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xyz_to_pdb.html
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<html>
<head>
<title>
XYZ_TO_PDB - Write PDB Atom Coordinates to XYZ File
</title>
</head>
<body bgcolor="#EEEEEE" link="#CC0000" alink="#FF3300" vlink="#000055">
<h1 align = "center">
XYZ_TO_PDB <br> Write PDB Atom Coordinates to XYZ File
</h1>
<hr>
<p>
<b>XYZ_TO_PDB</b>
is a FORTRAN90 program which
reads an XYZ file
containing a list of spatial coordinates, and writes a
PDB file containing ATOM records with the given coordinates.
</p>
<p>
The PDB file has many fields that must be filled in. This
program attempts to fill in these fields with plausible values,
but really only the atomic coordinates will have any meaning.
</p>
<h3 align = "center">
Usage:
</h3>
<p>
<blockquote>
<b>xyz_to_pdb</b>
</blockquote>
starts the program, and prompts for the file names.
</p>
<p>
<blockquote>
<b>xyz_to_pdb</b> <i>file.xyz</i> <i>file.pdb</i>
</blockquote>
where
<ul>
<li>
<i>file.xyz</i> is the input coordinate data;
</li>
<li>
<i>file.pdb</i> is the PDB file created.
</li>
</ul>
illustrates how the filenames can be specified on the command line.
</p>
<h3 align = "center">
Licensing:
</h3>
<p>
The computer code and data files described and made available on this web page
are distributed under
<a href = "../../txt/gnu_lgpl.txt">the GNU LGPL license.</a>
</p>
<h3 align = "center">
Related Data and Programs:
</h3>
<p>
<a href = "../../data/pdb/pdb.html">
PDB</a>,
a data directory which
contains a description and examples of the PDB format.
</p>
<p>
<a href = "../../f_src/pdb_extract/pdb_extract.html">
PDB_EXTRACT</a>,
a FORTRAN90 program which
can extract certain records from a PDB file.
</p>
<p>
<a href = "../../f_src/pdb_read/pdb_read.html">
PDB_READ</a>,
a FORTRAN90 program which
can read the information
in a PDB file.
</p>
<p>
<a href = "../../f_src/pdb_to_xyz/pdb_to_xyz.html">
PDB_TO_XYZ</a>,
a FORTRAN90 program which
reads the ATOM records
from a PDB file, and writes the atomic coordinates to an XYZ file.
</p>
<p>
<a href = "../../data/xyz/xyz.html">
XYZ</a>,
a data directory which
contains a description and examples of the XYZ format.
</p>
<p>
<a href = "../../f_src/xyz_io/xyz_io.html">
XYZ_IO</a>,
a FORTRAN90 library which
reads and writes XYZ files.
</p>
<h3 align = "center">
Reference:
</h3>
<p>
<ol>
<li>
<a href = "../../txt/pdb_format.txt">
The PDB format</a>
</li>
<li>
<a href = "http://www.rcsb.org/pdb/">
http://www.rcsb.org/pdb/</a> <br>
The Protein Data Bank Home Page.
</li>
</ol>
</p>
<h3 align = "center">
Source Code:
</h3>
<p>
<ul>
<li>
<a href = "xyz_to_pdb.f90">xyz_to_pdb.f90</a>, the source code;
</li>
<li>
<a href = "xyz_to_pdb.sh">xyz_to_pdb.sh</a>,
commands to compile the source code;
</li>
</ul>
</p>
<h3 align = "center">
Examples and Tests:
</h3>
<p>
<b>TINY</b> is a sample XYZ file with 12 sets of 3D coordinates.
<ul>
<li>
<a href = "tiny.xyz">tiny.xyz</a>, a sample XYZ file;
</li>
<li>
<a href = "tiny.pdb">tiny.pdb</a>,
the corresponding PDB file.
</li>
</ul>
</p>
<p>
<b>MOMOMER</b> is a sample XYZ file with 888 sets of 3D coordinates.
<ul>
<li>
<a href = "monomer.xyz">monomer.xyz</a>, a sample XYZ file;
</li>
<li>
<a href = "monomer.pdb">monomer.pdb</a>,
the corresponding PDB file.
</li>
</ul>
</p>
<h3 align = "center">
List of Routines:
</h3>
<p>
<ul>
<li>
<b>MAIN</b> is the main program for XYZ_TO_PDB.
</li>
<li>
<b>CH_CAP</b> capitalizes a single character.
</li>
<li>
<b>CH_EQI</b> is a case insensitive comparison of two characters for equality.
</li>
<li>
<b>CH_TO_DIGIT</b> returns the integer value of a base 10 digit.
</li>
<li>
<b>GET_UNIT</b> returns a free FORTRAN unit number.
</li>
<li>
<b>S_EQI</b> is a case insensitive comparison of two strings for equality.
</li>
<li>
<b>S_TO_R8</b> reads an R8 from a string.
</li>
<li>
<b>S_TO_R8VEC</b> reads an R8VEC from a string.
</li>
<li>
<b>TIMESTAMP</b> prints the current YMDHMS date as a time stamp.
</li>
<li>
<b>TIMESTRING</b> writes the current YMDHMS date into a string.
</li>
<li>
<b>XYZ_TO_PDB_ATOM_TO_XYZ</b> writes XYZ data as ATOM records in a PDB file.
</li>
</ul>
</p>
<p>
You can go up one level to <a href = "../f_src.html">
the FORTRAN90 source codes</a>.
</p>
<hr>
<i>
Last revised on 09 January 2006.
</i>
<!-- John Burkardt -->
</body>
</html>