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Rcsb Pdb

by io.github.pipeworx-io

Recent Alerts

recent_alerts
Read-onlyIdempotent

Pull fired events from your subscription feed. Returns the most recent alerts the evaluator has written to your persisted feed — each carries source, citation_uri (pipeworx:// when available), and the raw event payload. Filter by type (e.g. "sec_8k") and/or since (ISO timestamp). Set mark_read:true to flag returned events read so the next call only shows newer ones. Polls work fine; the same feed is also at GET registry.pipeworx.io/alerts.json for scripts and dashboards.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
typeNoOptional — filter to one subscription type.
limitNoMax events to return (1-200, default 50).
sinceNoOptional ISO timestamp — return events fired_at >= this time.
mark_readNoFlag the returned events read in the same call (default false).
unread_onlyNoReturn only events where read_at is null (default false).

Schema Changelog

Changes observed during successful MCP inspections. Dates show when Glama detected each change.

  1. First observed

TDQS

A3.7/5.0
Behavior1/5

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

The description explicitly says mark_read:true flags events as read, which mutates state, but the annotations declare readOnlyHint:true. This is a direct contradiction, undermining the reliability of the safety hints.

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 three sentences, starts with the main purpose, and packs useful details without excessive verbosity. The final sentence is slightly long but still efficient.

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

Completeness4/5

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

The description covers return fields, filtering, mark_read behavior, polling suitability, and an alternative access method. With no output schema and 5 optional parameters, it provides enough context for typical use, though it doesn't explain 'source' or 'citation_uri' in depth.

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%, but the description adds a concrete example for 'type' (sec_8k) and clarifies that 'since' is an ISO timestamp. The behavior of mark_read is also reinforced, providing slight value 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 opens with 'Pull fired events from your subscription feed,' clearly specifying the verb and resource. It distinguishes itself from sibling tools by focusing on reading fired alerts, whereas siblings manage subscriptions or perform other actions.

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 states that it returns most recent alerts, supports filtering by type and since, and notes that polling works fine. It also mentions an alternative HTTP endpoint for scripts/dashboards, but does not explicitly name sibling tools or conditions for when to use this tool over them.

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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TDQS

A3.7/5.0
Disambiguation2/5

ask_pipeworx, ask_pipeworx_beta, and ask_pipeworx_grounded are nearly identical in purpose, and structure/summary both fetch PDB entries. The server name 'Rcsb Pdb' doesn't match most tools, which are Pipeworx data tools, compounding ambiguity.

Naming Consistency3/5

Mostly snake_case verb_noun, but verbs are inconsistent (ask, discover, generate, list, recall) and some names are noun phrases (entity_profile, polymarket_edges). No clear pattern unifies the set.

Tool Count2/5

37 tools is excessive for a server ostensibly about RCSB PDB; only 6 tools relate to PDB while 31 serve unrelated Pipeworx functionality. The count feels like a bundled grab-bag rather than a focused toolset.

Completeness3/5

The PDB-specific tools cover the core operations (search, fetch, assembly, ligand, polymer entity), so the structural biology surface is mostly complete. However, the server's overall purpose is muddled, and the Pipeworx tools are a separate domain that happens to be bundled in, making it unclear what 'completeness' even means for this server.

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