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<html> <head> <title>MayaChemTools: Documentation: README</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <div class="DocNav"> <table width="100%" border=0 cellpadding=0 cellspacing=2> <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> </table> </div> <h2>Introduction</h2> <p></p> <p>MayaChemTools is a growing collection of Perl scripts, modules, and classes to support day-to-day computational discovery needs. </p> <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> <p>Review the documentation for further details. </p> <p></p> <h2>Installation</h2> <p></p> <p> 1. Add <YOUR MAYACHEMTOOLS DIR>/bin to your PATH environment variable. <br \> 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> <p>That's it. And you're all set to try out the various scripts. </p> <p></p> <h2>Caveats</h2> <p></p> <p>All output files generated by MayaChemTools package contain UNIX style new line character; you can modify it using ModifyNewLineChar.pl script. </p> <p></p> <h2>Dependencies</h2> <p></p> <p>Perl v5.8 or higher. Additional Perl modules required to use database scripts: DBI, DBD-mysql and/or DBD-Oracle. </p> <p></p> <h2>Supported Platforms</h2> <p></p> <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> <p></p> <h2>Perl Download</h2> <p></p> <p><p><a href="http://www.cpan.org">www.cpan.org</a></p> </p> <p></p> <h2>Feedback</h2> <p></p> <p><p>Manish Sud <<a href="mailto:msud@san.rr.com">msud@san.rr.com</a>></p> </p> <p></p> <h2>Copyright & License</h2> <p></p> <p>Copyright (C) 2015 Manish Sud. All rights reserved. </p> <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> <div class="DocNav"> <table width="100%" border=0 cellpadding=0 cellspacing=2> <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> </table> </div> <br /> <center> <img src="../../images/h2o2.png"> </center> </body> </html>