Public record
Software health reportschema 0.11.0 · metrics 2.10.0 · 2026-07-15 12:10 UTC

haddocking / protein-quest

Python package to search/retrieve/filter proteins and protein structures

PythonApache-2.0★ 5 stars⑂ 0 forkssince Aug 2025View on GitHub ↗
KindLibraryhow this is determined

haddocking/protein-quest holds a health index of 81 out of 100, placing it in the Excellent band. It scores highest on Vitality (94/100) and lowest on Community & Adoption (45/100). It was last updated 1 day ago. A single contributor accounts for most of its recent work.

81
overall / 100
Excellent

Software health index

Metrics are grouped into weighted categories on one standardized 1–100 scale. Overall starts as their weighted mean, calibrated against the distribution of the public record so bands carry percentile meaning; when public evidence triggers the High-Risk Jurisdiction Policy, the rating is adjusted and receives an At Risk ceiling of 34.

81
Exceptional93-100The record's top tier (≈ top 5%); essentially all checked criteria met
Excellent80-92Strong across the board; minor gaps
Good65-79Healthy; gaps are limited and manageable
Moderate50-64Acceptable with notable gaps; review recommended
Weak35-49Material weaknesses across several areas
At Risk20-34Significant weaknesses; adoption warrants caution
Critical1-19Severe problems (abandoned, single-maintainer, no hygiene)
VitalityCommunity &AdoptionSustainability &GovernanceEngineeringQualitySecurityAI Readiness

Score profile

Each axis is a category. The shape matters more than the average — a healthy subject fills the whole shape, while a spike-and-crater profile means strength in one dimension is masking risk in another.

The weighted overall 69 is calibrated to 81 on the published index scale (record calibration 2026-08-02).

Ownership

HADDOCKOrganization
225 followers75 public repossince Oct 2013

This repository is backed by an organization — shared, accountable stewardship that can outlive any single maintainer.

Package ecosystems

RegistryPackageVersionDownloads / moVersionsLast publishTags
PyPIprotein_quest1.5.0-202 days agoalphafoldmmcifpdbproteinprotein-structureuniprot

Metrics by category

Vitality

Is the project alive — is code being written and are releases shipping?

94Exceptional · 21% of overall

Development activity

90Excellent
How it's scored
36/36Push recency — last push 1 days ago
25.6/36Commit cadence — 37/52 weeks with commits
18/18Commit volume — 677 commits in the last year
10/10OpenSSF Scorecard: Maintained — 30 commit(s) and 14 issue activity found in the last 90 days -- score normalized to 10
Inputs used
commits_last_year677
human_commit_share—
days_since_last_push1
active_weeks_last_year37

Release discipline

100Exceptional
How it's scored
27/27Ships releases — 20 releases published
36/36Release recency — latest release 2 days ago
27/27Release cadence — a release every ~27.1 days
0/10OpenSSF Scorecard: Signed-Releases — no data
Inputs used
releases_count20
latest_release_tagv1.5.0
releases_from_tagsno
days_since_latest_release2
mean_days_between_releases27.1
Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Signed-Releases. Remaining weights renormalized.

Community & Adoption

Does the project have users, downloads, attention, and a welcoming setup for contributors?

45Weak · 17% of overall

Popularity & adoption

10Critical
How it's scored
9.8/60Stars — 5 stars
0/25Forks — 0 forks
0/15Watchers — 1 watchers
Inputs used
forks0
stars5
watchers1
growth_stateunverified
growth_factor_pct100
growth_unverified_reasonno_history

Community health

85Excellent
How it's scored
22.5/22.5README
22.5/22.5License — recognized license (Apache-2.0)
18/18CONTRIBUTING guide
13.5/13.5Code of conduct
0/7.2Issue template
0/6.3PR template
Inputs used
has_readmeyes
has_licenseyes
readme_badges—
has_contributingyes
has_issue_templateno
has_code_of_conductyes
readme_badge_services—
has_pull_request_templateno

Sustainability & Governance

Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?

