def loadTrainInfo(item,
modProt,
modProtVer,
modelDir=settings.get('etoxlie_model_dir')):
protVer = '%04d' % modProtVer
pathParams = os.path.join(modelDir, modProt, protVer, 'params.pkl')
if os.path.exists(pathParams):
with open(pathParams, 'r') as inFile:
parms = pickle.load(inFile)
trainSet = parms[item]
else:
return (False, 'Model parameters not found (%s)' % pathParams)
return (True, trainSet)
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with eTOXlab. If not, see <http://www.gnu.org/licenses/>.
import sys
import os
import logging
from time import sleep
from eTOX_ALLIES.etox import settings
from eTOX_ALLIES.etox.core import jobHandler
from eTOX_ALLIES.etox.core.main import submitScreen, screenSDF
etoxlie_folder = settings.get('etoxlie_folder')
class imodel():
def __init__(self, vpath, jobid='<not defined>'):
"""
LIE settings
The jobid argument was added by Marc van Dijk, 21-10-2016.
It passes along the Celery job identifier responsible for
launching this calculation from the etoxwsapi side of things.
This API jobid is stored in the .dsr and .job files greated
by eTOXLie and enables API job cancelation by querying for
the jobid and touching an empty KILL file in the associated
eTOXlie job directory.
"""
def prepareMD(wdir,itpLig,pdbLig, proteinPoses,model,dirSimPref='sim',localExe=True,timeSim=1.0,\
scriptExe='lie_mdrun.sh',enePref='MD_ene', decPref='decomp',remoteSettings=None):
currDir = os.getcwd()
try:
topology = importlib.import_module("eTOX_ALLIES.etox.topology.%s" %
model['forceField'])
except Exception, e:
logging.error('Error in loading module "{0}": {1}'.format(
model['forceField'], e))
sys.exit()
listFiles = []
GMXMD = os.path.join(settings.get('etoxlie_root_dir'), 'bin/gmx45md.sh')
ENERGYANALYSIS = os.path.join(settings.get('etoxlie_root_dir'),
'bin/getEnergies.py')
GMXRC = settings.get('GMXRC')
listFiles.extend([GMXMD, ENERGYANALYSIS])
os.chdir(wdir)
#Fix topology ligand
itpOut = 'compound_ref.itp'
success, results = topology.correctItp(itpLig, itpOut, posre=True)
listFiles.append(results['itp']) # Ligand itp
if 'posre' in results:
listFiles.append(results['posre']) # ligand posre
if os.name == 'posix' and sys.version_info[0] < 3:
import subprocess32 as sp
else:
import subprocess as sp
import pybel as pb
import openbabel as ob
from glob import glob
from eTOX_ALLIES.etox import settings
from eTOX_ALLIES.etox.core import modelHandler
from eTOX_ALLIES.etox.topology.amber import refineTau
from eTOX_ALLIES.etox.core.geometry import findOcpd1, normhem, distance as dist
AMBERHOME = settings.get('AMBERHOME')
ACPYPE = settings.get('ACPYPE')
DATADIR = os.path.join(settings.get('etoxlie_root_dir'), 'bin/files/')
GROMACSHOME = settings.get('GROMACSHOME')
ob.obErrorLog.SetOutputLevel(0)
def prepareModel(modelDir, modelData, etoxlie_folder, radiusRes=16):
'''modelData={name: str, dockSoftware: str, timeSim: float, forceField:str, resSite: None or list
pH: float, pHCorr: bool, protConfs: list of dictionaries }
protConfs: [{'pdb' : str, 'center' : None / [X,Y,Z], 'radius' : float }]
'''
currDir = os.getcwd()
success = True
def linkElab(keyElab='ETOXLABHOME', overWrite=True):
eLabFn = 'imodel.py'
eLabVersions = 'service-version.txt'
eLabLabel = 'service-label.txt'
#Get list calibrated models
listModels = modelHandler.listModels(modelDir)
eLabDir = settings.get(keyElab)
if not os.path.isdir(str(eLabDir)):
msg = 'Specified folder in settings.py does not exists: {0}'.format(
eLabDir)
logging.error(msg)
return (False, msg)
try:
for model in listModels:
### Create service-label.txt; service-version.txt; models dir
modDir = os.path.join(eLabDir, model['name'])
if not os.path.isdir(modDir):
os.mkdir(modDir)
