assembly-index
Lee Cronin's Assembly Theory for molecular complexity measurement and
npx skills add majiayu000/claude-skill-registry --skill assembly-index --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Assembly Index Skill: Molecular Complexity Validation **Status**: ✅ Production Ready **Trit**: -1 (MINUS - validator/constraint) **Color**: #2626D8 (Blue) **Principle**: Complexity threshold → Life signature **Frame**: Assembly pathways with minimal step counting --- ## Overview **Assembly Index** measures molecular complexity by counting the minimum number of joining operations needed to construct a molecule from basic building blocks. Molecules with assembly index > 15 are biosignatures—too complex for random chemistry. 1. **Assembly pathway**: Shortest construction sequence 2. **Copy number threshold**: Abundance × complexity = life signal 3. **Molecular DAG**: Directed acyclic graph of substructures 4. **Mass spectrometry integration**: MA(m/z) measurement ## Core Formula ``` MA(molecule) = min |steps| to construct from primitives Life threshold: MA > 15 with copy_number > 1 ``` ```python def assembly_index(molecule: Molecule) -> int: """Compute minimum assembly steps via dynamic programming.""" substructures = enumerate_substructures(molecule) dag = build_assembly_dag(substructures) return shortest_path_length(dag, source="primitives", target=molecule) ``` ## Key Concepts ##
- Overview
- Core Formula
- Key Concepts
- 1. Assembly Pathway Enumeration
- 2. Copy Number Amplification
- 3. Tandem Mass Spectrometry Integration
- End-of-Skill Interface
- Commands
- Integration with GF(3) Triads
- Related Skills
- r2con Speaker Resources
- SDF Interleaving
- Primary Chapter: 1. Flexibility through Abstraction
- GF(3) Balanced Triad
Compute assembly index just assembly-index molecule.sdf Validate biosignature threshold just assembly-validate sample.ms2 Compare assembly pathways just assembly-compare mol1.sdf mol2.sdf
What does the assembly-index skill do?
Lee Cronin's Assembly Theory for molecular complexity measurement and
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill assembly-index --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.