Repository Analysis

Biohub/esm

13.1 Low AI signal View on GitHub

Analysis Overview

This report presents the forensic synthetic code analysis of Biohub/esm, a Jupyter Notebook project with 2,931 GitHub stars. SynthScan v2.0 examined 123,327 lines of code across 180 source files, recording 992 pattern matches distributed across 18 syntactic categories. The overall adjusted score of 13.1 places this repository in the Low AI signal band.

The scanner applied 160+ deterministic lexical heuristics, multi-line block detectors, abstract syntax tree depth profilers, and a cross-file Jaccard similarity matrix to construct a statistically normalised synthetic code estimate. All matches are individually weighted by severity coefficient and contextual multiplier before summation, and the resulting headline score is temporally discounted to account for the repository's development history relative to the commercial emergence of large language model coding tooling (November 2022 onward).

13.1
Adjusted Score
13.1
Raw Score
100%
Time Factor
2026-08-27
Last Push
2.9K
Stars
Jupyter Notebook
Language
123.3K
Lines of Code
180
Files
992
Pattern Hits
2026-08-29
Scan Date
0.04
HC Hit Rate

What These Metrics Mean

Adjusted Score
Primary synthetic code indicator. Raw score normalised per 1,000 lines of code and multiplied by the temporal discount factor. This is the definitive comparative metric — use it to rank repositories by AI authorship density.
Raw Score
The unmodified sum of all severity-weighted, context-multiplied pattern match scores before temporal discounting. Reflects the absolute signal strength independent of when the repository was last active.
Time Factor
The temporal discount multiplier (0–100%) applied to the raw score. Repositories last updated before ChatGPT's launch (Nov 2022) receive a 5% factor. Full signal is only assigned to repositories active in the post-adoption era (Jan 2024+).
Pattern Hits
Total count of individual pattern matches across all files and categories. A high hit count with a low score may indicate a very large codebase with isolated AI snippets; a low count with a high score indicates dense, concentrated AI signatures.
HC Hit Rate
High+Critical pattern hits per file, averaged across the repository. This orthogonal signal catches repositories where a few files are densely packed with high-severity AI tells — a strong indicator even when the normalised score appears moderate due to codebase size.
Lines of Code / Files
Total lines and files analysed. The scanner examines 94 file extensions. These denominators are used to normalise the score, enabling fair comparison between repositories of vastly different sizes.

Score History

This chart maps the temporal evolution of the adjusted synthetic code score across successive scan runs. An upward trajectory indicates ongoing incorporation of AI-generated code or expanding LLM-assisted scaffolding; a stable or declining trajectory may reflect active human refactoring, code removal, or the adoption of stricter authorship policies. The dashed secondary line (right axis) independently tracks total raw pattern hit count, which can diverge from the normalised score when codebase size changes significantly between scans.

Severity Breakdown

Classifies detected patterns by their diagnostic confidence and structural impact. CRITICAL patterns (coefficient 10) represent definitive synthetic signatures — hallucinated imports, explicit LLM attribution metadata — virtually never produced by human authors. HIGH (5) indicates strong structural tells such as cross-file repetition or cross-linguistic idioms. MEDIUM (2) covers recognisable conversational padding and AI-specific vocabulary. LOW (1) captures subtle indicators like tautological comments and generic boilerplate that require density to carry independent signal.

CRITICAL 0HIGH 8MEDIUM 283LOW 701

Directory Score Breakdown

This horizontal bar chart decomposes the repository's raw synthetic code score by top-level directory, allowing you to pinpoint precisely which modules or components carry the highest AI authorship density. Directories with disproportionately high scores relative to their size warrant targeted manual review: concentrated AI signatures often trace back to mass-generated configuration layers, auto-ported test suites, LLM-scaffolded boilerplate classes, or entire subsystems authored under heavy copilot assistance. Use this view to prioritise your human code-review effort.

Pattern Findings

The scanner identified 992 distinct pattern matches across 18 syntactic categories. Each entry below represents a discrete location in the source code where the engine recorded a statistically significant AI authorship indicator. 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 diagnostic confidence level (CRITICAL / HIGH / MEDIUM / LOW). The Context column identifies whether the match occurred inside executable code, an inline comment, or a string literal — comment-context matches receive a ×1.5 weight because LLMs systematically over-annotate. The ⚡ bolt icon marks clustered matches: three or more patterns within a 10-line window, each receiving an additional ×1.5 density multiplier as dense clusters constitute far stronger evidence of synthetic authorship than isolated hits.

