/var/lib/mobyle/programs/dssp.xml is in mobyle-programs 5.1.2-1.
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<!-- XML Authors: Corinne Maufrais, Nicolas Joly and Bertrand Neron, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>dssp</name>
<version>2000</version>
<doc>
<title>DSSP</title>
<description>
<text lang="en">Definition of secondary structure of proteins given a set of 3D coordinates</text>
</description>
<authors>W.Kabsch, C. Sander</authors>
<reference>Kabsch,W. and Sander,C. (1983) Biopolymers 22, 2577-2637.</reference>
<homepagelink>http://swift.cmbi.ru.nl/gv/dssp/</homepagelink>
<sourcelink>ftp://ftp.cmbi.ru.nl/pub/molbio/software/</sourcelink>
</doc>
<category>sequence:protein:2D_structure</category>
<category>structure:2D_structure</category>
<command>dssp</command>
</head>
<parameters>
<parameter issimple="1">
<name>pdbfile</name>
<prompt lang="en">PDB File</prompt>
<type>
<datatype>
<superclass>AbstractText</superclass>
<class>_3DStructure</class>
</datatype>
<dataFormat>PDB</dataFormat>
</type>
<format>
<code proglang="perl">(defined $value) ? " $value" : " -- "</code>
<code proglang="python">( " -- " , " " + str(value) )[ value is not None ]</code>
</format>
<ctrl>
<message>
<text lang="en">You must enter either the PDB data or the PDB id</text>
</message>
<code proglang="perl">not defined $pdbid and defined $pdbfile</code>
<code proglang="python">pdbfile is not None and pdbid is None</code>
</ctrl>
<argpos>10</argpos>
</parameter>
<parameter issimple="1">
<name>pdbid</name>
<prompt lang="en">or you can instead enter a PDB id.</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? "cat <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="../../Local/Services/Programs/Env/dssp_data.xml" xpointer="xpointer(/pdb_path/text())" />pdb$value.ent | " : ""</code>
<code proglang="python">( "" , "cat <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="../../Local/Services/Programs/Env/dssp_data.xml" xpointer="xpointer(/pdb_path/text())" />pdb" + str( value ).lower() + ".ent | " )[ value is not None ]</code>
</format>
<ctrl>
<message>
<text lang="en">You must enter either the PDB data or the PDB id</text>
</message>
<code proglang="perl">defined $pdbid and not defined $pdbfile</code>
<code proglang="python">pdbid is not None and pdbfile is None</code>
</ctrl>
<argpos>-1</argpos>
</parameter>
<paragraph>
<name>output</name>
<prompt lang="en">Output parameters</prompt>
<parameters>
<parameter>
<name>surface</name>
<prompt lang="en">Disables the calculation of accessible surface (-na)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -na " : ""</code>
<code proglang="python">( "" , " -na " )[ value ]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>classic</name>
<prompt lang="en">Classic (pre-July 1995) format (-c)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -c " : ""</code>
<code proglang="python">( "" , " -c " )[ value ]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>disulfide</name>
<prompt lang="en">Adds information about disulfide bonds to output file (-ssa)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -ssa " : ""</code>
<code proglang="python">( "" , " -ssa " )[ value ]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>sidechains2X</name>
<prompt lang="en">Renames residues with incomplete sidechains to 'X' (-x)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -x " : ""</code>
<code proglang="python">( "" , " -x " )[ value ]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>altLoc</name>
<prompt lang="en">Keeps an additional AltLoc indicator at the line ends (-alt2)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -alt2 " : ""</code>
<code proglang="python">( "" , " -alt2 " )[ value ]</code>
</format>
<argpos>1</argpos>
</parameter>
</parameters>
</paragraph>
<parameter isstdout="1">
<name>outfile</name>
<prompt lang="en">Standard output</prompt>
<type>
<datatype>
<class>DsspReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"dssp.out"</code>
<code proglang="python">"dssp.out"</code>
</filenames>
</parameter>
</parameters>
</program>
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