Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add skills/kdevos12/alkyl/rdkitnpx skills add Kdevos12/ALKYL --skill rdkitgit clone --depth 1 https://github.com/Kdevos12/ALKYLWhat it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5 | $0.00058 | $0.01151 |
| Opus 5 | $0.00029 | $0.00575 |
| Sonnet 5 | $0.00012 | $0.00230 |
| Haiku 4.5 | $0.00006 | $0.00115 |
Grade A, and why
rdkit scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 97 lines — stays where its author put it; the contents beside it link to each section on GitHub.
RDKit
The primary Python library for cheminformatics. Molecular manipulation, descriptors, fingerprints, 3D generation, reactions, and more.
When to Use This Skill
- Reading/writing molecules from SMILES, SDF, MOL, PDB files
- Calculating molecular properties and drug-likeness filters (Ro5, QED)
- Computing and comparing molecular fingerprints (Morgan/ECFP, MACCS, RDKit FP)
- Generating 3D conformers (ETKDG, MMFF, UFF)
- Substructure searching and SMARTS queries
- Maximum Common Substructure (MCS) analysis
- Chemical reactions via SMARTS or RXN files
- Molecular fragmentation (BRICS, RECAP, Murcko scaffolds)
- Stereochemistry assignment and analysis
- Tautomer enumeration and molecule standardization
- Molecular visualization (2D SVG/PNG, similarity maps)
Quick Start
from rdkit import Chem
from rdkit.Chem import AllChem, Descriptors, Draw, rdMolDescriptors
# Load molecule
mol = Chem.MolFromSmiles('CC(=O)Oc1ccccc1C(=O)O') # aspirin
# Basic properties
print(Descriptors.MolWt(mol)) # 180.16
print(Descriptors.MolLogP(mol)) # 1.31
print(rdMolDescriptors.CalcNumHBD(mol)) # 1
print(rdMolDescriptors.CalcNumHBA(mol)) # 4
print(rdMolDescriptors.CalcTPSA(mol)) # 63.6
# Morgan fingerprint (ECFP4-like)
fpgen = AllChem.GetMorganGenerator(radius=2)
fp = fpgen.GetFingerprint(mol)
# 2D image
img = Draw.MolToImage(mol, size=(300, 200))
Router — What to Read
| Task | Reference |
|---|---|
| SMILES, SDF, MOL, PDB, SMARTS I/O, serialization | references/io-molecules.md |
| Descriptors, Lipinski Ro5, QED, ADME, drug filters | references/properties-descriptors.md |
| Morgan, MACCS, RDKit FP, atom pair, similarity, diversity | references/fingerprints-similarity.md |
| 3D conformers (ETKDG), MMFF/UFF optimization, 3D descriptors | references/3d-conformers.md |
| Reactions (SMARTS), BRICS, RECAP, Murcko, tautomers, standardization | references/transformations.md |
| Substructure search (SMARTS), MCS, rings, stereochemistry, pharmacophores | references/analysis-search.md |
| Visualization: SVG/PNG, highlighting, similarity maps, grids | references/visualization.md |
What ships with it
7 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 2d ago First seen · 97 lines · 58 tokens per session scan A 3c1e9e5c3069
rdkit is a skill published in the GitHub repository Kdevos12/ALKYL (6 stars, last pushed 5mo ago), licensed MIT. It adds 58 tokens to every session and 1,151 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
Other skills, from other repositories
add-tool
Scaffold a new MCP tool definition. Use when the user asks to add a tool, create a new tool, or implement a new capability for the server.
api-errors
McpError constructor, JsonRpcErrorCode reference, and error handling patterns for @cyanheads/mcp-ts-core. Use when looking up error codes, understanding where errors should be thrown vs. caught, or using ErrorHandler.tryCatch in services.
field-test
Exercise tools, resources, and prompts against a live HTTP server via MCP JSON-RPC over curl. Starts the server, surfaces the catalog, runs real and adversarial inputs, and produces a tight report with concrete findings and numbered follow-up options. Use after adding or modifying definitions, or when the user asks to…
tool-defs-analysis
Read-only audit of MCP definition language across an existing surface — tools, resources, prompts, server instructions. Walks every definition file and checks 16 categories the LLM reads to decide whether and how to call: voice & tense, internal leaks, audience leaks, defaults, recovery hints, field descriptions…
add-service
Scaffold a new service integration. Use when the user asks to add a service, integrate an external API, or create a reusable domain module with its own initialization and state.
add-app-tool
Scaffold an MCP App tool + UI resource pair. Use when the user asks to add a tool with interactive UI, create an MCP App, or build a visual/interactive tool.