Repository Analysis

Biohub/esm

4.8 Likely human-written View on GitHub

Analysis Overview

This report presents the forensic synthetic code analysis of Biohub/esm, a Jupyter Notebook project with 2,844 GitHub stars. SynthScan v2.0 examined 100,047 lines of code across 132 source files, recording 364 pattern matches distributed across 15 syntactic categories. The overall adjusted score of 4.8 places this repository in the Likely human-written 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).

4.8
Adjusted Score
4.8
Raw Score
100%
Time Factor
2026-07-01
Last Push
2.8K
Stars
Jupyter Notebook
Language
100.0K
Lines of Code
132
Files
364
Pattern Hits
2026-07-14
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 5MEDIUM 49LOW 310

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 364 distinct pattern matches across 15 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.

Hyper-Verbose Identifiers147 hits · 144 pts
SeverityFileLineSnippetContext
LOWesm/utils/misc_test.py23def test_merge_annotations_gap():CODE
LOWesm/utils/misc.py40def slice_python_object_as_numpy(CODE
LOWesm/utils/misc.py180def stack_variable_length_tensors(CODE
LOWesm/utils/misc.py394def get_chainbreak_boundaries_from_sequence(sequence: Sequence[str]) -> np.ndarray:CODE
LOWesm/utils/misc.py444def 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() -> (CODE
LOWesm/utils/residue_constants.py1042def _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/msa/msa_test.py71def test_deletions_flow_through_featurization(tmp_path):CODE
LOWesm/utils/msa/msa_test.py78def test_from_sequences_has_no_deletions_and_recomputes():CODE
LOWesm/utils/msa/msa_test.py86def test_slicing_carries_deletions(tmp_path):CODE
LOWesm/utils/msa/msa_test.py98def test_sliced_deletions_flow_through_featurization(tmp_path):CODE
LOWesm/utils/msa/msa_test.py107def test_deletions_dropped_when_not_column_aligned():CODE
LOWesm/utils/msa/msa_test.py117def test_pad_to_depth_carries_deletions(tmp_path):CODE
LOWesm/utils/msa/msa_test.py126def test_stack_carries_deletions(tmp_path):CODE
LOWesm/utils/msa/msa_test.py135def test_stack_drops_deletions_if_any_missing(tmp_path):CODE
LOWesm/utils/msa/msa_test.py141def test_concat_carries_deletions_without_join_token(tmp_path):CODE
LOWesm/utils/msa/msa_test.py152def test_concat_drops_deletions_with_join_token(tmp_path):CODE
LOWesm/utils/msa/msa_test.py158def test_state_dict_round_trip(tmp_path):CODE
LOWesm/utils/msa/msa_test.py170def test_state_dict_omits_deletions_when_absent():CODE
LOWesm/utils/constants/models.py19def forge_only_return_single_layer_hidden_states(model_name: str):CODE
LOWesm/utils/constants/models.py23def 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.py83def serialize_structure_prediction_input(all_atom_input: StructurePredictionInput):CODE
LOWesm/utils/structure/input_builder.py157def 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/input_builder_test.py38def test_roundtrip_minimal_protein() -> None:CODE
LOWesm/utils/structure/input_builder_test.py43def test_roundtrip_protein_with_modifications() -> None:CODE
LOWesm/utils/structure/input_builder_test.py68def test_roundtrip_protein_with_msa() -> None:CODE
LOWesm/utils/structure/input_builder_test.py82def test_roundtrip_rna_dna_ligand() -> None:CODE
LOWesm/utils/structure/input_builder_test.py99def test_roundtrip_full_with_conditioning() -> None:CODE
LOWesm/utils/structure/input_builder_test.py140def test_unsupported_sequence_type_raises() -> None:CODE
LOWesm/utils/structure/protein_chain.py243 def residue_index_no_insertions(self) -> np.ndarray:CODE
LOWesm/utils/structure/protein_chain.py774 def chain_iterable_from_mmcif(CODE
LOWesm/utils/structure/protein_chain.py982 def from_backbone_atom_coordinates(CODE
LOWesm/utils/structure/protein_chain.py1369 def to_structure_encoder_inputs(CODE
LOWesm/utils/structure/protein_complex.py57def _parse_operation_expression(expression):CODE
87 more matches not shown…
Decorative Section Separators32 hits · 108 pts
SeverityFileLineSnippetContext
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/prepare_input.py60# =============================================================================COMMENT
