252 lines
8.5 KiB
Python
252 lines
8.5 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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from misc.common import get3DModel, CopyContentOfFolder, RemoveAllFilesMatching
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from misc.email import email
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from misc.config import iniConfig
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mycon = con.connect(host=iniConfig['DATABASE']['HOST'],user=iniConfig['DATABASE']['USER'],password=iniConfig['DATABASE']['PASSWORD'],port=iniConfig['DATABASE']['PORT'],database=iniConfig['DATABASE']['NAME'])
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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 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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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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cd = os.getcwd()
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f = os.path.join(cd,"static/uploads")
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scripts = os.path.join(cd,"scripts")
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reportDirectory = os.path.join(f,"reports")
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modelDirectory = os.path.join(f,"3DModels")
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import tempfile
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from shutil import make_archive, copyfile,copy
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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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try:
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pdbpath, pdbid = download_structure(inPDB)
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except:
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reason = "Could not download PDB with the id " + str(inPDB) + ". "
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email(toaddr,jobID,date,description,reason=reason)
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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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sys.exit(0)
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residues = getResidues(pdbpath)
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try:
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selectionResidues = get_select_command(residues,allResidues=False)
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except IndexError:
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reason = "Could not find binding site automatically. "
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email(toaddr,jobID,date,description,reason=reason)
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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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sys.exit(0)
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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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print("Ligand:",records[4])
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print(str(records[4]+".pdbqt"))
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CopyContentOfFolder(scripts,directory)
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os.system("./main.sh -r %s -l %s -c config.txt -dpi" % (pdbqt,str(records[4]+".pdbqt")))
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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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RemoveAllFilesMatching(directory,".py")
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RemoveAllFilesMatching(directory,".sh")
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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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try:
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copyfile("report.pdf",os.path.join(reportDirectory,(str(jobID)+".pdf")))
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except FileNotFoundError:
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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. "
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email(toaddr,jobID,date,description,zipArchive=zi,reason=reason)
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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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sys.exit(0)
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try:
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get3DModel(pdbpath,"%s_out.pdbqt"%(records[4]))
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except:
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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. "
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email(toaddr,jobID,date,description,zipArchive=zi,reason=reason)
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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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sys.exit(0)
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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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print("Generating 3D Model")
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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(toaddr,jobID,date,description,zipArchive=zi)
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mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID))
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mycon.commit() |