t-0hmura / pdb2reaction
End-to-end Reaction-Path Modeling from PDB Structures Using Machine-Learning Interatomic Potentials
t-0hmura/pdb2reaction holds a health index of 65 out of 100, placing it in the Good band. It scores highest on Vitality (91/100) and lowest on Security (31/100). It was last updated 3 days ago. A single contributor accounts for most of its recent work.
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.
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 60 is calibrated to 65 on the published index scale (record calibration 2026-08-02).
Ownership
This repository is owned by a personal account. A single-owner project carries more continuity risk than an organization-backed one.
Package ecosystems
| Registry | Package | Version | Downloads / mo | Versions | Last publish | Tags |
|---|---|---|---|---|---|---|
| PyPI | pdb2reaction | 0.4.13 | 378 | 25 | 3 days ago | computational-chemistryenzymereaction-mechanismtransition-statepdbmachine-learning-potentialmlip |
Metrics by category
Vitality
Is the project alive — is code being written and are releases shipping?
Development activity
How it's scored
| 36/36 | Push recency — last push 3 days ago |
| 27.7/36 | Commit cadence — 40/52 weeks with commits |
| 18/18 | Commit volume — 1,750 commits in the last year |
| 10/10 | OpenSSF Scorecard: Maintained — 30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10 |
Inputs used
| commits_last_year | 1,750 |
| human_commit_share | 1 |
| days_since_last_push | 3 |
| active_weeks_last_year | 40 |
Release discipline
How it's scored
| 27/27 | Ships releases — 24 releases published |
| 36/36 | Release recency — latest release 3 days ago |
| 27/27 | Release cadence — a release every ~7.1 days |
| 0/10 | OpenSSF Scorecard: Signed-Releases — Project has not signed or included provenance with any releases. |
Inputs used
| releases_count | 24 |
| latest_release_tag | v0.4.13 |
| releases_from_tags | no |
| days_since_latest_release | 3 |
| mean_days_between_releases | 7.1 |
Community & Adoption
Does the project have users, downloads, attention, and a welcoming setup for contributors?
Popularity & adoption
How it's scored
| 22.7/60 | Stars — 26 stars |
| 2.5/25 | Forks — 3 forks |
| 0/15 | Watchers — 1 watchers |
Inputs used
| forks | 3 |
| stars | 26 |
| watchers | 1 |
| growth_state | unverified |
| growth_factor_pct | 100 |
| growth_unverified_reason | no_history |
Community health
How it's scored
| 22.5/22.5 | README |
| 22.5/22.5 | License — recognized license (GPL-3.0) |
| 18/18 | CONTRIBUTING guide |
| 0/13.5 | Code of conduct |
| 0/7.2 | Issue template |
| 0/6.3 | PR template |
Inputs used
| has_readme | yes |
| has_license | yes |
| readme_badges | 1 |
| has_contributing | yes |
| has_issue_template | no |
| has_code_of_conduct | no |
| readme_badge_services | shields.io |
| has_pull_request_template | no |
How it's scored
| 34.4/80 | Monthly downloads — 378 downloads/month across pypi |
| 0/20 | Registry dependents — not reported by this ecosystem |
Inputs used
| packages | pdb2reaction |
| dependents | — |
| ecosystems | pypi |
| total_downloads | — |
| monthly_downloads | 378 |
| unverified_packages_excluded | — |
Sustainability & Governance
Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?
Maintainer resilience (bus factor)
How it's scored
| 9/54 | Bus factor — 1 contributor(s) cover half of all commits |
| 0/22.5 | Commit distribution — top contributor authored 100% of commits |
| 1.4/13.5 | Contributor breadth — 1 contributors |
| 3/10 | OpenSSF Scorecard: Contributors — project has 1 contributing companies or organizations -- score normalized to 3 |
Inputs used
| bus_factor | 1 |
| contributors_sampled | 1 |
| top_contributor_share | 1 |
Issue & PR responsiveness
How it's scored
| 42/42 | Issue resolution — 100% of issues closed |
| 28.8/30 | PR acceptance — 282/294 decided PRs merged |
| 0/13 | Newcomer PR acceptance — no first-time contributor's PR decided in 30d |
| 0/15 | OpenSSF Scorecard: Code-Review — Found 0/30 approved changesets -- score normalized to 0 |
Inputs used
| merged_prs | 282 |
| open_issues | 0 |
| closed_issues | 2 |
| prs_merged_7d | 0 |
| prs_decided_7d | 0 |
| prs_merged_30d | 0 |
| prs_decided_30d | 0 |
| issue_closed_ratio | 1 |
| closed_unmerged_prs | 12 |
| first_time_authors_30d | 0 |
| first_time_prs_merged_30d | 0 |
| first_time_prs_decided_30d | 0 |
Ownership & stewardship
How it's scored
| 10/30 | Ownership backing — personal (user) account |
| 0/20 | Verified domain — not applicable to user accounts |
| 8.7/25 | Owner reach — 15 followers of t-0hmura |
| 16.7/25 | Track record — 12 public repos, account ~4 yr old |
Inputs used
| followers | 15 |
| owner_type | User |
| is_verified | — |
| owner_login | t-0hmura |
| public_repos | 12 |
| account_age_days | 1,569 |
Package maintenance
How it's scored
| 25/25 | Published & resolvable — 1 package(s) on pypi |
| 35/35 | Publish recency — latest publish 3 days ago |
| 20/20 | Version history — 25 published versions |
| 20/20 | Not deprecated — active, not deprecated or yanked |
Inputs used
| packages | pdb2reaction |
| ecosystems | pypi |
| any_deprecated | no |
| min_days_since_publish | 3 |
Engineering Quality
Are baseline engineering and documentation practices in place?
