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Created June 25, 2024 13:22
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full_usage_example-Copy1.ipynb
{
"cells": [
{
"cell_type": "markdown",
"id": "consecutive-report",
"metadata": {},
"source": [
"## This notebook exemplifies full notebook usage of bbSelect"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "blind-divide",
"metadata": {},
"outputs": [],
"source": [
"import sys\n",
"import os\n",
"sys.path.append('../')\n",
"from bbSelectBuild import bbSelectBuild\n",
"from bbSelect import Picker\n",
"\n",
"import matplotlib.pyplot as plt\n",
"\n",
"plt.rcParams['figure.figsize'] = [15,10]"
]
},
{
"cell_type": "markdown",
"id": "guided-asian",
"metadata": {},
"source": [
"## Build the bbSelect database"
]
},
{
"cell_type": "markdown",
"id": "protecting-plane",
"metadata": {},
"source": [
"### Set the parameters for bbSelectBuild, which builds the bbSelect database"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "confident-moscow",
"metadata": {},
"outputs": [],
"source": [
"smiles_file = '../data/enamine_acids/enamine_acids_filtered.csv'\n",
"#for rdkit csv shoud be tsv format with smiles and ID column\n",
"smiles_file = '../data/enamine_acids/enamine_acids_filtered_rdkit_top2k.csv'\n",
"\n",
"output_root = '../data/enamine_acids/enamine_acids_full_usage_example'\n",
"cell_size = 1\n",
"num_cells = 20\n",
"ncpu = len(os.sched_getaffinity(0)) -1\n",
"\n",
"# Set the SMARTS that will be used to clip the \"core scaffold\" to [15CH3]. \n",
"# If using the results from an R-group decomposition, you need to generate the clipped smiles file yourself replacing * with [15CH3]\n",
"\n",
"rxn_smarts = '[C:1](=[O:2])[OH]>>[C:1](=[O:2])[15CH3]'\n",
"\n",
"# Below are the default settings for bbSelectBuild and do not need to be set if using default. \n",
"# However, if changing anything, these will need to be set\n",
"\n",
"#conformer_generation_program = 'omega' # Can be set to 'rdkit' if rdkit is to be used. Warning: this takes MUCH longer\n",
"conformer_generation_program = \"rdkit\"\n",
"# These are required to run omega from python\n",
"omega_load_command = 'module load openeye'\n",
"omega_run_command = 'omega2'\n",
"\n",
"# If the clipped smiles file has already been generated you can load that in and define the separator in the file\n",
"# If you are using the results of an R-group decomposition, the clipped file will need to be loaded in where * has been replaced by [15CH3]\n",
"clipped_smiles_file = None\n",
"clipped_smiles_file_sep = None\n",
"#clipped_smiles_file_sep = '\\t'\n",
"\n",
"# If the conformers, or the aligned conformers have already been generated, set the paths here\n",
"conformer_sdf = None\n",
"aligned_mols_sdf = None\n",
"\n",
"# If you would like to save the aligned conformers, you can set the path here\n",
"save_aligned_mols_sdf = None"
]
},
{
"cell_type": "markdown",
"id": "after-great",
"metadata": {},
"source": [
"### Initiate the bbSelectBuild class"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "worse-battlefield",
"metadata": {},
"outputs": [],
"source": [
"bbSelectBuilder = bbSelectBuild(\n",
" smiles_file = smiles_file, \n",
" output_root = output_root, \n",
" cell_size = cell_size, \n",
" num_cells = num_cells, \n",
" ncpu = ncpu,\n",
" rxn_smarts = rxn_smarts\n",
" )\n",
"\n",
"# Set options in bbSelectBuild\n",
"bbSelectBuilder.SetOption('conformer_generation_program', conformer_generation_program)\n",
"bbSelectBuilder.SetOption('omega_load_command', omega_load_command)\n",
"bbSelectBuilder.SetOption('omega_run_command', omega_run_command)\n",
"bbSelectBuilder.SetOption('clipped_smiles_file', clipped_smiles_file)\n",
"bbSelectBuilder.SetOption('clipped_smiles_file_sep', clipped_smiles_file_sep)\n",
"bbSelectBuilder.SetOption('conformer_sdf', conformer_sdf)\n",
"bbSelectBuilder.SetOption('aligned_mols_sdf', aligned_mols_sdf)\n",
"bbSelectBuilder.SetOption('save_aligned_mols_sdf', save_aligned_mols_sdf)\n",
"bbSelectBuilder.SetOption('smiles_file_sep', '\\t') # added"
]
},
{
"cell_type": "markdown",
"id": "minute-nevada",
"metadata": {},
"source": [
"### Run the bbSelectBuilder and get the location of the database"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "normal-czech",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"2024-06-25 19:47:05,417 - root - INFO - loading smiles file\n",
"2024-06-25 19:47:05,426 - root - INFO - clipping smiles file\n",
