funky

 

Function

Reads clean coordinate files and writes file of protein-heterogen contact data

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 funky:

% funky

Command line arguments

   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

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
aaindexextractExtract data from AAINDEX
cutgextractExtract data from CUTG
domainerReads protein coordinate files and writes domains coordinate files
groupsRemoves redundant hits from a scop families file
hetparseConverts raw dictionary of heterogen groups to a file in embl-like format
nrscopeConverts redundant EMBL-format SCOP file to non-redundant one
pdbparseParses pdb files and writes cleaned-up protein coordinate files
pdbtospConvert raw swissprot:pdb equivalence file to embl-like format
printsextractExtract data from PRINTS
prosextractBuilds the PROSITE motif database for patmatmotifs to search
rebaseextractExtract data from REBASE
scopeConvert raw scop classification file to embl-like format
scopnrRemoves redundant domains from a scop classification file
scopparseConverts raw scop classification files to a file in embl-like format
scopseqsAdds pdb and swissprot sequence records to a scop classification file
tfextractExtract data from TRANSFAC

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