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

The core set of command line Perl scripts available in the current release of MayaChemTools has no external dependencies and provide functionality for the following tasks:

• Manipulation and analysis of data in SD, CSV/TSV, sequence/alignments, and PDB files
• Listing information about data in SD, CSV/TSV, Sequence/Alignments, PDB, and fingerprints 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
• Generation of 2D fingerprints with atom types corresponding to atomic invariants, DREIDING, E-state, functional class, MMFF94, SLogP, SYBYL, TPSA and UFF
• Similarity searching and calculation of similarity matrices using available 2D fingerprints
• Listing properties of elements in the periodic table, amino acids, and nucleic acids
• Exporting data from relational database tables into text files

The command line Python scripts based on RDKit provide functionality for the following tasks:

• Calculation of molecular descriptors
• Comparison 3D molecules based on RMSD and shape
• Conversion between different molecular file formats
• Enumeration of compound libraries and stereoisomers
• Filtering molecules using SMARTS, PAINS, and names of functional groups
• Generation of graph and atomic molecular frameworks
• Generation of images for molecules
• Performing structure minimization and conformation generation based on distance geometry and forcefields
• Picking and clustering molecules based on 2D fingerprints and various clustering methodologies
• Removal of duplicate molecules

These invaluable scripts can be used in other applications, I've written a Vortex Script that uses them.