618 lines
16 KiB
Plaintext
618 lines
16 KiB
Plaintext
{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 4,
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||
"metadata": {},
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"outputs": [],
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"source": [
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"MD_finish = '''1ao7\n",
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"1mi5\n",
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"1oga\n",
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"2vlj\n",
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"2vlk\n",
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"3o41\n",
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"4ftv\n",
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"1bd2\n",
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"1fo0\n",
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"1j8h\n",
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"inam\n",
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"2bnr\n",
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"2iam\n",
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"2ol3\n",
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"2p5e\n",
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"2z31\n",
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"3h9s\n",
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"3hg1\n",
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"3kps\n",
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"3pwp\n",
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"3qdg\n",
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"3qdm\n",
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"3qib\n",
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"3vxm\n",
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"3vxs\n",
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"4jrx\n",
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"5brz\n",
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"5bs0\n",
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"4g9f\n",
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"5nht\n",
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"5nqk\n",
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"5isz\n",
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"3gsn\n",
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"1d9k\n",
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"1u3h\n",
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"3dxa\n",
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"3ffc\n",
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"3kpr\n",
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"3sjv\n",
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"3utt\n",
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"4eup\n",
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"4h1l\n",
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"4mji\n",
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"4qrp\n",
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"5c0a\n",
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"4ozf\n",
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"4pri\n",
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"5eu6\n",
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"5ivx\n",
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"5m02\n",
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"5men\n",
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"5tez\n",
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"5yxn\n",
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"6am5\n",
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"6amu\n",
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"6avf\n",
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"6cql\n",
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"6g9q\n",
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"6mtm\n",
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"6px6\n",
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"6py2\n",
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"6r0e\n",
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"6r2l\n",
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"6rpa\n",
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"6tro\n",
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"6vrm\n",
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"6vrn\n",
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"6zkw\n",
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"7dzm\n",
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"7jwj\n",
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"7n1e\n",
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"7n1f\n",
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"7n2n\n",
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"7na5\n",
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"7ndq\n",
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"7nme\n",
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"7ow5\n",
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"7qpj\n",
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"7rtr\n",
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"7sg0\n",
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"7t2c\n",
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"8gom\n",
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"8gvb\n",
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"1zgl\n",
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"1g6r\n",
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"3qiu\n",
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"4p2o\n",
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"6u3n\n",
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"2ypl'''"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 13,
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"metadata": {},
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"outputs": [],
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"source": [
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"run_MD = set(MD_finish.splitlines())"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 14,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"89"
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]
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},