MEDIUMesm/models/esmfold2/prepare_input.py62# =============================================================================COMMENT
MEDIUMesm/models/esmfold2/prepare_input.py107# =============================================================================COMMENT
MEDIUMesm/models/esmfold2/prepare_input.py109# =============================================================================COMMENT
MEDIUMesm/models/esmfold2/prepare_input.py186# =============================================================================COMMENT
MEDIUMesm/models/esmfold2/prepare_input.py188# =============================================================================COMMENT
MEDIUMesm/models/esmfold2/prepare_input.py670# =============================================================================COMMENT
MEDIUMesm/models/esmfold2/prepare_input.py672# =============================================================================COMMENT
MEDIUMesm/models/esmfold2/prepare_input.py820# =============================================================================COMMENT
MEDIUMesm/models/esmfold2/prepare_input.py822# =============================================================================COMMENT
MEDIUMesm/models/esmfold2/prepare_input.py1465# =============================================================================COMMENT
MEDIUMesm/models/esmfold2/prepare_input.py1467# =============================================================================COMMENT
MEDIUMesm/sdk/experimental/guided_generation.py107 # ----------------------------------------------COMMENT
MEDIUMesm/sdk/experimental/guided_generation.py109 # ----------------------------------------------COMMENT
MEDIUMesm/sdk/experimental/guided_generation.py119 # ----------------------------------------------COMMENT
MEDIUMesm/sdk/experimental/guided_generation.py121 # ----------------------------------------------COMMENT
MEDIUMcookbook/snippets/esmc.py21 # ================================================================COMMENT
MEDIUMcookbook/snippets/esmc.py23 # ================================================================COMMENT
MEDIUMcookbook/snippets/esmc.py63 # ================================================================COMMENT
MEDIUMcookbook/snippets/esmc.py65 # ================================================================COMMENT
Deep Nesting59 hits · 57 pts
SeverityFileLineSnippetContext
LOWesm/utils/generation.py37CODE
LOWesm/utils/generation.py66CODE
LOWesm/utils/generation.py130CODE
LOWesm/utils/sequential_dataclass.py97CODE
LOWesm/utils/residue_constants.py1118CODE
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.py83CODE
LOWesm/utils/structure/input_builder.py157CODE
LOWesm/utils/structure/molecular_complex.py447CODE
LOWesm/utils/structure/molecular_complex.py732CODE
LOWesm/utils/structure/molecular_complex.py895CODE
LOWesm/utils/structure/molecular_complex.py1065CODE
LOWesm/utils/structure/molecular_complex.py1298CODE
LOWesm/utils/structure/protein_chain.py88CODE
LOWesm/utils/structure/protein_chain.py905CODE
LOWesm/utils/structure/protein_chain.py1019CODE
LOWesm/utils/structure/protein_complex.py803CODE
LOWesm/utils/structure/molecular_complex_test.py304CODE
LOWesm/models/esmfold2/conformers.py268CODE
LOWesm/models/esmfold2/processor.py86CODE
LOWesm/models/esmfold2/paired_msa.py95CODE
LOWesm/models/esmfold2/prepare_input.py157CODE
LOWesm/models/esmfold2/prepare_input.py329CODE
LOWesm/models/esmfold2/prepare_input.py675CODE
LOWesm/models/esmfold2/prepare_input.py690CODE
LOWesm/models/esmfold2/prepare_input.py825CODE
LOWesm/models/esmfold2/prepare_input.py965CODE
LOWesm/models/esmfold2/prepare_input.py1105CODE
LOWesm/models/esmfold2/prepare_input.py1145CODE
LOWesm/models/esmfold2/output.py18CODE
LOWesm/models/esmfold2/output.py129CODE
LOWesm/tokenization/residue_tokenizer.py73CODE
LOWesm/sdk/forge.py133CODE
LOWesm/sdk/api.py56CODE
LOWesm/sdk/api.py165CODE
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
LOWesm/widgets/views/esm3_generation_launcher.py133CODE
LOWesm/widgets/views/inverse_folding.py14CODE
LOWesm/widgets/views/inverse_folding.py54CODE
LOWesm/widgets/views/esm3_prompt_preview.py74CODE
