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get_bound_molecule_interactions_api_pdb_bound_molecule_inter

Read-only

Retrieve composition, internal connectivity, and detected interactions (covalent, hydrogen-bond, polar, van der Waals, hydrophobic, atom-plane) for a specified bound molecule in a PDB entry.

Instructions

Returns composition and high-level interactions for a specific Bound Molecule ID (e.g., “bm1”) of a PDB entry ID. This includes its full composition (all covalently linked ligands with their CCD IDs), internal connectivity between those ligands (e.g: [“F1”, “F6”] means bound ligands identified by author_residue_number “1” and “6” in chain_id “F” are covalently bound), and all detected interactions between the bound molecule and surrounding residues or ligands (e.g., covalent, hydrogen-bond, polar, van der Waals, hydrophobic, and atom-plane interactions) calculated for the preferred assembly of the PDB entry.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pdb_idYes4-character PDB id code. title: Pdb Id description: 4-character PDB id code.
bm_idYesBound molecule ID (can be obtained from the output of bound_molecules call) title: Bm Id description: Bound molecule ID (can be obtained from the output of bound_molecules call)
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already provide readOnlyHint=true, and the description adds value by detailing what interactions are included (covalent, hydrogen-bond, etc.) and that they are calculated for the preferred assembly, going beyond annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single paragraph that front-loads the main purpose. It is informative but could be slightly more concise; however, it avoids unnecessary detail.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With no output schema, the description fully explains the return content: composition, internal connectivity, and various interaction types. It also specifies the calculation context (preferred assembly), making it complete for an agent.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100% with parameter descriptions. The description adds extra context by noting that bm_id can be obtained from bound_molecules output, which aids understanding beyond the schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool returns composition and high-level interactions for a specific Bound Molecule ID of a PDB entry, distinguishing it from sibling tools like get_bound_molecules which lists bound molecules without interaction details.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description mentions that bm_id can be obtained from bound_molecules call, providing implicit usage context. However, it does not explicitly state when to use this tool versus alternatives or provide exclusion criteria.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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