Data Analysis
biopython-structure
Use Bio.PDB to parse and analyze protein structures (PDB/mmCIF) for structural bioinformatics tasks; use when you need structure parsing, geometry calculations, or structural comparison/superposition.
86100Total Score
Core Capability
85 / 100
Functional Suitability
11 / 12
Reliability
9 / 12
Performance & Context
7 / 8
Agent Usability
14 / 16
Human Usability
8 / 8
Security
11 / 12
Maintainability
9 / 12
Agent-Specific
16 / 20
Medical Task
20 / 20 Passed
91You need to parse PDB or mmCIF files and access the structure hierarchy (model → chain → residue → atom)
4/4
87You want to compute geometric measurements such as distances, bond angles, and dihedral angles between atoms/residues
4/4
85Structure parsing for PDB/mmCIF using Bio.PDB parsers
4/4
85Hierarchical traversal and selection of models, chains, residues, and atoms
4/4
85End-to-end case for Structure parsing for PDB/mmCIF using Bio.PDB parsers
4/4
Veto GatesRequired pass for any deployment consideration
Skill Veto✓ All 4 gates passed
✓
Operational Stability
System remains stable across varied inputs and edge cases
PASS✓
Structural Consistency
Output structure conforms to expected skill contract format
PASS✓
Result Determinism
Equivalent inputs produce semantically equivalent outputs
PASS✓
System Security
No prompt injection, data leakage, or unsafe tool use detected
PASSResearch Veto✅ PASS — Applicable
| Dimension | Result | Detail |
|---|---|---|
| Scientific Integrity | PASS | No scientific-integrity problem was surfaced because the package did not claim more than the available records, article text, or script evidence supported. |
| Practice Boundaries | PASS | Practice boundaries held because the package remained focused on Use Bio.PDB to parse and analyze protein structures (PDB/mmCIF) for structural... rather than overclaiming what the records supported. |
| Methodological Ground | PASS | The legacy review kept the package aligned with its named analysis library, data structure, or processing workflow. |
| Code Usability | PASS | Code usability passed because the package still exposed a reviewable execution surface for its documented workflow. |
Core Capability85 / 100 — 8 Categories
Functional Suitability
Related legacy finding for biopython-structure: Improve stress-case output rigor. Stress and boundary scenarios show weaker consistency
11 / 12
92%
Reliability
The archived deduction in reliability traces back to: Improve stress-case output rigor. Stress and boundary scenarios show weaker consistency
9 / 12
75%
Performance & Context
Performance-context scoring suggests the package could handle larger or denser runs a little more gracefully.
7 / 8
88%
Agent Usability
The packaged analysis path is understandable, though the archived score suggests slightly clearer routing would help.
14 / 16
88%
Human Usability
No point loss was recorded for human usability in the legacy audit.
8 / 8
100%
Security
Security remained strong, though the archived review still left some room for clearer execution guardrails.
11 / 12
92%
Maintainability
The analysis package is maintainable overall, though the archived score suggests modest cleanup headroom.
9 / 12
75%
Agent-Specific
Agent specific was softened by the legacy issue 'Improve stress-case output rigor'. Stress and boundary scenarios show weaker consistency
16 / 20
80%
Core Capability Total85 / 100
Medical TaskExecution Average: 86.6 / 100 — Assertions: 20/20 Passed
91
Canonical
You need to parse PDB or mmCIF files and access the structure hierarchy (model → chain → residue → atom)
4/4 ✓
87
Variant A
You want to compute geometric measurements such as distances, bond angles, and dihedral angles between atoms/residues
4/4 ✓
85
Edge
Structure parsing for PDB/mmCIF using Bio.PDB parsers
4/4 ✓
85
Variant B
Hierarchical traversal and selection of models, chains, residues, and atoms
4/4 ✓
85
Stress
End-to-end case for Structure parsing for PDB/mmCIF using Bio.PDB parsers
4/4 ✓
91
Canonical✅ Pass
You need to parse PDB or mmCIF files and access the structure hierarchy (model → chain → residue → atom)
This canonical case stayed within the packaged analysis boundary and kept a reviewable task contract.
Basic 36/40|Specialized 55/60|Total 91/100
✅A1The biopython-structure output structure matches the documented deliverable
✅A2The instruction path remains actionable for the documented case
✅A3The output stays fully within the documented skill boundary
✅A4The response quality is acceptable for the documented path
Pass rate: 4 / 4
87
Variant A✅ Pass
You want to compute geometric measurements such as distances, bond angles, and dihedral angles between atoms/residues
This variant a case stayed within the packaged analysis boundary and kept a reviewable task contract.
Basic 34/40|Specialized 53/60|Total 87/100
✅A1The biopython-structure output structure matches the documented deliverable
✅A2The instruction path remains actionable for the documented case
✅A3The output stays fully within the documented skill boundary
✅A4The response quality is acceptable for the documented path
Pass rate: 4 / 4
85
Edge✅ Pass
Structure parsing for PDB/mmCIF using Bio.PDB parsers
This edge case stayed within the packaged analysis boundary and kept a reviewable task contract.
Basic 33/40|Specialized 52/60|Total 85/100
✅A1The biopython-structure output structure matches the documented deliverable
✅A2The instruction path remains actionable for the documented case
✅A3The output stays fully within the documented skill boundary
✅A4The response quality is acceptable for the documented path
Pass rate: 4 / 4
85
Variant B✅ Pass
Hierarchical traversal and selection of models, chains, residues, and atoms
This variant b case stayed within the packaged analysis boundary and kept a reviewable task contract.
Basic 32/40|Specialized 53/60|Total 85/100
✅A1The biopython-structure output structure matches the documented deliverable
✅A2The instruction path remains actionable for the documented case
✅A3The output stays fully within the documented skill boundary
✅A4The response quality is acceptable for the documented path
Pass rate: 4 / 4
85
Stress✅ Pass
End-to-end case for Structure parsing for PDB/mmCIF using Bio.PDB parsers
End-to-end case for Structure parsing for PDB/mmCIF using Bio.PDB... remained tied to the documented analysis contract even when the preserved evidence centered on instructions instead of a full rerun.
Basic 29/40|Specialized 56/60|Total 85/100
✅A1The biopython-structure output structure matches the documented deliverable
✅A2The instruction path remains actionable for the documented case
✅A3The output stays fully within the documented skill boundary
✅A4The response quality is acceptable for the documented path
Pass rate: 4 / 4
Medical Task Total86.6 / 100
Key Strengths
- Primary routing is Data Analysis with execution mode A
- Static quality score is 85/100 and dynamic average is 78.6/100
- Assertions and command execution outcomes are recorded per input for human review
- Execution verification summary: No script verification was applicable