File: psize.1.xml

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pdb2pqr 2.1.1%2Bdfsg-2
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<?xml version="1.0"?>
<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN" "http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [
<!ENTITY psize "<command>psize</command>">
]>
<refentry>
  <refentryinfo>
    <title>PDB2PQR Manual</title>
    <!-- "date" should be the date of the latest change -->
    <date>2008-06-04</date>
    <productname>psize</productname>
    <authorgroup>
      <author>
	<firstname>Manuel</firstname><surname>Prinz</surname>
	<contrib>Wrote this manpage for the Debian System.</contrib>
	<address><email>debian@pinguinkiste.de</email></address>
      </author>
    </authorgroup>
    <copyright><year>2008</year><holder>Manuel Prinz</holder></copyright>
  </refentryinfo>
  <refmeta>
    <refentrytitle>psize</refentrytitle>
    <manvolnum>1</manvolnum>
  </refmeta>
  <refnamediv>
    <refname>psize</refname>
    <refpurpose>Get dimensions and other information from <acronym>PQR</acronym> files</refpurpose>
  </refnamediv>
  <refsynopsisdiv>
    <cmdsynopsis>
      <command>psize</command>
      <arg choice="opt"><option>--cfact=<replaceable>value</replaceable></option></arg>
      <arg choice="opt"><option>--fadd=<replaceable>value</replaceable></option></arg>
      <arg choice="opt"><option>--space=<replaceable>value</replaceable></option></arg>
      <arg choice="opt"><option>--gememfac=<replaceable>value</replaceable></option></arg>
      <arg choice="opt"><option>--gememceil=<replaceable>value</replaceable></option></arg>
      <arg choice="opt"><option>--ofrac=<replaceable>value</replaceable></option></arg>
      <arg choice="opt"><option>--redfac=<replaceable>value</replaceable></option></arg>
      <arg choice="req"><option><replaceable>pqrfile</replaceable></option></arg>
    </cmdsynopsis>
    <cmdsynopsis>
      <command>psize</command>
      <group choice="req">
	<arg choice="plain"><option>--help</option></arg>
	<arg choice="plain"><option>-h</option></arg>
      </group>
    </cmdsynopsis>
  </refsynopsisdiv>
  <refsect1 id="description">
    <title>DESCRIPTION</title>
    <para>
      &psize; derives information from <acronym>PQR</acronym> files to preprare the models of proteins and chemicals for electrostatics calculations. The tool calculates dimensions for coarse and fine grids, grid spacings, box size and estimates the memory required to perform an electrostatics calculation.</para>
      <para>The calculation of this information can be influenced by giving constraints to &psize; as parameters.</para>
  </refsect1>
  <refsect1 id="options">
    <title>OPTIONS</title>
    <para>&psize; accepts the following options:</para>
    <variablelist>
      <varlistentry>
	<term><option>--help</option></term>
	<term><option>-h</option></term>
	<listitem>
	  <para>Print a help message and exit.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--cfact=<replaceable class="option">value</replaceable></option></term>
	<listitem>
	  <para>Factor by which to expand the molecule dimensions to get the coarse grid dimensions</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--fadd=<replaceable class="option">value</replaceable></option></term>
	<listitem>
	  <para>Amount to add to the molecule dimensions to get the fine grid dimensions.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--space=<replaceable class="option">value</replaceable></option></term>
	<listitem>
	  <para>Desired fine mesh resolution.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--gememfac=<replaceable class="option">value</replaceable></option></term>
	<listitem>
	  <para>Number of bytes per grid point required for sequential <acronym>MG</acronym> calculation.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--gememceil=<replaceable class="option">value</replaceable></option></term>
	<listitem>
	  <para>Maximum <acronym>MB</acronym> allowed for sequential <acronym>MG</acronym> calculation. Adjust this to force the script to perform faster calculations (which require more parallelism).</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--ofrac=<replaceable class="option">value</replaceable></option></term>
	<listitem>
	  <para>Overlap factor between mesh partitions.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--redfac=<replaceable class="option">value</replaceable></option></term>
	<listitem>
	  <para>Maximum factor by which a domain dimension can be reduced during focusing.</para>
	</listitem>
      </varlistentry>
    </variablelist>
  </refsect1>
  <refsect1 id="seealso">
    <title>SEE ALSO</title>
    <para><citerefentry><refentrytitle>apbs</refentrytitle><manvolnum>1</manvolnum></citerefentry>, <citerefentry><refentrytitle>pdb2pqr</refentrytitle><manvolnum>1</manvolnum></citerefentry></para>
  </refsect1>
</refentry>