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.