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CATHPARSE documentation |
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 [caths.list.v2.4] 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 [domlist.v2.4] 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 [CAT.names.all.v2.4] 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 [Ecath.dat] 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 [cathparse.log] 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 dying program messages
| 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 Generates DCF file from raw CATH files. Raw cath list file [caths.list.v2.4]: caths.list.small Raw cath domlist file [domlist.v2.4]: domlist.small Raw cath names file [CAT.names.all.v2.4]: CAT.names.all.small Domain classification output file [Ecath.dat]: Domainatrix log output file [cathparse.log]: |
Go to the input files for this example
Go to the output files for this example
| 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 | Sequence similarity data from all-versus-all comparison |
| cutgextract | Extract data from CUTG |
| domainer | Generates domain CCF files from protein CCF files |
| domainnr | Removes redundant domains from a DCF file |
| domainseqs | Adds sequence records to a DCF file |
| domainsse | Add secondary structure records to a DCF file |
| hetparse | Converts heterogen group dictionary to EMBL-like format |
| pdbparse | Parses PDB files and writes protein CCF files |
| pdbplus | Add accessibility & secondary structure to a CCF file |
| pdbtosp | Convert swissprot:PDB codes file to EMBL-like format |
| printsextract | Extract data from PRINTS |
| prosextract | Build the PROSITE motif database for use by patmatmotifs |
| rebaseextract | Extract data from REBASE |
| scopparse | Generate DCF file from raw SCOP files |
| seqnr | Removes redundancy from DHF files |
| sites | Generate residue-ligand CON files from CCF files |
| ssematch | Search a DCF file for secondary structure matches |
| tfextract | Extract data from TRANSFAC |
See also http://emboss.sourceforge.net/