{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# mqapRNA in rna-tools"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Single Model"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import rna_tools.rna_tools_lib as rtl"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"r = rtl.RNAStructure('../rna_tools/input/mq/5e3hBC.pdb')"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"RNAStructure /Users/magnus/work/src/rna-tools/rna_tools/input/mq/5e3hBC.pdb"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"r"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[-16410.4, 83589.0, -0.196323, 0.0, 0.0, 0.0]"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"r.mq(method=\"RASP\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"r.mq(method=\"Dfire\")"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"0.76172626"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"r.mq(method=\"rna3dcnn\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"r.mq(method=\"qrna\")"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"0.0"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"r.mq(method=\"clashscore\")"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"0.0"
]
},
"execution_count": 22,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"r.mq(method=\"analyzegeometry\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Multiple models"
]
},
{
"cell_type": "code",
"execution_count": 42,
"metadata": {},
"outputs": [],
"source": [
"rnas = rtl.load_rnas('../rna_tools/input/mq/*.pdb')"
]
},
{
"cell_type": "code",
"execution_count": 43,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"5e3hBC.pdb [-16410.4, 83589.0, -0.196323, 0.0, 0.0, 0.0]\n",
"S_000001_000.pdb [-15191.9, 460077.0, -0.0330204, 0.0, 0.0, 0.0]\n",
"1a9nR.pdb [-9869.61, 66447.0, -0.148534, 0.0, 0.0, 0.0]\n",
"3b58ABC.pdb [-31456.9, 344202.0, -0.0913908, 0.0, 0.0, 0.0]\n",
"1a9n.pdb [-9869.61, 66447.0, -0.148534, 0.0, 0.0, 0.0]\n"
]
}
],
"source": [
"for r in rnas:\n",
" print(r.name, r.mq(method=\"RASP\"))"
]
},
{
"cell_type": "code",
"execution_count": 58,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"5e3hBC.pdb -19451.089802\n",
"S_000001_000.pdb -52615.344214\n",
"1a9nR.pdb -12480.188898\n",
"3b58ABC.pdb -53013.816472\n",
"1a9n.pdb -12480.188898\n"
]
}
],
"source": [
"rnas_names = []\n",
"rnas_scores = []\n",
"for r in rnas:\n",
" print(r.name, r.mq(method=\"Dfire\"))\n",
" rnas_names.append(r.name)\n",
" rnas_scores.append(r.mq(method=\"Dfire\"))"
]
},
{
"cell_type": "code",
"execution_count": 86,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
"\n",
"
\n",
" \n",
" \n",
" | \n",
" Name | \n",
" Score | \n",
"
\n",
" \n",
" \n",
" \n",
" | 3 | \n",
" 3b58ABC.pdb | \n",
" -53013.816472 | \n",
"
\n",
" \n",
" | 1 | \n",
" S_000001_000.pdb | \n",
" -52615.344214 | \n",
"
\n",
" \n",
" | 0 | \n",
" 5e3hBC.pdb | \n",
" -19451.089802 | \n",
"
\n",
" \n",
" | 2 | \n",
" 1a9nR.pdb | \n",
" -12480.188898 | \n",
"
\n",
" \n",
" | 4 | \n",
" 1a9n.pdb | \n",
" -12480.188898 | \n",
"
\n",
" \n",
"
\n",
"