daimon

Personal Claude Code skill and prompt library for computational chemistry research.

Setup

bash setup.sh

Symlinks all skills into ~/.claude/skills/ and checks required plugins.

Structure

daimon/
├── brainstorm/skills/     # idea generation, hypothesis, planning
├── coding/skills/         # code generation and debugging
├── computation/skills/    # HPC, job submission, data processing
├── git/skills/            # git workflow automation
├── integrations/          # external tools (NotebookLM, etc.)
├── literature/
│   ├── skills/
│   │   ├── lit-search/    # multi-DB paper discovery + citation chase
│   │   ├── lit-bib/       # BibTeX generation + Zotero sync
│   │   ├── lit-watch/     # weekly new-paper monitor → vault digest
│   │   ├── lit-review/    # full pipeline: search → PRISMA → NLM → report
│   │   ├── lit-vault/     # papers.json → per-paper vault notes (20-Sources/papers/)
│   │   └── lit-annotate/  # fill Key points skeleton in vault notes after reading
│   ├── scripts/
│   │   └── papers_io.py   # shared papers.json read/write/merge
│   └── schemas/
│       └── papers.schema.json
├── theory/skills/         # theoretical chemistry, equations
├── vault/skills/          # Obsidian vault management and knowledge workflows
│   ├── galaxy/            # Draft 30-Galaxy/ concept skeletons from confirmed [[links]] in paper notes
│   ├── process-inbox/     # Route 00-Inbox/ notes
│   └── update-memory/     # End-of-session memory capture
└── writing/skills/        # scientific writing and figures
    ├── poster/            # beamerposter LaTeX conference poster
    ├── qr-code/           # QR code PNG/SVG + LaTeX snippet
    ├── review-tags-tex/   # process %CT: / %CQ: review tags in .tex
    └── workflow-diagram/  # TikZ workflow/scheme diagrams

Skills

User-authored (in this repo)

Domain	Skill	Description
literature	lit-search	Multi-DB paper discovery (arXiv, S2, OpenAlex, ChemRxiv, PubMed, WoS, Scopus) + citation chase (DOI/arXiv/PDF)
literature	lit-bib	BibTeX generation from papers.json/DOIs/arXiv IDs; Levenshtein validation; Zotero sync
literature	lit-watch	Weekly new-paper monitor → vault inbox digest; project-aware relevance scoring
literature	lit-review	Full pipeline: search → PRISMA screening → NotebookLM (batched) → report + .bib
literature	lit-vault	papers.json → per-paper Obsidian vault notes; full-text fetch (arXiv/Unpaywall); project-situated summaries; Galaxy link suggestions
literature	lit-annotate	Fill Key points skeleton in vault notes after reading; accepts user notes, PDF, or URL; project-context framing; approval-gated
vault	galaxy	Draft 30-Galaxy/ concept note skeletons from confirmed [[links]] in paper notes; approval-gated write
vault	process-inbox	Routes 00-Inbox/ notes and emails — conferences, tutor emails, source notes, Galaxy skeletons
vault	update-memory	End-of-session memory capture — writes/updates project memory files
writing	poster	Scientific conference poster (LaTeX/beamerposter) + optional abstract and Q&A prep
writing	qr-code	Generate QR code PNG/SVG from URL or text + LaTeX snippet
writing	review-tags-tex	Process %CT: / %CQ: review tags embedded in .tex files
writing	workflow-diagram	TikZ flowchart/scheme diagrams for LaTeX

Plugin-provided (install separately)

Not duplicated here. Install from Anthropic's official plugin registry.

Plugin	Skills	Source
claude-md-management	claude-md-improver	anthropics/claude-plugins-official

Vault context skills

Skills for Obsidian vault workflows. Pending migration to this repo.

Skill	Source	Target domain	Status
sci-lit-pipeline	user-authored	literature/skills/	superseded by lit-search + lit-review; pending migration
youtube-research-pipeline	user-authored	literature/skills/	BROKEN — missing youtube-search dep
claude-md-improver	claude-md-management plugin	—	plugin-provided, no migration

Config

Copy config/config.example → config/config.local and fill in values before running setup.sh.