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Generate new molecules de novo.
Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.
Based on SOC occupation classification
Predict the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of the input molecules.
Predict binding affinity between target protein sequence and small molecule SMILES using Boltz-2.
Predict protein structures with Chai-1 from sequence or FASTA input and return model scoring summaries.
Chroma toolkit skill covering chroma_monomer for single-chain generation, chroma_complex for multi-chain assembly generation, and chroma_symmetry for symmetry-constrained protein design.
Retrieve SMILES strings from PubChem database using compound names.
[CURRENTLY UNAVAILABLE] DiffDock protein-ligand docking. This tool is not deployed on the current MCP server. Use molclaw-quickvina-docking or molclaw-karmadock-tool as alternatives.
| name | molclaw-denovo-sampling |
| description | Generate new molecules de novo. |
| license | MIT license |
| metadata | {"skill-author":"PJLab"} |
Note:
molclaw-file-transfer before execution.molclaw-pdbfixer before execution.molclaw-scp-server to complete tool invocation.The description of tool reinvent_denovo_sampling.
Generate new molecules de novo.
Args:
n (int): Number of molecules for sampling
lipinski (bool): Whether to apply Lipinski's rule of five filtering, default is True
filter_preset (str): Filter preset, options: ['none', 'minimal', 'default', 'strict', 'druglike', 'all'], default is 'druglike'
Return:
status (str): success/error
msg (str): message
save_smiles_file (str): Path to the saved SMILES file
output_smiles_list (List[str]): List of generated SMILES strings
How to use tool reinvent_denovo_sampling :
response = await client.session.call_tool(
"reinvent_denovo_sampling",
arguments={
"n": n,
"lipinski": True,
"filter_preset": filter_type
}
)
result = client.parse_result(response)
output_smiles_list = result["output_smiles_list"]