252 lines
8.1 KiB
Python
252 lines
8.1 KiB
Python
import argparse
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import logging
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import multiprocessing
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import os
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import sys
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from argparse import ArgumentParser
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from collections import namedtuple
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import mysql.connector as con
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mycon = con.connect(host='192.168.1.6',user="curieweb",password="curie-web-russian-54",port=3306,database="curie")
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mycursor = mycon.cursor()
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sql_select_Query = "SELECT id,email,pdb,ligand_smile,ligand_name,description,date FROM curieweb WHERE pdb IS NOT NULL AND 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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records = records[0]
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print("Importing PLIP..",end="")
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from plip.basic import config, logger
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from plip.basic.config import __version__
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from plip.basic.parallel import parallel_fn
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from plip.basic.remote import VisualizerData
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from plip.exchange.webservices import fetch_pdb
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from plip.structure.preparation import create_folder_if_not_exists, extract_pdbid
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from plip.structure.preparation import tilde_expansion, PDBComplex
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print(".Done")
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def download_structure(inputpdbid):
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"""Given a PDB ID, downloads the corresponding PDB structure.
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Checks for validity of ID and handles error while downloading.
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Returns the path of the downloaded file."""
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try:
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if len(inputpdbid) != 4 or extract_pdbid(inputpdbid.lower()) == 'UnknownProtein':
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logger.error(f'invalid PDB-ID (wrong format): {inputpdbid}')
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sys.exit(1)
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pdbfile, pdbid = fetch_pdb(inputpdbid.lower())
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pdbpath = tilde_expansion('%s/%s.pdb' % (config.BASEPATH.rstrip('/'), pdbid))
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create_folder_if_not_exists(config.BASEPATH)
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with open(pdbpath, 'w') as g:
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g.write(pdbfile)
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return pdbpath, pdbid
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except ValueError: # Invalid PDB ID, cannot fetch from RCBS server
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logger.error(f'PDB-ID does not exist: {inputpdbid}')
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sys.exit(1)
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def bounding_box(receptor, residues):
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try:
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import pymol2
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except ImportError:
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raise ImportError("Failed to import PyMOL")
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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(pdbpath,"target")
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cmd.select("box",(selectionResidues))
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extent = 5
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([minX, minY, minZ],[maxX, maxY, maxZ]) = cmd.get_extent("box")
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minX = minX - float(extent)
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minY = minY - float(extent)
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minZ = minZ - float(extent)
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maxX = maxX + float(extent)
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maxY = maxY + float(extent)
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maxZ = maxZ + float(extent)
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SizeX = maxX - minX
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SizeY = maxY - minY
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SizeZ = maxZ - minZ
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CenterX = (maxX + minX)/2
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CenterY = (maxY + minY)/2
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CenterZ = (maxZ + minZ)/2
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session.stop()
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return {"size_x": SizeX, "size_y": SizeY, "size_z": SizeZ, "center_x": CenterX, "center_y": CenterY, "center_z": CenterZ}
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def get3DModel(protein,ligand):
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import pymol2
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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.gltf")
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session.stop()
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def removeWater(pdbpath):
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import pymol2
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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(pdbpath,"target")
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cmd.remove('resn HOH')
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cmd.save(pdbpath,"target")
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session.stop()
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def getResidues(pdbpath):
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mol = PDBComplex()
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mol.load_pdb(pdbpath)
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for ligand in mol.ligands:
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mol.characterize_complex(ligand)
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residues = []
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for x in range(len(mol.interaction_sets)):
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if len(mol.interaction_sets[list(mol.interaction_sets.keys())[x]].interacting_res) != 0:
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residues.append(mol.interaction_sets[list(mol.interaction_sets.keys())[x]].interacting_res)
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print(residues)
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return residues
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def get_select_command(residues,allResidues=False):
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residues.sort(key=len,reverse=True)
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selectionResidues = ""
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allRes = []
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if len(residues) == 0:
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#print("what the frick, no interacting ligands???")
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print("We could not find any binding sites within the structure.")
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else:
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for x in residues:
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selectionResidues = ""
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for y in x:
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selectionResidues += 'resi ' + y.replace("A","") + ' + '
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allRes.append(selectionResidues.strip()[:-1].strip())
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if allResidues == False:
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return allRes[0]
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return allRes
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def convert_pdb_pdbqt(pdbpath):
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import oddt
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from oddt.docking.AutodockVina import write_vina_pdbqt
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print(pdbpath)
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try:
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receptor = next(oddt.toolkit.readfile("pdb",pdbpath.split("./")[1]))
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"""
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# remove zero order bonds from metals
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for atom in receptor:
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if atom.atomicnum == 30: # Atomic num of treated metals
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for bond in atom.bonds:
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print("del")
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receptor.OBMol.DeleteBond(bond.OBBond)
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"""
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receptor.calccharges()
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except Exception:
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print("Molecule failed to charge, falling back to RDKit")
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receptor = next(oddt.toolkits.rdk.readfile("pdb",pdbpath.split("./")[1]))
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receptor.calccharges()
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path = write_vina_pdbqt(receptor,'./',flexible=False)
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return path
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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 = "navanchauhan@gmail.com"
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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('smtp.gmail.com', 587)
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s.starttls()
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s.login(fromaddr, 'okrs shoc ahtk idui')
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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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inPDB = records[2]
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jobID = records[0]
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toaddr = records[1]
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description = records[5]
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date = records[6]
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#pdb_file_name = pdbpath.split('/')[-1]
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#pdbpath="./6lu7.pdb"
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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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import tempfile
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from shutil import make_archive, copyfile
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import time
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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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pdbpath, pdbid = download_structure(inPDB)
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residues = getResidues(pdbpath)
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selectionResidues = get_select_command(residues,allResidues=False)
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#print(selectionResidues)
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removeWater(pdbpath)
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config = bounding_box(pdbpath,selectionResidues)
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print("Configuration:",config)
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pdbqt = convert_pdb_pdbqt(pdbpath)
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configuration = "size_x={}\nsize_y={}\nsize_z={}\ncenter_x={}\ncenter_y={}\ncenter_z={}".format(config["size_x"],config["size_y"],config["size_z"],config["center_x"],config["center_y"],config["center_z"])
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with open("config.txt","w") as file:
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file.write(configuration)
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os.system('obabel -:"%s" --gen3d -opdbqt -O%s.pdbqt' % (records[3],records[4]))
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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" % (pdbqt,str(records[4]+".pdbqt")))
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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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copyfile("report.pdf",os.path.join(reportDirectory,(str(jobID)+".pdf")))
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get3DModel(pdbpath,"%s_out.pdbqt"%(records[4]))
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copyfile("model.gltf",os.path.join(modelDirectory,(str(jobID)+".gltf")))
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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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copyfile("model.usdz",os.path.join(modelDirectory,(str(jobID)+".usdz")))
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#copy(("Curie_Web_Result_"+str(jobID)),f)
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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() |