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epik

Enumerate protonation and tautomeric states of ligands and estimate pKa values. Accepts .mae, .maegz, or .sdf files; returns a job ID for asynchronous processing.

Instructions

Enumerate protonation/tautomeric states and estimate pKa for ligands with Epik. Accepts a structure file (.mae/.maegz/.sdf — non-Maestro inputs are auto-converted). Long-running — returns a job_id; states with pKa/penalty properties in <output_name>.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
input_pathYes
phNo
ph_toleranceNo
max_statesNo
output_nameNoepik_out.maegz
Behavior3/5

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

No annotations provided, so description must carry the burden. It discloses long-running async behavior (returns job_id) and output file with properties. However, it does not mention side effects, authentication needs, or what exactly happens during processing.

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?

Three sentences, front-loaded with purpose, then input format, then async/output. No fluff, but could be more concise by merging sentences or adding parameter hints.

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

Completeness2/5

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

With 5 parameters, no output schema, and no annotations, the description only covers input format and async behavior. Missing explanations for ph, ph_tolerance, max_states, and exact return value structure. Incomplete for a complex computational tool.

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

Parameters2/5

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

Schema description coverage is 0%, so description should compensate. It only adds meaning to input_path ('non-Maestro inputs auto-converted') and output_name ('states with pKa/penalty properties'), but ignores ph, ph_tolerance, and max_states entirely.

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 enumerates protonation/tautomeric states and estimates pKa for ligands using Epik. This specific verb-resource combination distinguishes it from sibling tools like ligprep or glide_dock.

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?

No guidance on when to use this tool vs alternatives. The description mentions input format and auto-conversion but does not specify prerequisites, when not to use, or compare to similar tools like ligprep or jaguar_qm.

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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