Pdbtm Tools#

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

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

Available Tools#

PDBTM_get_topology (Type: PDBTMTool)#

Retrieve structure-derived transmembrane classification for one PDB entry from PDBTM: per-chain t…

PDBTM_get_topology tool specification

Tool Information:

  • Name: PDBTM_get_topology

  • Type: PDBTMTool

  • Description: Retrieve structure-derived transmembrane classification for one PDB entry from PDBTM: per-chain type (alpha-helical, beta-barrel, or not membrane-embedded) and transmembrane segment count, computed directly from coordinates. Example: pdb_id=’2por’ (porin) returns a 16-strand beta-barrel; pdb_id=’1prc’ (photosynthetic reaction centre) shows 5 TM helices each in the L and M subunits and 1 in H. Complements OPM_search_structures (geometry/energetics) and TopDB_get_topology (curated evidence).

Parameters:

  • pdb_id (string) (required) 4-character PDB identifier, e.g. ‘2por’, ‘1prc’.

Example Usage:

query = {
    "name": "PDBTM_get_topology",
    "arguments": {
        "pdb_id": "example_value"
    }
}
result = tu.run(query)