Comp2Prot_example.ipynb

{"cells":[{"cell_type":"markdown","id":"07cc8925","metadata":{},"source":["This example notebooks shows the local execution of Comp2Prot and of the singular databases "]},{"cell_type":"code","execution_count":3,"id":"14fade58","metadata":{"id":"14fade58"},"outputs":[],"source":["#General packages\n","import pandas as pd\n","from tqdm import tqdm\n","import os\n","from cpiextract import Comp2Prot\n","import time"]},{"cell_type":"markdown","id":"01326abe","metadata":{"id":"01326abe"},"source":["# Load in Required Datasets"]},{"cell_type":"code","execution_count":2,"id":"d92568f4","metadata":{"id":"d92568f4","outputId":"40a9f5c6-6e27-4f06-9437-896371506cfc","scrolled":false},"outputs":[{"name":"stderr","output_type":"stream","text":["C:\\Users\\andre\\AppData\\Local\\Temp\\ipykernel_25568\\4108575009.py:3: DtypeWarning: Columns (8,9,10,11,15,40,41) have mixed types. Specify dtype option on import or set low_memory=False.\n","  BDB_data=pd.read_csv(file_path,sep=',',usecols=['CID', 'Ligand SMILES','Ligand InChI','BindingDB MonomerID','Ligand InChI Key','BindingDB Ligand Name','Target Name Assigned by Curator or DataSource','Target Source Organism According to Curator or DataSource','Ki (nM)','IC50 (nM)','Kd (nM)','EC50 (nM)','pH','Temp (C)','Curation/DataSource','UniProt (SwissProt) Entry Name of Target Chain','UniProt (SwissProt) Primary ID of Target Chain'],on_bad_lines='skip')\n","C:\\Users\\andre\\AppData\\Local\\Temp\\ipykernel_25568\\4108575009.py:11: DtypeWarning: Columns (27,28,30,31,44,45) have mixed types. Specify dtype option on import or set low_memory=False.\n","  chembl_data=pd.read_csv(file_path,sep=',')\n","C:\\Users\\andre\\AppData\\Local\\Temp\\ipykernel_25568\\4108575009.py:18: DtypeWarning: Columns (0,1,8,14) have mixed types. Specify dtype option on import or set low_memory=False.\n","  DTC_data=pd.read_csv(file_path,sep=',',usecols=['CID', 'compound_id','standard_inchi_key','target_id','gene_names','wildtype_or_mutant','mutation_info','standard_type','standard_relation','standard_value','standard_units','activity_comment','pubmed_id','doc_type'])\n"]}],"source":["# Root data path\n","data_path = 'data/Databases/'\n","\n","#Downloaded from BindingDB on 3/30/2023\n","file_path=os.path.join(data_path, 'BindingDB.csv')\n","BDB_data=pd.read_csv(file_path,sep=',',usecols=['CID', 'Ligand SMILES','Ligand InChI','BindingDB MonomerID','Ligand InChI Key','BindingDB Ligand Name','Target Name Assigned by Curator or DataSource','Target Source Organism According to Curator or DataSource','Ki (nM)','IC50 (nM)','Kd (nM)','EC50 (nM)','pH','Temp (C)','Curation/DataSource','UniProt (SwissProt) Entry Name of Target Chain','UniProt (SwissProt) Primary ID of Target Chain'],on_bad_lines='skip')\n","\n","#Downloaded from STITCH on 2/22/2023\n","file_path=os.path.join(data_path, 'STITCH.tsv')\n","sttch_data=pd.read_csv(file_path,sep='\\t')\n","\n","#Downloaded from ChEMBL on 2/01/2024\n","file_path=os.path.join(data_path, 'ChEMBL.csv')\n","chembl_data=pd.read_csv(file_path,sep=',')\n","\n","file_path=os.path.join(data_path, 'CTD.csv')\n","CTD_data=pd.read_csv(file_path,sep=',')\n","\n","#Downloaded from DTC on 2/24/2023\n","file_path=os.path.join(data_path, 'DTC.csv')\n","DTC_data=pd.read_csv(file_path,sep=',',usecols=['CID', 'compound_id','standard_inchi_key','target_id','gene_names','wildtype_or_mutant','mutation_info','standard_type','standard_relation','standard_value','standard_units','activity_comment','pubmed_id','doc_type'])\n","\n","#Downloaded