{ "cells": [ { "cell_type": "markdown", "id": "834aeced-c3c5-42a0-bad1-41e009dd86ee", "metadata": {}, "source": [ "### Preprocessing" ] }, { "cell_type": "code", "execution_count": 1, "id": "86476f6e-802a-463b-a1b0-2ae228bb92af", "metadata": {}, "outputs": [], "source": [ "import pandas as pd" ] }, { "cell_type": "code", "execution_count": 12, "id": "9b2be11c-f4bb-4107-af49-abd78052afcf", "metadata": {}, "outputs": [], "source": [ "df = pd.read_table('pdbbind/data/index/INDEX_general_PL_data.2020',skiprows=4,sep=r'\\s+',usecols=[0,4]).drop(0)\n", "df = df.rename(columns={'#': 'name','release': 'affinity'})\n", "df_refined = pd.read_table('pdbbind/data/index/INDEX_refined_data.2020',skiprows=4,sep=r'\\s+',usecols=[0,4]).drop(0)\n", "df_refined = df_refined.rename(columns={'#': 'name','release': 'affinity'})\n", "df = pd.concat([df,df_refined])" ] }, { "cell_type": "code", "execution_count": 13, "id": "68983ab8-bf11-4ed6-ba06-f962dbdc077e", "metadata": {}, "outputs": [], "source": [ "quantities = ['ki','kd','ka','k1/2','kb','ic50','ec50']" ] }, { "cell_type": "code", "execution_count": 14, "id": "3acbca3c-9c0b-43a1-a45e-331bf153bcfa", "metadata": {}, "outputs": [], "source": [ "from pint import UnitRegistry\n", "ureg = UnitRegistry()\n", "\n", "def to_uM(affinity):\n", " val = ureg(affinity)\n", " try:\n", " return val.m_as(ureg.uM)\n", " except Exception:\n", " pass\n", " \n", " try:\n", " return 1/val.m_as(1/ureg.uM)\n", " except Exception:\n", " pass" ] }, { "cell_type": "code", "execution_count": 15, "id": "58e5748b-2cea-43ff-ab51-85a5021bd50b", "metadata": {}, "outputs": [], "source": [ "df['affinity_uM'] = df['affinity'].str.split('[=\\~><]').str[1].apply(to_uM)\n", "df['affinity_quantity'] = df['affinity'].str.split('[=\\~><]').str[0]" ] }, { "cell_type": "code", "execution_count": 16, "id": "d92f0004-68c1-4487-94b9-56b4fd598de4", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "" ] }, "execution_count": 16, "metadata": {}, "output_type": "execute_result" }, { "data": { "image/png": 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"text/plain": [ "
" ] }, "metadata": { "needs_background": "light" }, "output_type": "display_data" } ], "source": [ "df['affinity_quantity'].hist()" ] }, { "cell_type": "code", "execution_count": 17, "id": "aa358835-55f3-4551-9217-e76a15de4fe8", "metadata": {}, "outputs": [], "source": [ "df_filter = df[df['affinity_quantity'].str.lower().isin(quantities)]" ] }, { "cell_type": "code", "execution_count": 18, "id": "d6dda488-f709-4fe7-b372-080042cf7c66", "metadata": {}, "outputs": [], "source": [ "df_complex = pd.read_parquet('data/pdbbind_complex.parquet')" ] }, { "cell_type": "code", "execution_count": 20, "id": "df7929e3-c7fd-4e1b-a165-92f8d53b9011", "metadata": {}, "outputs": [], "source": [ "df_all = df_complex.merge(df_filter,on='name').drop('affinity',axis=1)" ] }, { "cell_type": "code", "execution_count": 21, "id": "41711825-b110-472b-a9f3-2eccc5afbfd9", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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nameseqsmilesaffinity_uMaffinity_quantity
02lbvMTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE...CCCCCCCCCCCCCCCCCCCC(=O)O0.02600Kd
11lt6APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE...OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]...500.00000IC50
24lwiVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE...COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)...0.02300IC50
33t4pAAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM...OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)C(=O)O)NC(=O)...6.43000Kd
46oyzYITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRKKYTPTMGGIVIL...CO[C@@H]1[C@H](O[C@H]([C@@H]1O)n1ccc(=O)[nH]c1...0.18500IC50
..................
