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HETPARSE documentation |
RESIDUE 061 58 CONECT N1 2 N2 C5 CONECT N2 2 N1 N3 CONECT N3 2 N2 N4 CONECT N4 3 N3 C5 HN4 CONECT C5 3 N1 N4 C6 CONECT C6 3 C5 C7 C11 CONECT C7 3 C6 C8 C12 CONECT C8 3 C7 C9 H8 CONECT C9 3 C8 C10 H9 CONECT C10 3 C9 C11 H10 CONECT C11 3 C6 C10 H11 CONECT C12 3 C7 C13 C17 CONECT C13 3 C12 C14 H13 CONECT C14 3 C13 C15 H14 CONECT C15 3 C14 C16 C18 CONECT C16 3 C15 C17 H16 CONECT C17 3 C12 C16 H17 CONECT C18 4 C15 N19 1H18 2H18 CONECT N19 3 C18 C20 C33 CONECT C20 3 N19 C21 N25 CONECT C21 4 C20 C22 1H21 2H21 CONECT C22 4 C21 C23 1H22 2H22 CONECT C23 4 C22 C24 1H23 2H23 CONECT C24 4 C23 1H24 2H24 3H24 CONECT N25 2 C20 C26 CONECT C26 3 N25 C27 C32 CONECT C27 3 C26 C28 H27 CONECT C28 3 C27 C29 H28 CONECT C29 3 C28 O30 C31 CONECT O30 2 C29 HOU CONECT C31 3 C29 C32 H31 CONECT C32 3 C26 C31 C33 CONECT C33 3 N19 C32 O34 CONECT O34 1 C33 CONECT HN4 1 N4 CONECT H8 1 C8 CONECT H9 1 C9 CONECT H10 1 C10 CONECT H11 1 C11 CONECT H13 1 C13 CONECT H14 1 C14 CONECT H16 1 C16 CONECT H17 1 C17 CONECT 1H18 1 C18 CONECT 2H18 1 C18 CONECT 1H21 1 C21 CONECT 2H21 1 C21 CONECT 1H22 1 C22 CONECT 2H22 1 C22 [Part of this file has been deleted for brevity] CONECT 2H6 1 C6 CONECT 1H8 1 C8 CONECT 2H8 1 C8 CONECT 1H9 1 C9 CONECT 2H9 1 C9 END HET 104 28 HETSYN 104 TRIENTINE HETNAM 104 N,N'-BIS(2-AMINOETHYL)-1,2-ETHANEDIAMINE FORMUL 104 C6 H18 N4 RESIDUE 105 32 CONECT B 3 O1 O2 C3 CONECT O1 2 B H1 CONECT O2 2 B H2 CONECT C3 4 B N4 1H3 2H3 CONECT N4 3 C3 C5 H4 CONECT C5 3 N4 O6 C7 CONECT O6 1 C5 CONECT C7 3 C5 C8 C12 CONECT N11 2 O10 C12 CONECT O10 2 N11 C8 CONECT C8 3 C7 O10 C9 CONECT C12 3 C7 N11 C13 CONECT C9 4 C8 1H9 2H9 3H9 CONECT C13 3 C12 C14 C18 CONECT C14 3 C13 C15 CL1 CONECT CL1 1 C14 CONECT C15 3 C14 C16 H15 CONECT C16 3 C15 C17 H16 CONECT C17 3 C16 C18 H17 CONECT C18 3 C13 C17 H18 CONECT H1 1 O1 CONECT H2 1 O2 CONECT 1H3 1 C3 CONECT 2H3 1 C3 CONECT H4 1 N4 CONECT 1H9 1 C9 CONECT 2H9 1 C9 CONECT 3H9 1 C9 CONECT H15 1 C15 CONECT H16 1 C16 CONECT H17 1 C17 CONECT H18 1 C18 END HET 105 32 HETSYN 105 CLOXACILLIN DERIVATIVE HETNAM 105 N-[5-METHYL-3-O-TOLYL-ISOXAZOLE-4-CARBOXYLIC ACID HETNAM 2 105 AMIDE] BORONIC ACID FORMUL 105 C12 H12 N2 O4 B1 CL1 |
ID 105 DE N-[5-METHYL-3-O-TOLYL-ISOXAZOLE-4-CARBOXYLIC ACIDAMIDE] BORONIC ACID SY CLOXACILLIN DERIVATIVE NN 0 // ID 104 DE N,N'-BIS(2-AMINOETHYL)-1,2-ETHANEDIAMINE SY TRIENTINE NN 0 // ID 103 DE 2',5'-DIDEOXY-ADENOSINE 3'-MONOPHOSPHATE SY . NN 0 // ID 102 DE GAMMA-DEOXY-GAMMA-SULFO-GUANOSINE-5'-TRIPHOSPHATE SY . NN 0 // ID 101 DE 2'-DEOXY-ADENOSINE 3'-MONOPHOSPHATE SY . NN 0 // ID 100 DE 1-(5-CHLOROINDOL-3-YL)-3-HYDROXY-3-(2H-TETRAZOL-5-YL)-PROPENONE SY . NN 0 // ID 074 DE [PROPYLAMINO-3-HYDROXY-BUTAN-1,4-DIONYL]-ISOLEUCYL-PROLINE SY CA-074; SY [N-(L-3-TRANS-PROPYLCARBAMOYL-OXIRANE-2-CARBONYL)-L-ISOLEUCYL-L-PROLINE] NN 0 // ID 072 DE DE (+/-)(2S,5S)-3-(4-(4-CARBOXYPHENYL)BUTYL)-2-HEPTYL-4-OXO-5-THIAZOLIDINE SY THIAZOLIDINONE; GW0072 NN 0 // ID 061 DE DE 2-BUTYL-6-HYDROXY-3-[2'-(1H-TETRAZOL-5-YL)-BIPHENYL-4-YLMETHYL]-3H-QUINAZOLIN-4-ONE SY L-159,061 NN 0 // |
Convert heterogen group dictionary to EMBL-like format.
