preview-molecular-structures

name	preview-molecular-structures
description	Preview supported molecular attachments or an explicit public PDB ID in Burrete's interactive viewer, or use the bounded hosted Ketcher editor for transient chemical sketches.

Preview molecular structures

Use Burrete for bounded molecular inspection and transient chemical sketching.

Choose the tool

• Use preview_molecular_file when the user provides one supported molecular structure attachment.
• Use preview_pdb_structure only when the user explicitly names a four-character PDB ID or clearly asks to open that public PDB entry.
• Use render_molecular_scene when the user asks to select or focus a typed chain, residue range, or component; clear a selection; reset the camera; or hide/show polymers, ligands, ions, or water. Pass the same PDB ID or authorized attachment again because the public server does not retain widget sessions.
• Use open_ketcher when the user asks to draw or edit a small chemical structure in the hosted widget. Seed only bounded inline KET, MOL, RXN, or SMILES content when it is supplied.
• Use control_ketcher for a follow-up Ketcher action. First use the current surfaceId and structureRevision from the editor snapshot; send a revision-checked set_structure, clear_structure, highlight_atoms, or get_structure action. request_persist only reaches a user-confirmation boundary and never writes silently.
• If several supported attachments are present and the target is unclear, ask which single structure to open.

Present the result

1. Call the selected tool once with the user's attachment or PDB ID.
2. Report the bounded composition summary returned by the tool. Do not infer counts that are absent from the result.
3. Let the interactive Burrete preview carry the detailed 3D inspection. The user can rotate, zoom, select residues, inspect the sequence, change representations, and use measurements directly in the result.
4. State format limitations or parser notes when the result includes them.
5. Treat burrete.activeSelection from widget context as the user's current selection. Do not claim an action succeeded until the widget reports its bounded scene result.

Boundaries

• Do not claim that this public plugin edits, overwrites, or deletes molecular source files. Ketcher edits exist only in the ephemeral hosted widget relay.
• Do not claim local macOS app control, docking, simulation, structure prediction, or remote job execution. Those are outside this hosted plugin.
• Do not treat a molecular preview as medical diagnosis, clinical advice, or proof of biological function.
• Do not request credentials, private URLs, local paths, health records, or other sensitive identifiers.
• Files larger than 3 MiB or unsupported formats need a smaller supported structure file.
• Arbitrary residue isolation and persistent representation overpaint are not available in the hosted action allowlist.