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