Deepchem molgraph featurization

Skill ma-compbio-lab/SkillFoundry/skills/computational-chemistry-and-molecular-simulation/deepchem-molgraph-featurization

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install

npx -y skills add ma-compbio-lab/SkillFoundry --skill deepchem-molgraph-featurization

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What its author says it does

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Use this skill to featurize SMILES strings into DeepChem molecular graph objects. Prefer it for local graph-based preprocessing before molecular machine-learning experiments.

SKILL.md

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Purpose

Create deterministic DeepChem molecular graph features from a small SMILES table using the repo-managed chemtools prefix.

When to use

You need a lightweight DeepChem starter without training a model.
You want to inspect graph sizes and node-feature dimensions before modeling.

When not to use

You need trained DeepChem models requiring TensorFlow or PyTorch.
You need dataset download or benchmark automation.

Inputs

A TSV file with molecule_id and smiles columns.

Outputs

A JSON summary with graph dimensions for each molecule.

Requirements

slurm/envs/chemtools
DeepChem and RDKit in that prefix

Procedure

Run slurm/envs/chemtools/bin/python skills/computational-chemistry-and-molecular-simulation/deepchem-molgraph-featurization/scripts/featurize_molecules.py --input skills/computational-chemistry-and-molecular-simulation/deepchem-molgraph-featurization/examples/molecules.tsv --out scratch/deepchem/featurization.json.
Inspect node counts, edge counts, and feature dimensions.
Use the feature summary as a preflight step before larger molecular ML runs.

Validation

The script exits successfully.
Each molecule yields graph metadata.
Node and edge counts are positive for valid molecules.

Failure modes and fixes

Missing optional ML backends: this skill only requires the featurizer path, not torch or tensorflow.
Invalid SMILES: correct the input row before featurization.

Provenance

DeepChem documentation: https://deepchem.readthedocs.io/en/latest/

Related skills

rdkit-molecular-descriptors