diff options
Diffstat (limited to 'app/dock-manual.py')
| -rw-r--r-- | app/dock-manual.py | 154 |
1 files changed, 154 insertions, 0 deletions
diff --git a/app/dock-manual.py b/app/dock-manual.py new file mode 100644 index 0000000..e2da478 --- /dev/null +++ b/app/dock-manual.py @@ -0,0 +1,154 @@ +import mysql.connector as con + +import configparser +iniConfig = configparser.ConfigParser() +iniConfig.read('config.ini') + +try: + iniConfig['DATABASE'] +except KeyError: + iniConfig.read("../config.ini") + +mycon = con.connect(host=iniConfig['DATABASE']['HOST'],user=iniConfig['DATABASE']['USER'],password=iniConfig['DATABASE']['PASSWORD'],port=iniConfig['DATABASE']['PORT'],database=iniConfig['DATABASE']['NAME']) +mycursor = mycon.cursor() + +sql_select_Query = "select * from curieweb where done=0 LIMIT 1" +mycursor.execute(sql_select_Query) + +records = mycursor.fetchall() +if records == []: + print("Empty Set 😳") + print("No active task, exitting gracefully") + exit(0) + +def email(zipArchive): + import smtplib + from email.mime.multipart import MIMEMultipart + from email.mime.text import MIMEText + from email.mime.base import MIMEBase + from email import encoders + + fromaddr = iniConfig['SMTP']['EMAIL'] + toaddr = toEmail + + msg = MIMEMultipart() + msg['From'] = fromaddr + msg['To'] = toaddr + msg['Subject'] = "Curie Web Results for Job ID " + str(jobID) + 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) + + msg.attach(MIMEText(body, 'plain')) + filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip" + p = MIMEBase('application', 'octet-stream') + with open((str(zipArchive) + ".zip"), "rb") as attachment: + p.set_payload((attachment).read()) + encoders.encode_base64(p) + p.add_header('Content-Disposition', "attachment; filename= %s" % filename) + msg.attach(p) + + s = smtplib.SMTP(iniConfig['SMTP']['SERVER'], iniConfig['SMTP']['PORT']) + s.starttls() + s.login(fromaddr, iniConfig['SMTP']['PASSWORD']) + text = msg.as_string() + + s.sendmail(fromaddr, toaddr, text) + s.quit() + +def get3DModel(protein,ligand): + try: + import pymol2 + except ImportError: + print("🤠PyMOL 2 has not been installed correctly") + return None + session = pymol2.PyMOL() + session.start() + cmd = session.cmd + cmd.load(protein,"target") + cmd.load(ligand,"ligand") + cmd.save("model.dae") + session.stop() + +def CopyContentOfFolder(sauce,destination): + src_files = os.listdir(sauce) + for file_name in src_files: + full_file_name = os.path.join(sauce, file_name) + if os.path.isfile(full_file_name): + copy(full_file_name, destination) + +def RemoveAllFilesMatching(directory,pattern): + print(directory+"/*"+pattern) + FileList = glob.glob(directory+"/*"+pattern) + for FilePath in FileList: + try: + print(FilePath) + os.remove(FilePath) + except: + print("Error in removing misc file") + +receptor_name = "protein.pdbqt" +ligand_name = "ligand.pdbqt" +description = "Curie Web Task" + +#print(records[0]) +r = records[0] +jobID = r[0] +toEmail = r[1] +targetB = r[2] +if r[3] is not None: + receptor_name = str(r[3]) +if r[6] is not None: + ligand_name = str(r[6]) +ligandB = r[4] +configB = r[7] +date = r[8] +if r[9] is not None: + description = r[9] + +import os,glob +cd = os.getcwd() +f = os.path.join(cd,"static/uploads") +reportDirectory = os.path.join(f,"reports") +scripts = os.path.join(cd,"scripts") +modelDirectory = os.path.join(f,"3DModels") +#t = os.path.join(f,"receptor",target) +#r = os.path.join(f,"ligands",ligand) +#c = os.path.join(f,"configs",config) +print(f) +import tempfile +from shutil import make_archive, copyfile,copy + +with tempfile.TemporaryDirectory() as directory: + print('The created temporary directory is %s' % directory) + os.chdir(directory) + with open(receptor_name,"wb") as file: + file.write(targetB) + with open(ligand_name,"wb") as file: + file.write(ligandB) + with open("config.txt","wb") as file: + file.write(configB) + # Legacy Docker Curie-Cli Run + #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)) + CopyContentOfFolder(scripts,directory) + os.system("./main.sh -r %s -l %s -c config.txt -dpi" % (receptor_name,ligand_name)) + RemoveAllFilesMatching(directory,".py") + RemoveAllFilesMatching(directory,".sh") + z = "Curie_Web_Result_"+str(jobID) + zi = os.path.join(f,z) + make_archive(zi, 'zip', directory) + copyfile("report.pdf",os.path.join(reportDirectory,(str(jobID)+".pdf"))) + get3DModel(receptor_name,ligand_name.replace(".pdbqt","_out.pdbqt")) + os.system("collada2gltf -i model.dae -o model.gltf") + copyfile("model.gltf",os.path.join(modelDirectory,(str(jobID)+".gltf"))) + arch = os.popen("uname -m").read() + print("Generating 3D Model") + if "x86" in arch: + os.system("docker run -it --rm -v $(pwd):/usr/app leon/usd-from-gltf:latest model.gltf model.usdz") + elif "aarch64" in arch: + os.system("docker run -it --rm -v $(pwd):/usr/app navanchauhan/usd-from-gltf:latest model.gltf model.usdz") + try: + copyfile("model.usdz",os.path.join(modelDirectory,(str(jobID)+".usdz"))) + except: + print("Could not generate USDZ file") + email(zi) + mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID)) + mycon.commit() |