67Good · 23% of overall

Maintainer resilience (bus factor)

23At Risk
How it's scored
9/54Bus factor — 1 contributor(s) cover half of all commits
0.2/22.5Commit distribution — top contributor authored 99% of commits
4.1/13.5Contributor breadth — 3 contributors
10/10OpenSSF Scorecard: Contributors — project has 18 contributing companies or organizations
Inputs used
bus_factor1
contributors_sampled3
top_contributor_share0.993

Issue & PR responsiveness

72Good
How it's scored
34.1/42Issue resolution — 81% of issues closed
28.9/30PR acceptance — 78/81 decided PRs merged
0/13Newcomer PR acceptance — no first-time contributor's PR decided in 30d
0/15OpenSSF Scorecard: Code-Review — Found 0/3 approved changesets -- score normalized to 0
Inputs used
merged_prs78
open_issues9
closed_issues39
prs_merged_7d—
prs_decided_7d—
prs_merged_30d—
prs_decided_30d—
issue_closed_ratio0.812
closed_unmerged_prs3
first_time_authors_30d—
first_time_prs_merged_30d—
first_time_prs_decided_30d—
Excluded from scoring (no data or not applicable): Newcomer PR acceptance. Remaining weights renormalized.

Ownership & stewardship

90Excellent
How it's scored
30/30Ownership backing — organization-owned
0/20Verified domain — verified-domain status not read for this organization
16.9/25Owner reach — 225 followers of haddocking
25/25Track record — 75 public repos, account ~12 yr old
Inputs used
followers225
owner_typeOrganization
is_verified—
owner_loginhaddocking
public_repos75
account_age_days4,663
Excluded from scoring (no data or not applicable): Verified domain. Remaining weights renormalized.

Package maintenance

100Exceptional
How it's scored
25/25Published & resolvable — 1 package(s) on pypi
35/35Publish recency — latest publish 2 days ago
20/20Version history — 20 published versions
20/20Not deprecated — active, not deprecated or yanked
Inputs used
packagesprotein_quest
ecosystemspypi
any_deprecatedno
min_days_since_publish2

Engineering Quality

Are baseline engineering and documentation practices in place?

88Excellent · 19% of overall

Engineering practices

94Exceptional
How it's scored
24/24CI workflows — 4 workflow(s)
24/24Tests present
16/16Linter config
9.6/9.6Pre-commit hooks
0/6.4.editorconfig
20/20OpenSSF Scorecard: CI-Tests — 3 out of 3 merged PRs checked by a CI test -- score normalized to 10
Inputs used
has_ciyes
has_testsyes
has_editorconfigno
has_linter_configyes
has_precommit_configyes

Documentation

80Excellent
How it's scored
30/30README
25/25Documentation directory
15/15Documentation / homepage site — http://www.bonvinlab.org/protein-quest/
10/10Repository description
0/10Topics
0/10Wiki
Inputs used
topics—
has_wikino
homepagehttp://www.bonvinlab.org/protein-quest/
docs_sitehttp://www.bonvinlab.org/protein-quest/
has_readmeyes
has_docs_diryes
has_descriptionyes

Security

Are visible security and supply-chain practices strong, without unresolved high-risk jurisdiction exposure?

48Weak · 16% of overall

Security posture

48Weak
How it's scored
7.5/7.5Binary-Artifacts — no binaries found in the repo
2.2/7.5Branch-Protection — branch protection is not maximal on development and all release branches
2.5/2.5CI-Tests — 3 out of 3 merged PRs checked by a CI test -- score normalized to 10
0/2.5CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected
0/7.5Code-Review — Found 0/3 approved changesets -- score normalized to 0
2.5/2.5Contributors — project has 18 contributing companies or organizations
10/10Dangerous-Workflow — no dangerous workflow patterns detected
0/7.5Dependency-Update-Tool — no update tool detected
0/5Fuzzing — project is not fuzzed
2.5/2.5License — license file detected
7.5/7.5Maintained — 30 commit(s) and 14 issue activity found in the last 90 days -- score normalized to 10
5/5Packaging — packaging workflow detected
0/5Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
0/5SAST — SAST tool is not run on all commits -- score normalized to 0
0/5Security-Policy — security policy file not detected
0/7.5Signed-Releases — no data
0/7.5Token-Permissions — detected GitHub workflow tokens with excessive permissions
7.5/7.5Vulnerabilities — 0 existing vulnerabilities detected
Inputs used
sourceopenssf_scorecard
checks_evaluated17
scorecard_versionv5.5.0
checks_inconclusive1
scorecard_aggregate4.8
Excluded from scoring (no data or not applicable): Signed-Releases. Remaining weights renormalized.

