                            PDBTOSP 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

   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

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

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:6.2.0

   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

