
                             EMBOSS: interface
     _________________________________________________________________
   
                               Program interface
                                       
Function

   Reads coordinate files and writes inter-chain contact files
   
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 interface:

% interface

Command line arguments

   Mandatory qualifiers:
  [-in]                infile     Coordinate file for input (embl-like format)
  [-out]               outfile    Contact file for output
  [-thresh]            float      Threshold contact distance

   Optional qualifiers: (none)
   Advanced qualifiers:
   -ignore             float      If any two atoms from two different residues
                                  are at least this distance apart then no
                                  futher inter-atomic contacts will be checked
                                  for for that residue pair . This speeds the
                                  calculation up considerably.
   -vdwf               string     Name of data file with van der Waals radii
   -conerrf            outfile    Name of log file for the build

   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
   [-in]
   (Parameter 1) Coordinate file for input (embl-like format) Input file
   test.pxyz
   [-out]
   (Parameter 2) Contact file for output Output file test.con
   [-thresh]
   (Parameter 3) Threshold contact distance Any integer value 6.0
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   -ignore If any two atoms from two different residues are at least this
   distance apart then no futher inter-atomic contacts will be checked
   for for that residue pair . This speeds the calculation up
   considerably. Any integer value 20.0
   -vdwf Name of data file with van der Waals radii Any string is
   accepted Evdw.dat
   -conerrf Name of log file for the build Output file interface.log
   
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 name Description
   contacts Reads coordinate files and writes contact files
   dichet Parse dictionary of heterogen groups
   psiblasts Runs PSI-BLAST given scopalign alignments
   scopalign Generate alignments for SCOP families
   seqsort Removes ambiguities from a set of hits resulting from a
   database search
   siggen Generates a sparse protein signature
   sigscan Scans a sparse protein signature against swissprot
   
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
