Skip to main content
Glama

submit_pka_workflow

Calculate site-specific pKa values for individual ionizable groups in molecules using microscopic pKa prediction to determine protonation states at specific pH levels.

Instructions

Submit a microscopic pKa prediction workflow using Rowan v2 API.

Microscopic pKa: "At what pH does this site lose its proton, given the current protonation state of the rest of the molecule?" Calculates site-specific pKa values for individual ionizable groups considering their local environment.

Args: initial_molecule: The molecule to calculate the pKa of. SMILES string. pka_range: pKa range [min, max] to search, e.g., [2, 12] deprotonate_elements: Atomic numbers to consider for deprotonation, e.g., "[7, 8, 16]" for N, O, S. Empty string uses defaults. protonate_elements: Atomic numbers to consider for protonation, e.g., "[7, 8]" for N, O. Empty string uses defaults. 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.

Returns: Workflow object representing the submitted workflow

Examples: # Phenol pKa result = submit_pka_workflow( initial_molecule="Oc1ccccc1", name="pKa phenol", deprotonate_elements="[8]" # Only consider oxygen )

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
initial_moleculeYesSMILES string of the molecule to calculate pKa
pka_rangeNopKa range [min, max] to search (e.g., [2, 12])
deprotonate_elementsNoComma-separated elements for deprotonation (e.g., 'N,O,S'). Empty for auto-detect
protonate_elementsNoComma-separated elements for protonation (e.g., 'N,O'). Empty for auto-detect
nameNoWorkflow name for identification and trackingpKa 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 well: it explains this is a workflow submission (implying asynchronous processing), mentions credit spending limits, and describes what microscopic pKa calculation entails. However, it doesn't disclose potential rate limits, authentication requirements, or error conditions.

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

Conciseness5/5

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

Perfectly structured: starts with purpose statement, provides conceptual explanation, lists parameters with examples, describes return value, and includes a practical code example. Every sentence earns its place with no redundancy or wasted words.

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 7-parameter workflow submission tool with no annotations and no output schema, the description does well: explains the calculation type, parameters, returns, and includes an example. However, it doesn't fully address what happens after submission (how to monitor workflow, typical runtime, or how to retrieve results).

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 baseline is 3. The description adds value by providing a clear conceptual explanation of microscopic pKa, practical examples of parameter values, and an example showing how to use the tool with specific parameters, going beyond the schema's technical descriptions.

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 microscopic pKa prediction workflow') and resource ('using Rowan v2 API'), with a detailed explanation of what microscopic pKa means. It distinguishes from siblings by focusing specifically on pKa prediction, unlike other workflow tools for different calculations like docking, ADMET, or protein operations.

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 for pKa prediction of molecules via SMILES strings, but doesn't explicitly state when to use this tool versus alternatives like submit_macropka_workflow (a sibling tool) or other chemical analysis workflows. The example provides a concrete use case but lacks broader contextual guidance.

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

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/k-yenko/rowan-mcp'

If you have feedback or need assistance with the MCP directory API, please join our Discord server