Protein Pkai Tools#

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

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

Available Tools#

PKAI_predict_sidechain_pka (Type: ProteinPKAITool)#

Predict six protein side-chain pKa types from one PDB with local CPU pKAI/pKAI+ weights. Returns …

PKAI_predict_sidechain_pka tool specification

Tool Information:

  • Name: PKAI_predict_sidechain_pka

  • Type: ProteinPKAITool

  • Description: Predict six protein side-chain pKa types from one PDB with local CPU pKAI/pKAI+ weights. Returns residue predictions and coverage. ARG/termini unsupported; not affinity or a complete pH binding cycle. Requires optional pKAI.

Parameters:

  • pdb_id ([‘string’, ‘null’]) (optional) Public four-character RCSB PDB ID; alternative to pdb_path/pdb_content. Only this option downloads public coordinates.

  • pdb_path ([‘string’, ‘null’]) (optional) Local single-model PDB file; no upload. Alternative to pdb_id/pdb_content.

  • pdb_content ([‘string’, ‘null’]) (optional) Single-model PDB text; processed locally without upload. Alternative to pdb_id/pdb_path.

  • python_executable ([‘string’, ‘null’]) (optional) Optional same-host Python interpreter with pKAI and torch installed; default current interpreter. No shell command.

  • model_variant ([‘string’, ‘null’]) (optional) pKAI+ (default) for single-structure diagnostics; pKAI for conformation sensitivity. Correlated variants of one model family.

  • threads ([‘integer’, ‘null’]) (optional) CPU threads, default1.

  • timeout_seconds ([‘integer’, ‘null’]) (optional) Finite worker timeout in seconds, default180.

Example Usage:

query = {
    "name": "PKAI_predict_sidechain_pka",
    "arguments": {
    }
}
result = tu.run(query)