def sample(self, val):
""" Set the 'sample' parameter to val."""
if val is None:
raise ValueError( "A sample must be defined.")
if val.split(".")[-1] == "pdb":
print("Checking presence of %s. Will query from PDB if not found in $PWD." % (val))
self.__sample = IOUtilities.checkAndGetPDB(val)
print("Sample path is set to %s." % (self.__sample))
def sample(self, val):
""" Set the 'sample' parameter to val."""
if val is None:
self.__sample = None
return
if val.split(".")[-1] == "pdb":
self.__sample = IOUtilities.checkAndGetPDB(val)
return
raise IOError("Samples must be in pdb format.")
def testQueryPDBTwice(self):
""" Check that we can do two subsequent queries (fails if urllib.urlcleanup is not called.) """
# Setup path to pdb file.
pdb_path = '5loy.pdb'
self.__files_to_remove.append(pdb_path)
self.__paths_to_remove.append('obsolete')
# Attempt to load it.
pdb_path = IOUtilities.checkAndGetPDB(pdb_path)
# Check it's there.
self.assertTrue( os.path.isfile( pdb_path ) )
# Remove it.
os.remove(pdb_path)
# Query again.
pdb_path = IOUtilities.checkAndGetPDB(pdb_path)
# Check it's there.
self.assertTrue( os.path.isfile( pdb_path ) )
def testQueryPDB(self):
""" Check that we can query a non-existing pdb from pdb.org and convert it to a dict. """
# Setup path to pdb file.
pdb_path = '5UDC.pdb'
self.__files_to_remove.append(pdb_path)
self.__paths_to_remove.append('obsolete')
# Attempt to load it.
pdb_path = IOUtilities.checkAndGetPDB(pdb_path)
# Check it's there.
self.assertTrue( os.path.isfile( pdb_path ) )
def sample(self, val):
""" Set the 'sample' parameter to val."""
if val is None:
raise ValueError( "A sample must be defined.")
if val.split(".")[-1] == "pdb":
self.__sample = IOUtilities.checkAndGetPDB(val)
def backengine(self):
""" This method drives the backengine singFEL."""
uniform_rotation = self.parameters.uniform_rotation
calculate_Compton = int(self.parameters.calculate_Compton)
slice_interval = self.parameters.slice_interval
number_of_slices = self.parameters.number_of_slices
pmi_start_ID = self.parameters.pmi_start_ID
pmi_stop_ID = self.parameters.pmi_stop_ID
number_of_diffraction_patterns = self.parameters.number_of_diffraction_patterns
if not os.path.isdir(self.output_path):
os.mkdir(self.output_path)
self.__output_dir = self.output_path
# If the sample is passed as a pdb, branch out to separate backengine implementation.
if self.input_path.split(".")[-1].lower() == 'pdb':
if not os.path.isfile(self.input_path):
# Attempt to query from pdb.
self.input_path = IOUtilities.checkAndGetPDB(self.input_path)
return self._backengineWithPdb()
# Ok, not a pdb, proceed.
# Serialize the geometry file.
beam_geometry_file = "tmp.geom"
self.parameters.detector_geometry.serialize(beam_geometry_file)
# Setup directory to pmi output.
# Backengine expects a directory name, so have to check if
# input_path is dir or file and handle accordingly.
if os.path.isdir(self.input_path):
input_dir = self.input_path
elif os.path.isfile(self.input_path):
input_dir = os.path.dirname(self.input_path)
config_file = '/dev/null'
# collect MPI arguments
if self.parameters.forced_mpi_command == "":
np, ncores = self.computeNTasks()
mpicommand = ParallelUtilities.prepareMPICommandArguments(np,1)
else:
mpicommand = self.parameters.forced_mpi_command
# collect program arguments
command_sequence = ['radiationDamageMPI',
'--inputDir', str(input_dir),
'--outputDir', str(self.__output_dir),
'--geomFile', str(beam_geometry_file),
'--configFile', str(config_file),
'--uniformRotation', str(uniform_rotation),
'--calculateCompton', str(calculate_Compton),
'--sliceInterval', str(slice_interval),
'--numSlices', str(number_of_slices),
'--pmiStartID', str(pmi_start_ID),
'--pmiEndID', str(pmi_stop_ID),
'--numDP', str(number_of_diffraction_patterns),
]
if self.parameters.beam_parameters is not None:
beam_parameter_file = "tmp.beam"
self.parameters.beam_parameters.serialize(beam_parameter_file)
command_sequence.append('--beamFile')
command_sequence.append(str(beam_parameter_file))
# put MPI and program arguments together
args = shlex.split(mpicommand) + command_sequence
if 'SIMEX_VERBOSE' in os.environ:
print(("SingFELPhotonDiffractor backengine command: "
+ " ".join(args)),flush=True)
# Run the backengine command.
proc = subprocess.Popen(args)
proc.wait()
# Return the return code from the backengine.
return proc.returncode