from DrugBank on 3/2/2022\n","file_path=os.path.join(data_path, 'DB.csv')\n","DB_data=pd.read_csv(file_path, sep=',')\n","\n","#Downloaded from DrugCentral on 2/25/2024\n","file_path=os.path.join(data_path, 'DrugCentral.csv')\n","DC_data=pd.read_csv(file_path, sep=',')\n"]},{"cell_type":"code","execution_count":3,"id":"bd616086","metadata":{},"outputs":[],"source":["dbs = {\n","    'chembl': chembl_data,\n","    'bdb': BDB_data,\n","    'stitch': sttch_data,\n","    'ctd': CTD_data,\n","    'dtc': DTC_data,\n","    'db': DB_data,\n","    'dc': DC_data\n","}"]},{"cell_type":"markdown","id":"6e683707","metadata":{"id":"6e683707"},"source":["## Load in Compound List"]},{"cell_type":"markdown","id":"eb140d3b","metadata":{},"source":["DrugBank compounds"]},{"cell_type":"code","execution_count":7,"id":"a0b84531","metadata":{"id":"a0b84531"},"outputs":[],"source":["chem_dat=pd.read_csv('data/input/db_compounds.csv')\n","output_path = 'data/output/C2P'"]},{"cell_type":"markdown","id":"e081b66f","metadata":{},"source":["FooDB compounds"]},{"cell_type":"code","execution_count":null,"id":"7af953cd","metadata":{},"outputs":[],"source":["chem_dat=pd.read_csv('data/input/foodb_compounds.csv')\n","output_path = 'data/output/foodb'"]},{"cell_type":"markdown","id":"8cf4a2e9","metadata":{"id":"8cf4a2e9"},"source":["## Run Comp2Prot on Compound List"]},{"cell_type":"code","execution_count":6,"id":"a70e2db7","metadata":{},"outputs":[],"source":["C2P = Comp2Prot('local', dbs=dbs)"]},{"cell_type":"code","execution_count":8,"id":"a77c159b","metadata":{},"outputs":[],"source":["times = {}"]},{"cell_type":"code","execution_count":null,"id":"f0f2f7b4","metadata":{},"outputs":[],"source":["c2p_dat=pd.DataFrame()\n","c2p_fail=pd.DataFrame()\n","states = pd.DataFrame()\n","\n","r=0\n","for h in tqdm(range(0, 10)):\n","\n","    try:\n","        inputid=int(chem_dat['cid'].iloc[h])\n","    except:\n","        continue\n","    start = time.time()\n","\n","    try:\n","        [comp_dat, state] = C2P.comp_interactions(inputid)\n","        end = time.time()\n","        times[h] = end-start\n","        states = pd.concat([states, state])\n","        c2p_dat=pd.concat([c2p_dat,comp_dat])\n","        print(f'{h} done')\n","    except:\n","        print(f'{h} failed')\n","        c2p_fail.loc[r,\"failed_id\"]=inputid #Collects failed inputids\n","        r=r+1\n","\n","    # Saves a file after a certain number of loops for insurance\n","    check=h/50 #automatically saves progress when on loop number set here\n","    if (check-int(check)==0)==True:\n","        filename=os.path.join(output_path, '_iter_'+str(h)+'.csv')\n","        c2p_dat.to_csv(filename,sep=',',index=False)\n","\n","# Save completed dataframe to file\n","filename=os.path.join(output_path, '.csv')\n","c2p_dat.to_csv(filename,sep=',',index=False)"]},{"cell_type":"code","execution_count":null,"id":"415bd6f2","metadata":{},"outputs":[],"source":["c2p_dat"]},{"cell_type":"code","execution_count":null,"id":"43fd25ca","metadata":{},"outputs":[],"source":["states"]},{"cell_type":"markdown","id":"f1450d59","metadata":{"id":"f1450d59"},"source":["# Run Comp2Prot on Single Compound"]},{"cell_type":"markdown","id":"69cdcdff","metadata":{"id":"69cdcdff"},"source":["## Comp2Prot with all Databases"]},{"cell_type":"markdown","id":"1d552625","metadata":{},"source":["### Test time