Merge pull request #60 from MDAnalysis/ccp4-int-57

fix reading of nrstart and ncstart in CCP4 format

Author: orbeckst

CHANGELOG

@@ -23,6 +23,7 @@ The rules for this file:
   * Fixed reading in DX files containing scientific notation (PR #52)
   * Added missing floordivision to Grid (PR #53)
   * fix test on ARM (#51)
+  * fix incorrect reading of ncstart and nrstart in CCP4 (#57)
 
   Changes (do not affect user)
 

gridData/CCP4.py

@@ -177,7 +177,7 @@ class CCP4(object):
             3: 'Transform of Complex Integer*2',
             4: 'Transform of Complex Reals',
             5: '0',
-        }), Record('ncstart', 'I'), Record('nrstart', 'I'),
+        }), Record('ncstart', 'i'), Record('nrstart', 'i'),
         Record('nsstart', 'I'), Record('nx', 'I'),  # Number of gridpoints.
         Record('ny', 'I'), Record('nz', 'I'), Record('xlen', 'f'),  # Angstroms.
         Record('ylen', 'f'), Record('zlen', 'f'), Record('alpha', 'f'),  # Degrees.

gridData/tests/datafiles/1jzv.ccp4

@@ -6,6 +6,9 @@
 
 DX = resource_filename(__name__, 'test.dx')
 CCP4 = resource_filename(__name__, 'test.ccp4')
+# from http://www.ebi.ac.uk/pdbe/coordinates/files/1jzv.ccp4
+# (see issue #57)
+CCP4_1JZV = resource_filename(__name__, '1jzv.ccp4')
 # water density around M2 TM helices of nAChR from MD simulations
 # [O. Beckstein and M. S. P. Sansom. Physical Biology 3(2):147-159, 2006]
 gOpenMol = resource_filename(__name__, 'nAChR_M2_water.plt')

gridData/tests/datafiles/__init__.py

@@ -1,5 +1,7 @@
 from __future__ import absolute_import, division
 
+import pytest
+
 import numpy as np
 from numpy.testing import (assert_almost_equal,
                            assert_equal)
@@ -8,14 +10,63 @@
 
 from . import datafiles
 
-def test_ccp4():
-    g = Grid(datafiles.CCP4)
+@pytest.fixture(scope="module")
+def g():
+    return Grid(datafiles.CCP4)
+
+def test_ccp4(g):
     POINTS = 192
     assert_equal(g.grid.flat, np.arange(1, POINTS+1))
     assert_equal(g.grid.size, POINTS)
     assert_almost_equal(g.delta, [3./4, .5, 2./3])
     assert_equal(g.origin, np.zeros(3))
 
+
+@pytest.fixture(scope="module")
+def ccp4data():
+    return CCP4.CCP4(datafiles.CCP4_1JZV)
+
+@pytest.mark.parametrize('name,value', [
+    ('nc', 96),
+    ('nr', 76),
+    ('ns', 70),
+    ('mode', 2),
+    ('ncstart', -4),
+    ('nrstart', -23),
+    ('nsstart', 102),
+    ('nx', 84),
+    ('ny', 84),
+    ('nz', 160),
+    ('xlen', 45.79999923706055),
+    ('ylen', 45.79999923706055),
+    ('zlen', 89.6500015258789),
+    ('alpha', 90.0),
+    ('beta', 90.0),
+    ('gamma', 90.0),
+    ('mapc', 2),
+    ('mapr', 1),
+    ('maps', 3),
+    ('amin', -0.9930942058563232),
+    ('amax', 9.050403594970703),
+    ('amean', -0.0005801090155728161),
+    ('ispg', 92),
+    ('nsymbt', 640),
+    ('lskflg', 0),
+    ('bsaflag', '@'),
+    ('skwmat', None),
+    ('skwtrn', None),
+    ('endianness', 'little'),
+    ('arms', 0.4034915268421173),
+    ('nlabl', 1),
+    ('label', ' Map from fft                                                                   '),
+])
+def test_ccp4_integer_reading(ccp4data, name, value):
+    if type(value) is float:
+        assert_almost_equal(ccp4data.header[name], value, decimal=6)
+    else:
+        assert_equal(ccp4data.header[name], value)
+
+
 def test_byteorder():
     with open(datafiles.CCP4, 'rb') as ccp4file:
         flag = CCP4.CCP4._detect_byteorder(ccp4file)