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"execution_count": 14,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"len(run_MD)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"metadata": {},
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/tmp/ipykernel_192237/2850835352.py:1: DeprecationWarning: \n",
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||
"Pyarrow will become a required dependency of pandas in the next major release of pandas (pandas 3.0),\n",
|
||
"(to allow more performant data types, such as the Arrow string type, and better interoperability with other libraries)\n",
|
||
"but was not found to be installed on your system.\n",
|
||
"If this would cause problems for you,\n",
|
||
"please provide us feedback at https://github.com/pandas-dev/pandas/issues/54466\n",
|
||
" \n",
|
||
" import pandas as pd\n"
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||
]
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||
},
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"<bound method NDFrame.head of pdb_id MHC_class TCR_alpha TCR_beta peptide MHC_alpha MHC_beta Beta2m \\\n",
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"0 1d9k 2 A B P C D NaN \n",
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"1 1g6r 1 A B P H NaN L \n",
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"2 1kj2 1 A B P H NaN L \n",
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"3 1mwa 1 A B P H NaN L \n",
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"4 1u3h 2 E F I G H NaN \n",
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".. ... ... ... ... ... ... ... ... \n",
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"141 7sg0 2 D E C A B NaN \n",
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"142 7t2c 2 D E C A B NaN \n",
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"143 8gom 1 D E C A NaN B \n",
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"144 8gvb 1 A B P H NaN L \n",
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"145 7phr 1 A B P H NaN L \n",
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"\n",
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" protein_type DOI ... No. of bonds Polar Surface Area \\\n",
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"0 m 10.7554/eLife.82934 ... NaN NaN \n",
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"1 m 10.7554/eLife.82916 ... 149.0 415.57 \n",
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"2 m 10.7554/eLife.82914 ... NaN NaN \n",
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"3 m 10.7554/eLife.82912 ... NaN NaN \n",
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"4 m 10.7554/eLife.82935 ... NaN NaN \n",
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".. ... ... ... ... ... \n",
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"141 s 10.1093/nar/gkad398 ... NaN NaN \n",
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"142 s 10.1093/nar/gkad401 ... NaN NaN \n",
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"143 s 10.1093/nar/gkad386 ... NaN NaN \n",
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"144 s 10.1093/nar/gkad383 ... NaN NaN \n",
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"145 m 10.1093/nar/gkad380 ... NaN NaN \n",
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"\n",
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" XLOGP3 open banel LogP HB donor HB acceptor Rotatable bonds \\\n",
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"0 NaN NaN NaN NaN NaN \n",
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"1 1.91 -0.09 12.0 13.0 40.0 \n",
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"2 NaN NaN NaN NaN NaN \n",
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"3 NaN NaN NaN NaN NaN \n",
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"4 NaN NaN NaN NaN NaN \n",
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".. ... ... ... ... ... \n",
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"141 NaN NaN NaN NaN NaN \n",
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"142 NaN NaN NaN NaN NaN \n",
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"143 NaN NaN NaN NaN NaN \n",
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"144 NaN NaN NaN NaN NaN \n",
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"145 NaN NaN NaN NaN NaN \n",
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"\n",
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" Canonical SMILES Unnamed: 49 \\\n",
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"0 NaN NaN \n",
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"1 CC[C@@H]([C@@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N... NaN \n",
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"2 NaN NaN \n",
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"3 NaN NaN \n",
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"4 NaN NaN \n",
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".. ... ... \n",
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"141 NaN NaN \n",
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"142 NaN NaN \n",
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"143 NaN NaN \n",
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"144 NaN NaN \n",
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"145 NaN NaN \n",
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"\n",
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" others \n",
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"0 NaN \n",
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"1 NaN \n",
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"2 NaN \n",
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"3 B链116，117动画缺失，文件正常 \n",
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"4 NaN \n",
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".. ... \n",
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"141 NaN \n",
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"142 NaN \n",
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"143 NaN \n",
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"144 NaN \n",
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"145 有peptides的结果中是否存在序列数目大于5的结果: 1 \\r\\n ['7phr'] \n",
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"\n",
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"[146 rows x 51 columns]>\n"
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]
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}
