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

<pise>

<head>
    <title>environ</title>
    <description>Calculates Energies Associated with Accessible as well as Buried Surface Areas in Proteins</description>
    <authors>P. Koehl, M. Delarue</authors>
    <reference>P. Koehl and M. Delarue, Proteins 20:264-278 (1994)</reference>
    <category>protein:3d structure</category>
  </head>


<command>environ</command>

<parameters>

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

	<format>
		<language>perl</language>
		<code> "environ &lt; params" </code>
	</format>
	<group>0</group>

</attributes>
</parameter>

<parameter type="Results">
<name>param</name>
<attributes>

	<filenames>params accessibility_per_residue accessibility_per_atom free_energy</filenames>

</attributes>
</parameter>

<parameter ismandatory="1" issimple="1" type="InFile">
<name>pdbfile</name>
<attributes>

	<prompt>PDB file</prompt>
	<format>
		<language>perl</language>
		<code>"$value\\n"</code>
	</format>
	<group>1</group>
	<paramfile>params</paramfile>
	<pipe>
		<pipetype>pdbfile</pipetype>
			<language>perl</language>
			<code>1</code>
	</pipe>

</attributes>
</parameter>

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

	<format>
		<language>perl</language>
		<code>"accessibility_per_residue\\n"</code>
	</format>
	<group>2</group>
	<paramfile>params</paramfile>

</attributes>
</parameter>

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

	<format>
		<language>perl</language>
		<code>"accessibility_per_atom\\n"</code>
	</format>
	<group>3</group>
	<paramfile>params</paramfile>

</attributes>
</parameter>

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

	<format>
		<language>perl</language>
		<code>"free_energy\\n"</code>
	</format>
	<group>4</group>
	<paramfile>params</paramfile>

</attributes>
</parameter>


</parameters>
</pise>
