def calc_arvo_geo_measures(self, radius):
"""
Calculates geometrical measures: volume, area
"""
_temp_file = Utilities.get_random_name()
_temp_file = "temp"
# TODO: Need a way set the surface radius for a each atom. Probably add it as
# as a new column in the atoms.in file.
# prepare a temporary file
self._writeATS(_temp_file, radius)
command = "%s protein=%s" % ("/Users/Tomas/git/Analysis-Toolkit/thirdparty/arvo_c/arvo_c", _temp_file)
output, stderr, status = Utilities.run_sub_process(command)
# if the execution of the was successful:
if not status:
output_array = output.split()
self.arvo_calc = True
self.arvo_volume = np.float64(output_array[1])
self.arvo_area = np.float64(output_array[3])
self.arvo_spheres = np.int16(output_array[6])
os.unlink(_temp_file)
def getSymmetry(self, clusterO):
"""
Evaluates the symmetry (point group) of a cluster.
"""
success = True
error = ""
symmetry = ""
if not self._globJVMOn:
success = False
error = "JVM is has not been initialized"
return success, error, symmetry
# Saves a cluster in to an xyz file.
cwd = os.getcwd()
tempClusterFile = "%s/%s.xyz" % (cwd, Utilities.get_random_name(10))
success, error = IO.writeXYZ(clusterO, tempClusterFile, scfDone=False)
if not success:
return success, error, symmetry
# Runs the symmetrizer to get the point group
try:
self._globJVMSymm.main(["-v", _verbose, "-t", _tolerance, tempClusterFile])
except:
#TODO: catch the Symmetrizer error
success = False
error = "error while running Symmetrizer"
return success, error, symmetry
IO.removeFile(tempClusterFile)
#TODO: In future this should be done via streams
success, error, symmetry = _getSymmetryFromFile(self._globJVMOutPath, self._globJVMErrPath)
self._clearJVMOutputFiles()
return success, error, symmetry
def __init__(self, options=None, args=None, standAlone=True): """ Constructor """ self.cwd = os.getcwd() self._globJVMOn = False self._globJVMSymm = None randomName = Utilities.get_random_name(8) self._globJVMOutPath = os.path.join(self.cwd, "jvm%s.out" % (randomName)) self._globJVMErrPath = os.path.join(self.cwd, "jvm%s.err" % (randomName)) self._options = options self._args = args self._input = None self.__startJVM()
