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pdb_extract.html
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<html>
<head>
<title>
PDB_EXTRACT - Extract data from PDB files
</title>
</head>
<body bgcolor="#EEEEEE" link="#CC0000" alink="#FF3300" vlink="#000055">
<h1 align = "center">
PDB_EXTRACT <br> Extract data from PDB files
</h1>
<hr>
<p>
<b>PDB_EXTRACT</b>
is a FORTRAN90 program which
extracts certain columns from certain lines of a
Protein Data Bank file.
</p>
<p>
Right now, the controls for which lines are to be considered, and what
data is to be extracted, are hardwired into the code. For instance, we
might want to consider every line in which the fourth word is "CA", and
for those lines, we would write out columns 9 and 10.
</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_read/pdb_read.html">
PDB_READ</a>,
a FORTRAN90 program which
can read 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 coordinates of atoms in a PDB file
and writes them out as an XYZ file.
</p>
<p>
<a href = "../../f_src/xyz_to_pdb/xyz_to_pdb.html">
XYZ_TO_PDB</a>,
a FORTRAN90 program which
reads an XYZ file and
writes the data as coordinates of atoms in a PDB file.
</p>
<h3 align = "center">
Reference:
</h3>
<p>
<ol>
<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 = "pdb_extract.f90">pdb_extract.f90</a>, the source code;
</li>
<li>
<a href = "pdb_extract.sh">pdb_extract.sh</a>,
commands to compile and load the source code;
</li>
</ul>
</p>
<h3 align = "center">
Examples and Tests:
</h3>
<p>
<ul>
<li>
<a href = "input.txt">input.txt</a>, a sample input PDB file;
</li>
<li>
<a href = "output.txt">output.txt</a>, a sample output file;
</li>
</ul>
</p>
<h3 align = "center">
List of Routines:
</h3>
<p>
<ul>
<li>
<b>MAIN</b> is the main program for PDB_EXTRACT.
</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_TO_R8</b> reads an R8 from a string.
</li>
<li>
<b>TIMESTAMP</b> prints the current YMDHMS date as a time stamp.
</li>
<li>
<b>WORD_FIND</b> finds the word of a given index in a string.
</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>