247544j46GTIYPRNPAMYSEEARLKSFQNWPDYAHLTPRELASAGLYYTGIGD...CC[C@@H]([C@@H](C(=O)O)NC(=O)[C@@H]1CCCN1C(=O)...5.24000Ki
247552c80DHIKVIYFNGRGRAESIRMTLVAAGVNYEDERISFQDWPKIKPTIP...CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(...4.70000Kd
247562c80DHIKVIYFNGRGRAESIRMTLVAAGVNYEDERISFQDWPKIKPTIP...CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(...4.70000Kd
247575wl0NDDIDQSLIIAARNIVRRASVSADPLASLLEMCHSTQIGGTRMVDI...OC(=O)[C@H]1[C@@H]2CC[C@H]([C@@H]1Nc1nc(ncc1F)...0.00067Kd
247585wl0NDDIDQSLIIAARNIVRRASVSADPLASLLEMCHSTQIGGTRMVDI...OC(=O)[C@H]1[C@@H]2CC[C@H]([C@@H]1Nc1nc(ncc1F)...0.00067Kd
\n", "

24759 rows × 5 columns

\n", "
" ], "text/plain": [ " name seq \\\n", "0 2lbv MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE... \n", "1 1lt6 APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE... \n", "2 4lwi VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE... \n", "3 3t4p AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM... \n", "4 6oyz YITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRKKYTPTMGGIVIL... \n", "... ... ... \n", "24754 4j46 GTIYPRNPAMYSEEARLKSFQNWPDYAHLTPRELASAGLYYTGIGD... \n", "24755 2c80 DHIKVIYFNGRGRAESIRMTLVAAGVNYEDERISFQDWPKIKPTIP... \n", "24756 2c80 DHIKVIYFNGRGRAESIRMTLVAAGVNYEDERISFQDWPKIKPTIP... \n", "24757 5wl0 NDDIDQSLIIAARNIVRRASVSADPLASLLEMCHSTQIGGTRMVDI... \n", "24758 5wl0 NDDIDQSLIIAARNIVRRASVSADPLASLLEMCHSTQIGGTRMVDI... \n", "\n", " smiles affinity_uM \\\n", "0 CCCCCCCCCCCCCCCCCCCC(=O)O 0.02600 \n", "1 OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]... 500.00000 \n", "2 COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)... 0.02300 \n", "3 OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)C(=O)O)NC(=O)... 6.43000 \n", "4 CO[C@@H]1[C@H](O[C@H]([C@@H]1O)n1ccc(=O)[nH]c1... 0.18500 \n", "... ... ... \n", "24754 CC[C@@H]([C@@H](C(=O)O)NC(=O)[C@@H]1CCCN1C(=O)... 5.24000 \n", "24755 CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(... 4.70000 \n", "24756 CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(... 4.70000 \n", "24757 OC(=O)[C@H]1[C@@H]2CC[C@H]([C@@H]1Nc1nc(ncc1F)... 0.00067 \n", "24758 OC(=O)[C@H]1[C@@H]2CC[C@H]([C@@H]1Nc1nc(ncc1F)... 0.00067 \n", "\n", " affinity_quantity \n", "0 Kd \n", "1 IC50 \n", "2 IC50 \n", "3 Kd \n", "4 IC50 \n", "... ... \n", "24754 Ki \n", "24755 Kd \n", "24756 Kd \n", "24757 Kd \n", "24758 Kd \n", "\n", "[24759 rows x 5 columns]" ] }, "execution_count": 21, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df_all" ] }, { "cell_type": "code", "execution_count": 53, "id": "4d105c42-0d11-49db-9012-52fafc9cd299", "metadata": {}, "outputs": [], "source": [ "df_all.to_parquet('data/pdbbind.parquet')" ] }, { "cell_type": "code", "execution_count": 54, "id": "2955b056-26dd-45fa-8d74-f17661253a9a", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "24759" ] }, "execution_count": 54, "metadata": {}, "output_type": "execute_result" } ], "source": [ "len(df_all)" ] }, { "cell_type": "code", "execution_count": null, "id": "ed3fe035-6035-4d39-b072-d12dc0a95857", "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": "3.9.4" } }, "nbformat": 4, "nbformat_minor": 5 }