Public record
Software health reportschema 0.34.0 · metrics 2.10.0 · 2026-09-13 11:05 UTC

Acellera / moleculekit

MoleculeKit: Your favorite molecule manipulation kit

PythonCustom license★ 243 stars⑂ 35 forkssince Mar 2019View on GitHub ↗
KindWeb interfacehow this is determined
#molecule#machine-learning#proteins#drug-discovery#molecular-modeling#molecular-simulation

Acellera/moleculekit holds a health index of 84 out of 100, placing it in the Excellent band. It scores highest on Vitality (91/100) and lowest on Community & Adoption (54/100). It was last updated 2 days ago. A single contributor accounts for most of its recent work.

84
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.

84
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 71 is calibrated to 84 on the published index scale (record calibration 2026-08-02).

Ownership

AcelleraOrganization
68 followers39 public repossince Jun 2014

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

Package ecosystems

RegistryPackageVersionDownloads / moVersionsLast publish
PyPImoleculekit1.17.68,8492482 days ago
PyPImolkitten0.0.71011504 days ago

Metrics by category

Vitality

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

91Excellent · 21% of overall

Development activity

86Excellent
How it's scored
36/36Push recency — last push 2 days ago
22.2/36Commit cadence — 32/52 weeks with commits
18/18Commit volume — 319 commits in the last year
10/10OpenSSF Scorecard: Maintained — 30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10
Inputs used
commits_last_year319
human_commit_share0.96
days_since_last_push2
active_weeks_last_year32

Release discipline

98Exceptional
How it's scored
27/27Ships releases — 33 releases published
36/36Release recency — latest release 2 days ago
27/27Release cadence — a release every ~12.3 days
8/10OpenSSF Scorecard: Signed-Releases — 5 out of the last 5 releases have a total of 5 signed artifacts.
Inputs used
releases_count33
latest_release_tagv1.17.6
releases_from_tagsno
days_since_latest_release2
mean_days_between_releases12.3

Community & Adoption

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

54Moderate · 17% of overall

Popularity & adoption

56Moderate
How it's scored
38.7/60Stars — 243 stars
12.8/25Forks — 35 forks
5/15Watchers — 9 watchers
Inputs used
forks35
stars243
watchers9
growth_stateunverified
growth_factor_pct100
growth_unverified_reasonno_history

Community health

44Weak
How it's scored
22.5/22.5README
16.9/22.5License — license file present, not a recognized license
0/18CONTRIBUTING guide
0/13.5Code of conduct
0/7.2Issue template
0/6.3PR template
Inputs used
has_readmeyes
has_licenseyes
readme_badges0
has_contributingno
has_issue_templateno
has_code_of_conductno
readme_badge_services—
has_pull_request_templateno

Ecosystem adoption (downloads)

66Good
How it's scored
52.6/80Monthly downloads — 8,859 downloads/month across pypi
0/20Registry dependents — not reported by this ecosystem
Inputs used
packagesmoleculekit, molkitten
dependents—
ecosystemspypi
total_downloads—
monthly_downloads8,859
unverified_packages_excluded—
Excluded from scoring (no data or not applicable): Registry dependents. Remaining weights renormalized.

Sustainability & Governance

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

63Moderate · 23% of overall

Maintainer resilience (bus factor)

28At Risk
How it's scored
9/54Bus factor — 1 contributor(s) cover half of all commits
0.4/22.5Commit distribution — top contributor authored 98% of commits
12.2/13.5Contributor breadth — 9 contributors
6/10OpenSSF Scorecard: Contributors — project has 2 contributing companies or organizations -- score normalized to 6
Inputs used
bus_factor1
contributors_sampled9
top_contributor_share0.981

Issue & PR responsiveness

72Good
How it's scored
39.1/42Issue resolution — 93% of issues closed
23.7/30PR acceptance — 41/52 decided PRs merged
0/13Newcomer PR acceptance — no first-time contributor's PR decided in 30d
0/15OpenSSF Scorecard: Code-Review — Found 0/29 approved changesets -- score normalized to 0
Inputs used
merged_prs41
open_issues7
closed_issues96
prs_merged_7d0
prs_decided_7d0
prs_merged_30d0
prs_decided_30d0
issue_closed_ratio0.932
closed_unmerged_prs11
first_time_authors_30d0
first_time_prs_merged_30d0
first_time_prs_decided_30d0
Excluded from scoring (no data or not applicable): Newcomer PR acceptance. Remaining weights renormalized.