LOWesm/widgets/views/esm3_prompt_preview.py133CODE
LOWcookbook/tutorials/binder_design.py828CODE
Unused Imports52 hits · 52 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/molecular_complex.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/esmc.py1CODE
LOWesm/models/esmfold2/conformers.py7CODE
LOWesm/models/esmfold2/__init__.py1CODE
LOWesm/models/esmfold2/__init__.py2CODE
LOWesm/models/esmfold2/__init__.py3CODE
LOWesm/models/esmfold2/__init__.py3CODE
LOWesm/models/esmfold2/__init__.py4CODE
LOWesm/models/esmfold2/__init__.py4CODE
LOWesm/models/esmfold2/__init__.py5CODE
LOWesm/models/esmfold2/__init__.py5CODE
LOWesm/models/esmfold2/__init__.py5CODE
LOWesm/models/esmfold2/__init__.py5CODE
LOWesm/models/esmfold2/__init__.py5CODE
LOWesm/models/esmfold2/__init__.py5CODE
LOWesm/models/esmfold2/__init__.py5CODE
LOWesm/models/esmfold2/__init__.py5CODE
LOWesm/models/esmfold2/__init__.py5CODE
LOWesm/models/esmfold2/__init__.py16CODE
LOWesm/models/esmfold2/__init__.py16CODE
LOWesm/models/esmfold2/__init__.py16CODE
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/prepare_input.py7CODE
LOWesm/sdk/forge.py1CODE
LOWesm/sdk/api.py1CODE
LOWesm/sdk/experimental/__init__.py1CODE
LOWesm/sdk/experimental/__init__.py1CODE
LOWesm/sdk/experimental/__init__.py1CODE
LOWesm/sdk/experimental/__init__.py6CODE
LOWesm/sdk/experimental/__init__.py6CODE
LOWesm/sdk/experimental/constrained_generation.py1CODE
Excessive Try-Catch Wrapping31 hits · 38 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.py1061 except Exception:CODE
LOWesm/utils/structure/molecular_complex.py1133 except Exception as e:CODE
LOWesm/models/esmfold2/conformers.py59 except Exception as e:CODE
LOWesm/sdk/forge.py939 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.py128 except Exception as e:CODE
LOWesm/sdk/base_forge_client.py158 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
Self-Referential Comments7 hits · 21 pts
SeverityFileLineSnippetContext
MEDIUMesm/utils/residue_constants.py494 # Create a fast lookup dict for bond lengths.COMMENT
MEDIUMesm/utils/residue_constants.py870# 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
AI Structural Patterns11 hits · 11 pts
SeverityFileLineSnippetContext
LOWesm/layers/transformer_stack.py26CODE
LOWesm/layers/blocks.py73CODE
LOWesm/utils/structure/protein_complex.py936CODE
LOWesm/models/esm3.py267CODE
LOWesm/models/vqvae.py49CODE
LOWesm/models/esmc.py191CODE
LOWesm/models/esmfold2/processor.py327CODE
LOWesm/sdk/forge.py1232CODE
LOWesm/sdk/sagemaker.py59CODE
LOWesm/sdk/sagemaker.py119CODE
LOWesm/widgets/utils/drawing/draw_category_array.py13CODE
Docstring Block Structure2 hits · 10 pts
SeverityFileLineSnippetContext
HIGHesm/utils/residue_constants.py798Maps 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
SeverityFileLineSnippetContext
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.py1168 # Check if both tokens have atomsCOMMENT
LOWesm/utils/structure/molecular_complex.py1236 # Check if both tokens have atomsCOMMENT
LOWesm/models/esmfold2/prepare_input.py226 # 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.py137 "To try this script with a Forge/Biohub Platform API, please run ESM_API_KEY=your_api_key python esm3.py"CODE
Modern Structural Boilerplate7 hits · 7 pts
SeverityFileLineSnippetContext
LOWesm/utils/msa/__init__.py3__all__ = ["MSA", "FastMSA", "remove_insertions_from_sequence"]CODE
LOWesm/models/esmfold2/__init__.py22__all__ = [CODE
LOWesm/models/esmfold2/processor.py422__all__ = ["ESMFold2InputBuilder", "clean_esmfold2_input"]CODE
LOWesm/models/esmfold2/types.py22__all__ = [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.py66logger = logging.getLogger(__name__)CODE
Cross-Language Confusion1 hit · 5 pts
SeverityFileLineSnippetContext
HIGHcookbook/tutorials/binder_design.py1185 .run_commands("apt update && apt install -y git build-essential")CODE
AI Slop Vocabulary2 hits · 4 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
Modern AI Meta-Vocabulary2 hits · 4 pts
SeverityFileLineSnippetContext
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
Over-Commented Block2 hits · 2 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