102 lines
1.9 KiB
Plaintext
102 lines
1.9 KiB
Plaintext
{
|
|
"cells": [
|
|
{
|
|
"cell_type": "markdown",
|
|
"metadata": {},
|
|
"source": [
|
|
"# DeepDrug3D"
|
|
]
|
|
},
|
|
{
|
|
"cell_type": "code",
|
|
"execution_count": 1,
|
|
"metadata": {},
|
|
"outputs": [],
|
|
"source": [
|
|
"import numpy as np"
|
|
]
|
|
},
|
|
{
|
|
"cell_type": "markdown",
|
|
"metadata": {},
|
|
"source": [
|
|
"## Create pocket lists\n",
|
|
"4 pockets are created :\n",
|
|
" + control\n",
|
|
" + steroid\n",
|
|
" + heme\n",
|
|
" + nucleotide"
|
|
]
|
|
},
|
|
{
|
|
"cell_type": "code",
|
|
"execution_count": 3,
|
|
"metadata": {},
|
|
"outputs": [],
|
|
"source": [
|
|
"with open(\"control.list\", \"r\") as filin:\n",
|
|
" control = filin.read()\n",
|
|
"control = control.split(\"\\n\")\n",
|
|
"control.pop()"
|
|
]
|
|
},
|
|
{
|
|
"cell_type": "code",
|
|
"execution_count": null,
|
|
"metadata": {},
|
|
"outputs": [],
|
|
"source": [
|
|
"with open(\"steroid.list\", \"r\") as filin:\n",
|
|
" steroid = filin.read()\n",
|
|
"steroid = steroid.split(\"\\n\")\n",
|
|
"steroid.pop()"
|
|
]
|
|
},
|
|
{
|
|
"cell_type": "code",
|
|
"execution_count": null,
|
|
"metadata": {},
|
|
"outputs": [],
|
|
"source": [
|
|
"with open(\"heme.list\", \"r\") as filin:\n",
|
|
" heme = filin.read()\n",
|
|
"heme = heme.split(\"\\n\")\n",
|
|
"heme.pop()"
|
|
]
|
|
},
|
|
{
|
|
"cell_type": "code",
|
|
"execution_count": null,
|
|
"metadata": {},
|
|
"outputs": [],
|
|
"source": [
|
|
"with open(\"nucleotide.list\", \"r\") as filin:\n",
|
|
" nucleotide = filin.read()\n",
|
|
"nucleotide = nucleotide.split(\"\\n\")\n",
|
|
"nucleotide.pop()"
|
|
]
|
|
}
|
|
],
|
|
"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": "3.7.4"
|
|
}
|
|
},
|
|
"nbformat": 4,
|
|
"nbformat_minor": 4
|
|
}
|