Ownership & stewardship

67Good
How it's scored
30/30Ownership backing — organization-owned
0/20Verified domain
13.2/25Owner reach — 68 followers of Acellera
23.7/25Track record — 39 public repos, account ~12 yr old
Inputs used
followers68
owner_typeOrganization
is_verifiedno
owner_loginAcellera
public_repos39
account_age_days4,485

Package maintenance

100Exceptional
How it's scored
25/25Published & resolvable — 2 package(s) on pypi
35/35Publish recency — latest publish 2 days ago
20/20Version history — 248 published versions
20/20Not deprecated — active, not deprecated or yanked
Inputs used
packagesmoleculekit, molkitten
ecosystemspypi
any_deprecatedno
min_days_since_publish2

Engineering Quality

Are baseline engineering and documentation practices in place?

75Good · 19% of overall

Engineering practices

68Good
How it's scored
24/24CI workflows — 6 workflow(s)
24/24Tests present
0/16Linter config
0/9.6Pre-commit hooks
0/6.4.editorconfig
20/20OpenSSF Scorecard: CI-Tests — 1 out of 1 merged PRs checked by a CI test -- score normalized to 10
Inputs used
has_ciyes
has_testsyes
has_editorconfigno
has_linter_configno
has_precommit_configno

Documentation

85Excellent
How it's scored
30/30README
25/25Documentation directory
0/15Documentation / homepage site
10/10Repository description
10/10Topics — 6 topics
10/10Wiki
Inputs used
topicsmolecule, machine-learning, proteins, drug-discovery, molecular-modeling, molecular-simulation
has_wikiyes
homepage—
docs_site—
has_readmeyes
has_docs_diryes
has_descriptionyes

Security

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

69Good · 16% of overall

Security posture

61Moderate
How it's scored
7.5/7.5Binary-Artifacts — no binaries found in the repo
0/7.5Branch-Protection — no data
2.5/2.5CI-Tests — 1 out of 1 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 0/29 approved changesets -- score normalized to 0
1.5/2.5Contributors — project has 2 contributing companies or organizations -- score normalized to 6
10/10Dangerous-Workflow — no dangerous workflow patterns detected
7.5/7.5Dependency-Update-Tool — update tool detected
0/5Fuzzing — project is not fuzzed
2.2/2.5License — license file detected
7.5/7.5Maintained — 30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10
0/5Packaging — no data
0/5Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
5/5SAST — SAST tool is run on all commits
0/5Security-Policy — security policy file not detected
6/7.5Signed-Releases — 5 out of the last 5 releases have a total of 5 signed artifacts.
0/7.5Token-Permissions — detected GitHub workflow tokens with excessive permissions
6.8/7.5Vulnerabilities — 1 existing vulnerabilities detected
Inputs used
sourceopenssf_scorecard
checks_evaluated16
scorecard_versionv5.5.0
checks_inconclusive2
scorecard_aggregate6.1
Excluded from scoring (no data or not applicable): Branch-Protection, Packaging. Remaining weights renormalized.

Dependency advisories

100Exceptional
How it's scored
35/35Direct dependencies free of known advisories — no direct dependency carries a known advisory
25/25Indirect dependencies free of known advisories — no indirect dependency carries a known advisory
0/40No advisories left outstanding — no advisory carries a publication date
Inputs used
sourceosv
advisories0
affected_packages0
assessed_packages28
unassessed_packages0
affected_by_severitynone
direct_affected_packages0
Excluded from scoring (no data or not applicable): No advisories left outstanding. Remaining weights renormalized. Matched the pypi:moleculekit@1.17.6 runtime dependency closure — what installing the published package pulls in — 28 packages. Reachability is not analyzed.

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.

74Good · 4% of overall

Agent context & guidance

61Moderate
How it's scored
45/45Agent instructions — AGENTS.md
15/15Machine-readable docs (llms.txt) — llms.txt present
0.6/40Legible commit history — 1 of 96 human commits state their intent (structured subject or explanatory body)
Inputs used
has_llms_txtyes
llms_txt_url—
legible_history_share0.01
agent_instruction_filesAGENTS.md
agent_instruction_max_bytes9,201

Verify loop (build / test / typecheck)

