============================================================================COMMENT
MEDIUMesm/models/esmfold2/constants.py304# =============================================================================COMMENT
MEDIUM⚡esm/models/esmfold2/layers.py409# ===========================================================================COMMENT
MEDIUM⚡esm/models/esmfold2/layers.py411# ===========================================================================COMMENT
MEDIUM⚡esm/models/esmfold2/layers.py1685 # ------------------------------------------------------------------COMMENT
MEDIUM⚡esm/models/esmfold2/layers.py1687 # ------------------------------------------------------------------COMMENT
MEDIUM⚡esm/models/esmfold2/layers.py2494# ===========================================================================COMMENT
MEDIUM⚡esm/models/esmfold2/layers.py2496# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py149# ---------------------------------------------------------------------------COMMENT
MEDIUMesm/models/esmfold2/layers.py151# ---------------------------------------------------------------------------COMMENT
MEDIUMesm/models/esmfold2/layers.py175# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py177# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py230# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py232# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py339# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py341# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py362# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py364# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py385# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py387# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py453# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py455# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py536# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py538# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py556# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py558# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py652# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py654# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py780# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py782# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py942# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py944# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py1014# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py1016# ===========================================================================COMMENT
224 more matches not shown…
Hyper-Verbose Identifiers467 hits · 443 pts
SeverityFileLineSnippetContext
LOWesm/utils/misc.py40def slice_python_object_as_numpy(CODE
LOWesm/utils/misc.py180def stack_variable_length_tensors(CODE
LOWesm/utils/misc.py409def get_chainbreak_boundaries_from_sequence(sequence: Sequence[str]) -> np.ndarray:CODE
LOWesm/utils/misc.py459def iterate_with_intermediate(CODE
LOWesm/utils/system.py10def run_subprocess_with_errorcheck(CODE
LOWesm/utils/encoding.py26def get_default_secondary_structure(sequence_length: int) -> str:CODE
LOWesm/utils/encoding.py100def tokenize_secondary_structure(CODE
LOWesm/utils/encoding.py138def tokenize_function_annotations(CODE
LOWesm/utils/encoding.py156def get_default_sequence_tokens(CODE
LOWesm/utils/encoding.py172def get_default_structure_tokens(CODE
LOWesm/utils/encoding.py185def get_default_secondary_structure_tokens(CODE
LOWesm/utils/encoding.py206def get_default_function_tokens(CODE
LOWesm/utils/encoding.py219def get_default_residue_annotation_tokens(CODE
LOWesm/utils/generation.py37def _trim_sequence_tensor_dataclass(o: Any, sequence_len: int):CODE
LOWesm/utils/generation.py240def _get_iterative_sampling_mask_for_prompt_and_step(CODE
LOWesm/utils/generation.py349def _get_annealed_temperature(step: int, num_steps: int, initial_temperature: float):CODE
LOWesm/utils/generation.py354def iterative_sampling_tokens(CODE
LOWesm/utils/decoding.py172def decode_secondary_structure(CODE
LOWesm/utils/decoding.py211def decode_function_annotations(CODE
LOWesm/utils/decoding.py228def decode_residue_annotations(CODE
