comparison mayachemtools/README.txt @ 0:73ae111cf86f draft

Uploaded

0:73ae111cf86f

INTRODUCTION

MayaChemTools is a growing collection of Perl scripts, modules, and classes
to support day-to-day computational discovery needs.

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.

Review the documentation for further details.

INSTALLATION

1. Add <YOUR MAYACHEMTOOLS DIR>/bin to your PATH environment variable.
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.

That's it. And you're all set to try out the various scripts.

CAVEATS

All output files generated by MayaChemTools package contain UNIX style new line
character; you can modify it using ModifyNewLineChar.pl script.

DEPENDENCIES

Perl v5.8 or higher. Additional Perl modules required to use database scripts: DBI,
DBD-mysql and/or DBD-Oracle. 

SUPPORTED PLATFORMS

Whatever Perl supports: www.cpan.org/ports/. It includes support for various
flavors of UNIX, LINUX, Windows, and Mac operating systems running on all kinds
of hardware platforms.

PERL DOWNLOAD

www.cpan.org

FEEDBACK

Manish Sud<[e-mail]>

COPYRIGHT & LICENSE

Copyright (C) 2015 Manish Sud. All rights reserved.

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.