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 nameDescription
contactsReads coordinate files and writes contact files
dichetParse dictionary of heterogen groups
psiblastsRuns PSI-BLAST given scopalign alignments
scopalignGenerate alignments for SCOP families
seqsortRemoves ambiguities from a set of hits resulting from a database search
siggenGenerates a sparse protein signature
sigscanScans 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