AI Readiness

How well is the repo equipped to be developed and maintained with AI coding agents? Carries a deliberately small weight (4%): agent tooling is a real maintenance signal, but a repository with none can still reach 100/100.

54Moderate · 4% of overall

Agent context & guidance

1Critical
How it's scored
0/45Agent instructions — no CLAUDE.md / AGENTS.md / editor rules
0/15Machine-readable docs (llms.txt)
0/40Legible commit history — no data
Inputs used
has_llms_txtno
llms_txt_url—
legible_history_share—
agent_instruction_files—
agent_instruction_max_bytes—
Excluded from scoring (no data or not applicable): Legible commit history. Remaining weights renormalized.

Verify loop (build / test / typecheck)

66Good
How it's scored
0/18One-command bootstrap
22/22Automated tests
11/11Lint / format config
11/11Static type checking — src/protein_quest/py.typed
10/10Reproducible environment — lockfile
0/10Demonstrated agent practice — no data
0/8Automated maintenance — no data
0/10OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
Inputs used
has_nixno
has_testsyes
lockfilesuv.lock
has_dockerfileno
typed_languageno
bootstrap_files—
has_devcontainerno
has_linter_configyes
typecheck_configssrc/protein_quest/py.typed
agent_commit_share—
toolchain_manifests—
dependency_bot_commit_share—
Excluded from scoring (no data or not applicable): Demonstrated agent practice, Automated maintenance. Remaining weights renormalized.

Code legibility for models

82Excellent
How it's scored
27/45Type-checkable code — Python with type-check config (src/protein_quest/py.typed)
55/55Manageable file sizes — 0/93 source files over 60KB
Inputs used
primary_languagePython
largest_source_bytes38,744
source_files_sampled93
oversized_source_files0

Machine-readable interfaces

100Exceptional
How it's scored
0/40API schema (OpenAPI/GraphQL/proto) — not applicable to this kind of software
20/20MCP server
40/40Runnable examples — notebooks
Inputs used
example_dirsnotebooks
has_mcp_signalyes
api_schema_files—
interfaces_expected_of—
Excluded from scoring (no data or not applicable): API schema (OpenAPI/GraphQL/proto). Remaining weights renormalized.

Key facts

5GitHub stars
3contributors
677commits, last 12 months
1days since last push
20releases
1bus factor
9open issues
PyPIpackage ecosystems

More detail

OpenSSF Scorecard 4.8 / 10
4.8aggregate

Independent, tool-agnostic security assessment from the open-source OpenSSF Scorecard. Each check rewards a security practice, not a specific vendor's tool. Checks Scorecard could not determine are marked n/a and excluded from the security score (never counted as zero).Scorecard v5.5.0 · 2026-07-15 12:10 UTC

10Binary-Artifactsno binaries found in the repo
3Branch-Protectionbranch protection is not maximal on development and all release branches
10CI-Tests3 out of 3 merged PRs checked by a CI test -- score normalized to 10
0CII-Best-Practicesno effort to earn an OpenSSF best practices badge detected
0Code-ReviewFound 0/3 approved changesets -- score normalized to 0
10Contributorsproject has 18 contributing companies or organizations
10Dangerous-Workflowno dangerous workflow patterns detected
0Dependency-Update-Toolno update tool detected
0Fuzzingproject is not fuzzed
10Licenselicense file detected
10Maintained30 commit(s) and 14 issue activity found in the last 90 days -- score normalized to 10
10Packagingpackaging workflow detected
0Pinned-Dependenciesdependency not pinned by hash detected -- score normalized to 0
0SASTSAST tool is not run on all commits -- score normalized to 0
0Security-Policysecurity policy file not detected
n/aSigned-Releasesno releases found
0Token-Permissionsdetected GitHub workflow tokens with excessive permissions
10Vulnerabilities0 existing vulnerabilities detected
Direct dependencies 18
RegistryPackageVersion constraintManifest
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All dependencies 195

Full resolved dependency set from the GitHub dependency graph: 18 direct and 177 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.

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Raw JSON report machine-readable

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Scores are signals, not warranties. They reflect publicly visible practices on GitHub — not a code audit, and not a security guarantee.

Missing data is excluded and weights renormalized, never scored as zero. Methodology is versioned and open: metrics v2.10.0, schema v0.11.0 — full methodology · metrics wiki.

How one result sits in the wider record: aggregate statistics — PyPI.