"2024-06-25 19:47:05,600 - root - INFO - 1999 compounds clipped in 0.17309832572937012 seconds\n",
"2024-06-25 19:47:05,600 - root - INFO - clipped smiles saved at ../data/enamine_acids/enamine_acids_filtered_rdkit_top2k_clipped.tsv\n",
"2024-06-25 19:47:05,603 - root - INFO - generating conformers\n",
"2024-06-25 19:47:05,603 - root - INFO - Starting conformer generation with rdkit over 19 cores.\n",
"2024-06-25 21:24:39,811 - root - INFO - loading conformer sdf\n",
"2024-06-25 21:24:41,860 - root - INFO - 26852 conformers loaded in 2.047424554824829 seconds\n",
"2024-06-25 21:24:41,861 - root - INFO - Running alignment over 19 cores\n",
"2024-06-25 21:24:45,371 - root - INFO - 26852 compounds aligned over 19 CPU cores in 3.510171890258789 seconds\n",
"2024-06-25 21:24:45,674 - root - INFO - getting pharmacophore_features\n",
"2024-06-25 21:24:45,675 - root - INFO - Capturing pharmacophores over 19 cores\n",
"2024-06-25 21:24:48,979 - root - INFO - 26852 pharmacophores captured over 19 cores in 3.304802656173706 seconds\n",
"2024-06-25 21:24:48,981 - root - INFO - generating fingerprints\n",
"2024-06-25 21:24:49,076 - root - INFO - 1999 fingerprints generated over 1 CPU core in 0.09395861625671387 seconds\n",
"2024-06-25 21:24:49,077 - root - INFO - writing bbSelect DB\n",
"2024-06-25 21:24:49,416 - root - INFO - 1999 fingerprints written in 0.338761568069458 seconds\n",
"2024-06-25 21:24:49,416 - root - INFO - Writing reference file\n",
"2024-06-25 21:24:49,591 - root - INFO - Reference file written\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"step1\n",
"step2\n",
"../data/enamine_acids/enamine_acids_full_usage_example.bin ../data/enamine_acids/enamine_acids_full_usage_example.ref\n"
]
}
],
"source": [
"bbSelect = bbSelectBuilder.Run()\n",
"print('step1')\n",
"bin_file = bbSelect.GetBinLocation()\n",
"print('step2')\n",
"ref_file = bbSelect.GetRefLocation()\n",
"print(bin_file, ref_file)"
]
},
{
"cell_type": "markdown",
"id": "parental-facility",
"metadata": {},
"source": [
"## Select compounds from the bbSelect database"
]
},
{
"cell_type": "markdown",
"id": "covered-pontiac",
"metadata": {},
"source": [
"### Set the parameters for bbSelect, which performs the selection"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "bound-advocacy",
"metadata": {},
"outputs": [],
"source": [
"n_select = 48\n",
"ncpu = len(os.sched_getaffinity(0)) -1\n",
"sort = 'MPO'\n",
"tanimoto = 0.9\n",
"pharmacophores = '*'\n",
"method = 'classic'\n",
"use_coverage = False"
]
},
{
"cell_type": "markdown",
"id": "physical-following",
"metadata": {},
"source": [
"### Run the selection"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "animal-wiring",
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"2024-06-25 21:26:31,113 - root - INFO - Beginning generation of query fingerprints\n",
"2024-06-25 21:26:31,118 - root - INFO - Starting set-driven division of area\n",
"2024-06-25 21:26:31,438 - root - INFO - Generation of query fingerprints execution time = 0.32 seconds\n",
"2024-06-25 21:26:31,439 - root - INFO - Starting fingerprint matching algorithm over 19 cores\n",
"2024-06-25 21:26:34,069 - root - INFO - fingerprint matching execution time = 2.63 seconds\n",
"2024-06-25 21:26:34,070 - root - INFO - Starting selection algorithm\n",
"2024-06-25 21:26:34,331 - root - INFO - selection execution time = 0.26 seconds\n",
"2024-06-25 21:26:34,332 - root - DEBUG - skip 13 rows\n"
]
},
{
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"</svg>"
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"text/plain": [
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]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"bbSelection = Picker(ref_file = ref_file, \n",
" bin_file = bin_file, \n",
" n = n_select, # How many compounds to select\n",
" method = 'som', # Which clustering method to use\n",
" pharmacophores = pharmacophores, # Which pharmacophore to select from,\n",
" ncpu = ncpu, # Number of cpus to use,\n",
" sort = sort,\n",
" tanimoto = tanimoto,\n",
" use_coverage = use_coverage)\n",
"\n",
"bbSelection.DrawSelectedMols(align_smiles = 'CC(=O)O')"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "8a190b21-c40b-4051-b174-1eb58673cc03",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "0c7dc1c8-bd40-4170-bfc5-416acacafd2d",
"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": "3.9.19"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
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