pdb-get-info [-datadir dir] [-pdbinfodir dir] [-pdbdir dir] [-pdbmoddir dir] [-cat] pdbid
Get the path to a PDB info RDB file. PDB info files reside in a directory
pdbinfo/dir, where dir is
directory name of the pdb directory that was used. The PDB directory to use is
established by checking:
pdbid.pdb-rdb.gz. If the PDB file is newer than PDB
info file, the info file will be built. If the info file exists but the PDB
file is missing, the info file is considered current.
This deals with the the mapping of SEQRES residues to ATOM residue
by aligning the SEQRES and ATOM residue strings using SAM.
-datadir dir -
Specifies the directory contain the other data directories. The default
is /projects/compbio/data.
-pdbinfodir dir -
The directory to store the PDB info files in.
The default is ${datadir}/pdbinfo.
-pdbdir dir -
Specifies an alternate PDB directory if the. The default is the same
as pdb-get.
-pdbmoddir dir -
Specified a directory that will be checked for modified
PDB files. A file here overrides the file in -pdbdir. The default is
the same as pdb-get.
-cat -
Instead of returning the file name, uncompress the file to stdout.
pdbid -
PDB four character identifier plus chain of the file to get.
-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:
pdb-get-info -cat 1ceo | row SEQNUM ne ""