File: read.xml

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<cmdsynopsis>
	<command>READ</command>
	<arg choice="opt" rep="repeat"><replaceable>keywords</replaceable></arg>
	<command>END</command>
</cmdsynopsis>
<para>One of these sections must be present for every molecule involved in the
	APBS calculation. Molecule and "map" IDs are assigned implicitly assigned for
	each molecule/map read, based on order and starting at 1.  This section has
	the following keywords:</para>
<itemizedlist>
	<listitem>
		<cmdsynopsis id="read-mol">
			<command>mol</command>
			<arg choice="req"><replaceable>format</replaceable></arg>
			<arg choice="req"><replaceable>path</replaceable></arg>
		</cmdsynopsis>
		<para>This command specifies the molecular data to be read into APBS.  The
			arguments are: 
			<variablelist>
				<varlistentry> <term><replaceable>format</replaceable></term>
					<listitem>
						<para>The format of the input data.  Acceptable flags include:
							<variablelist>
								<varlistentry>
									<term><type>pqr</type></term>
									<listitem>
										<para>Molecular data is in <link linkend="pqr-format">PQR format</link> 
										</para> 
									</listitem>
								</varlistentry>
								<varlistentry>
									<term><type>pdb</type></term>
									<listitem>
										<para>Molecular data is in <ulink url="http://www.rcsb.org/pdb/info.html#File_Formats_and_Standards">PDB format</ulink>.
											<warning>
												<para>We do not completely follow the PDB format, as
													specified in the above link.  Specifically, we allow
													general whitespace-, tab-, or newline-delimited
													format, thereby permitting the manipulation of
													molecules with coordinates outside the &plusmn;999
													range.  </para>
											</warning>

										</para>
									</listitem>
								</varlistentry>
							</variablelist>
							<note>
								<para>Beginning with APBS 0.5.0, the optional use of the
									chain ID field is now supported in both PDB and PQR formats.</para>
							</note>
						</para>
					</listitem>
				</varlistentry>
				<varlistentry>
					<term><replaceable>path</replaceable></term>
					<listitem>
						<para>The location of the molecular data file.  This pathname should not include spaces. </para>
					</listitem>
				</varlistentry>
			</variablelist>
		</para>
	</listitem>

	<listitem>
		<cmdsynopsis id="parm">
			<command>parm</command>
			<arg choice="req"><replaceable>format</replaceable></arg>
			<arg choice="req"><replaceable>path</replaceable></arg>
		</cmdsynopsis>
		<para>This command specifies the charge and radius data to be used with
			PDB-format molecule files.  The arguments are: 
			<variablelist>
				<varlistentry>
					<term><replaceable>format</replaceable></term>
					<listitem>
						<para>The format of the parameter file.  Acceptable flags include:
							<variablelist>
								<varlistentry>
									<term><type>flat</type></term>
									<listitem>
										<para>APBS
											<link
												linkend="parm-flat-format">flat-file
												parameter
												format</link></para>
									</listitem>
								</varlistentry>
								<varlistentry>
									<term><type>xml</type></term>
									<listitem>
										<para>APBS
											<link
												linkend="parm-xml-format">XML
												parameter
												format</link></para>
									</listitem>
								</varlistentry>
							</variablelist>
						</para>
					</listitem>
				</varlistentry>
				<varlistentry>
					<term><replaceable>path</replaceable></term>
					<listitem>
						<para>The location of the parameter data file.  This pathname should not include spaces. </para>
					</listitem>
				</varlistentry>
			</variablelist>
		</para>
	</listitem>

	<listitem>
		<cmdsynopsis id="diel">
			<command>diel</command>
			<arg choice="req"><replaceable>format</replaceable></arg>
			<arg choice="req"><replaceable>path-x</replaceable></arg>
			<arg choice="req"><replaceable>path-y</replaceable></arg>
			<arg choice="req"><replaceable>path-z</replaceable></arg>
		</cmdsynopsis>
		<para>This command allows APBS to read the dielectric function 
			<inlineequation>
				<alt>\epsilon(x)</alt>
				<graphic fileref="images/epsilon_of_x.gif" valign="bottom"/>
			</inlineequation>
			mapped to 3 meshes shifted by one-half grid spacing in the x, y, and z
			directions.  The inputs are maps of dielectric variables between the
			solvent and biomolecular dieletric constants; these values are unitless.
			In general, this command will read dielectric maps written by 
			<link linkend="elec-write"><command>write</command></link>
			commands in earlier APBS calculations.  
			<note>
				<para>NOTE:  if you choose this option and have a non-zero ionic
					strength, you must also include a 
					<link linkend="kappa"><command>read kappa</command></link>
					statement</para>
			</note>
			Arguments for this command are:
			<variablelist>
				<varlistentry>
					<term><replaceable>format</replaceable></term>
					<listitem>
						<para>The format of the dielectric map.  Acceptable values include:
							<variablelist>
								<varlistentry>
									<term><type>dx</type></term>
									<listitem>
										<para> <link linkend="opendx-format">OpenDX format</link>
											(see <link linkend="opendx-format">Formats
												section</link>)</para>
									</listitem>
								</varlistentry>
							</variablelist>
						</para>
					</listitem>
				</varlistentry>
				<varlistentry>
					<term><replaceable>path-x</replaceable></term>
					<listitem>
						<para>The location of the x-shifted dielectric map file.  This pathname should not include spaces. </para>
					</listitem>
				</varlistentry>
				<varlistentry>
					<term><replaceable>path-y</replaceable></term>
					<listitem>
						<para>The location of the y-shifted dielectric map file.  This pathname should not include spaces. </para>
					</listitem>
				</varlistentry>
				<varlistentry>
					<term><replaceable>path-z</replaceable></term>
					<listitem>
						<para>The location of the z-shifted dielectric map file.  This pathname should not include spaces. </para>
					</listitem>
				</varlistentry>
			</variablelist>
		</para>
	</listitem>

