def process(self, mol, port):
try:
# The copy of the dictionary option as local variable
# is necessary to avoid filename collisions due to
# the parallel cube processes
opt = dict(self.opt)
if utils.PackageOEMol.checkTags(mol, ['Structure']):
gd = utils.PackageOEMol.unpack(mol)
opt['outfname'] = '{}-{}'.format(gd['IDTag'],
self.opt['outfname'])
mdData = utils.MDData(mol)
opt['molecule'] = mol
self.log.info('START NPT SIMULATION %s' % gd['IDTag'])
simtools.simulation(mdData, **opt)
packedmol = mdData.packMDData(mol)
self.success.emit(packedmol)
except Exception as e:
# Attach error message to the molecule that failed
self.log.error(traceback.format_exc())
mol.SetData('error', str(e))
# Return failed mol
self.failure.emit(mol)
return
def process(self, mol, port):
try:
# The copy of the dictionary option as local variable
# is necessary to avoid filename collisions due to
# the parallel cube processes
opt = dict(self.opt)
# Update cube simulation parameters with the eventually molecule SD tags
new_args = {
dp.GetTag(): dp.GetValue()
for dp in oechem.OEGetSDDataPairs(mol)
if dp.GetTag() in ["temperature", "pressure"]
}
if new_args:
for k in new_args:
try:
new_args[k] = float(new_args[k])
except:
pass
self.log.info(
"Updating parameters for molecule: {}\n{}".format(
mol.GetTitle(), new_args))
opt.update(new_args)
if utils.PackageOEMol.checkTags(mol, ['Structure']):
gd = utils.PackageOEMol.unpack(mol)
opt['outfname'] = '{}-{}'.format(gd['IDTag'],
self.opt['outfname'])
mdData = utils.MDData(mol)
opt['molecule'] = mol
self.log.info('START NPT SIMULATION %s' % gd['IDTag'])
simtools.simulation(mdData, **opt)
packedmol = mdData.packMDData(mol)
self.success.emit(packedmol)
except Exception as e:
# Attach error message to the molecule that failed
self.log.error(traceback.format_exc())
mol.SetData('error', str(e))
# Return failed mol
self.failure.emit(mol)
return