Getting StartedΒΆ

This example provides the fastest way to run MHCXGraph with a minimal manifest configuration. It uses the multiple mode, reads structures from examples/input/renumbered, applies the predefined MHC1 selector, and writes the results to examples/results/minimal.

Before running this example, make sure the input structures have already been renumbered if you intend to use the MHC1 selector. The predefined MHC1 and MHC2 selectors follow IMGT numbering, as described in Using hotspot residue selectors.

Run the example with:

MHCXGraph run examples/manifests/manifest-minimal.json

The corresponding manifest is shown below:

{
  "settings": {
    "run_mode": "multiple",
    "run_name": "minimal",
    "output_path": "examples/results/minimal",
    "edge_threshold": 8.5,
    "node_granularity": "all_atoms",
    "triad_rsa": false,
    "rsa_filter": 0.1,
    "global_distance_diff_threshold": 2.0,
    "local_distance_diff_threshold": 1.0,
    "distance_bin_width": 2
  },

  "inputs": [
    {
      "path": "examples/input/renumbered",
      "enable_tui": false,
      "extensions": [".pdb", ".cif"],
      "selectors": [
        { "name": "MHC1" }
      ]
    }
  ],

  "selectors": {
    "MHC1": {
      "chains": ["C"],
      "residues": {
        "A": [18, 19, 42, 43, 44, 54, 55, 56, 58, 59, 61, 62, 63, 64, 65, 66,
              68, 69, 70, 71, 72, 73, 75, 76, 79, 80, 83, 84, 89, 108, 109,
              142, 143, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155,
              156, 157, 158, 159, 161, 162, 163, 165, 166, 167, 169, 170, 171]
      }
    },

    "MHC2": {
      "chains": ["C"],
      "residues": {
        "A": [37, 51, 52, 53, 55, 56, 58, 59, 60, 62, 63, 65, 66, 67, 69],
        "B": [56, 57, 59, 60, 61, 62, 63, 65, 66, 67, 68, 69, 70, 71, 72, 73,
              74, 77, 78, 81]
      }
    },

    "general": {
      "chains": ["C"],
      "structures": ["helix"],
      "residues": {}
    }
  }
}

This manifest is intentionally minimal. It includes only the parameters required for a basic execution, while leaving the remaining options at their default values.

The main settings used in this example are:

Field

Description

run_mode

Uses the multiple execution mode.

run_name

Sets the name of the run to minimal.

output_path

Writes the output to examples/results/minimal.

edge_threshold

Sets the distance cutoff used to define graph edges.

node_granularity

Uses all_atoms to compute residue centroids.

triad_rsa

Disables RSA-based features in the triad token.

rsa_filter

Restricts the analysis to solvent-exposed canonical residues.

global_distance_diff_threshold

Sets the global distance consistency threshold used during frame generation.

local_distance_diff_threshold

Sets the local distance consistency threshold used during triad comparison.

distance_bin_width

Defines the discretization width for distance values.

For a complete description of these fields, see Execution configuration (Manifest).