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'\" t
.\" Title: SCOPPARSE
.\" Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
.\" Date: 08/11/2010
.\" Manual: EMBOSS Manual for Debian
.\" Source: DOMAINATRIX 0.1.0+20100721
.\" Language: English
.\"
.TH "SCOPPARSE" "1e" "08/11/2010" "DOMAINATRIX 0.1.0+20100721" "EMBOSS Manual for Debian"
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.ie \n(.g .ds Aq \(aq
.el .ds Aq '
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.nh
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.\" * MAIN CONTENT STARTS HERE *
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.SH "NAME"
scopparse \- Generate DCF file from raw SCOP files\&.
.SH "SYNOPSIS"
.HP \w'\fBscopparse\fR\ 'u
\fBscopparse\fR \fB\-classfile\ \fR\fB\fIinfile\fR\fR \fB\-desinfile\ \fR\fB\fIinfile\fR\fR \fB\-nosegments\ \fR\fB\fIboolean\fR\fR \fB\-nomultichain\ \fR\fB\fIboolean\fR\fR [\fB\-nominor\ \fR\fB\fIboolean\fR\fR] \fB\-dcffile\ \fR\fB\fIoutfile\fR\fR
.HP \w'\fBscopparse\fR\ 'u
\fBscopparse\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBscopparse\fR
is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-classfile\fR \fIinfile\fR
.RS 4
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\&.
.RE
.PP
\fB\-desinfile\fR \fIinfile\fR
.RS 4
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\&.
.RE
.SS "Required section"
.PP
\fB\-nosegments\fR \fIboolean\fR
.RS 4
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
.RE
.PP
\fB\-nomultichain\fR \fIboolean\fR
.RS 4
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
.RE
.SS "Additional section"
.PP
\fB\-nominor\fR \fIboolean\fR
.RS 4
This option specifies whether to omit domains from minor classes (defined as anything not in class \*(AqAll alpha proteins\*(Aq, \*(AqAll beta proteins\*(Aq, \*(AqAlpha and beta proteins (a/b)\*(Aq or \*(AqAlpha and beta proteins (a+b)\*(Aq)\&. This is necessary or appropriate for many analyses\&. Default value: N
.RE
.SS "Output section"
.PP
\fB\-dcffile\fR \fIoutfile\fR
.RS 4
This option specifies the name of SCOP DCF file (domain classification file) (output)\&. A \*(Aqdomain classification file\*(Aq 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
.RE
.SH "BUGS"
.PP
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)\&.
.SH "SEE ALSO"
.PP
scopparse is fully documented via the
\fBtfm\fR(1)
system\&.
.SH "AUTHOR"
.PP
\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
.SH "COPYRIGHT"
.br
.PP
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\&.
.sp
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