EMBASSY: PDBTOSP documentation.

PDBTOSP documentation

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

Convert raw swissprot:PDB equivalence file to EMBL-like format. Convert swissprot:PDB codes file to EMBL-like format

2.0 INPUTS & OUTPUTS

PDBTOSP parses the swissprot:PDB equivalence table available at http://www.expasy.ch/cgi-bin/lists?pdbtosp.txt and writes the data out in EMBL-like format. The raw (input) file can be obtained by doing a "save as ... text format" from the web page. No changes are made to the data other than changing the format in which it is held. The input and output files are specified by the user.

3.0 INPUT FILE FORMAT

An excerpt from the raw swissprot:PDB equivalence file is shown (Figure 1).

Input files for usage example

File: pdbtosp.txt

  ------------------------------------------------------------------------
   ExPASy Home page   Site Map    Search ExPASy   Contact us    SWISS-PROT

 Hosted by SIB       Mirror                                        USA[new]
 Switzerland         sites:      AustraliaCanada China Korea Taiwan
  ------------------------------------------------------------------------

----------------------------------------------------------------------------
        SWISS-PROT Protein Knowledgebase
        Swiss Institute of Bioinformatics (SIB); Geneva, Switzerland
        European Bioinformatics Institute (EBI); Hinxton, United Kingdom
----------------------------------------------------------------------------

Description: Index of Protein Data Bank (PDB) entries referenced in
             SWISS-PROT
Name:        PDBTOSP.TXT
Release:     40.9 of 31-Jan-2002

----------------------------------------------------------------------------

The PDB database is available at the following URL:

USA:  http://www.rcsb.org/pdb/
EBI:  http://www2.ebi.ac.uk/pdb/

 - Number of PDB entries referenced in SWISS-PROT: 9901
 - Number of SWISS-PROT entries with one or more pointers to PDB: 3260

PDB   Last revision
code  date           SWISS-PROT entry name(s)
____  ___________    __________________________________________
101M  (08-APR-98)  : MYG_PHYCA   (P02185)
102L  (31-OCT-93)  : LYCV_BPT4   (P00720)
102M  (08-APR-98)  : MYG_PHYCA   (P02185)
103L  (31-OCT-93)  : LYCV_BPT4   (P00720)
103M  (08-APR-98)  : MYG_PHYCA   (P02185)
9XIA  (15-JUL-92)  : XYLA_STRRU  (P24300)
9XIM  (15-JUL-93)  : XYLA_ACTMI  (P12851)

----------------------------------------------------------------------------
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institutions as long as its  content is in no way modified. Usage by and for
commercial entities requires a license agreement.  For information about the
licensing  scheme  see: http://www.isb-sib.ch/announce/ or send  an email to
license@isb-sib.ch.
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  ------------------------------------------------------------------------
   ExPASy Home page   Site Map    Search ExPASy   Contact us    SWISS-PROT

 Hosted by SIB       Mirror                                        USA[new]
 Switzerland         sites:      AustraliaCanada China Korea Taiwan
  ------------------------------------------------------------------------

4.0 OUTPUT FILE FORMAT

An excerpt from the swissprot:PDB equivalence file in EMBL-like format is shown (Figure 2).

Output files for usage example

File: Epdbtosp.dat

EN   101M
XX
NE   1
XX
IN   MYG_PHYCA ID; P02185 ACC;
XX
//
EN   102L
XX
NE   1
XX
IN   LYCV_BPT4 ID; P00720 ACC;
XX
//
EN   102M
XX
NE   1
XX
IN   MYG_PHYCA ID; P02185 ACC;
XX
//
EN   103L
XX
NE   1
XX
IN   LYCV_BPT4 ID; P00720 ACC;
XX
//
EN   103M
XX
NE   1
XX
IN   MYG_PHYCA ID; P02185 ACC;
XX
//
EN   9XIA
XX
NE   1
XX
IN   XYLA_STRRU ID; P24300 ACC;
XX
//
EN   9XIM
XX
NE   1
XX
IN   XYLA_ACTMI ID; P12851 ACC;
XX
//

5.0 DATA FILES

No data files are used by PDBTOSP.

6.0 USAGE

Convert swissprot:PDB codes file to EMBL-like format.
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-infile]            infile     This option specifies the name of raw
                                  swissprot:PDB equivalence file (input).
                                  HETPARSE parses this file, which is
                                  available at URL
                                  http://www.expasy.ch/cgi-bin/lists?pdbtosp.txt
  [-outfile]           outfile    [Epdbtosp.dat] This option specifies the
                                  name of swissprot:PDB equivalence file
                                  (EMBL-like format). This is the PDBTOSP
                                  output file.

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-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 raw swissprot:PDB equivalence file (input). HETPARSE parses this file, which is available at URL http://www.expasy.ch/cgi-bin/lists?pdbtosp.txt	Input file	Required
[-outfile] (Parameter 2)	outfile	This option specifies the name of swissprot:PDB equivalence file (EMBL-like format). This is the PDBTOSP output file.	Output file	Epdbtosp.dat
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-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 PDBTOSP is shown below. Here is a sample session with pdbtosp

% pdbtosp Convert swissprot:PDB codes file to EMBL-like format. Swissprot:pdb equivalence table file: pdbtosp.txt Swissprot:pdb equivalence output file [Epdbtosp.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

PDBTOSP is used to create the EMBOSS data file Epdbtosp.dat that is included in the EMBOSS distribution.

8.1 GLOSSARY OF FILE TYPES

FILE TYPE	FORMAT	DESCRIPTION	CREATED BY	SEE ALSO
swissprot:PDB equivalence file	EMBL-like format.	A file containing swissprot identifiers for PDB codes.	Included in the EMBOSS distribution	N.A.

None

9.0 DESCRIPTION

Some research applications require knowledge of the database sequence(s) that corresponds to the sequence(s) given in a PDB file. A 'swissprot:PDB equivalence' file listing accession numbers and swissprot database identifiers for certain PDB codes is available, but is not in a format that is consistent with flat file formats used for protein structural data in emboss. PDBTOSP parses the swissprot:PDB equivalence in its raw format and converts it to an EMBL-like format.

10.0 ALGORITHM

PDBTOSP relies on finding a line beginning with '____ _' in the input file (all lines up to and including this one are ignored). Lines of code data are then parsed, up until the first blank line.

11.0 RELATED APPLICATIONS

Program name	Description
aaindexextract	Extract amino acid property data from AAINDEX
allversusall	Sequence similarity data from all-versus-all comparison
cathparse	Generates DCF file from raw CATH files
cutgextract	Extract codon usage tables from CUTG database
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
jaspextract	Extract data from JASPAR
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	Processes 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	Removes 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