MayaChemTools: An Open Source Package for Computational Drug Discovery.

MayaChemTools is a growing collection of Perl scripts, modules, and classes to support a variety of computational drug discovery needs, such as manipulation and analysis of data, generation of two-dimensional (2D) fingerprints, similarity searching, and calculation of physicochemical properties. MayaChemTools provides command line scripts for the following tasks: manipulation and analysis of data in SD, CSV/TSV, sequence/alignments, and PDB files; calculation of a key set of physicochemical properties, such as molecular weight, hydrogen bond donors and acceptors, logP, and topological polar surface area; generation of 2D fingerprints corresponding to atom neighborhoods, atom types, E-state indices, extended connectivity, MACCS keys, path lengths, topological atom pairs, topological atom triplets, topological atom torsions, topological pharmacophore atom pairs, and topological pharmacophore atom triplets; similarity searching and calculation of similarity matrices using available 2D fingerprints; listing properties of elements in the periodic table, amino acids, and nucleic acids; and exporting data from relational databases. An extensive set of modules and classes are also available for custom development. MayaChemTools is freely available online at www.MayaChemTools.org, under the terms of the GNU LGPL, as published by the Free Software Foundation.