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submit_macropka_workflow

Calculate pKa values and ionization states to determine pH-dependent solubility, with options for fast qualitative analysis or detailed quantitative solubility predictions.

Instructions

Submit a Macroscopic pKa workflow using Rowan v2 API.

Calculates pKa values, microstate populations, and net charge across pH range. PERFORMANCE: compute_aqueous_solubility=False is 8x faster (~5 min vs ~40 min).

Fast mode (False): pKa values, ionization states, isoelectric point. Sufficient to determine which pH has highest/lowest solubility (ionization dominates).

Slow mode (True): Adds conformer search + solvation free energies for quantitative solubility predictions (mg/mL). Only needed for absolute values or fold-changes.

Args: initial_smiles: SMILES string min_pH: Minimum pH (default: 0) max_pH: Maximum pH (default: 14) min_charge: Minimum charge (default: -2) max_charge: Maximum charge (default: 2) compute_solvation_energy: Compute solvation energy corrections (default: False) compute_aqueous_solubility: Enable quantitative solubility mode (default: False) name: Workflow name folder_uuid: Folder UUID (empty = default) max_credits: Credit limit (0 = no limit)

Returns: Workflow object. WAIT ~5 min (fast) or ~40 min (slow) before checking results. Use workflow_is_finished() to poll (not more than once per minute to avoid loops).

Examples: # Fast: "At which pH is solubility highest?" submit_macropka_workflow(initial_smiles=smiles, compute_aqueous_solubility=False)

# Slow: "What is solubility at pH 7 in mg/mL?"
submit_macropka_workflow(initial_smiles=smiles, compute_aqueous_solubility=True)

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
initial_smilesYesSMILES string of the molecule for macropKa calculation
min_pHNoMinimum pH value for the calculation range
max_pHNoMaximum pH value for the calculation range
min_chargeNoMinimum molecular charge to consider
max_chargeNoMaximum molecular charge to consider
compute_solvation_energyNoWhether to compute solvation energy corrections
compute_aqueous_solubilityNoCompute quantitative pH-dependent solubility. False (default, 5min): pKa+ionization only, sufficient for 'which pH' questions. True (40min): adds conformer search+solvation energies for absolute mg/mL values
nameNoWorkflow name for identification and trackingMacropka 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
Behavior4/5

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

With no annotations provided, the description carries full burden and does an excellent job disclosing key behavioral traits: performance characteristics (8x speed difference, ~5 min vs ~40 min runtime), waiting requirements ('WAIT ~5 min (fast) or ~40 min (slow)'), polling guidance ('Use workflow_is_finished() to poll'), and rate limit warnings ('not more than once per minute to avoid loops'). It doesn't cover all possible edge cases, but provides substantial operational context.

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, performance, modes, args, returns, examples) and every sentence adds value. It could be slightly more concise in the parameter explanation section, but overall it's efficiently organized with no wasted text.

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?

For a complex 10-parameter workflow tool with no annotations and no output schema, the description provides excellent context: clear purpose, detailed usage guidelines, performance expectations, runtime behavior, and practical examples. The main gap is the lack of information about the return format ('Workflow object' is vague), but given the comprehensive operational guidance, this is a minor limitation.

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 100% schema description coverage, the baseline is 3. The description adds significant value by explaining the practical implications of key parameters: it clarifies that compute_aqueous_solubility=False enables 'fast mode' for relative comparisons while True enables 'slow mode' for absolute values, and provides performance context. However, it doesn't add meaningful context for all 10 parameters beyond what the schema provides.

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 a Macroscopic pKa workflow') and resource ('using Rowan v2 API'), with detailed explanation of what it calculates (pKa values, microstate populations, net charge across pH range). It effectively distinguishes from siblings by focusing on macroscopic pKa calculations, unlike other workflow tools for different purposes like docking or solubility.

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

Usage Guidelines5/5

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

The description provides explicit guidance on when to use fast vs. slow modes: 'Fast mode (False): ... Sufficient to determine which pH has highest/lowest solubility' and 'Slow mode (True): ... Only needed for absolute values or fold-changes.' It also includes practical examples with specific use cases, making it clear when to choose each alternative.

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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