Pdb Stereochemistry Tools#

Configuration File: pdb_stereochemistry_tools.json Tool Type: Local Tools Count: 2

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

Available Tools#

PDB_check_alpha_stereochemistry (Type: PDBStereochemistryTool)#

Check C-alpha orientation in local legacy PDB or public 1UBQ. Reports L/D mirrors, degenerate cen…

PDB_check_alpha_stereochemistry tool specification

Tool Information:

  • Name: PDB_check_alpha_stereochemistry

  • Type: PDBStereochemistryTool

  • Description: Check C-alpha orientation in local legacy PDB or public 1UBQ. Reports L/D mirrors, degenerate centers, altloc and missing-atom coverage. Distance checks miss reflections. No reconstruction, full stereochemistry or binding validation.

Parameters:

  • pdb_path ([‘string’, ‘null’]) (optional) Local legacy PDB path; stays local. Exactly one input source.

  • pdb_content ([‘string’, ‘null’]) (optional) Inline legacy PDB coordinates; stays local. Exactly one input source.

  • pdb_id ([‘string’, ‘null’]) (optional) Four-character public RCSB identifier, e.g. 1UBQ; downloads only this public PDB.

  • model_index ([‘integer’, ‘null’]) (optional) Model by file order, default 1. Models are never pooled.

  • protein_residue_aliases ([‘object’, ‘null’]) (optional) Caller declarations mapping nonstandard protein names to canonical 3-letter amino acids; e.g. NLN to ASN for a known GLYCAM input.

  • max_residue_details ([‘integer’, ‘null’]) (optional) Bound residue detail lists, default 100. Counts and coordinate sequences stay complete; truncation is reported.

  • expected_orientation ([‘string’, ‘null’]) (optional) Expected C-alpha geometric orientation, default L for natural encoded proteins; D is also supported. This is not formal CIP R/S.

  • degenerate_tolerance_A3 ([‘number’, ‘null’]) (optional) Absolute N/CA/C/CB determinant tolerance in A^3 for degenerate centers, default 1e-6.

  • minimum_normalized_volume ([‘number’, ‘null’]) (optional) Minimum absolute determinant divided by product of CA-N/CA-C/CA-CB lengths. Default0.1 flags near-planar centers;0 requests orientation only. A geometric diagnostic, not a calibrated energy cutoff.

Example Usage:

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

PDB_check_beta_stereochemistry (Type: PDBStereochemistryTool)#

Check natural Ile/Thr C-beta orientation in local legacy PDB or public1UBQ. Reports inverted/plan…

PDB_check_beta_stereochemistry tool specification

Tool Information:

  • Name: PDB_check_beta_stereochemistry

  • Type: PDBStereochemistryTool

  • Description: Check natural Ile/Thr C-beta orientation in local legacy PDB or public1UBQ. Reports inverted/planar centers, missing-atom coverage, altlocs and no-site applicability. Complements C-alpha checking; no repair or binding validation.

Parameters:

  • pdb_path ([‘string’, ‘null’]) (optional) Local legacy PDB path; stays local. Exactly one input source.

  • pdb_content ([‘string’, ‘null’]) (optional) Inline legacy PDB coordinates; stays local. Exactly one input source.

  • pdb_id ([‘string’, ‘null’]) (optional) Four-character public RCSB identifier, e.g. 1UBQ; downloads only this public PDB.

  • model_index ([‘integer’, ‘null’]) (optional) Model by file order, default 1. Models are never pooled.

  • protein_residue_aliases ([‘object’, ‘null’]) (optional) Caller declarations mapping nonstandard protein names to canonical 3-letter amino acids; e.g. NLN to ASN for a known GLYCAM input.

  • max_residue_details ([‘integer’, ‘null’]) (optional) Bound residue detail lists, default 100. Counts and coordinate sequences stay complete; truncation is reported.

  • expected_orientation ([‘string’, ‘null’]) (optional) Expected Ile/Thr beta geometry, default natural; opposite is supported. Independent of alpha L/D labels and not formal CIP R/S.

  • degenerate_tolerance_A3 ([‘number’, ‘null’]) (optional) Absolute CB/CA/CG1-or-OG1/CG2 determinant tolerance in A^3 for degenerate beta centers, default1e-6.

  • minimum_normalized_volume ([‘number’, ‘null’]) (optional) Minimum absolute beta determinant divided by product of center-neighbor lengths; default0.1 flags near-planar centers,0 requests orientation only. Geometric diagnostic, not an energy cutoff.

Example Usage:

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