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],
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"source": [
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"import pandas as pd\n",
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"\n",
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"# 假设Excel文件的路径为'path_to_excel_file.xlsx'\n",
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"file_path = 'TCR-pMHC4.xlsx'\n",
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"\n",
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"# 读取名为'sheet1'的工作表，第一行作为列名\n",
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"df = pd.read_excel(file_path, sheet_name='Sheet1', header=0, engine='calamine')\n",
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"\n",
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"# 显示数据帧以确认加载正确\n",
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"print(df.head)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 15,
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"metadata": {},
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"outputs": [],
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"source": [
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"column_set = set(df['pdb_id'])"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 16,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"146"
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]
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},
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"execution_count": 16,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"len(column_set)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 21,
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"metadata": {},
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"outputs": [
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||
{
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||
"data": {
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||
"text/plain": [
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||
"89"
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||
]
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||
},
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||
"execution_count": 21,
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||
"metadata": {},
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||
"output_type": "execute_result"
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}
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],
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"source": [
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||
"len(run_MD)"
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]
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},
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{
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"cell_type": "code",
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||
"execution_count": 18,
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||
"metadata": {},
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"outputs": [],
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"source": [
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||
"diff = column_set - run_MD"
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]
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||
},
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{
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"cell_type": "code",
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||
"execution_count": 20,
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||
"metadata": {},
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||
"outputs": [
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||
{
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||
"data": {
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||
"text/plain": [
|
||
"59"
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||
]
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||
},
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||
"execution_count": 20,
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||
"metadata": {},
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||
"output_type": "execute_result"
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||
}
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||
],
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||
"source": [
|
||
"len(diff)"
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||
]
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||
},
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||
{
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||
"cell_type": "code",
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||
"execution_count": 24,
|
||
"metadata": {},
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||
"outputs": [
|
||
{
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||
"data": {
|
||
"text/plain": [
|
||
"110"
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||
]
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||
},
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||
"execution_count": 24,
|
||
"metadata": {},
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||
"output_type": "execute_result"
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||
}
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||
],
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||
"source": [
|
||
"len(df[df['MHC_class'] == 1])"
|
||
]
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||
},
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||
{
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||
"cell_type": "code",
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||
"execution_count": 25,
|
||
"metadata": {},
|
||
"outputs": [
|
||
{
|
||
"data": {
|
||
"text/plain": [
|
||
"36"
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||
]
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||
},
|
||
"execution_count": 25,
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||
"metadata": {},
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||
"output_type": "execute_result"
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||
}
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||
],
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||
"source": [
|
||
"len(df[df['MHC_class'] == 2])"