outFn = os.path.join(modDir, eLabVersions)
outFileVers = open(outFn, 'w')
# For eTOXlab compatibility
fakever = 'version%04d' % 0
modDirVer = os.path.join(modDir, fakever)
if not os.path.isdir(modDirVer):
os.mkdir(modDirVer)
outFileVers.write('0\t0\n')
for version in model['vers']:
vers = 'version%04d' % version
modDirVer = os.path.join(modDir, vers)
if not os.path.isdir(modDirVer):
os.mkdir(modDirVer)
outFn = os.path.join(modDirVer, eLabFn)
sourceTmpl = getsource(
importlib.import_module("etox.core.imodel"))
sourceTmpl = sourceTmpl.replace('REPLACE_PROTEIN',
model['name'])
sourceTmpl = sourceTmpl.replace('REPLACE_VERSION',
str(model['vers'][0]))
if os.path.exists(outFn):
logging.info('%s is already present in %s' %
(eLabFn, modDirVer))
if not overWrite:
logging.warn('%s/%s will not be overwrite' %
(modDirVer, eLabFn))
continue
with open(outFn, 'w') as outFile:
outFile.write(sourceTmpl)
outFileVers.write('%d\t0\n' % version)
outFileVers.close()
### Versioning and labelling services
# full tag: e.g. /ADME/Metabolism/Phase I/CYP 1A2 Affinity/1
outFn = os.path.join(modDir, eLabLabel)
with open(outFn, 'w') as outFile:
outFile.write('/ADME/Metabolism/Phase I/%s Affinity/1\n' %
model['name'])
outFile.write('quantitative')
except exception, e:
return (False, e)
import os, sys
import importlib
from inspect import getsource
from eTOX_ALLIES.etox import settings
from eTOX_ALLIES.etox.core import modelHandler
modelDir = settings.get('etoxlie_model_dir')
def linkElab(keyElab='ETOXLABHOME', overWrite=True):
eLabFn = 'imodel.py'
eLabVersions = 'service-version.txt'
eLabLabel = 'service-label.txt'
#Get list calibrated models
listModels = modelHandler.listModels(modelDir)
eLabDir = settings.get(keyElab)
if not os.path.isdir(str(eLabDir)):
msg = 'Specified folder in settings.py does not exists: {0}'.format(
eLabDir)
logging.error(msg)
return (False, msg)
try:
for model in listModels:
### Create service-label.txt; service-version.txt; models dir
modDir = os.path.join(eLabDir, model['name'])
if not os.path.isdir(modDir):
os.mkdir(modDir)
default=None)
parser.add_argument('-o',
'--output',
dest='outPref',
required=False,
default='')
args = parser.parse_args()
logging.basicConfig(level='DEBUG')
if args.job and args.model:
logging.error(
'Analysis of a job or a model cannot be done simultaneously')
sys.exit(1)
if args.job is not None:
extractJob(args.job,
settings.get('tmpFolder'),
settings.get('etoxlie_model_dir'),
outPref=args.outPref)
if args.model is not None:
try:
ver = int(args.version)
except:
logging.error('A model version should be provide "e.g. -v 1"')
sys.exit(1)
extractModel(args.model, ver, modelDir)
import logging
import pybel as pb
import openbabel as ob
import time
import numpy as np
from eTOX_ALLIES.etox import settings
from eTOX_ALLIES.etox.core import jobHandler
from eTOX_ALLIES.etox.core.modelHandler import loadModel, saveModel, listModels
from eTOX_ALLIES.etox.core.docking import dockLie
from eTOX_ALLIES.etox.core.MDrunner import *
from eTOX_ALLIES.etox.core.utility_lie import calibrateLie, predictLie, predictError
from eTOX_ALLIES.etox.core.utility_AD import calibrateAD, predictAD
etoxlie_folder = settings.get('etoxlie_folder')
modelDir = settings.get('etoxlie_model_dir')
statEndJob = ['FAILED', 'CANCELLED', 'DONE']
def protonate(sdf, fileOut, pHcorr=True, pH=7.5):
'''If necessary converts the 2D structure of the molecule to 3D and protonation by pybel/openbabel
input:
sdf: sdf file as string
neutral: boolean; if molecule should be protonate according to pH is False
pH: pH for protonation
the result is a tuple containing:
1) True/False: describes the success of the operation
2) (if True ) The name of the 3D molecule
(if False) The error message
'''