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scopparse

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 EMBOSS Packaging Team <pkg-emboss-devel@lists.alioth.debian.org>

Wrote the script used to autogenerate this manual page.

COPYRIGHT

Copyright © 2007 Debian EMBOSS Packaging Team

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.