73Good
How it's scored
18/18One-command bootstrap — Makefile, doc/Makefile
22/22Automated tests
0/11Lint / format config
11/11Static type checking — viewer-frontend/tsconfig.json
10/10Reproducible environment — Dockerfile, lockfile
4/10Demonstrated agent practice — 2 of the last 100 commits agent-authored or agent-credited
8/8Automated maintenance — 4 of the last 100 commits are automated dependency updates
0/10OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
Inputs used
has_nixno
has_testsyes
lockfilespackage-lock.json
has_dockerfileyes
typed_languageno
bootstrap_filesMakefile, doc/Makefile
has_devcontainerno
has_linter_configno
typecheck_configsviewer-frontend/tsconfig.json
agent_commit_share0.02
toolchain_manifests—
dependency_bot_commit_share0.04

Code legibility for models

78Good
How it's scored
27/45Type-checkable code — Python with type-check config (viewer-frontend/tsconfig.json)
51/55Manageable file sizes — 16/221 source files over 60KB
Inputs used
primary_languagePython
largest_source_bytes2,745,702
source_files_sampled221
oversized_source_files16

Machine-readable interfaces

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

Key facts

243GitHub stars
9contributors
319commits, last 12 months
2days since last push
33releases
1bus factor
7open issues
npm, PyPIpackage ecosystems

Data collection warnings

  • Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token

More detail

Star and fork history 0 ★ / 35 ⇿
0Stars
35Forks
25Releases

When each star and fork was added, collected from GitHub and bucketed by day. Cumulative growth sits directly above the daily additions it is made of, so the two read against each other: steady organic accretion looks nothing like an abrupt, short-lived burst. Where that difference is measurable, it is reported as growth authenticity.

01325383422019-052022-122026-07
Major 0Minor 1Patch 24

Each point covers 7 days.

OpenSSF Scorecard 6.1 / 10
6.1aggregate

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 · 2026-09-13 11:05 UTC

10Binary-Artifactsno binaries found in the repo
n/aBranch-Protectioninternal error: error during branchesHandler.setup: internal error: some github tokens can't read classic branch protection rules: https://github.com/ossf/scorecard-action/blob/main/docs/authentication/fine-grained-auth-token.md
10CI-Tests1 out of 1 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 0/29 approved changesets -- score normalized to 0
6Contributorsproject has 2 contributing companies or organizations -- score normalized to 6
10Dangerous-Workflowno dangerous workflow patterns detected
10Dependency-Update-Toolupdate tool detected
0Fuzzingproject is not fuzzed
9Licenselicense file detected
10Maintained30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10
n/aPackagingpackaging workflow not detected
0Pinned-Dependenciesdependency not pinned by hash detected -- score normalized to 0
10SASTSAST tool is run on all commits
0Security-Policysecurity policy file not detected
8Signed-Releases5 out of the last 5 releases have a total of 5 signed artifacts.
0Token-Permissionsdetected GitHub workflow tokens with excessive permissions
9Vulnerabilities1 existing vulnerabilities detected
Direct dependencies 15
RegistryPackageVersion constraintManifest
PyPInumpy>=1.23.5pyproject.toml
PyPIpandas>=1.1.2pyproject.toml
PyPInetworkx—pyproject.toml
PyPItqdm—pyproject.toml
PyPImsgpack—pyproject.toml
PyPIrequests—pyproject.toml
PyPImatplotlib—pyproject.toml
PyPIrdkit>=2020.09.5pyproject.toml
PyPImdtraj—pyproject.toml
PyPIacellera-propka—pyproject.toml
PyPIacellera-pdb2pqr>=3.7.1.post2pyproject.toml
PyPIbiopython—pyproject.toml
npmmolstar^5.7.0viewer-frontend/package.json
npmreact^19.2.4viewer-frontend/package.json
npmreact-dom^19.2.4viewer-frontend/package.json
All dependencies 312

Full resolved dependency set from the GitHub dependency graph: 8 direct and 304 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.

