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[Update] Check for spacegroup and box angles when reading in CCP4 den… #1

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Jan 16, 2017
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[Update] Check for spacegroup and box angles when reading in CCP4 den… #1

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17 changes: 12 additions & 5 deletions powerfit/volume.py
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Original file line number Diff line number Diff line change
Expand Up @@ -272,6 +272,14 @@ def __init__(self, fid):
self._get_endiannes()
# get the header
self._get_header()
# Symmetry and non-rectangular boxes are not supported.
error = (self.header['ispg'] != 1 or
self.header['alpha'] != self.header['beta'] !=
self.header['gamma'] != 90)
if error:
msg = "Only densities with P1-symmetry in rectangular boxes are supported."
raise ValueError(msg)

# check the order of axis in the file
self._get_order()
# determine the voxelspacing and origin
Expand Down Expand Up @@ -326,8 +334,7 @@ def _get_density(self):
elif mode == 2:
dtype = 'f4'

density = np.fromfile(self.fhandle,
dtype=self._endian + dtype).reshape(self.shape)
density = np.fromfile(self.fhandle, dtype=self._endian + dtype).reshape(self.shape)
if self.order == (1, 3, 2):
self.density = np.swapaxes(self.density, 0, 1)
elif self.order == (2, 1, 3):
Expand Down Expand Up @@ -512,11 +519,11 @@ def _get_header(self):

line = volume.readline()
header['xlength'] = float(line[0:12])
header['ylength'] = float(line[12:24])
header['ylength'] = float(line[12:24])
header['zlength'] = float(line[24:36])
header['alpha'] = float(line[36:48])
header['alpha'] = float(line[36:48])
header['beta'] = float(line[48:60])
header['gamma'] = float(line[60:72])
header['gamma'] = float(line[60:72])

header['order'] = volume.readline()[0:3]

Expand Down