137 lines
4.6 KiB
Python
137 lines
4.6 KiB
Python
import mysql.connector as con
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import configparser
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config = configparser.ConfigParser()
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config.read('config.ini')
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try:
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config['DATABASE']
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except KeyError:
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config.read("../config.ini")
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mycon = con.connect(host=config['DATABASE']['HOST'],user=config['DATABASE']['USER'],password=config['DATABASE']['PASSWORD'],port=config['DATABASE']['PORT'],database=config['DATABASE']['NAME'])
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mycursor = mycon.cursor()
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sql_select_Query = "select * from curieweb where done=0 LIMIT 1"
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mycursor.execute(sql_select_Query)
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records = mycursor.fetchall()
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if records == []:
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print("Empty Set 😳")
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print("No active task, exitting gracefully")
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exit(0)
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def email(zipArchive):
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import smtplib
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from email.mime.multipart import MIMEMultipart
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from email.mime.text import MIMEText
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from email.mime.base import MIMEBase
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from email import encoders
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fromaddr = config['SMTP']['EMAIL']
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toaddr = toEmail
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msg = MIMEMultipart()
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msg['From'] = fromaddr
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msg['To'] = toaddr
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msg['Subject'] = "Curie Web Results for Job ID " + str(jobID)
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body = "Attached Zip contains the docked files, PLIP report and PyMOL Visualisations. If the ZIP file does not contain these files, please report this issue by replying to this email. Job was submitted on {} with the description {}".format(date, description)
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msg.attach(MIMEText(body, 'plain'))
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filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip"
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p = MIMEBase('application', 'octet-stream')
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with open((str(zipArchive) + ".zip"), "rb") as attachment:
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p.set_payload((attachment).read())
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encoders.encode_base64(p)
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p.add_header('Content-Disposition', "attachment; filename= %s" % filename)
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msg.attach(p)
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s = smtplib.SMTP(config['SMTP']['SERVER'], config['SMTP']['PORT'])
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s.starttls()
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s.login(fromaddr, config['SMTP']['PASSWORD'])
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text = msg.as_string()
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s.sendmail(fromaddr, toaddr, text)
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s.quit()
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def get3DModel(protein,ligand):
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try:
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import pymol2
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except ImportError:
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print("🤭 PyMOL 2 has not been installed correctly")
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return None
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session = pymol2.PyMOL()
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session.start()
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cmd = session.cmd
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cmd.load(protein,"target")
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cmd.load(ligand,"ligand")
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cmd.save("model.dae")
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session.stop()
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receptor_name = "protein.pdbqt"
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ligand_name = "ligand.pdbqt"
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description = "Curie Web Task"
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#print(records[0])
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r = records[0]
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jobID = r[0]
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toEmail = r[1]
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targetB = r[2]
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if r[3] is not None:
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receptor_name = str(r[3])
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if r[6] is not None:
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ligand_name = str(r[6])
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ligandB = r[4]
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configB = r[7]
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date = r[8]
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if r[9] is not None:
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description = r[9]
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import os
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cd = os.getcwd()
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f = os.path.join(cd,"static/uploads")
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reportDirectory = os.path.join(f,"reports")
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modelDirectory = os.path.join(f,"3DModels")
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#t = os.path.join(f,"receptor",target)
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#r = os.path.join(f,"ligands",ligand)
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#c = os.path.join(f,"configs",config)
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print(f)
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import tempfile
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from shutil import make_archive, copyfile
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with tempfile.TemporaryDirectory() as directory:
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print('The created temporary directory is %s' % directory)
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os.chdir(directory)
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# copy(t,os.getcwd())
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# copy(r,os.getcwd())
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# copy(c, os.getcwd())
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with open(receptor_name,"wb") as file:
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file.write(targetB)
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with open(ligand_name,"wb") as file:
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file.write(ligandB)
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with open("config.txt","wb") as file:
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file.write(configB)
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os.system("docker run --rm -v ${PWD}:/results -w /results -u $(id -u ${USER}):$(id -g ${USER}) navanchauhan/curie-cli -r %s -l %s -c config.txt -dpi" % (receptor_name,ligand_name))
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#copy("report.pdf",f)
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z = "Curie_Web_Result_"+str(jobID)
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zi = os.path.join(f,z)
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make_archive(zi, 'zip', directory)
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#copy(("Curie_Web_Result_"+str(jobID)),f)
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copyfile("report.pdf",os.path.join(reportDirectory,(str(jobID)+".pdf")))
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get3DModel(receptor_name,ligand_name.replace(".pdbqt","_out.pdbqt"))
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os.system("collada2gltf -i model.dae -o model.gltf")
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copyfile("model.gltf",os.path.join(modelDirectory,(str(jobID)+".gltf")))
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arch = os.popen("uname -m").read()
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if "x86" in arch:
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os.system("docker run -it --rm -v $(pwd):/usr/app leon/usd-from-gltf:latest model.gltf model.usdz")
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elif "aarch64" in arch:
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os.system("docker run -it --rm -v $(pwd):/usr/app navanchauhan/usd-from-gltf:latest model.gltf model.usdz")
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try:
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copyfile("model.usdz",os.path.join(modelDirectory,(str(jobID)+".usdz")))
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except:
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print("Could not generate USDZ file")
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email(zi)
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#print((str(zi) + ".zip"))
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mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID))
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mycon.commit()
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