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name: structure-generation description: "Guides agents using datamol to generate and manipulate molecular structures, including conformers, SASA, alignment, fragmentation, scaffolds, reactions, attachments, and isomer enumeration." disable-model-invocation: true metadata: disco-role: operating license: Apache 2.0

Datamol Structure Generation

Use this sub-skill when a task asks to create, enumerate, transform, align, fragment, assemble, scaffold, or react molecular structures with datamol beyond basic molecule conversion.

Route By Task

• Conformers and 3D features: Use dm.conformers.generate, dm.conformers.cluster, dm.conformers.rmsd, dm.conformers.sasa, dm.conformers.get_coords, dm.conformers.center_of_mass, and dm.conformers.keep_conformers; see workflows and API guidance.
• Alignment and atom ordering: Use dm.align.template_align, dm.align.auto_align_many, dm.conformers.align_conformers, and dm.reorder_mol_from_template; see workflows and API guidance.
• Fragmentation and assembly: Use dm.fragment.brics, frag, recap, anybreak, mmpa_cut, break_mol, build, and assemble_fragment_order; see workflows and API guidance.
• Scaffolds and fuzzy scaffolds: Use dm.to_scaffold_murcko, dm.make_scaffold_generic, dm.strip_mol_to_core, dm.compute_ring_system, and dm.scaffold.fuzzy_scaffolding; see workflows.
• Reactions and attachments: Use dm.reactions.rxn_from_smarts, apply_reaction, select_reaction_output, is_reaction_ok, can_react, inverse_reaction, convert_attach_to_isotope, num_attachment_points, and open_attach_points; see workflows.
• Isomer enumeration: Use dm.enumerate_tautomers, dm.enumerate_stereoisomers, dm.count_stereoisomers, dm.enumerate_structisomers, dm.canonical_tautomer, and dm.remove_stereochemistry; see workflows.

Boundaries

• For SMILES parsing, molecule cleaning, neutralization, salt removal, or SDF/dataframe I/O, use the sibling molecule-io-prep skill before this one.
• For fingerprints, pairwise distances, clustering generated sets by similarity, or diversity selection, use the sibling fingerprints-similarity skill after structure generation.
• For drawing products, conformers, highlights, or scaffold grids, use the sibling visualization-utilities skill after this one.

Safety Defaults

• Convert inputs with dm.to_mol, then sanitize or standardize through molecule-io-prep before reactions, conformers, and enumeration.
• Bound expensive operations with small n_confs, n_variants, depth, timeout_seconds, max_n_mols, rms_cutoff, and num_threads=1 until the workflow is proven.
• Treat reaction SMARTS, structural isomer enumeration, fuzzy scaffolds, MCS alignment, and fragment assembly as potentially combinatorial.
• See troubleshooting when embedding fails, no conformers exist, template matches are ambiguous, reactions return no products, or enumeration grows too large.

Bundled Smoke Script

Run a deterministic tiny exercise of conformer generation, scaffold extraction, reaction application, and isomer counting:

python sub-skills/structure-generation/scripts/structure_generation_smoke.py --help
python sub-skills/structure-generation/scripts/structure_generation_smoke.py

The script prints JSON and uses only local CPU chemistry operations.