LOWesm/utils/sequential_dataclass.py97 def _check_sequence_lengths_match(self):CODE
LOWesm/utils/residue_constants.py429def load_stereo_chemical_props() -> Tuple[CODE
LOWesm/utils/residue_constants.py1038def _make_rigid_group_constants():CODE
LOWesm/utils/sampling.py109def get_default_sampling_config(CODE
LOWesm/utils/sampling.py241def sample_residue_annotation_logits(CODE
LOWesm/utils/msa/msa.py25def remove_insertions_from_sequence(seq: str) -> str:CODE
LOWesm/utils/constants/models.py20def forge_only_return_single_layer_hidden_states(model_name: str):CODE
LOWesm/utils/constants/models.py24def model_is_locally_supported(x: str):CODE
LOWesm/utils/function/encode_decode.py13def encode_function_annotations(CODE
LOWesm/utils/function/encode_decode.py136def decode_residue_annotation_tokens(CODE
LOWesm/utils/structure/mmcif_parsing.py384 def _parse_nonpoly_from_mmcif(self) -> dict[tuple, bs.AtomArray]:CODE
LOWesm/utils/structure/input_builder.py133def serialize_structure_prediction_input(all_atom_input: StructurePredictionInput):CODE
LOWesm/utils/structure/input_builder.py207def deserialize_structure_prediction_input(CODE
LOWesm/utils/structure/protein_structure.py70def compute_alignment_tensors(CODE
LOWesm/utils/structure/protein_structure.py165def compute_rmsd_no_alignment(CODE
LOWesm/utils/structure/protein_structure.py263def compute_gdt_ts_no_alignment(CODE
LOWesm/utils/structure/protein_chain.py243 def residue_index_no_insertions(self) -> np.ndarray:CODE
LOWesm/utils/structure/protein_chain.py775 def chain_iterable_from_mmcif(CODE
LOWesm/utils/structure/protein_chain.py983 def from_backbone_atom_coordinates(CODE
LOWesm/utils/structure/protein_chain.py1378 def to_structure_encoder_inputs(CODE
LOWesm/utils/structure/protein_complex.py57def _parse_operation_expression(expression):CODE
LOWesm/utils/structure/protein_complex.py89def _apply_transformations_fast(chains, transformation_dict, operations):CODE
LOWesm/utils/structure/protein_complex.py380 def normalize_chain_ids_for_pdb(self):CODE
LOWesm/utils/structure/protein_complex.py393 def find_assembly_ids_with_chain(self, id: str) -> list[str]:CODE
LOWesm/utils/structure/protein_complex.py695 def _sanity_check_complexes_are_comparable(self, other: ProteinComplex):CODE
LOWesm/utils/structure/protein_complex.py1245def protein_chain_to_protein_complex(chain: ProteinChain) -> ProteinComplex:CODE
LOWesm/utils/structure/normalize_coordinates.py34def get_protein_normalization_frame(coords: Tensor) -> Affine3D:CODE
LOWesm/utils/structure/predicted_aligned_error.py37def compute_predicted_aligned_error(CODE
LOWesm/models/hub.py115 def _materialize_uninitialized(self, device: torch.device | str = "cpu") -> None:CODE
LOWesm/models/hub.py136 def _normalize_checkpoint_layout(CODE
LOWesm/models/esmfold2/hf_adapter.py104def _sampler_config_overrides(CODE
LOW⚡esm/models/esmfold2/experimental.py537 def _normalize_checkpoint_layout(CODE
LOWesm/models/esmfold2/experimental.py736 def _output_to_molecular_complex(output: dict, features: dict, chain_infos: list):CODE
LOWesm/models/esmfold2/experimental.py829 def _compute_lm_hidden_states(CODE
LOWesm/models/esmfold2/conformers.py87def _get_ccd_mol_with_significant_h(comp_id: str):CODE
LOWesm/models/esmfold2/conformers.py176def get_ligand_idealized_atom_pos(res_name: str, atom_name: str) -> np.ndarray | None:CODE
LOWesm/models/esmfold2/conformers.py195def get_ligand_ccd_atoms_with_charges(CODE
LOWesm/models/esmfold2/model.py582 def _normalize_checkpoint_layout(CODE
LOWesm/models/esmfold2/model.py850 def _compute_lm_hidden_states(CODE
LOWesm/models/esmfold2/paired_msa.py24def protein_letter_to_res_type() -> dict[str, int]:CODE
407 more matches not shown…
Unused Imports95 hits · 92 pts
SeverityFileLineSnippetContext
LOWesm/utils/types.py1CODE
LOWesm/utils/msa/msa.py1CODE
LOWesm/utils/msa/__init__.py1CODE
LOWesm/utils/msa/__init__.py1CODE
LOWesm/utils/msa/__init__.py1CODE
LOWesm/utils/structure/aligner.py1CODE
LOWesm/utils/structure/mmcif_parsing.py1CODE
LOWesm/utils/structure/affine3d.py1CODE
LOWesm/utils/structure/protein_structure.py1CODE
LOWesm/utils/structure/protein_chain.py1CODE
LOWesm/utils/structure/protein_complex.py1CODE
LOWesm/models/esm3.py1CODE
