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3 <title>MayaChemTools: Documentation: README</title>
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4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
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5 <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css">
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6 </head>
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7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
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8 <br/>
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9 <center>
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10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
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11 </center>
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12 <br/>
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13 <div class="DocNav">
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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./index.html" title="Table of Contents">TOC</a> <a href="./AnalyzeSDFilesData.html" title="AnalyzeSDFilesData.html">Next</a></td><td width="34%" align="middle"><strong>README</strong></td><td width="33%" align="right"><a href="./../pdf/README.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/README.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/README.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/README.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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16 </table>
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17 </div>
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18 <h2>Introduction</h2>
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19 <p></p>
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20 <p>MayaChemTools is a growing collection of Perl scripts, modules, and classes to support day-to-day computational discovery needs. </p>
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21 <p>The current release of MayaChemTools provides command line scripts for the following tasks: Manipulation of SD, CSV/TSV, Sequence/Alignments, and PDB files; Analysis of data in SD, CSV/TSV, and Sequence/Alignments files; Information about data in SD, CSV/TSV, Sequence/Alignments, PDB, and fingerprints files; Exporting data from Oracle and MySQL tables into text files Properties of periodic table elements, amino acids, and nucleic acids; Elemental analysis;Generation of fingerprints corresponding to atom neighborhoods, atom types, E-state indicies, extended connectivity, MACCS keys, path lengths, topological atom pairs, topological atom triplets, topological atom torsions, topological pharmacophore atom pairs, and topological pharmacophore atom triplets; Generation of fingerprints with atom types corresponding to atomic invariants, DREIDING, E-state, functional class, MMFF94, SLogP, SYBYL, TPSA and UFF; Calculation of similarity matrices using a variety of similarity and distance coefficients; Calculation of physicochemical properties including rotatable bonds, van der Waals molecular volume, hydrogen bond donors, hydrogen bond acceptors, SLogP, TPSA, molecular complexity and so on; Similarity searching using fingerprints. </p>
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22 <p>Review the documentation for further details. </p>
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23 <p></p>
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24 <h2>Installation</h2>
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25 <p></p>
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26 <p>
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27 1. Add <YOUR MAYACHEMTOOLS DIR>/bin to your PATH environment variable. <br \>
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28 2. And check to make sure PATH doesn't contain multiple entries for MayaChemTools package, and all *.pl files in <YOUR MAYACHEMTOOLS DIR>/bin are executable. </p>
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29 <p>That's it. And you're all set to try out the various scripts. </p>
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30 <p></p>
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31 <h2>Caveats</h2>
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32 <p></p>
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33 <p>All output files generated by MayaChemTools package contain UNIX style new line character; you can modify it using ModifyNewLineChar.pl script. </p>
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34 <p></p>
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35 <h2>Dependencies</h2>
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36 <p></p>
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37 <p>Perl v5.8 or higher. Additional Perl modules required to use database scripts: DBI, DBD-mysql and/or DBD-Oracle. </p>
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38 <p></p>
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39 <h2>Supported Platforms</h2>
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40 <p></p>
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41 <p>Whatever Perl supports: <a href="http://www.cpan.org/ports/">www.cpan.org/ports/</a>. It includes support for various flavors of UNIX, LINUX, Windows, and Mac operating systems running on all kinds of hardware platforms. </p>
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42 <p></p>
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43 <h2>Perl Download</h2>
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44 <p></p>
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45 <p><p><a href="http://www.cpan.org">www.cpan.org</a></p>
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46 </p>
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47 <p></p>
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48 <h2>Feedback</h2>
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49 <p></p>
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50 <p><p>Manish Sud <<a href="mailto:msud@san.rr.com">msud@san.rr.com</a>></p>
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51 </p>
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52 <p></p>
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53 <h2>Copyright & License</h2>
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54 <p></p>
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55 <p>Copyright (C) 2015 Manish Sud. All rights reserved. </p>
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56 <p>MayaChemTools is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License. Please see GNULICENSE.txt file for additional information. </p>
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57 <div class="DocNav">
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58 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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59 <tr align="left" valign="top"><td width="33%" align="left"><a href="./index.html" title="Table of Contents">TOC</a> <a href="./AnalyzeSDFilesData.html" title="AnalyzeSDFilesData.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>README</strong></td></tr>
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60 </table>
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61 </div>
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62 <br />
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63 <center>
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64 <img src="../../images/h2o2.png">
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65 </center>
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66 </body>
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67 </html>
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