	<listitem>
		<cmdsynopsis id="kappa">
			<command>kappa</command>
			<arg choice="req"><replaceable>format</replaceable></arg>
			<arg choice="req"><replaceable>path</replaceable></arg>
		</cmdsynopsis>
		<para>This command allows APBS to read the ion-accessibility function 
			<inlineequation>
				<alt>\overline{\kappa}^2(x)</alt>
				<graphic fileref="images/overline_kappa_2_of_x.gif" valign="bottom"/>
			</inlineequation>
			mapped to a mesh.  The inputs are maps of ion accessibility values which
			range between 0 and the build Debye-H&uuml;ckel screening parameter;
			these values have units of &Aring;<superscript>-2</superscript>.  In
			general, this command will read kappa-maps written by 
			<link linkend="elec-write"><command>write</command></link>
			commands in earlier APBS calculations.  
			<note>
				<para>NOTE:  if you choose this option, you must also include a 
					<link linkend="diel"><command>read diel</command></link>
					statement</para>
			</note>
			Arguments for this command are:
			<variablelist>
				<varlistentry>
					<term><replaceable>format</replaceable></term>
					<listitem>
						<para>The format of the kappa map.  Acceptable values include:
							<variablelist>
								<varlistentry>
									<term><type>dx</type></term>
									<listitem>
										<para><link linkend="opendx-format">OpenDX format</link>
											(see <link linkend="opendx-format">Formats section</link>)
										</para>
									</listitem>
								</varlistentry>
							</variablelist>
						</para>
					</listitem>
				</varlistentry>
				<varlistentry>
					<term><replaceable>path</replaceable></term>
					<listitem>
						<para>The location of the kappa map file. This pathname should not include spaces.</para>
					</listitem>
				</varlistentry>
			</variablelist>
		</para>
	</listitem>

	<listitem>
		<cmdsynopsis id="charge">
			<command>charge</command>
			<arg choice="req"><replaceable>format</replaceable></arg>
			<arg choice="req"><replaceable>path</replaceable></arg>
		</cmdsynopsis>
		<para>This command allows APBS to read the fixed (molecular) charge density
			function mapped to a mesh.  The inputs are maps of charge densities; 
			these values have units of e<subscript>c</subscript> (electron charge) per
			Angstrom<superscript>3</superscript>.
			In general, this command will read charge-maps written by 
			<link linkend="elec-write"><command>write</command></link>
			commands in earlier APBS calculations.  Arguments for this command are:
			<variablelist>
				<varlistentry>
					<term><replaceable>format</replaceable></term>
					<listitem>
						<para>The format of the charge map.  Acceptable values include:
							<variablelist>
								<varlistentry>
									<term><type>dx</type></term>
									<listitem>
										<para> <link linkend="opendx-format">OpenDX format</link>
											(see <link linkend="opendx-format">Formats section</link>)
										</para>
									</listitem>
								</varlistentry>
							</variablelist>
						</para>
					</listitem>
				</varlistentry>
				<varlistentry>
					<term><replaceable>path</replaceable></term>
					<listitem>
						<para>The location of the charge map file.  This pathname should not include spaces. </para>
					</listitem>
				</varlistentry>
			</variablelist>
		</para>
	</listitem>

	<listitem>
		<cmdsynopsis id="mesh">
			<command>mesh</command>
			<arg choice="req"><replaceable>format</replaceable></arg>
			<arg choice="req"><replaceable>path</replaceable></arg>
		</cmdsynopsis>
		<para>This command allows APBS to read a finite element mesh to use as a starting point for <link linkend="fe-manual">finite element</link> calculations.  The input is simply the mesh geometry; e.g., as produced by a finite element mesh generation program such as <ulink url="http://ccvweb.csres.utexas.edu/ccv/projects/project.php?proID=10">LBIE-Mesher</ulink> or <ulink url="http://fetk.org/codes/gamer/index.html">GAMer</ulink>.
			Arguments for this command are:
			<variablelist>
				<varlistentry>
					<term><replaceable>format</replaceable></term>
					<listitem>
						<para>The format of the input mesh.  Acceptable values include:
							<variablelist>
								<varlistentry>
									<term><type>mcsf</type></term>
									<listitem>
										<para> MCSF format (description coming soon!) </para>
									</listitem>
								</varlistentry>
							</variablelist>
						</para>
					</listitem>
				</varlistentry>
				<varlistentry>
					<term><replaceable>path</replaceable></term>
					<listitem>
						<para>The location of the meshes file.  This path should not include spaces.</para>
					</listitem>
				</varlistentry>
			</variablelist>
		</para>
	</listitem>


</itemizedlist>