LOWesm/models/esmfold2/config.py16CODE
LOWesm/models/esmfold2/experimental.py24CODE
LOWesm/models/esmfold2/conformers.py7CODE
LOWesm/models/esmfold2/__init__.py1CODE
LOWesm/models/esmfold2/__init__.py1CODE
LOWesm/models/esmfold2/__init__.py1CODE
LOWesm/models/esmfold2/__init__.py6CODE
LOWesm/models/esmfold2/__init__.py7CODE
LOWesm/models/esmfold2/__init__.py8CODE
LOWesm/models/esmfold2/__init__.py9CODE
LOWesm/models/esmfold2/__init__.py10CODE
LOWesm/models/esmfold2/__init__.py11CODE
LOWesm/models/esmfold2/__init__.py11CODE
LOWesm/models/esmfold2/__init__.py12CODE
LOWesm/models/esmfold2/__init__.py12CODE
LOWesm/models/esmfold2/__init__.py13CODE
LOWesm/models/esmfold2/__init__.py13CODE
LOWesm/models/esmfold2/__init__.py13CODE
LOWesm/models/esmfold2/__init__.py13CODE
LOWesm/models/esmfold2/__init__.py13CODE
LOWesm/models/esmfold2/__init__.py13CODE
LOWesm/models/esmfold2/__init__.py13CODE
LOWesm/models/esmfold2/__init__.py13CODE
LOWesm/models/esmfold2/__init__.py13CODE
LOWesm/models/esmfold2/__init__.py24CODE
LOWesm/models/esmfold2/__init__.py24CODE
LOWesm/models/esmfold2/__init__.py24CODE
LOWesm/models/esmfold2/types.py9CODE
LOWesm/models/esmfold2/types.py10CODE
LOWesm/models/esmfold2/types.py11CODE
LOWesm/models/esmfold2/types.py11CODE
LOWesm/models/esmfold2/types.py11CODE
LOWesm/models/esmfold2/types.py11CODE
LOWesm/models/esmfold2/types.py11CODE
LOWesm/models/esmfold2/types.py11CODE
LOWesm/models/esmfold2/types.py11CODE
LOWesm/models/esmfold2/types.py11CODE
LOWesm/models/esmfold2/protein_utils.py17CODE
LOWesm/models/esmfold2/layers.py11CODE
LOWesm/models/esmfold2/prepare_input.py7CODE
LOWesm/models/esmfold2/kernels/fused_dual_gemm.py13CODE
LOWesm/models/esmfold2/kernels/trimul_with_residual.py37CODE
LOWesm/models/esmfold2/kernels/fused_dropout_residual.py26CODE
LOWesm/models/esmfold2/kernels/__init__.py11CODE
LOWesm/models/esmfold2/kernels/__init__.py12CODE
LOWesm/models/esmfold2/kernels/__init__.py13CODE
LOWesm/models/esmfold2/kernels/__init__.py14CODE
LOWesm/models/esmfold2/kernels/fused_lnlin_swiglu.py27CODE
35 more matches not shown…
Deep Nesting71 hits · 68 pts
SeverityFileLineSnippetContext
LOWesm/utils/generation.py37CODE
LOWesm/utils/generation.py66CODE
LOWesm/utils/generation.py130CODE
LOWesm/utils/sequential_dataclass.py97CODE
LOWesm/utils/residue_constants.py1114CODE
LOWesm/utils/sampling.py133CODE
LOWesm/utils/forge_context_manager.py88CODE
LOWesm/utils/constants/esm3.py105CODE
LOWesm/utils/structure/mmcif_parsing.py101CODE
LOWesm/utils/structure/mmcif_parsing.py146CODE
LOWesm/utils/structure/mmcif_parsing.py202CODE
LOWesm/utils/structure/mmcif_parsing.py384CODE
LOWesm/utils/structure/mmcif_parsing.py449CODE
LOWesm/utils/structure/input_builder.py133CODE
LOWesm/utils/structure/input_builder.py207CODE
LOWesm/utils/structure/molecular_complex.py473CODE
LOWesm/utils/structure/molecular_complex.py745CODE
LOWesm/utils/structure/molecular_complex.py908CODE
LOWesm/utils/structure/molecular_complex.py1078CODE
LOWesm/utils/structure/molecular_complex.py1311CODE
LOWesm/utils/structure/protein_chain.py88CODE
LOWesm/utils/structure/protein_chain.py906CODE
LOWesm/utils/structure/protein_chain.py1056CODE
LOWesm/utils/structure/protein_complex.py815CODE
LOWesm/models/esmfold2/experimental.py850CODE
LOWesm/models/esmfold2/conformers.py268CODE
LOWesm/models/esmfold2/processor.py87CODE
LOWesm/models/esmfold2/model.py410CODE
LOWesm/models/esmfold2/model.py420CODE
LOWesm/models/esmfold2/paired_msa.py95CODE
LOWesm/models/esmfold2/prepare_input.py158CODE
LOWesm/models/esmfold2/prepare_input.py330CODE
LOWesm/models/esmfold2/prepare_input.py676CODE
LOWesm/models/esmfold2/prepare_input.py811CODE
LOWesm/models/esmfold2/prepare_input.py951CODE
LOWesm/models/esmfold2/prepare_input.py1120CODE
LOWesm/models/esmfold2/prepare_input.py1160CODE
LOWesm/models/esmfold2/output.py18CODE
LOWesm/models/esmfold2/output.py129CODE
LOWesm/models/esmfold2/distributed/utils.py173CODE
LOWesm/models/esmfold2/distributed/manager.py126CODE
LOWesm/models/esmfold2/distributed/manager.py569CODE
LOWesm/models/esmfold2/distributed/recycle.py153CODE
LOWesm/models/esmc/checkpoint_layout.py145CODE
LOWesm/models/esmc/model.py711CODE
LOWesm/tokenization/residue_tokenizer.py73CODE
