1cuk03 1 10 8 10 1 1 1 48 1.900 1hjp03 1 10 8 10 1 1 2 44 2.500 |
1cuk00 D03 F00 1 0 1 - 0 66 - 1 0 67 - 0 142 - 1 0 156 - 0 203 - 1hjp00 D03 F01 1 0 1 - 0 66 - 1 0 67 - 0 158 - 1 0 159 - 0 202 - 0 203 - 0 203 - (1) |
1.10.8 1cuk03 :Helicase, Ruva Protein, domain 3 1.10.8.10 1cuk03 :DNA helicase RuvA subunit, C-terminal domain 0001 2ccyA0 :Mainly Alpha 0001.0010 1eca00 :Orthogonal Bundle |
ID 1CUK03 XX EN 1CUK XX TY CATH XX CI 1 CL; 10 AR; 8 TP; 10 SF; 1 FA; 1 NI;1 IF; XX CL Mainly Alpha XX AR Orthogonal Bundle XX TP Helicase, Ruva Protein, domain 3 XX SF DNA helicase RuvA subunit, C-terminal domain XX NR 48 XX NC 1 XX CN [1] XX CH 0 CHAIN; 156 START; 203 END; // ID 1HJP03 XX EN 1HJP XX TY CATH XX CI 1 CL; 10 AR; 8 TP; 10 SF; 1 FA; 1 NI;2 IF; XX CL Mainly Alpha XX AR Orthogonal Bundle XX TP Helicase, Ruva Protein, domain 3 XX SF DNA helicase RuvA subunit, C-terminal domain XX NR 44 XX NC 1 XX CN [1] XX CH 0 CHAIN; 159 START; 202 END; // |
1.10.8.10 1.10.8 0001.0010 0001 1.10.8.10 1.10.8 0001.0010 0001 |
Standard (Mandatory) qualifiers: [-listfile] infile This option specifies the name of raw CATH classification file (caths.list.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4"). [-domfile] infile This option specifies the name of raw CATH classification file (domlist.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4"). [-namesfile] infile This option specifies the name of raw CATH classification file (CAT.names.all.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4"). [-outfile] outfile This option specifies the name of CATH 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. -logfile outfile This option specifies the name of the CATHPARSE log file. Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-outfile" associated qualifiers -odirectory4 string Output directory "-logfile" associated qualifiers -odirectory 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
Standard (Mandatory) qualifiers | Allowed values | Default | |
---|---|---|---|
[-listfile] (Parameter 1) |
This option specifies the name of raw CATH classification file (caths.list.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4"). | Input file | caths.list.v2.4 |
[-domfile] (Parameter 2) |
This option specifies the name of raw CATH classification file (domlist.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4"). | Input file | domlist.v2.4 |
[-namesfile] (Parameter 3) |
This option specifies the name of raw CATH classification file (CAT.names.all.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4"). | Input file | CAT.names.all.v2.4 |
[-outfile] (Parameter 4) |
This option specifies the name of CATH 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. | Output file | Ecath.dat |
-logfile | This option specifies the name of the CATHPARSE log file. | Output file | CATHPARSE.log |
Additional (Optional) qualifiers | Allowed values | Default | |
(none) | |||
Advanced (Unprompted) qualifiers | Allowed values | Default | |
(none) |
% cathparse Reads raw CATH classification files and writes DCF file (domain classification file). Name of raw CATH classification file (caths.list.vX.X) (input). [caths.list.v2.4]: caths.list.small Name of raw CATH classification file (domlist.vX.X) (input). [domlist.v2.4]: domlist.small Name of raw CATH classification file (CAT.names.all.vX.X) (input). [CAT.names.all.v2.4]: CAT.names.all.small Name of CATH DCF file (domain classification file) (output). [Ecath.dat]: Name of CATHPARSE log file [CATHPARSE.log]: |
Go to the input files for this example
Go to the output files for this example
The raw CATH classification files caths.list.small, domlist.small
and CAT.names.all.small were read from test_data/ directory and and a
domain classification file in DCF format called
/test_data/cathparse/all.scop was written. The log file
test_data/cathparse/CATHPARSE.log was written.
FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO |
SCOP parsable files | CATH format. | Raw CATH classification data. | Available from ftp.biochem.ucl.ac.uk (e.g. /pub/cathdata/v2.4) | N.A. |
Domain classification file (for CATH) | DCF format (EMBL-like). | Classification and other data for domains from CATH. | CATHPARSE | Domain sequence information can be added to the file by using DOMAINSEQS. |
Program name | Description |
---|---|
aaindexextract | Extract data from AAINDEX |
allversusall | Does an all-versus-all global alignment for each set of sequences in an input directory and writes files of sequence similarity values |
cutgextract | Extract data from CUTG |
domainer | Reads CCF files (clean coordinate files) for proteins and writes CCF files for domains, taken from a DCF file (domain classification file) |
domainnr | Removes redundant domains from a DCF file (domain classification file). The file must contain domain sequence information, which can be added by using DOMAINSEQS |
domainseqs | Adds sequence records to a DCF file (domain classification file) |
domainsse | Adds secondary structure records to a DCF file (domain classification file) |
hetparse | Converts raw dictionary of heterogen groups to a file in EMBL-like format |
pdbparse | Parses PDB files and writes CCF files (clean coordinate files) for proteins |
pdbplus | Add residue solvent accessibility and secondary structure data to a CCF file (clean coordinate file) for a protein or domain |
pdbtosp | Convert raw swissprot:PDB equivalence file to EMBL-like format |
printsextract | Extract data from PRINTS |
prosextract | Builds the PROSITE motif database for patmatmotifs to search |
rebaseextract | Extract data from REBASE |
scopparse | Reads raw SCOP classification files and writes a DCF file (domain classification file) |
seqnr | Removes redundancy from DHF files (domain hits files) or other files of sequences |
sites | Reads CCF files (clean coordinate files) and writes CON files (contact files) of residue-ligand contact data for domains in a DCF file (domain classification file) |
ssematch | Searches a DCF file (domain classification file) for secondary structure matches |
tfextract | Extract data from TRANSFAC |