Protein Ph Linkage Tools#

Configuration File: protein_ph_linkage_tools.json Tool Type: Local Tools Count: 1

This page contains all tools defined in the protein_ph_linkage_tools.json configuration file.

Available Tools#

Protein_calculate_pH_linkage (Type: ProteinPHLinkageTool)#

Integrate matched bound/free protein pKas into reference-normalized pH linkage curves, with decla…

Protein_calculate_pH_linkage tool specification

Tool Information:

  • Name: Protein_calculate_pH_linkage

  • Type: ProteinPHLinkageTool

  • Description: Integrate matched bound/free protein pKas into reference-normalized pH linkage curves, with declared inventory, component and terminal breakdowns. Postprocessing only; no pKa prediction, absolute affinity or experimental validation.

Parameters:

  • bound_groups (array) (required) No description

  • free_groups (array) (required) No description

  • expected_groups (array) (required) No description

  • reference_kind (string) (required) Both modes use titrating pKas; same-coordinate means component extraction, never a frozen protonation state.

  • ph_values (array) (required) No description

  • reference_ph (number) (required) No description

  • temperature_kelvin ([‘number’, ‘null’]) (optional) Defaults to 298.15 K; used only to convert the conditional logarithmic trend to kcal/mol.

  • provenance (object) (required) No description

Example Usage:

query = {
    "name": "Protein_calculate_pH_linkage",
    "arguments": {
        "bound_groups": ["item1", "item2"],
        "free_groups": ["item1", "item2"],
        "expected_groups": ["item1", "item2"],
        "reference_kind": "example_value",
        "ph_values": ["item1", "item2"],
        "reference_ph": "example_value",
        "provenance": "example_value"
    }
}
result = tu.run(query)