LOWesm/sdk/forge.py142CODE
LOWesm/sdk/api.py56CODE
LOWesm/sdk/api.py165CODE
LOWesm/sdk/base_forge_client.py298CODE
LOWesm/sdk/base_forge_client.py338CODE
LOWesm/sdk/base_forge_client.py479CODE
LOWesm/sdk/base_forge_client.py531CODE
LOWesm/widgets/utils/prompting.py385CODE
LOWesm/widgets/components/results_visualizer.py21CODE
LOWesm/widgets/components/results_visualizer.py55CODE
LOWesm/widgets/components/sequence_prompt_selector.py13CODE
LOWesm/widgets/components/sequence_prompt_selector.py96CODE
LOWesm/widgets/components/structure_prompt_selector.py19CODE
LOWesm/widgets/components/structure_prompt_selector.py94CODE
11 more matches not shown…
Modern Structural Boilerplate59 hits · 53 pts
SeverityFileLineSnippetContext
LOWesm/utils/msa/__init__.py3__all__ = ["MSA", "FastMSA", "remove_insertions_from_sequence"]CODE
LOWesm/models/esmfold2/hf_adapter.py197 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/hf_adapter.py416__all__ = ["EsmFold2HFAdapter", "translate_features", "upstream_available"]CODE
LOWesm/models/esmfold2/config.py107def _set_path(tree: dict, path: str, value) -> None:CODE
LOWesm/models/esmfold2/config.py563__all__ = [CODE
LOW⚡esm/models/esmfold2/experimental.py134 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOW⚡esm/models/esmfold2/experimental.py137 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/experimental.py387 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/models/esmfold2/experimental.py391 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/experimental.py472 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/models/esmfold2/experimental.py476 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/experimental.py623 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/models/esmfold2/experimental.py632 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/experimental.py1199__all__ = ["EsmFold2ExperimentalModel"]CODE
LOWesm/models/esmfold2/hf_checkpoint.py258__all__ = [CODE
LOWesm/models/esmfold2/__init__.py30__all__ = [CODE
LOWesm/models/esmfold2/processor.py449__all__ = ["ESMFold2InputBuilder", "clean_esmfold2_input"]CODE
LOWesm/models/esmfold2/types.py22__all__ = [CODE
LOWesm/models/esmfold2/model.py90 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/model.py158 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/models/esmfold2/model.py161 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/model.py697 def set_esmc_precision(self, precision: str = "bf16") -> None:CODE
LOWesm/models/esmfold2/model.py770 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/models/esmfold2/model.py841 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/model.py1453 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/models/esmfold2/model.py1457 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/model.py1512 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/models/esmfold2/model.py1516 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOW⚡esm/models/esmfold2/layers.py1682 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOW⚡esm/models/esmfold2/layers.py2478 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOW⚡esm/models/esmfold2/layers.py2487 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOW⚡esm/models/esmfold2/layers.py2623 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/layers.py1057 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/models/esmfold2/layers.py1307 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/models/esmfold2/layers.py1520 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/models/esmfold2/layers.py2381 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/layers.py2511 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/layers.py2514 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/models/esmfold2/layers.py2610 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/models/esmfold2/layers.py2691 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/models/esmfold2/layers.py2695 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/layers.py2756 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOW…m/models/esmfold2/kernels/fused_attention_pair_bias.py696__all__ = ["FusedPairBias", "fused_attention_pair_bias", "fused_pair_bias"]CODE
