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<html>
<head>
<title>Working with Fragment Catalogs</title>
<link rel="stylesheet" type="text/css" href="RD.css">
</head>
<body bgcolor="#ffffff">
<h1>Working with Fragment Catalogs</h1>
<center>Document Version: $Revision: 1.1 $</center>
To start from scratch, the tool requires a CSV file with a SMILES
column and an activity column. It's perfectly ok to have other
columns as well, you specify these two columns using the
<tt>--smiCol</tt> and <tt>--actCol</tt> arguments.
<p>There are four steps to the process:
<ol>
<li> Build the fragment catalog, command line argument <tt>-b</tt>
<p> This loops through a set of molecules and builds a fragment
catalog containing all unique fragments found in the molecules.
<p> <b>Requirements:</b>
<ul>
<li> InData
</ul>
<p> <b>Important arguments:</b>
<ul>
<li> <tt>-n</tt>: specifies the maximum number of molecules to be considered
<li> <tt>--catalog=[filename]</tt>: provides the name of the file to be used to store the pickled catalog.
</ul>
<li> Score molecules against the catalog, command line argument <tt>-s</tt>
<p>
<p> <b>Requirements:</b>
<ul>
<li> InData
<li> A Catalog
</ul>
<p> <b>Important arguments:</b>
<ul>
<li> <tt>-n</tt>: specifies the maximum number of molecules to be considered
<li> <tt>--catalog=[filename]</tt>: provides the name of the file containing a
pickled catalog.
<li> <tt>--scores=[filename]</tt>: provides the name of the file to be used to store
the pickled compound scores
<li> <tt>--onbits=[filename]</tt>: provides the name of the file to be used for
pickled OnBit lists (lists with the bits set by each molecule screened). Providing this
option can save a lot of time.
</ul>
<li> Calculate information gains for the molecules, command line argument <tt>-g</tt>
<p>
<p> <b>Requirements:</b>
<ul>
<li> Scores
</ul>
<p> <b>Important arguments:</b>
<ul>
<li> <tt>--scores=[filename]</tt>: provides the name of the file containing pickled compound scores
<li> <tt>--gains=[filename]</tt>: provides the name of the file to be used to store
the gains (a csv file).
</ul>
<li> Display details about the fragments, command line argument <tt>-d</tt>
<p>
<p> <b>Requirements:</b>
<ul>
<li> Catalog
<li> Gains
</ul>
<p> <b>Important arguments:</b>
<ul>
<li> <tt>--nBits=[value]</tt>: provide the maximum number of bits on which to report
(they are presented in order of decreasing Gain).
<li> <tt>--catalog=[filename]</tt>: provides the name of the file containing pickled catalog
<li> <tt>--gains=[filename]</tt>: provides the name of the file containing the
calculated gains (a CSV file)
<li> <tt>--details=[filename]</tt>: provides the name of the file to be used to store
the details (a CSV file).
</ul>
</ol>
</body>
</html>
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