Document Files

Document files are keyed, formatted, sequential files created by the command line operations: SD, DOC CREATE, DOC SORT, DOC MERGE, DOC SUBTRACT, DOC MIRROR, SD SHUFFLE, and certain additional operations. Document files are used to permanently store information such as the contents of a group of SPIDER registers as, image numbers, angles, or any other such numerical listing. Each listing is identified by a key number. Any subsequent SPIDER run can retrieve the register values, etc., by their keys.

Document files are also used for communication between Web and SPIDER. For example the "particle picking" operation in Web creates a set of document files used by certain operations in SPIDER.

Document files may also be used to define a processing protocol; switch on and off the execution of procedure files, or include/exclude images of a series from processing depending on the result of previous operation.

FORMAT FOR DOC FILES

A new format was introduced in SPIDER 11.0 (Feb 2004) which has variable length columns with each column separated by at least one blank. (Previously under some circumstances columns could exist without any interspersed blank). We think that the implementation will successfully read all existing older document files and will support keys > 999999 and more than 9 register columns. The new format is also easier to parse outside of SPIDER.

In both formats lines with a ";" in the second col. are considered comment lines or 'comment key' lines.

A sample new document file follows:

 KEY#  REGS/  VALUE      VALUE      VALUE      VALUE      VALUE      VALUE  ... (no set limit)
       LINE
---------------------------------------------------------------------------------
 ;tst/tst   16-JUN-1999 AT 13:03:18   jnkdoc001.tst
    9 1  11.000    
   99 2  11.000      12.000    
  999 3  11.000      12.000      13.000    
 9999 4  11.000      12.000      13.000      14.000    
99999 5  11.000      12.000      13.000      14.000      15.000    
999999 6  11.000      12.000      13.000      14.000      15.000      16.000    
 ; /COMMENT KEY -88 CONTAINS -88                                                 
 ;-88 2 -88.000     -88.000    
 ;  KEY 5556 HAS 7 REGISTERS
 5556 7  5554.0      6.0000      13.000      14.000      15.000      16.000      16.000    
 ;  KEY 987654 HAS 11 REGISTERS
   987654 11    11.0 12.0 13.000  14.000 15.000 16.000 17.000 -1.76E-13 -19.0 10.0E2 21.2   

---------------------------------------------------------------------------------
Data columns (registers) are written into the new format using Fortran format specification 1PGE12.5 so there are 6 decimal places worth of precision in each value which is written by SPIDER.

The pre SPIDER 11.0 format was as follows:

123456789 123456789 123456789 123456789 123456789 1234565789 123456789 123456789

 KEY# REGS/  VALUE      VALUE      VALUE      VALUE      VALUE      VALUE (limit is 9)
     LINE
---------------------------------------------------------------------------------
 ;tst/tst   16-JUN-1999 AT 13:03:18   jnkdoc001.tst
    9 1  11.000    
   99 2  11.000      12.000    
  999 3  11.000      12.000      13.000    
 9999 4  11.000      12.000      13.000      14.000    
99999 5  11.000      12.000      13.000      14.000      15.000    
9999996  11.000      12.000      13.000      14.000      15.000      16.000    
 ; /COMMENT KEY -88 CONTAINS -88                                                 
 ;-88 2 -88.000     -88.000    
 ;  KEY 5556 HAS 7 REGISTERS
 5556 7  5554.0      6.0000      13.000      14.000      15.000      16.000      16.000    

---------------------------------------------------------------------------------

DATA IS WRITTEN WITH FORTRAN FORMAT: (I6,I1,9G12.3)

DOC. FILE HANDLING ROUTINES


Source: docfile.html     Page updated: 02/9/05     ArDean Leith
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