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||
]
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||
},
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||
{
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||
"cell_type": "code",
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||
"execution_count": 26,
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||
"metadata": {},
|
||
"outputs": [
|
||
{
|
||
"data": {
|
||
"text/plain": [
|
||
"{'1kj2',\n",
|
||
" '1mwa',\n",
|
||
" '1nam',\n",
|
||
" '2nx5',\n",
|
||
" '2vlr',\n",
|
||
" '3mbe',\n",
|
||
" '3mv7',\n",
|
||
" '3mv8',\n",
|
||
" '3mv9',\n",
|
||
" '3o4l',\n",
|
||
" '3pqy',\n",
|
||
" '4e41',\n",
|
||
" '4gg6',\n",
|
||
" '4ozi',\n",
|
||
" '4p2q',\n",
|
||
" '4p2r',\n",
|
||
" '4z7u',\n",
|
||
" '4z7v',\n",
|
||
" '4z7w',\n",
|
||
" '5c07',\n",
|
||
" '5c08',\n",
|
||
" '5c09',\n",
|
||
" '5c0b',\n",
|
||
" '5c0c',\n",
|
||
" '5d2l',\n",
|
||
" '5d2n',\n",
|
||
" '5e6i',\n",
|
||
" '5e9d',\n",
|
||
" '5euo',\n",
|
||
" '5jhd',\n",
|
||
" '5ks9',\n",
|
||
" '5ksa',\n",
|
||
" '5ksb',\n",
|
||
" '5nme',\n",
|
||
" '5nmg',\n",
|
||
" '5wkh',\n",
|
||
" '5wlg',\n",
|
||
" '6avg',\n",
|
||
" '6bga',\n",
|
||
" '6bj2',\n",
|
||
" '6rp9',\n",
|
||
" '6rpb',\n",
|
||
" '6rsy',\n",
|
||
" '6u3o',\n",
|
||
" '6uk4',\n",
|
||
" '6uln',\n",
|
||
" '6uon',\n",
|
||
" '6vm8',\n",
|
||
" '6vmx',\n",
|
||
" '6vqo',\n",
|
||
" '7l1d',\n",
|
||
" '7n6e',\n",
|
||
" '7phr',\n",
|
||
" '7rdv',\n",
|
||
" '7rk7',\n",
|
||
" '7rrg',\n",
|
||
" '7sg1',\n",
|
||
" '7t2b',\n",
|
||
" '7z50'}"
|
||
]
|
||
},
|
||
"execution_count": 26,
|
||
"metadata": {},
|
||
"output_type": "execute_result"
|
||
}
|
||
],
|
||
"source": [
|
||
"diff"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 33,
|
||
"metadata": {},
|
||
"outputs": [],
|
||
"source": [
|
||
"!rm -rf ./fixed/*"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 34,
|
||
"metadata": {},
|
||
"outputs": [],
|
||
"source": [
|
||
"!cp single_polymeric_fix/*.pdb ./fixed\n",
|
||
"!cp multimer_polymeric_fix/*.pdb ./fixed"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 36,
|
||
"metadata": {},
|
||
"outputs": [
|
||
{
|
||
"data": {
|
||
"text/plain": [
|
||
"146"
|
||
]
|
||
},
|
||
"execution_count": 36,
|
||
"metadata": {},
|
||
"output_type": "execute_result"
|
||
}
|
||
],
|
||
"source": [
|
||
"from pathlib import Path\n",
|
||
"len(list(Path('fixed').glob('*.pdb')))"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 37,
|
||
"metadata": {},
|
||
"outputs": [],
|
||
"source": [
|
||
"!mkdir -p notrunMD"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 38,
|
||
"metadata": {},
|
||
"outputs": [],
|
||
"source": [
|
||
"from pathlib import Path\n",
|
||
"import shutil\n",
|
||
"\n",
|
||
"for i in diff:\n",
|
||
" shutil.copy(Path('./fixed').joinpath(f'{i}.modellerfix.pdb').as_posix(), Path('./notrunMD').joinpath(f'{i}.modellerfix.pdb').as_posix())"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 40,
|
||
"metadata": {},
|
||
"outputs": [
|
||
{
|
||
"data": {
|
||
"text/plain": [
|
||
"59"
|
||
]
|
||
},
|
||
"execution_count": 40,
|
||
"metadata": {},
|
||
"output_type": "execute_result"
|
||
}
|
||
],
|
||
"source": [
|
||
"len(list(Path('./notrunMD').glob('*.pdb')))"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 39,
|
||
"metadata": {},
|
||
"outputs": [
|
||
{
|
||
"name": "stdout",
|
||
"output_type": "stream",
|
||
"text": [
|
||
"notrunMD/\n",
|
||
"notrunMD/6uln.modellerfix.pdb\n",
|
||
"notrunMD/5ks9.modellerfix.pdb\n",
|
||
"notrunMD/1mwa.modellerfix.pdb\n",
|
||
"notrunMD/4z7w.modellerfix.pdb\n",
|
||
"notrunMD/7rdv.modellerfix.pdb\n",
|
||
"notrunMD/4z7u.modellerfix.pdb\n",
|
||
"notrunMD/5euo.modellerfix.pdb\n",
|
||
"notrunMD/5c08.modellerfix.pdb\n",
|
||
"notrunMD/6bga.modellerfix.pdb\n",
|
||
"notrunMD/1nam.modellerfix.pdb\n",
|
||
"notrunMD/5c07.modellerfix.pdb\n",
|
||
"notrunMD/7l1d.modellerfix.pdb\n",
|
||
"notrunMD/6vm8.modellerfix.pdb\n",
|
||
"notrunMD/7rk7.modellerfix.pdb\n",
|
||
"notrunMD/1kj2.modellerfix.pdb\n",
|
||
"notrunMD/6rpb.modellerfix.pdb\n",
|
||
"notrunMD/5nme.modellerfix.pdb\n",
|
||
"notrunMD/3mbe.modellerfix.pdb\n",
|
||
"notrunMD/6avg.modellerfix.pdb\n",
|
||
"notrunMD/5jhd.modellerfix.pdb\n",
|
||
"notrunMD/4p2r.modellerfix.pdb\n",
|
||
"notrunMD/3pqy.modellerfix.pdb\n",
|
||
"notrunMD/5e9d.modellerfix.pdb\n",
|
||
"notrunMD/3mv7.modellerfix.pdb\n",
|
||
"notrunMD/3mv9.modellerfix.pdb\n",
|
||
"notrunMD/2nx5.modellerfix.pdb\n",
|
||
"notrunMD/6rsy.modellerfix.pdb\n",
|
||
"notrunMD/7phr.modellerfix.pdb\n",
|
||
"notrunMD/6rp9.modellerfix.pdb\n",
|
||
"notrunMD/7rrg.modellerfix.pdb\n",
|
||
"notrunMD/5d2n.modellerfix.pdb\n",
|
||
"notrunMD/4ozi.modellerfix.pdb\n",
|
||
"notrunMD/2vlr.modellerfix.pdb\n",
|
||
"notrunMD/3o4l.modellerfix.pdb\n",
|
||
"notrunMD/5ksa.modellerfix.pdb\n",
|
||
"notrunMD/7n6e.modellerfix.pdb\n",
|
||
"notrunMD/4p2q.modellerfix.pdb\n",
|
||
"notrunMD/6uk4.modellerfix.pdb\n",
|
||
"notrunMD/6vmx.modellerfix.pdb\n",
|
||
"notrunMD/7z50.modellerfix.pdb\n",
|
||
"notrunMD/5d2l.modellerfix.pdb\n",
|
||
"notrunMD/4z7v.modellerfix.pdb\n",
|
||
"notrunMD/5e6i.modellerfix.pdb\n",
|
||
"notrunMD/6uon.modellerfix.pdb\n",
|
||
"notrunMD/6vqo.modellerfix.pdb\n",
|
||
"notrunMD/5wkh.modellerfix.pdb\n",
|
||
"notrunMD/5ksb.modellerfix.pdb\n",
|
||
"notrunMD/6bj2.modellerfix.pdb\n",
|
||
"notrunMD/7sg1.modellerfix.pdb\n",
|
||
"notrunMD/5c09.modellerfix.pdb\n",
|
||
"notrunMD/3mv8.modellerfix.pdb\n",
|
||
"notrunMD/4gg6.modellerfix.pdb\n",
|
||
"notrunMD/5nmg.modellerfix.pdb\n",
|
||
"notrunMD/5c0b.modellerfix.pdb\n",
|
||
"notrunMD/5c0c.modellerfix.pdb\n",
|
||
"notrunMD/5wlg.modellerfix.pdb\n",
|
||
"notrunMD/6u3o.modellerfix.pdb\n",
|
||
"notrunMD/7t2b.modellerfix.pdb\n",
|
||
"notrunMD/4e41.modellerfix.pdb\n"
|
||
]
|
||
}
|
||
],
|
||
"source": [
|
||
"!tar zcvf notrunMD.tar.gz notrunMD/"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": null,
|
||
"metadata": {},
|
||
"outputs": [],
|
||
"source": []
|
||
}
|
||
],
|
||
"metadata": {
|
||
"kernelspec": {
|
||
"display_name": "Python 3",
|
||
"language": "python",
|
||
"name": "python3"
|
||
},
|
||
"language_info": {
|
||
"codemirror_mode": {
|
||
"name": "ipython",
|
||
"version": 3
|
||
},
|
||
"file_extension": ".py",
|
||
"mimetype": "text/x-python",
|
||
"name": "python",
|
||
"nbconvert_exporter": "python",
|
||
"pygments_lexer": "ipython3",
|
||
"version": "3.10.13"
|
||
}
|
||
},
|
||
"nbformat": 4,
|
||
"nbformat_minor": 2
|
||
}
|