LOWesm/models/esmfold2/kernels/__init__.py18__all__ = [CODE
LOWesm/models/esmfold2/distributed/msa_wrapper.py98 def set_chunk_size(self, _chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/distributed/msa_wrapper.py101 def set_kernel_backend(self, _backend: str | None) -> None:CODE
LOWesm/models/esmfold2/distributed/structure_wrapper.py85 def set_kernel_backend(self, _backend: str | None) -> None:CODE
LOWesm/models/esmfold2/distributed/structure_wrapper.py88 def set_chunk_size(self, _chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/distributed/__init__.py41__all__ = [CODE
LOWesm/models/esmfold2/distributed/utils.py441 def set_kernel_backend(self, _backend: str | None) -> None:CODE
LOWesm/models/esmfold2/distributed/utils.py444 def set_chunk_size(self, _chunk_size: int | None) -> None:CODE
LOWesm/models/esmc/__init__.py23__all__ = [CODE
LOWesm/models/esmc/model.py311 def set_input_embeddings(self, value: nn.Embedding) -> None:CODE
LOWesm/models/esmc/model.py601 def set_output_embeddings(self, new_embeddings: nn.Linear) -> None:CODE
LOWesm/models/esmc/kernels.py25logger = logging.getLogger(__name__)CODE
LOWesm/models/esmc/layers.py106 def _update_cos_sin_cache(self, seqlen: int, device=None, dtype=None) -> None:CODE
LOWesm/sdk/experimental/__init__.py8__all__ = [CODE
LOWesm/sdk/experimental/constrained_generation.py72 def update_lambda(self, g: float, eta: float, gamma: float) -> None:CODE
LOWcookbook/tutorials/binder_design.py64logger = logging.getLogger(__name__)CODE
Excessive Try-Catch Wrapping36 hits · 42 pts
SeverityFileLineSnippetContext
LOWesm/utils/forge_context_manager.py137 except Exception as e:CODE
LOWesm/utils/structure/mmcif_parsing.py98 except Exception as e:CODE
LOWesm/utils/structure/mmcif_parsing.py142 except Exception:CODE
LOWesm/utils/structure/mmcif_parsing.py191 except Exception:CODE
LOWesm/utils/structure/mmcif_parsing.py495 except Exception:CODE
LOWesm/utils/structure/molecular_complex.py488 except Exception:CODE
LOWesm/utils/structure/molecular_complex.py552 except Exception:CODE
LOWesm/utils/structure/molecular_complex.py1074 except Exception:CODE
LOWesm/utils/structure/molecular_complex.py1146 except Exception as e:CODE
LOWesm/models/esmfold2/conformers.py59 except Exception as e:CODE
LOWesm/models/esmfold2/layers.py2437 except Exception as e:CODE
LOWesm/models/esmfold2/distributed/manager.py582 except Exception:CODE
LOWesm/sdk/forge.py964 except Exception as e:STRING
LOWesm/sdk/retry.py34 except Exception:CODE
MEDIUMesm/sdk/retry.py31def log_retry_attempt(retry_state):CODE
LOWesm/sdk/sagemaker.py46 except Exception as e:CODE
LOWesm/sdk/sagemaker.py108 except Exception as e:CODE
LOWesm/sdk/base_forge_client.py178 except Exception as e:CODE
LOWesm/sdk/base_forge_client.py216 except Exception as e:CODE
LOWesm/sdk/base_forge_client.py398 except Exception as e:CODE
LOWesm/sdk/base_forge_client.py428 except Exception as e:CODE
LOWesm/widgets/utils/protein_import.py110 except Exception as e:CODE
MEDIUMesm/widgets/utils/protein_import.py112 wrapped_print(f"Error: {e}")CODE
LOWesm/widgets/utils/protein_import.py148 except Exception as e:CODE
MEDIUMesm/widgets/utils/protein_import.py150 wrapped_print(f"Error: {e}")CODE
MEDIUMesm/widgets/utils/protein_import.py132def on_upload(self, _):CODE
LOWesm/widgets/components/structure_prompt_selector.py190 except Exception as e:CODE
LOWesm/widgets/components/structure_prompt_selector.py331 except Exception as e:CODE
LOWesm/widgets/components/function_annotator.py123 except Exception as e:CODE
MEDIUMesm/widgets/components/function_annotator.py125 print(f"Error: {e}")CODE
LOWesm/widgets/views/prediction.py149 except Exception as e:CODE
MEDIUMesm/widgets/views/prediction.py80def on_click_predict(_):CODE
LOWesm/widgets/views/esm3_generation_launcher.py185 except Exception:CODE
LOWesm/widgets/views/inverse_folding.py86 except Exception as e:CODE
MEDIUMesm/widgets/views/inverse_folding.py54def on_click_inverse_fold(_):CODE
LOW.github/scripts/airtable_issue_sync.py404 except Exception as err: # noqa: BLE001CODE
Over-Commented Block44 hits · 41 pts
SeverityFileLineSnippetContext
LOWesm/layers/rotary.py1# Copyright 2022 EleutherAI and the HuggingFace Inc. team. All rights reserved.COMMENT
