diff options
| -rw-r--r-- | app/dock-manual.py | 99 | ||||
| -rw-r--r-- | app/dock-single.py | 112 | ||||
| -rw-r--r-- | app/misc/__init__.py | 0 | ||||
| -rw-r--r-- | app/misc/common.py | 33 | ||||
| -rw-r--r-- | app/misc/email.py | 48 |
5 files changed, 147 insertions, 145 deletions
diff --git a/app/dock-manual.py b/app/dock-manual.py index c953a36..0734b14 100644 --- a/app/dock-manual.py +++ b/app/dock-manual.py @@ -1,6 +1,10 @@ import mysql.connector as con - +from misc.common import get3DModel, CopyContentOfFolder, RemoveAllFilesMatching +from misc.email import email +import os import configparser +import sys + iniConfig = configparser.ConfigParser() iniConfig.read('config.ini') @@ -21,69 +25,6 @@ if records == []: 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: - os.remove(FilePath) - except: - print("Error in removing misc file") - receptor_name = "protein.pdbqt" ligand_name = "ligand.pdbqt" description = "Curie Web Task" @@ -92,6 +33,7 @@ description = "Curie Web Task" r = records[0] jobID = r[0] toEmail = r[1] +toaddr = toEmail targetB = r[2] if r[3] is not None: receptor_name = str(r[3]) @@ -102,17 +44,15 @@ configB = r[7] date = r[8] if r[9] is not None: description = r[9] +else: + description = "not specified" -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 @@ -134,14 +74,27 @@ with tempfile.TemporaryDirectory() as directory: 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")) + try: + copyfile("report.pdf",os.path.join(reportDirectory,(str(jobID)+".pdf"))) + except: + reason = "Could not generate the report, this could be because of a failed docking job. Please check the ZIP archive for the configuration and converted PDBQTs and try submitting manually. " + email(toaddr,jobID,date,description,zipArchive=zi,reason=reason) + mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID)) + mycon.commit() + sys.exit(0) + res = get3DModel(receptor_name,ligand_name.replace(".pdbqt","_out.pdbqt")) + if res == None: + reason = "Could not generate the report, this could be because of a failed docking job. Please check the ZIP archive for the configuration and converted PDBQTs and try submitting manually. " + email(toaddr,jobID,date,description,zipArchive=zi,reason=reason) + mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID)) + mycon.commit() + sys.exit(0) os.system("collada2gltf -i model.dae -o model.gltf") try: copyfile("model.gltf",os.path.join(modelDirectory,(str(jobID)+".gltf"))) except: print("Does not have Collada2GLTF Installed") - email(zi) + email(toaddr,jobID,date,description,zipArchive=zi) mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID)) mycon.commit() exit(0) @@ -155,6 +108,6 @@ with tempfile.TemporaryDirectory() as directory: copyfile("model.usdz",os.path.join(modelDirectory,(str(jobID)+".usdz"))) except: print("Could not generate USDZ file") - email(zi) + email(toaddr,jobID,date,description,zipArchive=zi) mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID)) mycon.commit() diff --git a/app/dock-single.py b/app/dock-single.py index 90031a1..024cd8f 100644 --- a/app/dock-single.py +++ b/app/dock-single.py @@ -5,9 +5,9 @@ import os import sys from argparse import ArgumentParser from collections import namedtuple - +from misc.common import get3DModel, CopyContentOfFolder, RemoveAllFilesMatching import mysql.connector as con - +from misc.email import email import configparser iniConfig = configparser.ConfigParser() iniConfig.read('config.ini') @@ -36,7 +36,6 @@ records = records[0] print("Importing PLIP..",end="") from plip.basic import config, logger - from plip.basic.config import __version__ from plip.basic.parallel import parallel_fn from plip.basic.remote import VisualizerData @@ -99,15 +98,6 @@ def bounding_box(receptor, residues): return {"size_x": SizeX, "size_y": SizeY, "size_z": SizeZ, "center_x": CenterX, "center_y": CenterY, "center_z": CenterZ} -def get3DModel(protein,ligand): - import pymol2 - session = pymol2.PyMOL() - session.start() - cmd = session.cmd - cmd.load(protein,"target") - cmd.load(ligand,"ligand") - cmd.save("model.dae") - session.stop() def removeWater(pdbpath): import pymol2 @@ -176,83 +166,47 @@ def convert_pdb_pdbqt(pdbpath): return path -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'] - - 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 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: - os.remove(FilePath) - except: - print("Error in removing misc file") - inPDB = records[2] jobID = records[0] toaddr = records[1] description = records[5] date = records[6] -#pdb_file_name = pdbpath.split('/')[-1] -#pdbpath="./6lu7.pdb" -import os,glob cd = os.getcwd() f = os.path.join(cd,"static/uploads") scripts = os.path.join(cd,"scripts") reportDirectory = os.path.join(f,"reports") 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) import tempfile from shutil import make_archive, copyfile,copy import time + + with tempfile.TemporaryDirectory() as directory: print('The created temporary directory is %s' % directory) os.chdir(directory) - pdbpath, pdbid = download_structure(inPDB) + + try: + pdbpath, pdbid = download_structure(inPDB) + except: + reason = "Could not download PDB with the id " + str(inPDB) + ". " + email(toaddr,jobID,date,description,reason=reason) + mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID)) + mycon.commit() + sys.exit(0) + residues = getResidues(pdbpath) - selectionResidues = get_select_command(residues,allResidues=False) + + try: + selectionResidues = get_select_command(residues,allResidues=False) + except IndexError: + reason = "Could not find binding site automatically. " + email(toaddr,jobID,date,description,reason=reason) + mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID)) + mycon.commit() + sys.exit(0) #print(selectionResidues) removeWater(pdbpath) config = bounding_box(pdbpath,selectionResidues) @@ -272,8 +226,22 @@ with tempfile.TemporaryDirectory() as directory: 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(pdbpath,"%s_out.pdbqt"%(records[4])) + try: + copyfile("report.pdf",os.path.join(reportDirectory,(str(jobID)+".pdf"))) + except: + reason = "Could not generate the report, this could be because of a failed docking job. Please check the ZIP archive for the configuration and converted PDBQTs and try submitting manually. " + email(toaddr,jobID,date,description,zipArchive=zi,reason=reason) + mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID)) + mycon.commit() + sys.exit(0) + try: + get3DModel(pdbpath,"%s_out.pdbqt"%(records[4])) + except: + reason = "Could not generate the report, this could be because of a failed docking job. Please check the ZIP archive for the configuration and converted PDBQTs and try submitting manually. " + email(toaddr,jobID,date,description,zipArchive=zi,reason=reason) + mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID)) + mycon.commit() + sys.exit(0) 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() @@ -286,6 +254,6 @@ with tempfile.TemporaryDirectory() as directory: copyfile("model.usdz",os.path.join(modelDirectory,(str(jobID)+".usdz"))) except: print("Could not generate USDZ file") - email(zi) + email(toaddr,jobID,date,description,zipArchive=zi) mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID)) mycon.commit()
\ No newline at end of file diff --git a/app/misc/__init__.py b/app/misc/__init__.py new file mode 100644 index 0000000..e69de29 --- /dev/null +++ b/app/misc/__init__.py diff --git a/app/misc/common.py b/app/misc/common.py new file mode 100644 index 0000000..1463c73 --- /dev/null +++ b/app/misc/common.py @@ -0,0 +1,33 @@ +import os +import glob +from shutil import copy + +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: + os.remove(FilePath) + except: + print("Error in removing misc file") + +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()
\ No newline at end of file diff --git a/app/misc/email.py b/app/misc/email.py new file mode 100644 index 0000000..d2967bb --- /dev/null +++ b/app/misc/email.py @@ -0,0 +1,48 @@ +import smtplib +from email.mime.multipart import MIMEMultipart +from email.mime.text import MIMEText +from email.mime.base import MIMEBase +from email import encoders + +import configparser +iniConfig = configparser.ConfigParser() +iniConfig.read('config.ini') + +try: + iniConfig['DATABASE'] +except KeyError: + iniConfig.read("../config.ini") + + +def email(toaddr,jobID,date,description,zipArchive=None,complete=True,reason=None): + fromaddr = iniConfig['SMTP']['EMAIL'] + + msg = MIMEMultipart() + msg['From'] = fromaddr + msg['To'] = toaddr + msg['Subject'] = "Curie Web Results for Job ID " + str(jobID) + if complete: + 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) + else: + body = "Task unsuccessful :( \n Job was submitted on {} with the description {}".format(date, description) + + if reason != None: + body = reason + str(body) + + msg.attach(MIMEText(body, 'plain')) + if zipArchive != None: + 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() |