SCOPPARSE(1e)
NAME
scopparse - Generate DCF file from raw SCOP files.
SYNOPSIS
scopparse -classfile infile -desinfile infile -nosegments boolean -nomultichain boolean [-nominor boolean] -dcffile outfile scopparse -help
DESCRIPTION
scopparse is a command line program from EMBOSS ("the European
Molecular Biology Open Software Suite"). It is part of the
"Utils:Database creation" command group(s).
OPTIONS
- Input section
- -classfile infile
This option specifies the name of raw SCOP classification file
dir.cla.scop.txt_X.XX (input). This is the raw SCOP classification file available at
http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.57. - -desinfile infile
This option specifies the name of raw SCOP description file
dir.des.scop.txt_X.XX (input). This is the raw SCOP description
file available at
http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.57. - Required section
- -nosegments boolean
This option specifies whether to omit domains comprising of more
than one segment. This is necessary if a continuous residue
sequence is required. Default value: N - -nomultichain boolean
This option specifies whether to omit domains comprising segments
from more than one chain. This is necessary if a continuous residue sequence is required. Default value: N - Additional section
- -nominor boolean
This option specifies whether to omit domains from minor classes
(defined as anything not in class 'All alpha proteins', 'All beta
proteins', 'Alpha and beta proteins (a/b)' or 'Alpha and beta
proteins (a+b)'). This is necessary or appropriate for many
analyses. Default value: N - Output section
- -dcffile outfile
This option specifies the name of SCOP DCF file (domain
classification file) (output). A 'domain classification file'
contains classification and other data for domains from the SCOP or CATH databases. The file is generated by using DOMAINER and is in
DCF format (EMBL-like). Domain sequence information can be added to the file by using DOMAINSEQS. Default value: test.scop
BUGS
Bugs can be reported to the Debian Bug Tracking system
(http://bugs.debian.org/emboss), or directly to the EMBOSS developers
(http://sourceforge.net/tracker/?group_id=93650&atid=605031).
SEE ALSO
scopparse is fully documented via the tfm(1) system.
AUTHOR
- Debian Med Packaging Team
<debian-med-packaging@lists.alioth.debian.org> - Wrote the script used to autogenerate this manual page.
COPYRIGHT
- This manual page was autogenerated from an Ajax Control Definition of
the EMBOSS package. It can be redistributed under the same terms as
EMBOSS itself.