{ "cells": [ { "cell_type": "markdown", "id": "ab81b2f5", "metadata": {}, "source": [ "# Summary of *apo*-*holo* data" ] }, { "cell_type": "markdown", "id": "2bfa6a6f", "metadata": {}, "source": [ "## Introduction\n", "\n", "In this notebook, we look at the data used to create the *apo*-*holo* comparisons, generating plots and summary statistics." ] }, { "cell_type": "code", "execution_count": 1, "id": "b7b751a5", "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "Matplotlib is building the font cache; this may take a moment.\n" ] } ], "source": [ "import os\n", "import subprocess\n", "import tempfile\n", "\n", "import logomaker\n", "import matplotlib.pyplot as plt\n", "import networkx as nx\n", "import numpy as np\n", "import openchord\n", "import pandas as pd\n", "from IPython.display import display, Markdown\n", "from pyxdameraulevenshtein import damerau_levenshtein_distance\n", "\n", "from tcr_pmhc_interface_analysis.utils import mhc_slug_to_code" ] }, { "cell_type": "code", "execution_count": 2, "id": "38a0b629", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | file_name | \n", "pdb_id | \n", "structure_type | \n", "state | \n", "alpha_chain | \n", "beta_chain | \n", "antigen_chain | \n", "mhc_chain1 | \n", "mhc_chain2 | \n", "cdr_sequences_collated | \n", "peptide_sequence | \n", "mhc_slug | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "1ao7_D-E-C-A-B_tcr_pmhc.pdb | \n", "1ao7 | \n", "tcr_pmhc | \n", "holo | \n", "D | \n", "E | \n", "C | \n", "A | \n", "B | \n", "DRGSQS-IYSNGD-AVTTDSWGKLQ-MNHEY-SVGAGI-ASRPGLA... | \n", "LLFGYPVYV | \n", "hla_a_02_01 | \n", "
1 | \n", "1b0g_C-A-B_pmhc.pdb | \n", "1b0g | \n", "pmhc | \n", "apo | \n", "NaN | \n", "NaN | \n", "C | \n", "A | \n", "B | \n", "NaN | \n", "ALWGFFPVL | \n", "hla_a_02_01 | \n", "
2 | \n", "1b0g_F-D-E_pmhc.pdb | \n", "1b0g | \n", "pmhc | \n", "apo | \n", "NaN | \n", "NaN | \n", "F | \n", "D | \n", "E | \n", "NaN | \n", "ALWGFFPVL | \n", "hla_a_02_01 | \n", "
3 | \n", "1bd2_D-E-C-A-B_tcr_pmhc.pdb | \n", "1bd2 | \n", "tcr_pmhc | \n", "holo | \n", "D | \n", "E | \n", "C | \n", "A | \n", "B | \n", "NSMFDY-ISSIKDK-AAMEGAQKLV-MNHEY-SVGAGI-ASSYPGG... | \n", "LLFGYPVYV | \n", "hla_a_02_01 | \n", "
4 | \n", "1bii_P-A-B_pmhc.pdb | \n", "1bii | \n", "pmhc | \n", "apo | \n", "NaN | \n", "NaN | \n", "P | \n", "A | \n", "B | \n", "NaN | \n", "RGPGRAFVTI | \n", "h2_dd | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
386 | \n", "7rtd_C-A-B_pmhc.pdb | \n", "7rtd | \n", "pmhc | \n", "apo | \n", "NaN | \n", "NaN | \n", "C | \n", "A | \n", "B | \n", "NaN | \n", "YLQPRTFLL | \n", "hla_a_02_01 | \n", "
387 | \n", "7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "7rtr | \n", "tcr_pmhc | \n", "holo | \n", "D | \n", "E | \n", "C | \n", "A | \n", "B | \n", "DRGSQS-IYSNGD-AVNRDDKII-SEHNR-FQNEAQ-ASSPDIEQY | \n", "YLQPRTFLL | \n", "hla_a_02_01 | \n", "
388 | \n", "8gvb_A-B-P-H-L_tcr_pmhc.pdb | \n", "8gvb | \n", "tcr_pmhc | \n", "holo | \n", "A | \n", "B | \n", "P | \n", "H | \n", "L | \n", "YGATPY-YFSGDTLV-AVGFTGGGNKLT-SEHNR-FQNEAQ-ASSD... | \n", "RYPLTFGW | \n", "hla_a_24_02 | \n", "
389 | \n", "8gvg_A-B-P-H-L_tcr_pmhc.pdb | \n", "8gvg | \n", "tcr_pmhc | \n", "holo | \n", "A | \n", "B | \n", "P | \n", "H | \n", "L | \n", "YGATPY-YFSGDTLV-AVGFTGGGNKLT-SEHNR-FQNEAQ-ASSD... | \n", "RFPLTFGW | \n", "hla_a_24_02 | \n", "
390 | \n", "8gvi_A-B-P-H-L_tcr_pmhc.pdb | \n", "8gvi | \n", "tcr_pmhc | \n", "holo | \n", "A | \n", "B | \n", "P | \n", "H | \n", "L | \n", "YGATPY-YFSGDTLV-AVVFTGGGNKLT-SEHNR-FQNEAQ-ASSL... | \n", "RYPLTFGW | \n", "hla_a_24_02 | \n", "
391 rows × 12 columns
\n", "\n", " | MHC Allele | \n", "Peptide | \n", "
---|---|---|
Index | \n", "\n", " | \n", " |
1 | \n", "h2_db | \n", "ASNENMETM | \n", "
2 | \n", "h2_db | \n", "KAPANFATM | \n", "
3 | \n", "h2_db | \n", "KAPFNFATM | \n", "
4 | \n", "h2_db | \n", "KAPYDYAPI | \n", "
5 | \n", "h2_db | \n", "KAPYNFATM | \n", "
... | \n", "... | \n", "... | \n", "
77 | \n", "hla_b_51_01 | \n", "TAFTIPSI | \n", "
78 | \n", "hla_b_53_01 | \n", "QASQEVKNW | \n", "
79 | \n", "hla_b_81_01 | \n", "TPQDLNTML | \n", "
80 | \n", "hla_c_08_02 | \n", "GADGVGKSAL | \n", "
81 | \n", "hla_e_01_03 | \n", "RLPAKAPLL | \n", "
81 rows × 2 columns
\n", "