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submit_ion_mobility_workflow

Submit a workflow to predict collision cross-section values for ion mobility mass spectrometry using conformational averaging and theoretical calculations.

Instructions

Submit an ion mobility (CCS) prediction workflow using Rowan v2 API.

Args: initial_molecule: SMILES string of the molecule for collision cross-section prediction temperature: Temperature in Kelvin for CCS calculation (default: 300K) protonate: Whether to automatically protonate the molecule (default: False) do_csearch: Whether to perform conformational search (default: True) do_optimization: Whether to optimize geometry (default: True) name: Workflow name for identification and tracking folder_uuid: UUID of folder to organize this workflow. Empty string uses default folder. max_credits: Maximum credits to spend on this calculation. 0 for no limit.

Predicts collision cross-section (CCS) values for ion mobility mass spectrometry using conformational averaging and theoretical calculations. Useful for:

  • Validating experimental IM-MS data

  • Predicting CCS values for method development

  • Structural characterization of biomolecules

Returns: Workflow object representing the submitted workflow

Examples: # Pyridinium CCS result = submit_ion_mobility_workflow( initial_molecule="c1ccccn1", protonate=True, name="pyridinium CCS" )

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
initial_moleculeYesSMILES string of the molecule for ion mobility prediction
temperatureNoTemperature in Kelvin for CCS calculation
protonateNoWhether to automatically protonate the molecule
do_csearchNoWhether to perform conformational search before CCS calculation
do_optimizationNoWhether to optimize molecular geometry before CCS calculation
nameNoWorkflow name for identification and trackingIon-Mobility Workflow
folder_uuidNoUUID of folder to organize this workflow. Empty string uses default folder
max_creditsNoMaximum credits to spend on this calculation. 0 for no limit
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 mentions that the tool 'submits' a workflow and returns a 'Workflow object,' implying a write operation with tracking, but lacks details on permissions, rate limits, costs (beyond credits), or error handling. The example adds some practical context but doesn't fully compensate for the missing annotation coverage.

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 (purpose, args, use cases, returns, example) and avoids redundancy. However, it could be more front-loaded by moving the 'Useful for' bullet points earlier for quicker scanning, and the example is detailed but necessary for clarity.

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

Completeness3/5

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

Given the complexity (8 parameters, workflow submission), no annotations, and no output schema, the description is adequate but has gaps. It explains the purpose, parameters, and use cases well, but lacks details on behavioral aspects like authentication, response format beyond 'Workflow object,' or error scenarios, making it minimally viable but not 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 100%, so the schema already documents all parameters thoroughly. The description adds marginal value by grouping parameters in an 'Args:' section and providing an example that illustrates usage with 'initial_molecule,' 'protonate,' and 'name,' but doesn't significantly enhance understanding beyond the schema. The baseline is 3, but the example and clear parameter listing justify a slight bump.

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 specific action ('Submit an ion mobility (CCS) prediction workflow') and resource ('using Rowan v2 API'), distinguishing it from siblings like 'submit_admet_workflow' or 'submit_docking_workflow' by focusing on collision cross-section prediction for ion mobility mass spectrometry.

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 for when to use this tool ('Predicts collision cross-section (CCS) values... Useful for: - Validating experimental IM-MS data - Predicting CCS values for method development - Structural characterization of biomolecules'), but does not explicitly mention when not to use it or name specific alternatives among the sibling tools.

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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