The following module was proposed for inclusion in the Module List:
modid: HackaMol
DSLIP: adpOp
description: Moose Library for Molecular Hacking
userid: DEMIAN (Demian Riccardi)
chapterid: 23 (Miscellaneous_Modules)
communities:
none yet
similar:
PerlMol and Chemistry::Obabel are two libraries predating Moose with
narrower focus (cheminformatics) that have some overlap with
HackaMol. BioPerl has some overlap with Hackamol, but is specialized
to biological molecules.
rationale:
The HackaMol library was originally developed to manage quantum
chemical studies of mercury chemistry that resulted in two
publications (one in Journal of Chemical Theory and Computation and
the other in Journal of Physical Chemistry Letters). The core,
written in Moose, has been refactored from that work to be made
publicly available. The HackaMol library enables users to build
simple, yet powerful scripts for carrying out computational work on
molecules at multiple scales. This is where this library differs
significantly from PerlMol which is tailored more to
Cheminformatics. The molecular object system organizes atoms within
molecules and seeks to provide intuitive attributes and methods that
may be harnessed to coerce computational chemistry through a common
core. By using Moose, I have been able to create a sophisticated
molecule object system (I think so anyway!) that is surprisingly
powerful and flexible. Chemistry::Obabel provides C++ bindings to
the Open Babel library, which is slightly trickier to install than
typical CPAN modules. HackaMol extensions will use Open Babel and
may use or port functionality of PerlMol.
My plans:
I would like the library to be organized into two regions:
HackaMol, the core that contains classes for molecules, and
HackaMolX, the extensions, such as HackaMolX::PDBParser, a parser
for protein databank files, and HackaMolX::Calculator that use the
core. The three major goals of the core are for it to be
well-tested, well-documented, and easy to install. The goal of the
extensions is to provide a more flexible space for researchers to
develop and share new methods (that may not be well tested, well
documented or easy to install). The library will be maintained on
GitHub and released to CPAN as soon as I can finish writing the
announcement paper describing it.
The namespace is inspired by that of Moose itself. So this is a
request for not one, but two namespaces: HackaMol and HackaMolX
Demian
enteredby: DEMIAN (Demian Riccardi)
enteredon: Mon Sep 9 14:11:07 2013 UTC
The resulting entry would be:
HackaMol adpOp Moose Library for Molecular Hacking DEMIAN
Thanks for registering,
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