| ## HETPARSE documentation

## 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

Converts raw dictionary of heterogen groups EMBL-like format. Convert heterogen group dictionary to EMBL-like format

## 2.0 INPUTS & OUTPUTS

HETPARSE parse the dictionary of heterogen groups available at http://pdb.rutgers.edu/het_dictionary.txt and writes a file containing the group names, synonyms and 3-letter codes in EMBL-like format. Optionally, HETPARSE will search a directory of PDB files and will count the number of files that each heterogen appears in. The path and extension of the PDB files and the names of the input and output files are user- specified (file extension is set in the ACD file).

## 3.0 INPUT FILE FORMAT

An excerpt from the raw dictionary of heterogen group is shown (Figure 1).

### Input files for usage example

### File: het.txt

    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

## 4.0 OUTPUT FILE FORMAT

The records used in the output file (Figure 2) are as follows:

- ID - 3-character abbreviation of heterogen
- DE - full description
- SY - synonym
- NN - number of files which this heterogen appears in

### Output files for usage example

### File: Ehet.dat

    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
    //

## 5.0 DATA FILES

HETPARSE does not use a data file.

## 6.0 USAGE

    Convert heterogen group dictionary to EMBL-like format.
    Version: EMBOSS:6.6.0.0

       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

### 6.1 COMMAND LINE ARGUMENTS

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

### 6.2 EXAMPLE SESSION

An example of interactive use of HETPARSE is shown below. Here is a sample session with hetparse

    % 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

## 7.0 KNOWN BUGS & WARNINGS

None.

## 8.0 NOTES

HETPARSE is used to create the EMBOSS data file Ehet.dat that is included in the EMBOSS distribution.

### 8.1 GLOSSARY OF FILE TYPES

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.

None

## 9.0 DESCRIPTION

Some research applications require knowledge of the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files. A dictionary of such groups containing various data for all of the heterogens found in PDB is available, but is not in a convenient format. HETPARSE parses the dictionary in its raw format and converts it to an EMBL-like format.

## 10.0 ALGORITHM

None.

## 11.0 RELATED APPLICATIONS

## See also

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

## 12.0 DIAGNOSTIC ERROR MESSAGES

None.

## 13.0 AUTHORS

Jon Ison (jison@ebi.ac.uk)
The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD UK

## 14.0 REFERENCES

Please cite the authors and EMBOSS.
Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.

See also http://emboss.sourceforge.net/

### 14.1 Other useful references