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DOMAINREP documentation
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CONTENTS
1.0 SUMMARY
2.0 INPUTS & OUTPUTS
3.0 INPUT FILE FORMAT
4.0 OUTPUT FILE FORMAT
5.0 DATA FILES
6.0 USAGE
7.0 KNOWN BUGS & WARNINGS
8.0 NOTES
9.0 DESCRIPTION
10.0 ALGORITHM
11.0 RELATED APPLICATIONS
12.0 DIAGNOSTIC ERROR MESSAGES
13.0 AUTHORS
14.0 REFERENCES
1.0 SUMMARY
Reorder DCF file (domain classification file) so that the representative structure of each user-specified node is given first
2.0 INPUTS & OUTPUTS
DOMAINREP reads a DCF file (domain classification file) and writes a
DCF file containing the same data except that the order of domains
within each user-specified node (e.g. family) in the hierarchy may be
changed so that the representative structure of each node is given
first. The representative structure is found by using stamp and this
application must be installed on the system that is running DOMAINREP
and correctly configured (see 'Notes' below). A 'domain PDB file' for
each domain in the DCF file must exist in a directory specified in the
stamp "pdb.directories" file (see 'Notes' below). The domain PDB file
contains coordinate data for a single domain from SCOP or CATH, in PDB
format. The input and output files are specified by the user.
3.0 INPUT FILE FORMAT
The format of the DCF file is described in the SCOPPARSE documentation.
Input files for usage example
File: all.scop
ID D1CS4A_
XX
EN 1CS4
XX
TY SCOP
XX
SI 53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD;
XX
CL Alpha and beta proteins (a+b)
XX
FO Ferredoxin-like
XX
SF Adenylyl and guanylyl cyclase catalytic domain
XX
FA Adenylyl and guanylyl cyclase catalytic domain
XX
DO Adenylyl cyclase VC1, domain C1a
XX
OS Dog (Canis familiaris)
XX
NC 1
XX
CN [1]
XX
CH A CHAIN; . START; . END;
//
ID D1II7A_
XX
EN 1II7
XX
TY SCOP
XX
SI 53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL Alpha and beta proteins (a+b)
XX
FO Metallo-dependent phosphatases
XX
SF Metallo-dependent phosphatases
XX
FA DNA double-strand break repair nuclease
XX
DO Mre11
XX
OS Archaeon Pyrococcus furiosus
XX
NC 1
XX
CN [1]
XX
CH A CHAIN; . START; . END;
//
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4.0 OUTPUT FILE FORMAT
The format of the DCF file is described in the SCOPPARSE documentation.
Output files for usage example
File: all_rep1st.scop
ID D1CS4A_
XX
EN 1CS4
XX
TY SCOP
XX
SI 53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD;
XX
CL Alpha and beta proteins (a+b)
XX
FO Ferredoxin-like
XX
SF Adenylyl and guanylyl cyclase catalytic domain
XX
FA Adenylyl and guanylyl cyclase catalytic domain
XX
DO Adenylyl cyclase VC1, domain C1a
XX
OS Dog (Canis familiaris)
XX
NC 1
XX
CN [1]
XX
CH A CHAIN; . START; . END;
//
ID D1II7A_
XX
EN 1II7
XX
TY SCOP
XX
SI 53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL Alpha and beta proteins (a+b)
XX
FO Metallo-dependent phosphatases
XX
SF Metallo-dependent phosphatases
XX
FA DNA double-strand break repair nuclease
XX
DO Mre11
XX
OS Archaeon Pyrococcus furiosus
XX
NC 1
XX
CN [1]
XX
CH A CHAIN; . START; . END;
//
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5.0 DATA FILES
DOMAINREP does not use any data files but does make use of the stamp
"pdb.directories" file (see 'Notes').
6.0 USAGE
6.1 COMMAND LINE ARGUMENTS
Standard (Mandatory) qualifiers:
[-dcfinfile] infile This option specifies the name of DCF file
(domain classification file) (input). A
'domain classification file' contains
classification and other data for domains
from SCOP or CATH, in DCF format
(EMBL-like). The files are generated by
using SCOPPARSE and CATHPARSE. Domain
sequence information can be added to the
file by using DOMAINSEQS.
-node menu This option specifies the node fore
reordering the file. Reordering can be done
for any specified node in the SCOP or CATH
hierarchies. For example by selecting
'Class' entries belonging to the same Class
will be reordered in turn.
[-dcfoutfile] outfile This option specifies the name of DCF file
(domain classification file) (output). A
'domain classification file' contains
classification and other data for domains
from SCOP or CATH, in DCF format
(EMBL-like). The files are generated by
using SCOPPARSE and CATHPARSE. Domain
sequence information can be added to the
file by using DOMAINSEQS.
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-dcfoutfile" associated qualifiers
-odirectory2 string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report deaths
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