Just noticed this paper.
MayaChemTools: An Open Source Package for Computational Drug Discovery 10.1021/acs.jcim.6b00505">DOI.
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 is freely available online at www.MayaChemTools.org, under the terms of the GNU LGPL, as published by the Free Software Foundation.
It is possible to access them using a Vortex script.
To be honest I can't remember when I last used Perl but this publication brought back a few memories DOI.
HackaMol is an open source, object-oriented toolkit written in Modern Perl that organizes atoms within molecules and provides chemically intuitive attributes and methods.
There is also a very interesting extension HackaMol::X::Vina, a structured class that provides an interface with the AutoDock Vina docking program