{
"cells": [
{
"cell_type": "markdown",
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},
"source": [
"# TCRen potential & contact-statistics analysis\n",
"\n",
"Reproduces the core TCRen-manuscript analyses from the committed contact data\n",
"(`data/contact_maps_PDB.csv` + `data/summary_PDB_structures.csv`):\n",
"\n",
"- the TCRen potential (re-derived) and its agreement with the published values;\n",
"- the Miyazawa-Jernigan and Keskin reference potentials;\n",
"- the distribution of TCR-peptide contacts per structure and per TCR region;\n",
"- how contacts distribute over peptide and CDR3 positions as a function of length."
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "20a57c9e",
"metadata": {
"execution": {
"iopub.execute_input": "2026-06-12T07:24:11.181863Z",
"iopub.status.busy": "2026-06-12T07:24:11.181788Z",
"iopub.status.idle": "2026-06-12T07:24:11.917509Z",
"shell.execute_reply": "2026-06-12T07:24:11.917273Z"
},
"language": "python"
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"python 3.12.12 | polars 1.39.3 | tcren 0.1.0\n"
]
},
{
"data": {
"text/html": [
"\n",
"
shape: (5, 8)| pdb.id | chain.type.from | region.type.from | residue.aa.from | residue.aa.to | peptide_pos | peptide_len | cdr3_len |
|---|
| str | str | str | str | str | i64 | u32 | u32 |
| "5m01" | "TRA" | "CDR3" | "Y" | "K" | 0 | 9 | 12 |
| "5m01" | "TRA" | "CDR3" | "Y" | "K" | 0 | 9 | 12 |
| "5m01" | "TRA" | "CDR3" | "Y" | "A" | 1 | 9 | 12 |
| "5m01" | "TRA" | "CDR3" | "Y" | "A" | 1 | 9 | 12 |
| "5m01" | "TRA" | "CDR3" | "G" | "A" | 3 | 9 | 12 |