LOWesm/utils/residue_constants.py1# Copyright 2025 EvolutionaryScaleCOMMENT
LOWesm/utils/residue_constants.py861# 1-to-1 mapping of 3 letter names to one letter names. The latter containsCOMMENT
LOWesm/models/esmfold2/config.py1# Copyright 2026 Biohub. All rights reserved.COMMENT
LOWesm/models/esmfold2/experimental.py1# coding=utf-8COMMENT
LOWesm/models/esmfold2/protein_utils.py1# coding=utf-8COMMENT
LOWesm/models/esmfold2/distributed/msa_wrapper.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOWesm/models/esmfold2/distributed/structure_wrapper.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOWesm/models/esmfold2/distributed/comm.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOWesm/models/esmfold2/distributed/esmc_tp.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOWesm/models/esmfold2/distributed/__init__.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOWesm/models/esmfold2/distributed/utils.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOWesm/models/esmfold2/distributed/utils.py401 )COMMENT
LOWesm/models/esmfold2/distributed/distogram_wrapper.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOWesm/models/esmfold2/distributed/confidence_wrapper.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOWesm/models/esmfold2/distributed/manager.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOWesm/models/esmfold2/distributed/recycle.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOWesm/models/esmfold2/distributed/recycle.py241 if isinstance(pair_mask, DTensor):COMMENT
LOWesm/models/esmfold2/distributed/model/__init__.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOW…mfold2/distributed/model/layers/attention_pair_bias.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOW…ls/esmfold2/distributed/model/layers/pair_averaging.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOW…s/esmfold2/distributed/model/layers/triangular_mult.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOW…/models/esmfold2/distributed/model/layers/layernorm.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOWesm/models/esmfold2/distributed/model/layers/linear.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOW…m/models/esmfold2/distributed/model/layers/__init__.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOW…odels/esmfold2/distributed/model/layers/msa_encoder.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOW…ls/esmfold2/distributed/model/layers/single_to_pair.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOW…/models/esmfold2/distributed/model/layers/pair_init.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOW…models/esmfold2/distributed/model/layers/pairformer.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOW…old2/distributed/model/layers/row_attention_pooling.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOW…old2/distributed/model/layers/diffusion_transformer.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOW…smfold2/distributed/model/layers/outer_product_mean.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOW…/esmfold2/distributed/model/layers/confidence_zbase.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOW…ld2/distributed/model/layers/diffusion_conditioning.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOW…els/esmfold2/distributed/model/layers/atom_to_token.py1# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.COMMENT
LOWtests/conftest.py41# ---------------------------------------------------------------------------COMMENT
LOWtests/conftest.py241 reference[name] = {COMMENT
LOWtests/models/esmfold2_execution_test.py61COMMENT
LOWtests/models/esmfold2_execution_test.py501 # would otherwise only show up as a diffuse shift in every radius.COMMENT
LOWtests/models/esmfold2_sampler_test.py181COMMENT
LOWtests/models/esmfold2_sampler_test.py481 for a in apartCOMMENT
LOWtests/models/esmfold2_test.py1221 candidate = run()COMMENT
LOWtests/models/esmfold2_builds_test.py481# What a CUDA build can be held to against the CPU / fp32 result, and on whichCOMMENT
LOWtests/models/esmfold2_builds_test.py501#COMMENT
Empty Error Handlers6 hits · 30 pts
SeverityFileLineSnippetContext