required"]},{"cell_type":"code","execution_count":null,"id":"b8a26437","metadata":{"id":"b8a26437"},"outputs":[],"source":["#inputid='AAWZDTNXLSGCEK-WYWMIBKRSA-N'\n","import cProfile\n","inputid=5350"]},{"cell_type":"code","execution_count":null,"id":"769cb120","metadata":{},"outputs":[],"source":["cProfile.run('C2P.comp_interactions(inputid)')"]},{"cell_type":"markdown","id":"d936730a","metadata":{},"source":["### Run pipeline"]},{"cell_type":"code","execution_count":null,"id":"2e15318c","metadata":{},"outputs":[],"source":["inputid = 317"]},{"cell_type":"code","execution_count":null,"id":"4054df29","metadata":{},"outputs":[],"source":["C2P = Comp2Prot('local', dbs=dbs)"]},{"cell_type":"code","execution_count":null,"id":"6ea9b205","metadata":{"id":"6ea9b205","outputId":"41fcf465-5aad-41e6-b3a1-842bd9efb64d"},"outputs":[],"source":["[comp_dat,states]=C2P.comp_interactions(input_id=inputid)"]},{"cell_type":"code","execution_count":null,"id":"855fc158","metadata":{},"outputs":[],"source":["states"]},{"cell_type":"code","execution_count":null,"id":"6f7a6ca2","metadata":{},"outputs":[],"source":["comp_dat"]},{"cell_type":"markdown","id":"d9359a6c","metadata":{"id":"d9359a6c"},"source":["### Comp2Prot with select Databases"]},{"cell_type":"code","execution_count":null,"id":"503fe22b","metadata":{},"outputs":[],"source":["C2P = Comp2Prot('local', dbs=dbs)"]},{"cell_type":"code","execution_count":null,"id":"e60c3450","metadata":{"id":"e60c3450"},"outputs":[],"source":["#inputid='AAWZDTNXLSGCEK-WYWMIBKRSA-N'\n","inputid=39929"]},{"cell_type":"code","execution_count":null,"id":"91a1b222","metadata":{"id":"91a1b222"},"outputs":[],"source":["#The second argument is a string listing the databases needed.\n","#Underscore is required to separate the databases.\n","[comp_dat,states]=C2P.comp_interactions_select(inputid,'ctd')"]},{"cell_type":"code","execution_count":null,"id":"20b8f1a2","metadata":{"id":"20b8f1a2"},"outputs":[],"source":["comp_dat"]},{"cell_type":"markdown","id":"ea10576b","metadata":{"id":"ea10576b"},"source":["# Run each step/database separately (for troubleshooting)"]},{"cell_type":"code","execution_count":null,"id":"2ac270fb","metadata":{"id":"2ac270fb","scrolled":true},"outputs":[],"source":["#inp='AAWZDTNXLSGCEK-WYWMIBKRSA-N'\n","import pandas as pd\n","import os\n","from cpiextract.databases import *\n","from cpiextract.utils import compound_identifiers\n","inp=2830389\n","comp_ids=compound_identifiers(inp)"]},{"cell_type":"markdown","id":"054a9bdd","metadata":{"id":"054a9bdd"},"source":["### Run PubChem only"]},{"cell_type":"code","execution_count":null,"id":"d2d8a708","metadata":{"id":"d2d8a708","scrolled":true},"outputs":[],"source":["pubchem = PubChem()\n","pc_dat, pc_state, pc_raw = pubchem.interactions(input_comp=comp_ids, pChEMBL_thres=0)"]},{"cell_type":"code","execution_count":null,"id":"cd8b7ae7","metadata":{},"outputs":[],"source":["pc_dat"]},{"cell_type":"code","execution_count":null,"id":"ccc8dfc6","metadata":{},"outputs":[],"source":["pc_dat"]},{"cell_type":"code","execution_count":null,"id":"27104fdb","metadata":{},"outputs":[],"source":["pc_state"]},{"cell_type":"markdown","id":"c1cb637b","metadata":{},"source":[]},{"cell_type":"markdown","id":"54c291e7","metadata":{"id":"54c291e7"},"source":["### Run ChEMBL only"]},{"cell_type":"code","execution_count":null,"id":"9da0d85b","metadata":{},"outputs":[],"source":["chembl_ids = []"]},{"cell_type":"code","execution_count":null,"id":"a67a6400","metadata":{},"outputs":[],"source":["file_path=os.path.expanduser(os.getcwd()+'data\\\\Databases\\\\ChEMBL.csv')\n","chembl_data=pd.read_csv(file_path,sep=',')"]},{"cell_type":"code","execution_count":null,"id":"983755e0","metadata":{"id":"983755e0","scrolled":true},"outputs":[],"source":["chembl = ChEMBL(database=chembl_data)\n","[chembl_dat, chembl_state, chembl_raw] = chembl.interactions(input_comp=comp_ids, pChEMBL_thres=0, chembl_ids=chembl_ids)"]},{"cell_type":"code","execution_count":null,"id":"d8f7c952","metadata":{},"outputs":[],"source":["chembl_dat"]},{"cell_type":"code","execution_count":null,"id":"7de1ccf4","metadata":{},"outputs":[],"source":["chembl_state"]},{"cell_type":"markdown","id":"ed8bacdc","metadata":{"id":"ed8bacdc","scrolled":true},"source":["### Run BindingDB only"]},{"cell_type":"code","execution_count":null,"id":"2efba0b1","metadata":{},"outputs":[],"source":["#Downloaded from BindingDB on 3/30/2023\n","file_path=os.path.expanduser(os.getcwd()+'\\\\data\\\\Databases\\\\BindingDB_All.tsv')\n","BDB_data=pd.read_csv(file_path,sep='\\t',usecols=['Ligand SMILES','Ligand InChI','BindingDB MonomerID','Ligand InChI Key','BindingDB Ligand Name','Target Name Assigned by Curator or DataSource','Target Source Organism According to Curator or DataSource','Ki (nM)','IC50 (nM)','Kd (nM)','EC50 (nM)','pH','Temp (C)','Curation/DataSource','UniProt (SwissProt) Entry Name of Target Chain','UniProt (SwissProt) Primary ID of Target Chain'],on_bad_lines='skip')"]},{"cell_type":"code","execution_count":null,"id":"f76b79ef","metadata":{"id":"f76b79ef","scrolled":true},"outputs":[],"source":["bdb = BindingDB(database=BDB_data)\n","[bdb_dat, bdb_state, bdb_raw] = bdb.interactions(input_comp=comp_ids, pChEMBL_thres=0)"]},{"cell_type":"code","execution_count":null,"id":"15c3af12","metadata":{},"outputs":[],"source":["bdb_raw"]},{"cell_type":"code","execution_count":null,"id":"b53759ae","metadata":{},"outputs":[],"source":["bdb_state"]},{"cell_type":"code","execution_count":null,"id":"371a9c1b","metadata":{},"outputs":[],"source":["bdb_dat"]},{"cell_type":"markdown","id":"1d7c2216","metadata":{"id":"1d7c2216","scrolled":true},"source":["### Run STITCH only"]},{"cell_type":"code","execution_count":null,"id":"3edbfc57","metadata":{},"outputs":[],"source":["#Downloaded from STITCH on 2/22/2023\n","file_path=os.path.expanduser(os.getcwd()+'\\\\data\\\\Databases\\\\STITCH.tsv')\n","sttch_data=pd.read_csv(file_path,sep='\\t')"]},{"cell_type":"code","execution_count":null,"id":"3d336b9f","metadata":{},"outputs":[],"source":["stitch = Stitch(database=sttch_data)"]},{"cell_type":"code","execution_count":null,"id":"2ee0de86","metadata":{"id":"2ee0de86","scrolled":true},"outputs":[],"source":["[sttch_dat, sttch_state, sttch_raw] = stitch.interactions(input_comp=comp_ids, set_stereo=1)"]},{"cell_type":"code","execution_count":null,"id":"adf3a452","metadata":{"id":"adf3a452","outputId":"beff9b83-406a-4af5-bbc9-5ddef0f5dc05"},"outputs":[],"source":["sttch_dat"]},{"cell_type":"markdown","id":"37047848","metadata":{"id":"37047848"},"source":["### Run CTD only"]},{"cell_type":"code","execution_count":null,"id":"591c71a9","metadata":{},"outputs":[],"source":["#Downloaded from CTD on 2/24/2023\n","file_path=os.path.expanduser(os.getcwd()+'\\\\data\\\\Databases\\\\CTD.csv')\n","CTD_data=pd.read_csv(file_path,sep=',')"]},{"cell_type":"code","execution_count":null,"id":"d6759cd0","metadata":{"id":"d6759cd0","scrolled":true},"outputs":[],"source":["ctd = CTD(database=CTD_data)\n","[ctd_dat, ctd_state, ctd_raw] = ctd.interactions(input_comp=comp_ids)"]},{"cell_type":"code","execution_count":null,"id":"9560edf7","metadata":{},"outputs":[],"source":["ctd_dat"]},{"cell_type":"markdown","id":"1591a344","metadata":{"id":"1591a344","scrolled":true},"source":["### Run DTC only"]},{"cell_type":"code","execution_count":null,"id":"da52d804","metadata":{},"outputs":[],"source":["#Downloaded from DTC on 2/24/2023\n","file_path=os.path.expanduser(os.getcwd()+'\\\\data\\\\Databases\\\\DTC.csv')\n","DTC_data=pd.read_csv(file_path,sep=',',usecols=['compound_id','standard_inchi_key','target_id','gene_names','wildtype_or_mutant','mutation_info','standard_type','standard_relation','standard_value','standard_units','activity_comment','pubmed_id','doc_type'])"]},{"cell_type":"code","execution_count":null,"id":"ff6800b3","metadata":{"id":"ff6800b3","scrolled":true},"outputs":[],"source":["dtc = DTC(database=DTC_data)\n","[dtc_dat, dtc_state, dtc_raw] = dtc.interactions(input_comp=comp_ids, chembl_ids=[], pChEMBL_thres=0)"]},{"cell_type":"code","execution_count":null,"id":"f5bdc2ec","metadata":{},"outputs":[],"source":["dtc_dat"]},{"cell_type":"markdown","id":"63cc2b75","metadata":{"id":"63cc2b75"},"source":["### Run OTP only"]},{"cell_type":"code","execution_count":null,"id":"3ebcfa20","metadata":{"id":"3ebcfa20"},"outputs":[],"source":["otp = OTP()\n","[otp_dat, otp_state, otp_raw] = otp.interactions(input_comp=comp_ids, chembl_ids=[], intqual=2)"]},{"cell_type":"code","execution_count":null,"id":"d7bb183f","metadata":{"id":"d7bb183f","outputId":"0d363315-3fff-4cd3-8c3d-b4797f804fba"},"outputs":[],"source":["otp_dat"]},{"cell_type":"markdown","id":"45320498","metadata":{},"source":["### Run DrugCentral only"]},{"cell_type":"code","execution_count":null,"id":"dbb661cb","metadata":{},"outputs":[],"source":["# File obtained in the last cells of this notebook\n","file_path=os.path.expanduser(os.getcwd()+'\\\\data\\\\Databases\\\\DrugCentral.csv')\n","DC_data=pd.read_csv(file_path, sep=',')"]},{"cell_type":"code","execution_count":null,"id":"880906d2","metadata":{},"outputs":[],"source":["dc = DrugCentral(database=DC_data)\n","[DC_dat, DC_state, DC_raw] = dc.interactions(input_comp=comp_ids)"]},{"cell_type":"code","execution_count":null,"id":"f6308a36","metadata":{},"outputs":[],"source":["DC_dat"]},{"cell_type":"code","execution_count":null,"id":"cd2d712e","metadata":{},"outputs":[],"source":["DC_state"]},{"cell_type":"markdown","id":"4ded8d71","metadata":{"id":"4ded8d71"},"source":["### Run DrugBank only"]},{"cell_type":"code","execution_count":null,"id":"02967e3e","metadata":{},"outputs":[],"source":["#Downloaded from DrugBank on 3/2/2022\n","file_path=os.path.expanduser(os.getcwd()+'\\\\data\\\\Databases\\\\DB.csv')\n","DB_data = pd.read_csv(file_path, sep=',')"]},{"cell_type":"code","execution_count":null,"id":"2f22a67f","metadata":{"id":"2f22a67f"},"outputs":[],"source":["db = DB(database=DB_data)\n","[DB_dat, DB_state, DB_raw] = db.interactions(input_comp=comp_ids)"]},{"cell_type":"code","execution_count":null,"id":"5ab014ca","metadata":{},"outputs":[],"source":["DB_dat"]},{"cell_type":"code","execution_count":null,"id":"f5331d40","metadata":{},"outputs":[],"source":["DB_state"]}],"metadata":{"colab":{"provenance":[]},"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":"3.10.14"}},"nbformat":4,"nbformat_minor":5}