<?xml version="1.0" encoding="ISO-8859-1" ?>
<!DOCTYPE pise SYSTEM "PARSER/pise.dtd">

<pise>

  <head>
    <title>STAMP</title>
    <version>4.2</version>
    <description>pdbc</description>
    <authors>Russell, Barton</authors>
  </head>

  <command>pdbc</command>

<parameters>

<parameter iscommand="1" ishidden="1" issimple="1" type="String">
<name>pdbc</name>
<attributes>

	<format>
		<language>seqlab</language>
		<code>pdbc</code>
		<language>perl</language>
		<code>"pdbc"</code>
	</format>
	<group>0</group>

</attributes>
</parameter>

<parameter ismandatory="1" issimple="1" type="String">
<name>code</name>
<attributes>

	<prompt>4 letter PDB code</prompt>
	<format>
		<language>perl</language>
		<code>" $value"</code>
	</format>
	<group>2</group>

</attributes>
</parameter>

<parameter ishidden="1" isstandout="1" type="OutFile">
<name>outfile</name>
<attributes>

	<format>
		<language>perl</language>
		<code>""</code>
	</format>
	<vdef><value>"pdbc.out"</value></vdef>
	<pipe>
		<pipetype>stamp_domains_file</pipetype>
			<language>perl</language>
			<code>1</code>
	</pipe>

</attributes>
</parameter>

<parameter ishidden="1" type="String">
<name>loadresult</name>
<attributes>

	<format>
		<language>perl</language>
		<code>" &gt; load_result"</code>
	</format>
	<group>20</group>

</attributes>
</parameter>

<parameter ismandatory="1" issimple="1" type="Excl">
<name>choice</name>
<attributes>

	<prompt>Choices</prompt>
	<format>
		<language>perl</language>
		<code>" $value"</code>
	</format>
	<vdef><value>-d</value></vdef>
	<group>1</group>
	<vlist>
		<value>-m</value>
		<label>-m minimalist mode (just report file locations)</label>
		<value>-d</value>
		<label>-d write in STAMP database format</label>
		<value>-r</value>
		<label>-r write out chain, resolution, R-factor, etc.</label>
		<value>-q</value>
		<label>-q verbose mode</label>
	</vlist>

</attributes>
</parameter>

<parameter type="InFile">
<name>domains_file</name>
<attributes>

	<prompt>Already loaded domains</prompt>
	<format>
		<language>perl</language>
		<code>($value)? "; cat $domains_file load_result" : "; cat load_result" </code>
	</format>
	<group>40</group>
	<comment>
		<value>You don't need to enter this parameter. </value>
		<value>This is the intermediate file containing already loaded domains.</value>
	</comment>
	<pipe>
		<pipetype>stamp_domains_file</pipetype>
			<language>perl</language>
			<code>1</code>
	</pipe>

</attributes>
</parameter>


</parameters>
</pise>