HIGHesm/utils/structure/mmcif_parsing.py142except Exception:CODE
HIGHesm/utils/structure/mmcif_parsing.py120except ValueError:CODE
HIGHesm/utils/structure/mmcif_parsing.py131except ValueError:CODE
HIGHesm/utils/structure/molecular_complex.py552except Exception:CODE
HIGHesm/models/esmfold2/prepare_input.py609except (RuntimeError, ValueError):CODE
HIGHesm/models/esmfold2/distributed/manager.py582except Exception:CODE
AI Structural Patterns29 hits · 26 pts
SeverityFileLineSnippetContext
LOWesm/layers/transformer_stack.py26CODE
LOWesm/layers/blocks.py73CODE
LOWesm/utils/structure/protein_complex.py949CODE
LOWesm/models/esm3.py267CODE
LOWesm/models/vqvae.py49CODE
LOWesm/models/esmfold2/hf_adapter.py210CODE
LOWesm/models/esmfold2/experimental.py850CODE
LOWesm/models/esmfold2/processor.py338CODE
LOWesm/models/esmfold2/model.py1008CODE
LOWesm/models/esmfold2/layers.py718CODE
LOWesm/models/esmfold2/layers.py797CODE
LOWesm/models/esmfold2/layers.py950CODE
LOWesm/models/esmfold2/layers.py1443CODE
LOWesm/models/esmfold2/layers.py1791CODE
LOW…m/models/esmfold2/kernels/fused_attention_pair_bias.py693CODE
LOWesm/models/esmfold2/distributed/manager.py126CODE
LOWesm/models/esmc/sae.py211CODE
LOWesm/models/esmc/model.py221CODE
LOWesm/models/esmc/model.py414CODE
LOWesm/models/esmc/model.py608CODE
LOWesm/models/esmc/model.py711CODE
LOWesm/models/esmc/model.py811CODE
LOWesm/sdk/forge.py1259CODE
LOWesm/sdk/forge.py1434CODE
LOWesm/sdk/sagemaker.py59CODE
LOWesm/sdk/sagemaker.py119CODE
LOWesm/sdk/base_forge_client.py228CODE
LOWesm/widgets/utils/drawing/draw_category_array.py13CODE
LOWcookbook/tutorials/binder_design.py1436CODE
Verbosity Indicators16 hits · 25 pts
SeverityFileLineSnippetContext
LOW⚡esm/models/esmfold2/layers.py1570 # Step 2: normalize noisy coordsCOMMENT
LOW⚡esm/models/esmfold2/layers.py1574 # Step 3: atom encoderCOMMENT
LOW⚡esm/models/esmfold2/layers.py1590 # Step 4: add conditioned sCOMMENT
LOW⚡esm/models/esmfold2/layers.py1593 # Step 5: token transformerCOMMENT
LOW⚡esm/models/esmfold2/layers.py1603 # Step 6: token normCOMMENT
LOW⚡esm/models/esmfold2/layers.py1606 # Step 7: atom decoderCOMMENT
LOWesm/models/esmfold2/layers.py1558 # Step 1: conditioning (pair z is cached across diffusion steps)COMMENT
LOWesm/models/esmfold2/layers.py1618 # Step 8: compute denoised outputCOMMENT
LOWesm/models/esmfold2/distributed/structure_wrapper.py156 # Step 1: conditioning -> full s, sharded (padded) z. Only materialise +COMMENT
LOW⚡esm/models/esmfold2/distributed/structure_wrapper.py188 # Step 2: normalise noisy coords (replicated)COMMENT
LOW⚡esm/models/esmfold2/distributed/structure_wrapper.py192 # Step 3: atom encoder (replicated, full)COMMENT
LOW⚡esm/models/esmfold2/distributed/structure_wrapper.py208 # Step 4: add conditioned s (replicated)COMMENT
LOW⚡esm/models/esmfold2/distributed/structure_wrapper.py211 # Step 5: token transformer (distributed). Pad token axis; row-shard a/s/COMMENT
LOW⚡esm/models/esmfold2/distributed/structure_wrapper.py225 # Step 6: token norm (replicated)COMMENT
LOW⚡esm/models/esmfold2/distributed/structure_wrapper.py228 # Step 7: atom decoder (replicated, full)COMMENT
LOWesm/models/esmfold2/distributed/structure_wrapper.py240 # Step 8: denoised output (replicated)COMMENT
Structural Annotation Overuse16 hits · 25 pts
SeverityFileLineSnippetContext
LOW⚡esm/models/esmfold2/layers.py1570 # Step 2: normalize noisy coordsCOMMENT
LOW⚡esm/models/esmfold2/layers.py1574 # Step 3: atom encoderCOMMENT
LOW⚡esm/models/esmfold2/layers.py1590 # Step 4: add conditioned sCOMMENT
LOW⚡esm/models/esmfold2/layers.py1593 # Step 5: token transformerCOMMENT
LOW⚡esm/models/esmfold2/layers.py1603 # Step 6: token normCOMMENT
LOW⚡esm/models/esmfold2/layers.py1606 # Step 7: atom decoderCOMMENT
LOWesm/models/esmfold2/layers.py1558 # Step 1: conditioning (pair z is cached across diffusion steps)COMMENT
LOWesm/models/esmfold2/layers.py1618 # Step 8: compute denoised outputCOMMENT
LOWesm/models/esmfold2/distributed/structure_wrapper.py156 # Step 1: conditioning -> full s, sharded (padded) z. Only materialise +COMMENT
LOW⚡esm/models/esmfold2/distributed/structure_wrapper.py188 # Step 2: normalise noisy coords (replicated)COMMENT
