AutoResearchClaw chemistry-rdkit

Computational chemistry with RDKit for molecular analysis, descriptors, fingerprints, and substructure search. Use when working with SMILES, drug discovery, or cheminformatics tasks.

install

source · Clone the upstream repo

git clone https://github.com/aiming-lab/AutoResearchClaw

Claude Code · Install into ~/.claude/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/aiming-lab/AutoResearchClaw "$T" && mkdir -p ~/.claude/skills && cp -r "$T/researchclaw/skills/builtin/domain/chemistry-rdkit" ~/.claude/skills/aiming-lab-autoresearchclaw-chemistry-rdkit-7cae29 && rm -rf "$T"

manifest: researchclaw/skills/builtin/domain/chemistry-rdkit/SKILL.md

source content

RDKit Cheminformatics Best Practice

Molecular I/O

Create molecules from SMILES:
```
mol = Chem.MolFromSmiles('CCO')
```
Always check for None:
```
MolFromSmiles
```
returns None on invalid input
Convert to canonical SMILES:
```
Chem.MolToSmiles(mol)
```
Read SDF files:
```
suppl = Chem.SDMolSupplier('file.sdf')
```

Read SMILES files:

suppl = Chem.SmilesMolSupplier('file.smi')

Write molecules:
```
writer = Chem.SDWriter('output.sdf')
```

Molecular Descriptors

Molecular weight:
```
Descriptors.MolWt(mol)
```
LogP (lipophilicity):
```
Descriptors.MolLogP(mol)
```
TPSA (polar surface area):
```
Descriptors.TPSA(mol)
```

H-bond donors/acceptors:

Descriptors.NumHDonors(mol)

Descriptors.NumHAcceptors(mol)

Rotatable bonds:
```
Descriptors.NumRotatableBonds(mol)
```
Lipinski Rule of 5: MW <= 500, LogP <= 5, HBD <= 5, HBA <= 10

Fingerprints and Similarity

Morgan (circular) fingerprints:

AllChem.GetMorganFingerprintAsBitVect(mol, radius=2, nBits=2048)

RDKit fingerprints:
```
Chem.RDKFingerprint(mol)
```
MACCS keys:
```
MACCSkeys.GenMACCSKeys(mol)
```

Tanimoto similarity:

DataStructs.TanimotoSimilarity(fp1, fp2)

Use radius=2 (ECFP4 equivalent) as default for most applications
For virtual screening, Tanimoto > 0.7 suggests structural similarity

Substructure Search

SMARTS patterns:
```
pattern = Chem.MolFromSmarts('[OH]')
```
Check match:
```
mol.HasSubstructMatch(pattern)
```
Get all matches:
```
mol.GetSubstructMatches(pattern)
```
Common SMARTS:
```
[#6](=O)[OH]
```
(carboxylic acid),
```
[NH2]
```
(primary amine)
Filter compound libraries by functional group presence

Property Calculation Patterns

Batch processing: iterate over SDMolSupplier, skip None entries
Use
```
Chem.Descriptors.descList
```
for all available descriptors
For ADMET filtering, calculate Lipinski, Veber, and PAINS filters

Generate 3D coordinates:

AllChem.EmbedMolecule(mol, AllChem.ETKDG())

Minimize energy:
```
AllChem.MMFFOptimizeMolecule(mol)
```

Common Pitfalls

Always sanitize molecules (default behavior) — disable only when needed
Add hydrogens explicitly for 3D work:
```
Chem.AddHs(mol)
```
Handle stereochemistry: use
```
Chem.AssignStereochemistry(mol)
```
Large SDF files: use
```
ForwardSDMolSupplier
```
for memory efficiency
Kekulization errors usually indicate invalid SMILES input