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 infileThis 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 booleanThis 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 booleanThis 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 outfileThis 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.08/11/2010 | DOMAINATRIX 0.1.0+20100721 |