Engineering practices
How it's scored
| 24/24 | CI workflows — 5 workflow(s) |
| 24/24 | Tests present |
| 0/16 | Linter config |
| 0/9.6 | Pre-commit hooks |
| 0/6.4 | .editorconfig |
| 0/20 | OpenSSF Scorecard: CI-Tests — no data |
Inputs used
| has_ci | yes |
| has_tests | yes |
| has_editorconfig | no |
| has_linter_config | no |
| has_precommit_config | no |
Documentation
How it's scored
| 30/30 | README |
| 25/25 | Documentation directory |
| 15/15 | Documentation / homepage site — https://t-0hmura.github.io/pdb2reaction/ |
| 10/10 | Repository description |
| 10/10 | Topics — 7 topics |
| 0/10 | Wiki |
Inputs used
| topics | computational-chemistry, enzyme, mlip, pdb, reaction-mechanism, transition-states, machine-learning-interatomic-potential |
| has_wiki | no |
| homepage | https://t-0hmura.github.io/pdb2reaction/ |
| docs_site | https://t-0hmura.github.io/pdb2reaction/ |
| has_readme | yes |
| has_docs_dir | yes |
| has_description | yes |
Security
Are visible security and supply-chain practices strong, without unresolved high-risk jurisdiction exposure?
Security posture
How it's scored
| 7.5/7.5 | Binary-Artifacts — no binaries found in the repo |
| 0/7.5 | Branch-Protection — branch protection not enabled on development/release branches |
| 0/2.5 | CI-Tests — no data |
| 0/2.5 | CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected |
| 0/7.5 | Code-Review — Found 0/30 approved changesets -- score normalized to 0 |
| 0.8/2.5 | Contributors — project has 1 contributing companies or organizations -- score normalized to 3 |
| 0/10 | Dangerous-Workflow — dangerous workflow patterns detected |
| 0/7.5 | Dependency-Update-Tool — no update tool detected |
| 0/5 | Fuzzing — project is not fuzzed |
| 2.5/2.5 | License — license file detected |
| 7.5/7.5 | Maintained — 30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10 |
| 5/5 | Packaging — packaging workflow detected |
| 0.5/5 | Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 1 |
| 0/5 | SAST — no SAST tool detected |
| 0/5 | Security-Policy — security policy file not detected |
| 0/7.5 | Signed-Releases — Project has not signed or included provenance with any releases. |
| 0/7.5 | Token-Permissions — detected GitHub workflow tokens with excessive permissions |
| 7.5/7.5 | Vulnerabilities — 0 existing vulnerabilities detected |
Inputs used
| source | openssf_scorecard |
| checks_evaluated | 17 |
| scorecard_version | v5.5.0 |
| checks_inconclusive | 1 |
| scorecard_aggregate | 3 |
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.
