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Created a Jupyter Notebook containing an minimal example of how to ex…
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…ecute each measure
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@mikicanyelles
mikicanyelles committed Jan 25, 2024
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Easy MD Analysis Example Notebook"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/mcanyelles/miniconda3/envs/rcbs/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
" from .autonotebook import tqdm as notebook_tqdm\n",
"/home/mcanyelles/miniconda3/envs/rcbs/lib/python3.11/site-packages/MDAnalysis/topology/TPRParser.py:161: DeprecationWarning: 'xdrlib' is deprecated and slated for removal in Python 3.13\n",
" import xdrlib\n"
]
}
],
"source": [
"from EMDA.emda import EMDA"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"parameters = 'parameters.prmtop'\n",
"trajectory = 'trajectory.nc'"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Trajectory has been loaded!\n"
]
}
],
"source": [
"emda = EMDA(parameters=parameters, trajectory=trajectory)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"emda.select('C10', 'C10', sel_type='at_name')\n",
"emda.select('C11', 'C11', sel_type='at_name')\n",
"emda.select('C12', 'C12', sel_type='at_name')\n",
"emda.select('C13', 'C13', sel_type='at_name')\n",
"emda.select('C14', 'C14', sel_type='at_name')\n",
"\n",
"emda.select('H12', ['H12A', 'H12B'], sel_type='at_name')\n",
"emda.select('Fe', 10596, sel_type='at_num')\n",
"\n",
"emda.select('cof', 10597, sel_type='at_num')\n",
"\n",
"emda.select('COO', [10599, 10600, 10601], sel_type='at_num')\n",
"\n",
"\n",
"emda.select('subs', 666, sel_type='res_num')\n",
"\n",
"emda.select('protein', 'protein')\n"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[1mMethod: add_RMSD\u001b[0m\n",
"Help:\n",
"DESCRIPTION:\n",
" This function outputs the RMSD of a selection\n",
"\n",
"No usage available.\n",
"\n",
"\n",
"\u001b[1mMethod: add_angle\u001b[0m\n",
"Help:\n",
"DESCRIPTION:\n",
" This functions measures the angle between 3 specified atoms and returns the value between 0 and 360 degrees.\n",
" The input selections have to be single atoms.\n",
"\n",
"No usage available.\n",
"\n",
"\n",
"\u001b[1mMethod: add_contacts\u001b[0m\n",
"Help:\n",
"DESCRIPTION:\n",
" This function takes a Universe, a selection and a radius and returns the list of residues nearer than the specified radius.\n",
"\n",
"No usage available.\n",
"\n",
"\n",
"\u001b[1mMethod: add_dihedral\u001b[0m\n",
"Help:\n",
"DESCRIPTION:\n",
" This functions measures the dihedral angle between 4 specified atoms and returns the dihedral value between 0 and 360 degrees.\n",
" The input selections have to be single atoms.\n",
"\n",
"No usage available.\n",
"\n",
"\n",
"\u001b[1mMethod: add_distWATbridge\u001b[0m\n",
"Help:\n",
"DESCRIPTION\n",
" This function takes a Universe, two selections and the size of their environments and returns the nearest bridging water between the two selections and the distance to both of them.\n",
"\n",
"No usage available.\n",
"\n",
"\n",
"\u001b[1mMethod: add_distance\u001b[0m\n",
"Help:\n",
"DESCRIPTION:\n",
" This function outputs the minimum measured distance between the two input selections or coordinates or their combination.\n",
"\n",
"USAGE:\n",
" EMDA.add_distance(name, sel1, sel2, type=['min' | 'cog' | 'com'])\n",
"\n",
"\n",
"\u001b[1mMethod: add_pKa\u001b[0m\n",
"Help:\n",
"DESCRIPTION:\n",
" This function allows the prediction of the pKa using PROpKa3 of the protein for each frame.\n",
"\n",
"No usage available.\n",
"\n",
"\n",
"\u001b[1mMethod: add_planar_angle\u001b[0m\n",
"Help:\n",
"DESCRIPTION:\n",
" This function measures the angle between two planes specified by three atoms each one and returns the angle.\n",
" The input selections have to contain three atoms.\n",
"\n",
"No usage available.\n",
"\n",
"\n",
"Use '>>> help(EMDA.add_***)' to get the complete information of an adder.\n"
]
}
],
"source": [
"emda.print_available_adders()"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
"emda.add_distance('dist_H12_cof', 'H12', 'cof', type='min')\n",
"emda.add_angle('ang_C12_cof_Fe', 'Fe', 'cof', 'C12')\n",
"emda.add_dihedral('dihe_C10C14', 'C10', 'C11', 'C13', 'C14', domain=180)\n",
"emda.add_contacts('contacts_COO', 'COO', sel_env=5, interactions='all', include_WAT=True)\n",
"emda.add_contacts('contacts_protein', 'protein')\n",
"emda.add_pKa('pka_protein', 'protein', )\n",
"emda.add_RMSD('rmsd_subs', 'subs', )"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{'contacts_COO', 'contacts_protein', 'dihe_C10C14', 'dist_H12_cof', 'ang_C12_cof_Fe'}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Measuring: 100%|██████████| 10/10 [00:17<00:00, 1.70s/Frame]\n"
]
}
],
"source": [
"emda.run()"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{'dist_H12_cof': Measure dataclass with:\n",
"\tName: dist_H12_cof\n",
"\tType: distance\n",
"\tSel: [<AtomGroup with 2 atoms>, <AtomGroup with 1 atom>]\n",
"\tStatus: Calculated\n",
", 'ang_C12_cof_Fe': Measure dataclass with:\n",
"\tName: ang_C12_cof_Fe\n",
"\tType: angle\n",
"\tSel: [<AtomGroup with 1 atom>, <AtomGroup with 1 atom>, <AtomGroup with 1 atom>]\n",
"\tStatus: Calculated\n",
", 'dihe_C10C14': Measure dataclass with:\n",
"\tName: dihe_C10C14\n",
"\tType: dihedral\n",
"\tSel: [<AtomGroup with 1 atom>, <AtomGroup with 1 atom>, <AtomGroup with 1 atom>, <AtomGroup with 1 atom>]\n",
"\tStatus: Calculated\n",
", 'contacts_COO': Measure dataclass with:\n",
"\tName: contacts_COO\n",
"\tType: contacts\n",
"\tSel: [<AtomGroup with 3 atoms>, <AtomGroup with 77 atoms, with selection 'around 5 group select' on the entire Universe.>]\n",
"\tStatus: Calculated\n",
", 'contacts_protein': Measure dataclass with:\n",
"\tName: contacts_protein\n",
"\tType: contacts\n",
"\tSel: [<AtomGroup with 10510 atoms>, 3]\n",
"\tStatus: Calculated\n",
", 'pka_protein': Measure dataclass with:\n",
"\tName: pka_protein\n",
"\tType: pka\n",
"\tSel: [<AtomGroup with 10659 atoms>]\n",
"\tStatus: Not calculated\n",
", 'rmsd_subs': Measure dataclass with:\n",
"\tName: rmsd_subs\n",
"\tType: RMSD\n",
"\tSel: [<AtomGroup with 55 atoms>]\n",
"\tStatus: Not calculated\n",
"}\n"
]
}
],
"source": [
"print(emda.measures)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "markdown",
"metadata": {},
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "rcbs",
"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": "3.11.4"
}
},
"nbformat": 4,
"nbformat_minor": 2
}

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