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funky |
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)
% funky
Mandatory qualifiers: [-prot] string Location of protein coordinate files for input (embl-like format) [-protextn] string Extension of protein coordinate files (embl-like format) [-dom] string Location of domain coordinate files for input (embl-like format) [-domextn] string Extension of domain coordinate files (embl-like format) -dic infile Name of dictionary of heterogen groups -scop infile Name of scop file for input (embl-like format) -vdwf infile Name of data file with van der Waals radii -thresh float Threshold contact distance Optional qualifiers: (none) Advanced qualifiers: -outf outfile Name of output file -logf outfile Name of log file General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-prot] (Parameter 1) |
Location of protein coordinate files for input (embl-like format) | Any string is accepted | ./ |
[-protextn] (Parameter 2) |
Extension of protein coordinate files (embl-like format) | Any string is accepted | .pxyz |
[-dom] (Parameter 3) |
Location of domain coordinate files for input (embl-like format) | Any string is accepted | ./ |
[-domextn] (Parameter 4) |
Extension of domain coordinate files (embl-like format) | Any string is accepted | .pxyz |
-dic | Name of dictionary of heterogen groups | Input file | Ehet.dat |
-scop | Name of scop file for input (embl-like format) | Input file | Escop.dat |
-vdwf | Name of data file with van der Waals radii | Input file | Evdw.dat |
-thresh | Threshold contact distance | Any numeric value | 1.0 |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-outf | Name of output file | Output file | funky.out |
-logf | Name of log file | Output file | funky.log |
Program name | Description |
---|---|
aaindexextract | Extract data from AAINDEX |
cutgextract | Extract data from CUTG |
domainer | Reads protein coordinate files and writes domains coordinate files |
groups | Removes redundant hits from a scop families file |
hetparse | Converts raw dictionary of heterogen groups to a file in embl-like format |
nrscope | Converts redundant EMBL-format SCOP file to non-redundant one |
pdbparse | Parses pdb files and writes cleaned-up protein coordinate files |
pdbtosp | Convert raw swissprot:pdb equivalence file to embl-like format |
printsextract | Extract data from PRINTS |
prosextract | Builds the PROSITE motif database for patmatmotifs to search |
rebaseextract | Extract data from REBASE |
scope | Convert raw scop classification file to embl-like format |
scopnr | Removes redundant domains from a scop classification file |
scopparse | Converts raw scop classification files to a file in embl-like format |
scopseqs | Adds pdb and swissprot sequence records to a scop classification file |
tfextract | Extract data from TRANSFAC |