import argparse import logging import multiprocessing import os import sys from argparse import ArgumentParser from collections import namedtuple import mysql.connector as con from misc.common import get3DModel, CopyContentOfFolder, RemoveAllFilesMatching from misc.email import email from misc.config import iniConfig 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 id,email,pdb,ligand_smile,ligand_name,description,date FROM curieweb WHERE pdb IS NOT NULL AND 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) 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 from plip.exchange.webservices import fetch_pdb from plip.structure.preparation import create_folder_if_not_exists, extract_pdbid from plip.structure.preparation import tilde_expansion, PDBComplex print(".Done") def download_structure(inputpdbid): """Given a PDB ID, downloads the corresponding PDB structure. Checks for validity of ID and handles error while downloading. Returns the path of the downloaded file.""" try: if len(inputpdbid) != 4 or extract_pdbid(inputpdbid.lower()) == 'UnknownProtein': logger.error(f'invalid PDB-ID (wrong format): {inputpdbid}') sys.exit(1) pdbfile, pdbid = fetch_pdb(inputpdbid.lower()) pdbpath = tilde_expansion('%s/%s.pdb' % (config.BASEPATH.rstrip('/'), pdbid)) create_folder_if_not_exists(config.BASEPATH) with open(pdbpath, 'w') as g: g.write(pdbfile) return pdbpath, pdbid except ValueError: # Invalid PDB ID, cannot fetch from RCBS server logger.error(f'PDB-ID does not exist: {inputpdbid}') sys.exit(1) def bounding_box(receptor, residues): try: import pymol2 except ImportError: raise ImportError("Failed to import PyMOL") session = pymol2.PyMOL() session.start() cmd = session.cmd cmd.load(pdbpath,"target") cmd.select("box",(selectionResidues)) extent = 5 ([minX, minY, minZ],[maxX, maxY, maxZ]) = cmd.get_extent("box") minX = minX - float(extent) minY = minY - float(extent) minZ = minZ - float(extent) maxX = maxX + float(extent) maxY = maxY + float(extent) maxZ = maxZ + float(extent) SizeX = maxX - minX SizeY = maxY - minY SizeZ = maxZ - minZ CenterX = (maxX + minX)/2 CenterY = (maxY + minY)/2 CenterZ = (maxZ + minZ)/2 session.stop() return {"size_x": SizeX, "size_y": SizeY, "size_z": SizeZ, "center_x": CenterX, "center_y": CenterY, "center_z": CenterZ} def removeWater(pdbpath): import pymol2 session = pymol2.PyMOL() session.start() cmd = session.cmd cmd.load(pdbpath,"target") cmd.remove('resn HOH') cmd.save(pdbpath,"target") session.stop() def getResidues(pdbpath): mol = PDBComplex() mol.load_pdb(pdbpath) for ligand in mol.ligands: mol.characterize_complex(ligand) residues = [] for x in range(len(mol.interaction_sets)): if len(mol.interaction_sets[list(mol.interaction_sets.keys())[x]].interacting_res) != 0: residues.append(mol.interaction_sets[list(mol.interaction_sets.keys())[x]].interacting_res) print(residues) return residues def get_select_command(residues,allResidues=False): residues.sort(key=len,reverse=True) selectionResidues = "" allRes = [] if len(residues) == 0: #print("what the frick, no interacting ligands???") print("We could not find any binding sites within the structure.") else: for x in residues: selectionResidues = "" for y in x: selectionResidues += 'resi ' + y.replace("A","") + ' + ' allRes.append(selectionResidues.strip()[:-1].strip()) if allResidues == False: return allRes[0] return allRes def convert_pdb_pdbqt(pdbpath): import oddt from oddt.docking.AutodockVina import write_vina_pdbqt print(pdbpath) try: receptor = next(oddt.toolkit.readfile("pdb",pdbpath.split("./")[1])) """ # remove zero order bonds from metals for atom in receptor: if atom.atomicnum == 30: # Atomic num of treated metals for bond in atom.bonds: print("del") receptor.OBMol.DeleteBond(bond.OBBond) """ receptor.calccharges() except Exception: print("Molecule failed to charge, falling back to RDKit") receptor = next(oddt.toolkits.rdk.readfile("pdb",pdbpath.split("./")[1])) receptor.calccharges() path = write_vina_pdbqt(receptor,'./',flexible=False) return path inPDB = records[2] jobID = records[0] toaddr = records[1] description = records[5] date = records[6] cd = os.getcwd() print("Curie-Web Directory is:",cd) 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") 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) 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) 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) print("Configuration:",config) pdbqt = convert_pdb_pdbqt(pdbpath) 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"]) with open("config.txt","w") as file: file.write(configuration) os.system('obabel -:"%s" --gen3d -opdbqt -O%s.pdbqt' % (records[3],records[4])) print("Ligand:",records[4]) print(str(records[4]+".pdbqt")) CopyContentOfFolder(scripts,directory) os.system("./main.sh -r %s -l %s -c config.txt -dpi" % (pdbqt,str(records[4]+".pdbqt"))) #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"))) RemoveAllFilesMatching(directory,".py") RemoveAllFilesMatching(directory,".sh") z = "Curie_Web_Result_"+str(jobID) zi = os.path.join(f,z) make_archive(zi, 'zip', directory) try: copyfile("report.pdf",os.path.join(reportDirectory,(str(jobID)+".pdf"))) except FileNotFoundError: reason = "Could not generate the PDF 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: email(toaddr,jobID,date,description,zipArchive=zi) mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID)) mycon.commit() sys.exit(0) """ get3DModel(pdbpath,"%s_out.pdbqt"%(records[4])) 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 --rm -v $(pwd):/usr/app leon/usd-from-gltf:latest model.gltf model.usdz") elif "aarch64" in arch: os.system("docker run --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(toaddr,jobID,date,description,zipArchive=zi) mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID)) mycon.commit()