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PROGRAM:

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

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