Decorative Section Separators266 hits · 879 pts
SeverityFileLineSnippetContext
MEDIUMesm/models/esmfold2/config.py35# ---------------------------------------------------------------------------COMMENT
MEDIUMesm/models/esmfold2/config.py37# ---------------------------------------------------------------------------COMMENT
MEDIUMesm/models/esmfold2/config.py341# ---------------------------------------------------------------------------COMMENT
MEDIUMesm/models/esmfold2/config.py343# ---------------------------------------------------------------------------COMMENT
MEDIUMesm/models/esmfold2/experimental.py130 # ------------------------------------------------------------------COMMENT
MEDIUMesm/models/esmfold2/experimental.py132 # ------------------------------------------------------------------COMMENT
MEDIUMesm/models/esmfold2/experimental.py140 # ------------------------------------------------------------------COMMENT
MEDIUMesm/models/esmfold2/experimental.py142 # ------------------------------------------------------------------COMMENT
MEDIUMesm/models/esmfold2/experimental.py525# ===========================================================================COMMENT
MEDIUMesm/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
MEDIUMesm/models/esmfold2/constants.py6# =============================================================================COMMENT
MEDIUMesm/models/esmfold2/constants.py8# =============================================================================COMMENT
MEDIUMesm/models/esmfold2/constants.py15# =============================================================================COMMENT
MEDIUMesm/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
MEDIUMesm/models/esmfold2/layers.py409# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py411# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py1685 # ------------------------------------------------------------------COMMENT
MEDIUMesm/models/esmfold2/layers.py1687 # ------------------------------------------------------------------COMMENT
MEDIUMesm/models/esmfold2/layers.py2480# ===========================================================================COMMENT
MEDIUMesm/models/esmfold2/layers.py2482# ===========================================================================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
206 more matches not shown…
Hyper-Verbose Identifiers400 hits · 366 pts
SeverityFileLineSnippetContext
LOWesm/utils/misc.py40def slice_python_object_as_numpy(CODE
LOWesm/utils/misc.py180def stack_variable_length_tensors(CODE
LOWesm/utils/misc.py401def get_chainbreak_boundaries_from_sequence(sequence: Sequence[str]) -> np.ndarray:CODE
LOWesm/utils/misc.py451def 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.py206def decode_function_annotations(CODE
LOWesm/utils/decoding.py223def 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.py23def 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.py121def serialize_structure_prediction_input(all_atom_input: StructurePredictionInput):CODE
LOWesm/utils/structure/input_builder.py195def 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
LOWesm/models/esmfold2/experimental.py537 def _normalize_checkpoint_layout(CODE
LOWesm/models/esmfold2/experimental.py734 def _output_to_molecular_complex(output: dict, features: dict, chain_infos: list):CODE
LOWesm/models/esmfold2/experimental.py827 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.py540 def _normalize_checkpoint_layout(CODE
LOWesm/models/esmfold2/model.py796 def _compute_lm_hidden_states(CODE
LOWesm/models/esmfold2/paired_msa.py24def protein_letter_to_res_type() -> dict[str, int]:CODE
340 more matches not shown…
Unused Imports87 hits · 84 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
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Deep Nesting67 hits · 65 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.py121CODE
LOWesm/utils/structure/input_builder.py195CODE
LOWesm/utils/structure/molecular_complex.py447CODE
LOWesm/utils/structure/molecular_complex.py822CODE
LOWesm/utils/structure/molecular_complex.py985CODE
LOWesm/utils/structure/molecular_complex.py1155CODE
LOWesm/utils/structure/molecular_complex.py1388CODE
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.py848CODE
LOWesm/models/esmfold2/conformers.py268CODE
LOWesm/models/esmfold2/processor.py87CODE
LOWesm/models/esmfold2/model.py368CODE
LOWesm/models/esmfold2/model.py378CODE
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.py1091CODE
LOWesm/models/esmfold2/prepare_input.py1131CODE
LOWesm/models/esmfold2/output.py18CODE
LOWesm/models/esmfold2/output.py129CODE
LOWesm/models/esmc/checkpoint_layout.py145CODE
LOWesm/models/esmc/model.py675CODE
LOWesm/tokenization/residue_tokenizer.py73CODE
LOWesm/sdk/forge.py141CODE
LOWesm/sdk/api.py56CODE
LOWesm/sdk/api.py165CODE
LOWesm/sdk/base_forge_client.py245CODE
LOWesm/sdk/base_forge_client.py272CODE
LOWesm/sdk/base_forge_client.py385CODE
LOWesm/sdk/base_forge_client.py426CODE
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
LOWesm/widgets/components/structure_prompt_selector.py309CODE
LOWesm/widgets/views/prediction.py14CODE
LOWesm/widgets/views/prediction.py80CODE
LOWesm/widgets/views/esm3_generation_launcher.py21CODE
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Modern Structural Boilerplate52 hits · 46 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.py408__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.py559__all__ = [CODE
LOWesm/models/esmfold2/experimental.py134 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/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.py1178__all__ = ["EsmFold2ExperimentalModel"]CODE
LOWesm/models/esmfold2/hf_checkpoint.py258__all__ = [CODE
