Curie-Web/app/dock-single.py

260 lines
8.4 KiB
Python

import argparse
import logging
import multiprocessing
import os
import sys
from argparse import ArgumentParser
from collections import namedtuple
import mysql.connector as con
mycon = con.connect(host='192.168.1.6',user="curieweb",password="curie-web-russian-54",port=3306,database="curie")
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 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
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
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 = "navanchauhan@gmail.com"
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('smtp.gmail.com', 587)
s.starttls()
s.login(fromaddr, 'okrs shoc ahtk idui')
text = msg.as_string()
s.sendmail(fromaddr, toaddr, text)
s.quit()
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
cd = os.getcwd()
f = os.path.join(cd,"static/uploads")
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
import time
with tempfile.TemporaryDirectory() as directory:
print('The created temporary directory is %s' % directory)
os.chdir(directory)
pdbpath, pdbid = download_structure(inPDB)
residues = getResidues(pdbpath)
selectionResidues = get_select_command(residues,allResidues=False)
#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]))
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")))
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]))
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()
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")
#copy(("Curie_Web_Result_"+str(jobID)),f)
email(zi)
#print((str(zi) + ".zip"))
mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID))
mycon.commit()