EMBOSS: pdbtosp

Program pdbtosp

Function

Convert raw swissprot:pdb equivalence file to embl-like format

Description

This is part of Jon Ison's protein structure analysis package.

This package is still being developed.

Please ignore this program until further details can be documented.

All further queries should go to Jon Ison. (Jon Ison)

Usage

Here is a sample session with pdbtosp: 

% pdbtosp

Command line arguments 

   Mandatory qualifiers:
  [-infilea]           infile     Name of raw swissprot:pdb equivalence file
                                  (input)
  [-outfile]           outfile    Name of swissprot:pdb equivalence file
                                  (output)

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose

Mandatory qualifiers Allowed values Default
[-infilea]
(Parameter 1)		 Name of raw swissprot:pdb equivalence file (input) Input file pdbtosp.txt
[-outfile]
(Parameter 2)		 Name of swissprot:pdb equivalence file (output) Output file Epdbtosp.dat
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
(none)

Input file format

Output file format

Data files

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
cutgextractExtract data from CUTG
domainerBuild domain coordinate files
nrscopeConverts redundant EMBL-format SCOP file to non-redundant one
printsextractExtract data from PRINTS
prosextractBuilds the PROSITE motif database for patmatmotifs to search
rebaseextractExtract data from REBASE
scopeConvert raw scop classification file to embl-like format
scopparseReads raw-, and writes EMBL-like, scop classification files
seqnrConverts redundant database results to a non-redundant set of hits
tfextractExtract data from TRANSFAC

Author(s)

This application was written by Jon Ison (jison@hgmp.mrc.ac.uk)

History

Written (date) - author.

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments