scopparse1
Generate dcf file from raw scop files.
Usage
scopparse -classfile
infile
-desinfile
infile
-nosegments
boolean
-nomultichain
boolean
[-nominor
boolean]
-dcffile
outfile
scopparse -help
Overview
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