GARANT COMMANDS: report fragments - analyse assignments on the level of fragments

USAGE: report fragment

For each fragment a line is printed describing the quality of the assignment. 
The quality of the assignment is judged using criteria that must be defined 
using the criteria command. For each criterion a symbol is printed indicated 
whether the assignmnets conforms well, reasonably or badly to the criterion. 
In addition a comment can be printed for each criterion that gives additional 
information. The nature of this additional information depends on the type of 
the criterion. Prior to the use of this command the quality of the assignments 
must be evaluated using the 'report calculate' command.

EXAMPLE:
   	# define criterion, judging inta-residual assignments
   criteria fragment intrainter intra 0 0
   	# turn on the comment for this criterion
   criteria comment on intra
   	# define thresholds to classify into classes good,reasonable and bad
   criteria threshold intra 0.6 0.8
   	# define criterion, judging the sequential HB peaks
   criteria fragment template seqHB "HB(*) *(+1)"
   	# define criterion, judging the sequential HA peaks
   criteria fragment template seqHA "HA(*) *(+1)"
   	# define criterion, judging the sequential HA peaks
   criteria fragment template seqHN "HN(*) *(+1)"
	# define criterion to compare with the comparison assignments
   criteria fragment mapping map
   criteria comment on map

	# produce report
   report calculate
   report fragment



EXAMPLE OF OUTPUT:

            0 1 2 3 4
                     
            i s s s m
            n e e e a
            t q q q p
            r H H H  
            a B A N  
  ASP 1  :  . . . 0 .   | 0)      1 4)  CYS 73
  THR 2  :  - * . * .   | 0) 0.7759 4)  THR 3
  THR 3  :  * * * * .   | 0)  0.524 4)  THR 41
  VAL 4  :  . . . * .   | 0)  0.916 4)  VAL 4
  SER 5  :  - . . . .   | 0) 0.7804 4)  SER 5
  GLU 6  :  . 0 * - +   | 0) 0.8761 4)  GLU 6  PRO 7
  PRO 7  :  . . . 0 +   | 0)  0.913 4)  GLU 6  PRO 7  PRO 9
  ...


On the top of this list the names and numbers of the different criteria are 
given. Following are lines for each fragment. The name and number of the 
analysed fragment is given on the left of the ':'. Following is a summary of 
the quality of the different criterions for the given frgament. The signs have 
the following meaning:
	'*' ... bad assignment
	'-' ... reasonable assignment
	'.' ... good assignment
Comments to the different criteria are following the '|' sign. For example in 
the case of 'intrainter' criteria or of template criteria, the ratio of 
assigned peaks is listed. In the case of the map criterion a list of all 
fragments of the comparison assignments from which the assignments have been 
taken is given. For example, this means that THR 3 of the current assignment 
corresponds to THR 41 of the comparison assignment or that the current 
assignments of GLU 6 consists of parts of GLU 6 and of parts from PRO 7 from 
the comparison assignments.

SEE ALSO: report calculate, criteria ...