RegistryPackageVersionRelation
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npmreact-dom19.2.6direct
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PyPInetworkx—direct
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PyPIpandas—direct
PyPIrdkit—direct
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npmmicromark-factory-whitespace2.0.1indirect
npmmicromark-util-character2.1.1indirect
npmmicromark-util-chunked2.0.1indirect
npmmicromark-util-classify-character2.0.1indirect
npmmicromark-util-combine-extensions2.0.1indirect
npmmicromark-util-decode-numeric-character-reference2.0.2indirect
npmmicromark-util-decode-string2.0.1indirect
npmmicromark-util-encode2.0.1indirect
npmmicromark-util-html-tag-name2.0.1indirect
npmmicromark-util-normalize-identifier2.0.1indirect
npmmicromark-util-resolve-all2.0.1indirect
npmmicromark-util-sanitize-uri2.0.1indirect
npmmicromark-util-subtokenize2.1.0indirect
npmmicromark-util-symbol2.0.1indirect
npmmicromark-util-types2.0.2indirect
npmmime-db1.54.0indirect
npmmime-types3.0.2indirect
npmmoment2.30.1indirect
npmms2.0.0indirect
npmms2.1.3indirect
npmmutative1.3.0indirect
npmnanoid3.3.17indirect
npmnegotiator0.6.4indirect
npmnegotiator1.0.0indirect
npmobject-assign4.1.1indirect
npmobject-inspect1.13.4indirect
npmon-finished2.4.1indirect
npmon-headers1.1.0indirect
npmonce1.4.0indirect
npmpackage-name-regex2.0.6indirect
npmparse-entities4.0.2indirect
npmparseurl1.3.3indirect
npmpath-to-regexp8.4.2indirect
npmpicocolors1.1.1indirect
npmpicomatch4.0.4indirect
npmpostcss8.5.26indirect
npmproperty-information7.1.0indirect
npmproxy-addr2.0.7indirect
npmqs6.16.0indirect
npmrange-parser1.2.1indirect
npmraw-body3.0.2indirect
npmreact-markdown10.1.0indirect
npmremark-gfm4.0.1indirect
npmremark-parse11.0.0indirect
npmremark-rehype11.1.2indirect
npmremark-stringify11.0.0indirect
npmrolldown1.0.3indirect
npmrollup4.60.4indirect
npmrollup-plugin-license3.7.1indirect
npmrouter2.2.0indirect
npmrxjs7.8.2indirect
npmsafe-buffer5.2.1indirect
npmsafer-buffer2.1.2indirect
npmscheduler0.27.0indirect
npmsend1.2.1indirect
npmserve-static2.2.1indirect
npmsetprototypeof1.2.0indirect
npmside-channel1.1.1indirect
npmside-channel-list1.0.1indirect
npmside-channel-map1.0.1indirect
npmside-channel-weakmap1.0.2indirect
npmsource-map-js1.2.1indirect
npmspace-separated-tokens2.0.2indirect
npmspdx-compare1.0.0indirect
npmspdx-exceptions2.5.0indirect
npmspdx-expression-parse3.0.1indirect
npmspdx-expression-validate2.0.0indirect
npmspdx-license-ids3.0.23indirect
npmspdx-ranges2.1.1indirect
npmspdx-satisfies5.0.1indirect
npmstatuses2.0.2indirect
npmstringify-entities4.0.4indirect
npmstyle-to-js1.1.21indirect
npmstyle-to-object1.0.14indirect
npmswagger-ui-dist5.32.6indirect
npmtinyglobby0.2.17indirect
npmtoidentifier1.0.1indirect
npmtrim-lines3.0.1indirect
npmtrough2.2.0indirect
npmtslib2.8.1indirect
npmtype-is2.1.0indirect
npmtypescript5.9.3indirect
npmundici-types6.21.0indirect
npmundici-types7.16.0indirect
npmunified11.0.5indirect
npmunist-util-is6.0.1indirect
npmunist-util-position5.0.0indirect
npmunist-util-stringify-position4.0.0indirect
npmunist-util-visit5.1.0indirect
npmunist-util-visit-parents6.0.2indirect
npmunpipe1.0.0indirect
npmvary1.1.2indirect
npmvfile6.0.3indirect
npmvfile-message4.0.3indirect
npmvite8.0.16indirect
npmwrappy1.0.2indirect
npmzwitch2.0.4indirect
PyPIcython—indirect
PyPIipython—indirect
PyPInvidia-cuda-cupti-cu12—indirect
PyPInvidia-cuda-nvcc-cu12—indirect
PyPInvidia-cuda-nvrtc-cu12—indirect
PyPInvidia-cuda-runtime-cu12—indirect
PyPInvidia-nvjitlink-cu12—indirect
PyPIopenmm—indirect
PyPIpytest—indirect
PyPIscipy—indirect
PyPIsetuptools-scm—indirect
Dependency advisories 0

Installing pypi:moleculekit@1.17.6 pulls in 28 packages, direct and transitive: 0 carry known advisories, of which 0 are direct dependencies.

No known advisories affect the assessed dependencies.

An advisory means the version recorded in the dependency graph falls inside an advisory’s affected range. Reachability is not analysed, and the graph includes development and test pins — a finding may concern tooling rather than shipped software.

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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 v0.34.0 — full methodology · metrics wiki.

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