LOWesm/models/esmfold2/__init__.py30__all__ = [CODE
LOWesm/models/esmfold2/processor.py430__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.py643 def set_esmc_precision(self, precision: str = "bf16") -> None:CODE
LOWesm/models/esmfold2/model.py716 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/models/esmfold2/model.py787 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/model.py1241 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/models/esmfold2/model.py1245 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/model.py1300 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/models/esmfold2/model.py1304 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/layers.py1682 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/models/esmfold2/layers.py2464 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/models/esmfold2/layers.py2473 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/layers.py2609 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.py2367 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/layers.py2497 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/layers.py2500 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/models/esmfold2/layers.py2596 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/models/esmfold2/layers.py2677 def set_kernel_backend(self, backend: str | None) -> None:CODE
LOWesm/models/esmfold2/layers.py2681 def set_chunk_size(self, chunk_size: int | None) -> None:CODE
LOWesm/models/esmfold2/layers.py2742 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/esmc/__init__.py23__all__ = [CODE
LOWesm/models/esmc/model.py311 def set_input_embeddings(self, value: nn.Embedding) -> None:CODE
LOWesm/models/esmc/model.py565 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 Wrapping35 hits · 41 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.py476 except Exception:CODE
LOWesm/utils/structure/molecular_complex.py540 except Exception:CODE
LOWesm/utils/structure/molecular_complex.py1151 except Exception:CODE
LOWesm/utils/structure/molecular_complex.py1223 except Exception as e:CODE
LOWesm/models/esmfold2/conformers.py59 except Exception as e:CODE
LOWesm/models/esmfold2/layers.py2423 except Exception as e:CODE
LOWesm/sdk/forge.py967 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.py134 except Exception as e:CODE
LOWesm/sdk/base_forge_client.py165 except Exception as e:CODE
LOWesm/sdk/base_forge_client.py319 except Exception as e:CODE
LOWesm/sdk/base_forge_client.py349 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.py402 except Exception as err: # noqa: BLE001CODE
AI Structural Patterns28 hits · 24 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.py848CODE
LOWesm/models/esmfold2/processor.py328CODE
LOWesm/models/esmfold2/model.py929CODE
LOWesm/models/esmfold2/layers.py718CODE
LOWesm/models/esmfold2/layers.py797CODE
LOWesm/models/esmfold2/layers.py950CODE
LOWesm/models/esmfold2/layers.py1443CODE
LOWesm/models/esmfold2/layers.py1781CODE
LOW…m/models/esmfold2/kernels/fused_attention_pair_bias.py693CODE
LOWesm/models/esmc/sae.py201CODE
LOWesm/models/esmc/model.py221CODE
LOWesm/models/esmc/model.py376CODE
LOWesm/models/esmc/model.py572CODE
LOWesm/models/esmc/model.py675CODE
LOWesm/models/esmc/model.py775CODE
LOWesm/sdk/forge.py1262CODE
LOWesm/sdk/forge.py1435CODE
LOWesm/sdk/sagemaker.py59CODE
LOWesm/sdk/sagemaker.py119CODE
LOWesm/sdk/base_forge_client.py177CODE
LOWesm/widgets/utils/drawing/draw_category_array.py13CODE
LOWcookbook/tutorials/binder_design.py1436CODE
Self-Referential Comments7 hits · 21 pts
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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/utils/structure/molecular_complex.py580 # Create a mapping from chain_id to numeric indicesCOMMENT
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
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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
Over-Commented Block14 hits · 12 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
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.py501# reduction-order nondeterminism separates them), then the worst case across allCOMMENT
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.py1258 # Check if both tokens have atomsCOMMENT
LOWesm/utils/structure/molecular_complex.py1326 # 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
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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
Verbosity Indicators8 hits · 8 pts
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LOWesm/models/esmfold2/layers.py1570 # Step 2: normalize noisy coordsCOMMENT
LOWesm/models/esmfold2/layers.py1574 # Step 3: atom encoderCOMMENT
LOWesm/models/esmfold2/layers.py1590 # Step 4: add conditioned sCOMMENT
LOWesm/models/esmfold2/layers.py1593 # Step 5: token transformerCOMMENT
LOWesm/models/esmfold2/layers.py1603 # Step 6: token normCOMMENT
LOWesm/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
Structural Annotation Overuse8 hits · 8 pts
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LOWesm/models/esmfold2/layers.py1570 # Step 2: normalize noisy coordsCOMMENT
LOWesm/models/esmfold2/layers.py1574 # Step 3: atom encoderCOMMENT
LOWesm/models/esmfold2/layers.py1590 # Step 4: add conditioned sCOMMENT
LOWesm/models/esmfold2/layers.py1593 # Step 5: token transformerCOMMENT
LOWesm/models/esmfold2/layers.py1603 # Step 6: token normCOMMENT
LOWesm/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
AI Slop Vocabulary3 hits · 6 pts
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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.py1353 .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