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iwatobipen/qmgnnis.ipynb

Created January 31, 2025 12:36
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qmgnnis.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "f8aa916b",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.\n",
"Warning: Unable to load toolkit 'OpenEye Toolkit'. The Open Force Field Toolkit does not require the OpenEye Toolkits, and can use RDKit/AmberTools instead. However, if you have a valid license for the OpenEye Toolkits, consider installing them for faster performance and additional file format support: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html OpenEye offers free Toolkit licenses for academics: https://www.eyesopen.com/academic-licensing\n"
]
},
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "89f535e771594dc0b65de48b86b6184c",
"version_major": 2,
"version_minor": 0
},
"text/plain": []
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"import logging\n",
"from implicitml.calculator import ImplicitSolventCalculator, Solvent, Functional, BasisSet, SolventModel, logger\n",
"from implicitml.model import TinyModel\n",
"from implicitml.util import embedMolecule\n",
"from GNNImplicitSolvent import create_gnn_model, GNN3_Multisolvent_embedding_run_multiple_Delta, minimize_mol\n",
"from rdkit import Chem\n",
"from rdkit.Chem import AllChem\n",
"from rdkit.Chem.Draw import IPythonConsole\n",
"from Simulation.helper_functions import MODEL_PATH"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "b7c66f67",
"metadata": {},
"outputs": [],
"source": [
"import py3Dmol"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "584402bf",
"metadata": {},
"outputs": [
{
"data": {
"image/png": 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",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x76e20e4ce7a0>"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"smiles = \"COCCO\"\n",
"#smiles = \"c1cc(O)c(C(=O)NC)cc1\"\n",
"mol = Chem.MolFromSmiles(smiles)\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "3c2b63e4",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"0"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol = Chem.AddHs(mol)\n",
"AllChem.EmbedMolecule(mol,randomSeed=42)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "488780d8",
"metadata": {
"scrolled": true
},
"outputs": [
{
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" <p id=\"3dmolwarning_17383264601548843\" style=\"background-color:#ffcccc;color:black\">3Dmol.js failed to load for some reason. Please check your browser console for error messages.<br></p>\n",
" </div>\n",
"<script>\n",
"\n",
"var loadScriptAsync = function(uri){\n",
" return new Promise((resolve, reject) => {\n",
" //this is to ignore the existence of requirejs amd\n",
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"source": [
"calc = ImplicitSolventCalculator(Chem.Mol(mol))\n",
"calc.optimize_orca(Solvent.CHLOROFORM, Functional.BP86, BasisSet.def2_SVP, SolventModel.SMD, nprocs=1, maxcore=4096)"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "6f7b9107",
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},
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{
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{
"cell_type": "code",
"execution_count": 8,
"id": "f2b6c15d",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"-707031.3784966157\n"
]
}
],
"source": [
"calc.calculate_gibbs_free_energy(Solvent.CHLOROFORM, Functional.BP86, BasisSet.def2_SVP, SolventModel.COSMORS, nprocs=1, maxcore=4096)\n",
"print(calc.gibbs_free_energy)"
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "36c4cc12",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Using OpenFF forcefield: openff-2.0.0\n",
"using rdkit molecule\n",
"setting charges based on AM1BCC\n",
"Calculating TORCH\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/iwatobipen/miniforge3/envs/QMGNNIS/lib/python3.10/site-packages/torch/autograd/__init__.py:303: UserWarning: CUDA initialization: CUDA unknown error - this may be due to an incorrectly set up environment, e.g. changing env variable CUDA_VISIBLE_DEVICES after program start. Setting the available devices to be zero. (Triggered internally at /home/conda/feedstock_root/build_artifacts/pytorch-recipe_1680572619157/work/c10/cuda/CUDAFunctions.cpp:109.)\n",
" return Variable._execution_engine.run_backward( # Calls into the C++ engine to run the backward pass\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
" Step Time Energy fmax\n",
"BFGS: 0 21:29:19 -7329.877330 0.129892\n",
"Calculating TORCH\n",
"BFGS: 1 21:29:22 -7329.878128 0.063397\n",
"Calculating TORCH\n",
"BFGS: 2 21:29:25 -7329.878377 0.038203\n",
