Server Quality Checklist

Tool Scores

• get_protein_data_toolB
  3.1/5.0
  Behavior2/5

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

  No annotations are provided, so the description carries full burden. It mentions the tool returns a '完整蛋白质数据包' (complete protein data package) but doesn't disclose behavioral traits like rate limits, authentication requirements, error conditions, or whether it's a read-only operation. The description adds minimal context beyond basic functionality.

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

  Conciseness3/5

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

  The description is moderately structured with sections (Args, Returns, Examples) but includes some redundancy (e.g., repeating tool name in examples). The Chinese text is clear but could be more front-loaded; the core purpose is stated early but followed by less essential details. Some sentences like '这个工具是蛋白质数据获取的核心' add minimal value.

  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?

  Given the tool's moderate complexity (3 parameters, no annotations, but has output schema), the description is reasonably complete. It explains parameters well, provides examples, and states the return value. The output schema existence means it doesn't need to detail return structure. However, it lacks behavioral context and sibling tool differentiation.

  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?

  With 0% schema description coverage, the description compensates well by explaining all 3 parameters: pdb_id (with example), data_types (with detailed options and meanings), and chain_id (optional, with example). It provides clear semantic meaning beyond the bare schema, though it doesn't cover the ctx parameter mentioned in the description but not in the schema.

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

  Purpose4/5

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

  The description clearly states the tool's purpose: '获取完整蛋白质信息包' (get complete protein information package) and '一次性获取你需要的所有信息' (get all needed information at once). It specifies the resource (protein data) and action (retrieve), though it doesn't explicitly differentiate from sibling tools like download_structure_tool or find_protein_structures_tool.

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

  Usage Guidelines2/5

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

  The description provides no guidance on when to use this tool versus the sibling tools (download_structure_tool, find_protein_structures_tool). It mentions this is the '核心' (core) tool for protein data, but doesn't specify scenarios where alternatives might be more appropriate or any prerequisites for usage.

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

• download_structure_toolA
  3.5/5.0
  Behavior3/5

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

  With no annotations provided, the description carries the full burden. It discloses behavioral traits such as returning file content or download information with format explanations, and mentions progress feedback via ctx. However, it lacks details on error handling, rate limits, authentication needs, or what happens when save_local is true (e.g., file location, overwriting behavior). The description adds some context but is incomplete for a tool with mutation potential (saving files).

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

  Conciseness3/5

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

  The description is moderately structured with sections (Args, Returns, Examples), but includes redundant elements like '结构文件工具 - 下载和管理蛋白质结构文件' which repeats the title concept. The examples are helpful but verbose, and some sentences could be more front-loaded (e.g., the purpose statement is clear but not maximally efficient). It earns its place with parameter details but has room for trimming.

  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?

  Given the complexity (3 parameters, 0% schema coverage, no annotations, but has output schema), the description is fairly complete. It covers parameter meanings, return behavior, and usage examples. With an output schema present, it doesn't need to detail return values extensively. However, for a tool that can save files locally, it could better address potential side effects or error cases to be fully comprehensive.

  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 description coverage is 0%, so the description must compensate. It provides meaningful semantics for all parameters: pdb_id is explained with an example ('PDB ID (例如: "5G53")'), file_format includes detailed options with recommendations ('推荐，人类可读' for pdb, '现代标准' for mmcif, '二进制，速度快' for mmtf), and save_local clarifies behavior ('是否保存到本地文件 (默认False返回内容)'). This adds significant value beyond the bare schema, though it could specify default values more explicitly.

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

  Purpose4/5

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

  The description clearly states the tool's purpose as '处理所有文件相关的操作，从下载到格式说明' (handles all file-related operations from download to format explanation), which is specific about downloading and managing protein structure files. It distinguishes from siblings by focusing on file operations rather than searching (find_protein_structures_tool) or general data retrieval (get_protein_data_tool). However, it could be more precise about being primarily a download tool with format management.

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

  Usage Guidelines3/5

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

  The description implies usage through examples (e.g., '获取PDB文件内容' for getting content, '下载mmCIF格式并保存到本地' for saving locally), but lacks explicit guidance on when to use this tool versus alternatives like find_protein_structures_tool or get_protein_data_tool. It provides context for different scenarios (e.g., save_local parameter) but doesn't state when not to use it or compare with siblings.

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

• find_protein_structures_toolA
  3.8/5.0
  Behavior3/5

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

  With no annotations provided, the description carries the full burden of behavioral disclosure. It describes the tool's multi-functional nature (search, example, validation) and mentions default/max values for max_results, but doesn't cover important behavioral aspects like rate limits, authentication needs, error conditions, or what happens when multiple parameters are provided simultaneously.

  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 well-structured with clear sections (description, Args, Returns, Examples) and front-loads the main purpose. While comprehensive, some redundancy exists between the opening description and the examples section. Most sentences earn their place by adding value.

  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?

  Given the tool's moderate complexity (4 parameters, multi-functional) and the presence of an output schema, the description provides good coverage. It explains all parameters, shows usage examples, and describes the return value format. The main gap is lack of behavioral details that would be important for a discovery/validation tool.

  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?

  With 0% schema description coverage, the description compensates well by explaining all 4 parameters in the Args section with clear examples. It provides semantic meaning for keywords, category (with specific enum values), pdb_id, and max_results (including default and max values). The ctx parameter is mentioned but not fully explained.

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

  Purpose4/5

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

  The description clearly states the tool's purpose as a 'unified entry point for protein structure discovery' that helps 'discover and validate PDB structures.' It specifies the verb ('search, example, validate') and resource ('PDB structures'), though it doesn't explicitly differentiate from sibling tools like download_structure_tool or get_protein_data_tool.

  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 provides clear context on when to use the tool ('starting point for protein research') and includes examples showing different usage scenarios (searching by keywords, getting examples by category, validating PDB IDs). However, it doesn't explicitly state when NOT to use it or mention alternatives among sibling tools.

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