Agent context & guidance
How it's scored
| 0/45 | Agent instructions — no CLAUDE.md / AGENTS.md / editor rules |
| 0/15 | Machine-readable docs (llms.txt) |
| 2.1/40 | Legible commit history — 4 of 100 human commits state their intent (structured subject or explanatory body) |
Inputs used
| has_llms_txt | no |
| llms_txt_url | — |
| legible_history_share | 0.04 |
| agent_instruction_files | — |
| agent_instruction_max_bytes | — |
Verify loop (build / test / typecheck)
How it's scored
| 18/18 | One-command bootstrap — docs/Makefile |
| 22/22 | Automated tests |
| 0/11 | Lint / format config |
| 11/11 | Static type checking — pdb2reaction/py.typed |
| 0/10 | Reproducible environment |
| 8/10 | Demonstrated agent practice — 4 of the last 100 commits agent-authored or agent-credited |
| 0/8 | Automated maintenance — no automated dependency updates observed |
| 1/10 | OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 1 |
Inputs used
| has_nix | no |
| has_tests | yes |
| lockfiles | — |
| has_dockerfile | no |
| typed_language | no |
| bootstrap_files | docs/Makefile |
| has_devcontainer | no |
| has_linter_config | no |
| typecheck_configs | pdb2reaction/py.typed |
| agent_commit_share | 0.04 |
| toolchain_manifests | — |
| dependency_bot_commit_share | 0 |
How it's scored
| 27/45 | Type-checkable code — Python with type-check config (pdb2reaction/py.typed) |
| 52.4/55 | Manageable file sizes — 14/301 source files over 60KB |
Inputs used
| primary_language | Python |
| largest_source_bytes | 450,244 |
| source_files_sampled | 301 |
| oversized_source_files | 14 |
Machine-readable interfaces
How it's scored
| 0/40 | API schema (OpenAPI/GraphQL/proto) — not applicable to this kind of software |
| 20/20 | MCP server |
| 40/40 | Runnable examples — examples, notebooks |
Inputs used
| example_dirs | examples, notebooks |
| has_mcp_signal | yes |
| api_schema_files | — |
| interfaces_expected_of | — |
Key facts
Data collection warnings
- Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token
- GitHub dependency-graph SBOM unavailable (404); the dependency graph may be disabled for this repository
More detail
Star and fork history 0 ★ / 3 ⇿
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.
OpenSSF Scorecard 3.0 / 10
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).
| 10 | Binary-Artifacts | no binaries found in the repo |
| 0 | Branch-Protection | branch protection not enabled on development/release branches |
| n/a | CI-Tests | no pull request found |
| 0 | CII-Best-Practices | no effort to earn an OpenSSF best practices badge detected |
| 0 | Code-Review | Found 0/30 approved changesets -- score normalized to 0 |
| 3 | Contributors | project has 1 contributing companies or organizations -- score normalized to 3 |
| 0 | Dangerous-Workflow | dangerous workflow patterns detected |
| 0 | Dependency-Update-Tool | no update tool detected |
| 0 | Fuzzing | project is not fuzzed |
| 10 | License | license file detected |
| 10 | Maintained | 30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10 |
| 10 | Packaging | packaging workflow detected |
| 1 | Pinned-Dependencies | dependency not pinned by hash detected -- score normalized to 1 |
| 0 | SAST | no SAST tool detected |
| 0 | Security-Policy | security policy file not detected |
| 0 | Signed-Releases | Project has not signed or included provenance with any releases. |
| 0 | Token-Permissions | detected GitHub workflow tokens with excessive permissions |
| 10 | Vulnerabilities | 0 existing vulnerabilities detected |
Direct dependencies 24
| Registry | Package | Version constraint | Manifest |
|---|---|---|---|
| PyPI | fairchem-core | — | pyproject.toml |
| PyPI | pydmf | >=1.2 | pyproject.toml |
| PyPI | torch | ~=2.8.0 | pyproject.toml |
| PyPI | numpy | >=2.0,<2.5 | pyproject.toml |
| PyPI | biopython | — | pyproject.toml |
| PyPI | ase | >=3.26.0 | pyproject.toml |
| PyPI | pyyaml | — | pyproject.toml |
| PyPI | click | — | pyproject.toml |
| PyPI | plotly | >=6.1.1 | pyproject.toml |
| PyPI | kaleido | — | pyproject.toml |
| PyPI | autograd | — | pyproject.toml |
| PyPI | dask | — | pyproject.toml |
| PyPI | distributed | — | pyproject.toml |
| PyPI | h5py | — | pyproject.toml |
| PyPI | jinja2 | — | pyproject.toml |
| PyPI | natsort | — | pyproject.toml |
| PyPI | psutil | — | pyproject.toml |
| PyPI | pyparsing | — | pyproject.toml |
| PyPI | rmsd | — | pyproject.toml |
| PyPI | scipy | — | pyproject.toml |
| PyPI | sympy | — | pyproject.toml |
| PyPI | scikit-learn | — | pyproject.toml |
| PyPI | pandas | — | pyproject.toml |
| PyPI | pymsym | >=0.3.5,<0.4 | pyproject.toml |
All dependencies not collected
The resolved dependency set could not be collected for this report: GitHub dependency-graph SBOM unavailable (404); the dependency graph may be disabled for this repository
Raw JSON report machine-readable
Feedback
Spotted something off in this report, or have thoughts to share? Wrong measurements, missed tooling, ideas, questions — anything is welcome. Every message is read and gets a response.
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.