CCP4 — the CCP4 volumetric data format

New in version 0.3.0.

The module provides a simple implementation of a reader for CCP4 ccp4 files. CCP4 files are binary files. The CCP4 reader tries to guess the endianess of the file, but this can fail (with a TypeError); you are on your own in this case.

Only the reader is implemented. If you want to write gridded data use a format that is more standard, such as OpenDX (see OpenDX).

Background

CCP4 format: http://www.ccp4.ac.uk/html/maplib.html#description

Used to be more carefully documented at http://lsbr.niams.nih.gov/3demc/3demc_maplib.html but currently this is only accessible through the Google cache http://webcache.googleusercontent.com/search?q=cache:KRSvXB0S3dsJ:lsbr.niams.nih.gov/3demc/3demc_maplib.html

Grid data CCP4 file format

Copyright Science and Technologies Facilities Council, 2015.

The overall layout of the file is as follows:

File header (256 longwords)
Symmetry information
Map, stored as a 3-dimensional array

The header is organised as 56 words followed by space for ten 80 character text labels as follows:

 1      NC              # of Columns    (fastest changing in map)
 2      NR              # of Rows
 3      NS              # of Sections   (slowest changing in map)
 4      MODE            Data type
                          0 = envelope stored as signed bytes (from
                              -128 lowest to 127 highest)
                          1 = Image     stored as Integer*2
                          2 = Image     stored as Reals
                          3 = Transform stored as Complex Integer*2
                          4 = Transform stored as Complex Reals
                          5 == 0

                          Note: Mode 2 is the normal mode used in
                                the CCP4 programs. Other modes than 2 and 0
                                may NOT WORK

 5      NCSTART         Number of first COLUMN  in map
 6      NRSTART         Number of first ROW     in map
 7      NSSTART         Number of first SECTION in map
 8      NX              Number of intervals along X
 9      NY              Number of intervals along Y
10      NZ              Number of intervals along Z
11      X length        Cell Dimensions (Angstroms)
12      Y length                     "
13      Z length                     "
14      Alpha           Cell Angles     (Degrees)
15      Beta                         "
16      Gamma                        "
17      MAPC            Which axis corresponds to Cols.  (1,2,3 for X,Y,Z)
18      MAPR            Which axis corresponds to Rows   (1,2,3 for X,Y,Z)
19      MAPS            Which axis corresponds to Sects. (1,2,3 for X,Y,Z)
20      AMIN            Minimum density value
21      AMAX            Maximum density value
22      AMEAN           Mean    density value    (Average)
23      ISPG            Space group number
24      NSYMBT          Number of bytes used for storing symmetry operators
25      LSKFLG          Flag for skew transformation, =0 none, =1 if foll
26-34   SKWMAT          Skew matrix S (in order S11, S12, S13, S21 etc) if
                        LSKFLG .ne. 0.
35-37   SKWTRN          Skew translation t if LSKFLG .ne. 0.
                        Skew transformation is from standard orthogonal
                        coordinate frame (as used for atoms) to orthogonal
                        map frame, as

                                Xo(map) = S * (Xo(atoms) - t)

38      future use       (some of these are used by the MSUBSX routines
 .          "              in MAPBRICK, MAPCONT and FRODO)
 .          "   (all set to zero by default)
 .          "
52          "

53    MAP             Character string 'MAP ' to identify file type
54    MACHST          Machine stamp indicating the machine type
                        which wrote file
55      ARMS            Rms deviation of map from mean density
56      NLABL           Number of labels being used
57-256  LABEL(20,10)    10  80 character text labels (ie. A4 format)

Symmetry records follow - if any - stored as text as in International Tables, operators separated by * and grouped into ‘lines’ of 80 characters (i.e. symmetry operators do not cross the ends of the 80-character ‘lines’ and the ‘lines’ do not terminate in a *).

Map data array follows.

Note on the machine stamp: The machine stamp (word 54) is a 32-bit quantity containing a set of four ‘nibbles’ (half-bytes) - only half the space is used. Each nibble is a number specifying the representation of (in C terms) double (d), float (f), int (i) and unsigned char (c) types. Thus each stamp is of the form 0xdfic0000. For little endian hardware the stamp is 0x44, 0x41, 0x00, 0x00 while the big endian stamp is 0x11, 0x11, 0x00, 0x00.

Classes

class gridData.CCP4.CCP4(filename=None)[source]

A class to represent a CCP4 file.

Only reading is implemented; either supply a filename to the constructor
>>> G = CCP4(filename)
or load the file with the read method
>>> G = CCP4()
>>> G.read(filename)

The data is held in CCP4.array and all header information is in the dict CCP4.header.

CCP4.shape

D-tuplet describing size in each dimension

CCP4.origin

coordinates of the centre of the grid cell with index 0,0,…,0

CCP4.delta

DxD array describing the deltas

Note

The following features of the CCP4 format are not implemented: * triclinic boxes * symmetry records * index ordering besides standard column-major and row-major * non-standard fields, such any in filed in future use block

property edges

Edges of the grid cells, origin at centre of 0,0,..,0 grid cell.

Only works for regular, orthonormal grids.

histogramdd()[source]

Return array data as (edges,grid), i.e. a numpy nD histogram.

read(filename)[source]

Populate the instance from the ccp4 file filename.