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By molecule experiment work #10

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add by molecule experiment
jmaat Nov 19, 2020
0968569
by molecule update
jmaat Nov 24, 2020
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210 changes: 210 additions & 0 deletions by_molecule_experiment/.ipynb_checkpoints/kversusWBOplots-checkpoint.ipynb
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{
"cells": [
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"ename": "ModuleNotFoundError",
"evalue": "No module named 'plot_td_energies'",
"output_type": "error",
"traceback": [
"\u001b[0;31m-----------------------\u001b[0m",
"\u001b[0;31mModuleNotFoundError\u001b[0mTraceback (most recent call last)",
"\u001b[0;32m<ipython-input-6-b59dc60d8950>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 10\u001b[0m \u001b[0mProperTorsionHandler\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mImproperTorsionHandler\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 11\u001b[0m vdWHandler)\n\u001b[0;32m---> 12\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mplot_td_energies\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mcollect_td_targets_data\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mplot_td_targets_data\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 13\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpickle\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 14\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mmake_torsion_target_new\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'plot_td_energies'"
]
}
],
"source": [
"#imports\n",
"#Created by Jessica\n",
"\n",
"import os\n",
"import json\n",
"import tempfile\n",
"from openforcefield.topology import Molecule, Topology\n",
"from openforcefield.typing.engines.smirnoff import (ForceField,\n",
"UnassignedValenceParameterException, BondHandler, AngleHandler,\n",
"ProperTorsionHandler, ImproperTorsionHandler,\n",
"vdWHandler)\n",
"from plot_td_energies import collect_td_targets_data, plot_td_targets_data\n",
"import pickle\n",
"import make_torsion_target_new\n",
"\n",
"\n",
"force_balance_file = 'optimize.in'"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"#functions\n",
"sub_dir = [x[0] for x in os.walk(directory) if os.path.basename(x[0]).startswith('td')]\n",
"\n",
"def makePlots(ds, ff, param):\n",
" \"\"\"\n",
" Description: \n",
" -Create k versus WBO plots\n",
" -Create MM versus QM plots for each target \n",
" \n",
" \n",
" input:\n",
" ds: List of dataset names\n",
" ff: .offxml style format force field name\n",
" param: List of parameters to generate plots for\n",
" \"\"\"\n",
" \n",
" #make td Targets \n",
" \n",
" \n",
" \n",
" \n",
" \n",
" #Create targets folder in subdirectory \n",
" force_balance_file = 'optimize.in'\n",
"\n",
"\n",
" # Find which line of optimize.in the targets specificaiton begins at\n",
" with open(force_balance_file, 'r') as f:\n",
" replace_index = None\n",
" force_balance_lines = f.readlines()\n",
" for index,line in enumerate(force_balance_lines):\n",
" try:\n",
" #if 'name' in line[:4]:\n",
" if line.startswith('name'):\n",
" replace_index = index\n",
" break\n",
" except:\n",
" pass\n",
" #print(replace_index)\n",
"\n",
" count = 0\n",
" \n",
" \n",
"\n",
" \n",
" #run force balance \n",
" #store the k1 and k2 values\n",
" #getKval(k1, k2)=kval\n",
" \n",
" #store data in dictionary data {cmiles : [wbo, kval], }\n",
" \n",
" #create figure \n",
" \n",
" return \n",
" \n",
"def getKval(k1, k2):\n",
" \"\"\"\n",
" Determine the slope from the k1 and k2 value\n",
" \n",
" k1: \n",
" k2:\n",
" \"\"\"\n",
" \n",
" \n",
" \n",
"\n",
" return kval \n",
"\n",
"\n",
"def make_wbo_versus_k_plots(valDict):\n",
" \"\"\"\n",
" Description: Make plots of k versus WBO and save plots to .pdf \n",
" \n",
" \n",
" input: \n",
" valDict: Dictionary of cmiles as keys and list of [wbo, kval] as the items \n",
" \n",
" \"\"\"\n",
" \n",
" \n",
" \n",
" \n",
" return \n",
"\n",
"\n",
"\n",
"def make_MM_QM_plots(datasets):\n",
" \"\"\"\n",
" datasets: MM_QM_Plots\n",
" \n",
" \"\"\"\n",
"\n",
" \n",
" \n",
" \n",
" return \n",
"\n",
"\n",
"\n",
"\n",
"\n",
" \n",
"\n",
"\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"directory = '/Users/jessica/Downloads/release_1.2.0/fb-fit/targets/'\n",
"ff = '/Users/jessica/Documents/Grad_research/WBO_Torsions_ChayaPaper/release_1.3.0_2/fb-fit/fb-fit0/forcefield/test.offxml'\n",
"\n",
"#all of the molecules there is torsions \n",
"#break them out into subplots for the TIG parameters \n",
"\n",
"\n",
"#Plot for molecules that use TIG5a, but use the TIG-fit0 plots \n",
"#Plot for TIG3 \n",
"\n",
"#run the same experiments with Carbon-Nitrogen central bonds parameters \n",
"\n",
"\n",
"makePlots(datasets, ff, param)\n",
"\n",
"\n",
"\n",
"\n",
"\n",
"\n",
"\n"
]
},
{
"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": "3.7.6"
}
},
"nbformat": 4,
"nbformat_minor": 4
}
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