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EMBOSS: interface |
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)
% interface
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
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| 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 |
| 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 |