| ## 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