Molecule Io Core

What it does

When your agent uses it

• RDKit molecule creation
• File/string I/O
• Atom/bond/ring queries
• Substructure matching

Example prompts

• “/molecule-io-core”

Requirements

• Python 3

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

1. 1Parse input and immediately check for None before doing any chemistry.
2. 2Canonicalize with Chem.MolToSmiles(mol, isomericSmiles=True) when comparing or de-duplicating molecules.
3. 3Use suppliers defensively: iterate with indexes, skip or report None, and preserve molecule names/properties when writing SDF.
4. 4If using sanitize=False, run a deliberate Chem.SanitizeMol step before relying on valence, aromaticity, rings, descriptors, or…
5. 5For structural edits, edit a copy, call GetMol(), update property cache if needed, then sanitize or report the sanitization failure.

What it can do on your machine

Read from SKILL.md and the folder at commit ac3fe1a. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Ships 1 file in scripts/ (Python), which the agent can run.

  Shell commands in SKILL.md call:

  • python

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  No URLs in SKILL.md.

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Molecule Io Core loads about 936 tokens when it runs, and up to ~4.5k if it reads all its reference files. Until then it costs about 80 tokens; SKILL.md has 311 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~80

When it runs · the whole SKILL.md, loaded when a task matches

~936

With references · SKILL.md plus every file in references/, read only if the agent opens them

~4.5k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from VectorSpaceLab/AREX-Skill at commit ac3fe1a, republished under its BSD-3-Clause licence (© VectorSpaceLab). 311 words, ~936 tokens.

name

molecule-io-core

description

Use for RDKit molecule creation, file/string I/O, validation, sanitization, atom/bond/ring queries, substructure matching, hydrogens, and editable molecule workflows. Route descriptors/fingerprints, conformers/drawing, reactions/standardization, and R-group workflows to their dedicated RDKit sub-skills.

disable-model-invocation

true

metadata.disco-role

operating

license

BSD 3-Clause

from rdkit import Chem

mol = Chem.MolFromSmiles("CC(=O)O")
if mol is None:
    raise ValueError("invalid SMILES")
canonical = Chem.MolToSmiles(mol, isomericSmiles=True)

query = Chem.MolFromSmarts("[CX3](=O)[OX2H1]")
matches = mol.GetSubstructMatches(query)

edited = Chem.RWMol(mol)
atom_index = edited.AddAtom(Chem.Atom("Cl"))
edited.AddBond(0, atom_index, Chem.BondType.SINGLE)
new_mol = edited.GetMol()
Chem.SanitizeMol(new_mol)

python scripts/molecule_io_smoke.py --smiles "CCO" "c1ccccc1" --include-invalid

© VectorSpaceLab, BSD-3-Clause. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 4 other files (scripts, references) in skills/repositories/repo-skills/rdkit/sub-skills/molecule-io-core of VectorSpaceLab/AREX-Skill.

• SKILL.md
• references/molecule-io.md
• references/sanitization-and-queries.md
• references/troubleshooting.md
• scripts/molecule_io_smoke.py

Open the folder on GitHubat commit ac3fe1a