def surface_xtra(entity, **kwargs):
"""Runs the MSMS application to create the molecular surface, which is an
a numpy array of 3D-coordinates.
Arguments:
* entity - an ``Entity`` instance.
Additional keyworded arguments are for the ``Msms`` application controller.
Returns the numpy array and put it into entity.xtra['MSMS_SURFACE'].
"""
msms = Msms(**kwargs)
res = msms(entity)
surface = parse_VertFile(res['VertFile'])
entity.xtra['MSMS_SURFACE'] = surface
res.cleanUp() # remove all temporary files
return surface
def surface_xtra(entity, **kwargs):
"""Runs the MSMS application to create the molecular surface, which is an
a numpy array of 3D-coordinates.
Arguments:
* entity - an ``Entity`` instance.
Additional keyworded arguments are for the ``Msms`` application controller.
Returns the numpy array and put it into entity.xtra['MSMS_SURFACE'].
"""
msms = Msms(**kwargs)
res = msms(entity)
surface = parse_VertFile(res['VertFile'])
entity.xtra['MSMS_SURFACE'] = surface
res.cleanUp() # remove all temporary files
return surface
def test_parseVertFile(self):
out_arr = parse_VertFile(self.vertfile)
assert out_arr.dtype == 'float64'
assert out_arr.shape == (3,3)
assert out_arr[0][0] == 1.