"Calculating TORCH\n",
"BFGS: 3 21:29:28 -7329.878579 0.035754\n",
"Calculating TORCH\n",
"BFGS: 4 21:29:31 -7329.878747 0.035303\n",
"Calculating TORCH\n",
"BFGS: 5 21:29:34 -7329.878880 0.036228\n",
"Calculating TORCH\n",
"BFGS: 6 21:29:38 -7329.879034 0.038269\n",
"Calculating TORCH\n",
"BFGS: 7 21:29:41 -7329.879176 0.032033\n",
"Calculating TORCH\n",
"BFGS: 8 21:29:44 -7329.879320 0.027802\n",
"Calculating TORCH\n",
"BFGS: 9 21:29:47 -7329.879403 0.022712\n"
]
}
],
"source": [
"model = create_gnn_model(\n",
" mol,\n",
" solvent=\"tip3p\",\n",
" model_class=GNN3_Multisolvent_embedding_run_multiple_Delta,\n",
" model_dict=MODEL_PATH,\n",
" jit=False,\n",
")\n",
"\n",
"calc.optimize(Solvent.CHLOROFORM, Functional.BP86, BasisSet.def2_SVP, SolventModel.CPCM, model=model, nprocs=1, maxcore=4096, fmax=0.025)"
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "2a7f58db",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Calculating TORCH\n",
"(39, 39)\n",
"Calculating TORCH\n"
]
},
{
"data": {
"text/plain": [
"-707243.03466798986545"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from implicitml.util import normal_modes\n",
"from Simulation.helper_functions import calculate_entropy_from_frequencies\n",
"import numpy as np\n",
"calc.calculate_hessian(Solvent.CHLOROFORM, Functional.BP86, BasisSet.def2_SVP, SolventModel.CPCM, model=model, nprocs=1, maxcore=4096)\n",
"total_hessian = calc.QM_hessian*96.485332 + calc.GNN_hessian\n",
"print(total_hessian.shape)\n",
"masses = np.array([atom.GetMass() for atom in calc.molecule.GetAtoms()]).round(0)\n",
"indices = [atom.GetIdx() for atom in calc.molecule.GetAtoms()]\n",
"freqs, modes = normal_modes(total_hessian, indices,masses)\n",
"\n",
"freqs\n",
"entropy = calculate_entropy_from_frequencies(freqs)\n",
"calc.singlepoint(Solvent.CHLOROFORM, Functional.BP86, BasisSet.def2_SVP, SolventModel.CPCM, model=model, nprocs=1, maxcore=4096)\n",
"energy = calc.electronic_energy\n",
"gibbs_free_energy = energy - entropy\n",
"gibbs_free_energy"
]
},
{
"cell_type": "code",
"execution_count": 11,
"id": "01cc4c78",
"metadata": {},
"outputs": [
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"viewer_1738326636989299 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_1738326636989299\"),{backgroundColor:\"white\"});\n",
"viewer_1738326636989299.zoomTo();\n",
"\tviewer_1738326636989299.addModel(\"\\n RDKit 3D\\n\\n 13 12 0 0 0 0 0 0 0 0999 V2000\\n -1.8754 0.4803 0.2972 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.4926 0.3694 0.5533 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.1577 -0.5717 -0.2865 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6464 -0.4204 -0.0278 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.0803 0.8992 -0.3078 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.4092 -0.4871 0.4762 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.2866 1.2485 0.9879 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0809 0.7950 -0.7570 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.0652 -0.3503 -1.3608 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.1869 -1.6143 -0.0716 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.8592 -0.7174 1.0321 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.2147 -1.1136 -0.6876 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.4384 1.4825 0.1525 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 2 3 1 0\\n 3 4 1 0\\n 4 5 1 0\\n 1 6 1 0\\n 1 7 1 0\\n 1 8 1 0\\n 3 9 1 0\\n 3 10 1 0\\n 4 11 1 0\\n 4 12 1 0\\n 5 13 1 0\\nM END\\n\",\"sdf\",{\"keepH\": true});\n",
"\tviewer_1738326636989299.setStyle({\"line\": {\"linewidth\": 5}});\n",
"\tviewer_1738326636989299.setStyle({\"stick\": {}});\n",
"\tviewer_1738326636989299.setBackgroundColor(\"#ebf4fb\");\n",
"\tviewer_1738326636989299.setBackgroundColor(\"#f9f4fb\");\n",
"\tviewer_1738326636989299.setBackgroundColor(\"#e1e1e1\");\n",
"viewer_1738326636989299.render();\n",
"});\n",
"</script>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"view = py3Dmol.view()\n",
"view.addModel(Chem.MolToMolBlock(calc.molecule), 'sdf', {'keepH': True})\n",
"view.setStyle({'line': {'linewidth': 5}}, viewer=(0,0))\n",
"view.setStyle({'stick': {}}, viewer=(0,1))\n",
"view.setBackgroundColor('#ebf4fb', viewer=(0,0))\n",
"view.setBackgroundColor('#f9f4fb', viewer=(0,1))\n",
"view.setBackgroundColor('#e1e1e1', viewer=(0,2))\n",
"view.show()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "21931d02",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"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": "3.10.9"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
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