SCOPPARSE(1e) EMBOSS Manual for Debian 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.
DOMAINATRIX 0.1.0+20100721 08/11/2010 SCOPPARSE(1e)