Version: EMBOSS:6.5.0.0
Standard (Mandatory) qualifiers (* if not always prompted):
[-infile] infile This option specifies the name of input file
(raw dictionary of heterogen groups) to
parse, which should be of the format
specified at
http://pdb.rutgers.edu/het_dictionary.txt
-dogrep toggle [N] This option specifies whether to search
a directory of files (typically PDB files)
with keywords. If set, HETPARSE will search
the directory and will count the number of
files that each heterogen appears in.
* -dirlistpath dirlist [./] This option specifies the directory to
search with keywords.
[-outfile] outfile [Ehet.dat] This option specifies the name of
EMBL-like format dictionary of heterogen
groups.
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-dirlistpath" associated qualifiers
-extension string Default file extension
"-outfile" associated qualifiers
-odirectory2 string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to 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 and exit. 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
-version boolean Report version number and exit
|
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-infile] (Parameter 1) |
infile | This option specifies the name of input file (raw dictionary of heterogen groups) to parse, which should be of the format specified at http://pdb.rutgers.edu/het_dictionary.txt | Input file | Required |
| -dogrep | toggle | This option specifies whether to search a directory of files (typically PDB files) with keywords. If set, HETPARSE will search the directory and will count the number of files that each heterogen appears in. | Toggle value Yes/No | No |
| -dirlistpath | dirlist | This option specifies the directory to search with keywords. | Directory with files | ./ |
| [-outfile] (Parameter 2) |
outfile | This option specifies the name of EMBL-like format dictionary of heterogen groups. | Output file | Ehet.dat |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-dirlistpath" associated dirlist qualifiers | ||||
| -extension | string | Default file extension | Any string | ent |
| "-outfile" associated outfile qualifiers | ||||
| -odirectory2 -odirectory_outfile |
string | Output directory | Any string | |
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N |
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
| -warning | boolean | Report warnings | Boolean value Yes/No | Y |
| -error | boolean | Report errors | Boolean value Yes/No | Y |
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y |
| -version | boolean | Report version number and exit | Boolean value Yes/No | N |
% hetparse Convert heterogen group dictionary to EMBL-like format. Raw dictionary of heterogen groups file: het.txt Search a directory of PDB files with keywords? [N]: Y Pdb entry directories [./]: Dictionary of heterogen groups output file [Ehet.dat]: Ehet.dat |
Go to the input files for this example
Go to the output files for this example
| FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO |
| Dictionary of heterogen groups | A file of the dictionary of heterogen groups in PDB. | HETPARSE | N.A. |
| Program name | Description |
|---|---|
| aaindexextract | Extract amino acid property data from AAINDEX |
| allversusall | Sequence similarity data from all-versus-all comparison |
| cathparse | Generate DCF file from raw CATH files |
| cutgextract | Extract codon usage tables from CUTG database |
| domainer | Generate domain CCF files from protein CCF files |
| domainnr | Remove redundant domains from a DCF file |
| domainseqs | Add sequence records to a DCF file |
| domainsse | Add secondary structure records to a DCF file |
| jaspextract | Extract data from JASPAR |
| pdbparse | Parse PDB files and writes protein CCF files |
| pdbplus | Add accessibility and secondary structure to a CCF file |
| pdbtosp | Convert swissprot:PDB codes file to EMBL-like format |
| printsextract | Extract data from PRINTS database for use by pscan |
| prosextract | Process the PROSITE motif database for use by patmatmotifs |
| rebaseextract | Process the REBASE database for use by restriction enzyme applications |
| scopparse | Generate DCF file from raw SCOP files |
| seqnr | Remove redundancy from DHF files |
| sites | Generate residue-ligand CON files from CCF files |
| ssematch | Search a DCF file for secondary structure matches |
| tfextract | Process TRANSFAC transcription factor database for use by tfscan |
See also http://emboss.sourceforge.net/