LOW⚡esm/models/esmfold2/distributed/structure_wrapper.py192 # Step 3: atom encoder (replicated, full)COMMENT
LOW⚡esm/models/esmfold2/distributed/structure_wrapper.py208 # Step 4: add conditioned s (replicated)COMMENT
LOW⚡esm/models/esmfold2/distributed/structure_wrapper.py211 # Step 5: token transformer (distributed). Pad token axis; row-shard a/s/COMMENT
LOW⚡esm/models/esmfold2/distributed/structure_wrapper.py225 # Step 6: token norm (replicated)COMMENT
LOW⚡esm/models/esmfold2/distributed/structure_wrapper.py228 # Step 7: atom decoder (replicated, full)COMMENT
LOWesm/models/esmfold2/distributed/structure_wrapper.py240 # Step 8: denoised output (replicated)COMMENT
Self-Referential Comments6 hits · 18 pts
SeverityFileLineSnippetContext
MEDIUMesm/utils/residue_constants.py490 # Create a fast lookup dict for bond lengths.COMMENT
MEDIUMesm/utils/residue_constants.py866# Define a restype name for all unknown residues.COMMENT
MEDIUMesm/utils/structure/mmcif_parsing.py330 # Create a basic mapping based on the chain_dataCOMMENT
MEDIUMesm/models/esm3.py391 # The following methods are for the ESM3InferenceClient interfaceCOMMENT
MEDIUMesm/widgets/components/function_annotator.py33 # Create a text box input and a list of children to select fromCOMMENT
MEDIUMcookbook/snippets/sae_example.py19# Create a proteinCOMMENT
Cross-File Repetition3 hits · 15 pts
SeverityFileLineSnippetContext
HIGHtests/compatibility/esmfold2_hf_adapter_test.py0flash-attn imports on a cpu box but needs a cuda runtime to run.STRING
HIGHtests/models/esmfold2_msa_test.py0flash-attn imports on a cpu box but needs a cuda runtime to run.STRING
HIGHtests/models/esmfold2_api_test.py0flash-attn imports on a cpu box but needs a cuda runtime to run.STRING
Docstring Block Structure2 hits · 10 pts
SeverityFileLineSnippetContext
HIGHesm/utils/residue_constants.py794Maps the given sequence into a one-hot encoded matrix. Args: sequence: An amino acid sequence. mapping:STRING
HIGHesm/models/esm3.py283 Performs forward pass through the ESM3 model. Check utils to see how to tokenize inputs from raw data. STRING
Redundant / Tautological Comments7 hits · 10 pts
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LOWesm/utils/structure/mmcif_parsing.py286 # Check if there are duplicate residue numbers in this chainCOMMENT
LOWesm/utils/structure/molecular_complex.py298 # Check if token is a standard 3-letter amino acid codeCOMMENT
LOWesm/utils/structure/molecular_complex.py459 # Check if input is a file path or mmCIF string contentCOMMENT
LOWesm/utils/structure/molecular_complex.py1181 # Check if both tokens have atomsCOMMENT
LOWesm/utils/structure/molecular_complex.py1249 # Check if both tokens have atomsCOMMENT
LOWesm/models/esmfold2/prepare_input.py227 # Check if standard residue (has predefined atom list)COMMENT
LOWesm/widgets/components/sequence_prompt_selector.py123 a = 0.5 # Set alpha to 0.5CODE
Magic Placeholder Names2 hits · 10 pts
SeverityFileLineSnippetContext
HIGHcookbook/snippets/esm3.py204 "To try this script with a Forge/Biohub Platform API, please run ESM_API_KEY=your_api_key python esm3.py"CODE
HIGHcookbook/snippets/esmc.py147 "ESM_API_KEY=your_api_key python esmc.py"CODE
AI Slop Vocabulary3 hits · 6 pts
SeverityFileLineSnippetContext
LOWesm/utils/misc.py281 # For MPS, just return a no-op context manager (nullcontext) since MPS does not support autocast.COMMENT
MEDIUMesm/utils/structure/molecular_complex.py347 # Normalize to uppercase and strip whitespace for robust matchingCOMMENT
LOWesm/models/esmfold2/kernels/fused_lnlin_swiglu.py377 # If LN_B was None (no bias), ATen returns dLN_B=None and we just pass it through.COMMENT
Cross-Language Confusion1 hit · 5 pts
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HIGHcookbook/tutorials/binder_design.py1355 .run_commands("apt update && apt install -y git build-essential")CODE
Modern AI Meta-Vocabulary2 hits · 4 pts
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MEDIUMREADME.md35The **[ESM Atlas](https://biohub.ai/esm/protein/atlas)** is a map of 6.8 billion proteins covering the full breadth of lCODE
MEDIUMcookbook/tutorials/README.md38| Generating proteins with ESM3 | `esm3_generate.ipynb`<br>[![Open In Colab](https://colab.research.google.com/assets/cCODE