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1 INTRODUCTION
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2
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3 MayaChemTools is a growing collection of Perl scripts, modules, and classes
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4 to support day-to-day computational discovery needs.
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5
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6 The current release of MayaChemTools provides command line scripts for
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7 the following tasks: Manipulation of SD, CSV/TSV, Sequence/Alignments,
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8 and PDB files; Analysis of data in SD, CSV/TSV, and Sequence/Alignments
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9 files; Information about data in SD, CSV/TSV, Sequence/Alignments, PDB,
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10 and fingerprints files; Exporting data from Oracle and MySQL tables into text
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11 files Properties of periodic table elements, amino acids, and nucleic acids;
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12 Elemental analysis;Generation of fingerprints corresponding to atom
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13 neighborhoods, atom types, E-state indicies, extended connectivity,
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14 MACCS keys, path lengths, topological atom pairs, topological atom triplets,
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15 topological atom torsions, topological pharmacophore atom pairs, and
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16 topological pharmacophore atom triplets; Generation of fingerprints
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17 with atom types corresponding to atomic invariants, DREIDING, E-state,
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18 functional class, MMFF94, SLogP, SYBYL, TPSA and UFF; Calculation of
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19 similarity matrices using a variety of similarity and distance coefficients;
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20 Calculation of physicochemical properties including rotatable bonds,
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21 van der Waals molecular volume, hydrogen bond donors, hydrogen bond
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22 acceptors, SLogP, TPSA, molecular complexity and so on; Similarity
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23 searching using fingerprints.
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24
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25 Review the documentation for further details.
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26
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27 INSTALLATION
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28
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29 1. Add <YOUR MAYACHEMTOOLS DIR>/bin to your PATH environment variable.
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30 2. And check to make sure PATH doesn't contain multiple entries for MayaChemTools
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31 package, and all *.pl files in <YOUR MAYACHEMTOOLS DIR>/bin are executable.
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32
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33 That's it. And you're all set to try out the various scripts.
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34
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35 CAVEATS
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36
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37 All output files generated by MayaChemTools package contain UNIX style new line
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38 character; you can modify it using ModifyNewLineChar.pl script.
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39
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40 DEPENDENCIES
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41
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42 Perl v5.8 or higher. Additional Perl modules required to use database scripts: DBI,
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43 DBD-mysql and/or DBD-Oracle.
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44
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45 SUPPORTED PLATFORMS
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46
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47 Whatever Perl supports: www.cpan.org/ports/. It includes support for various
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48 flavors of UNIX, LINUX, Windows, and Mac operating systems running on all kinds
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49 of hardware platforms.
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50
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51 PERL DOWNLOAD
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52
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53 www.cpan.org
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54
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55 FEEDBACK
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56
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57 Manish Sud<msud@san.rr.com>
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58
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59 COPYRIGHT & LICENSE
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60
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61 Copyright (C) 2015 Manish Sud. All rights reserved.
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62
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63 MayaChemTools is free software; you can redistribute it and/or modify it under
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64 the terms of the GNU Lesser General Public License. Please see GNULICENSE.txt
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65 file for additional information.
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