dssp-get

dssp-get [-pdbdir dir] [-cat] pdbid

Get the path to a DSSP file. If the file already exists in the specified DSSP directory, it is used, otherwise the file is downloaded. The resulting file will be named in the form pdbid.dssp.gz and will always be gzipped.

Arguments

-dsspdir dir - Specifies an alternate DSSP directory. The default is /projects/compbio/data/dssp.
-cat - Instead of returning the file name, uncompress the file to stdout.
pdbid - PDB four character identifier of the file to get. Trailing chain identifiers and other garbage is dropped. Maybe upper or lower case.

Output

If successful, the full path to the DSSP file or the contents of the file if -cat is specified is written to stdout. If an error occurs, a message is written to stderr. This idea is that the output of this script is used to get the file name to open or to the actual data stream. For example:

       dssp-get -cat 1ceo | egrep '^AUTHOD
       some-prog `dssp-get 1ceo`

Exit codes

1 - file not found.
2 - Other ftp error.
3 - Error uncompressing, compressing or installing file.
4 - bad command line argument.

Source

CVS module xssp-tools.

Contact

Mark Diekhans