HackaMol on github

[Demian Riccardi]

Hello!

I finally pushed my Perl 5, Moose library for OO molecules to GitHub:

https://github.com/demianriccardi/HackaMol

I'm still updating the documentation and tests, among other things, and I'm trying to get it ready for release on CPAN.  If anyone more experienced has time to poke around, I'd be forever grateful.  This is my first distribution and getting everything this close has been far more work than I imagined!  The library is inspired by PerlMol, BioPerl, and MMTSB (a Perl library developed by Michael Feig and coworkers), my own experiences working on projects ranging from quantum chemistry to biophysical chemistry using hybrid potentials to the biophysics of coarse-grained biomolecular crystals, and an addiction to Perl and Moose.   

 

Long term goals of the library:

To be a solid core set of classes (the above linked) for developing new capabilities that are truly multiscale.    

Description of the library:

Written using open-source modules developed for modern object-oriented Perl on the Central Perl Archive Network (CPAN), the HackaMol library enables users to build simple, yet powerful scripts for carrying out computational work on molecules at multiple scales. 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. The library is 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, 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.  

I use Math::Vector::Real for all the vector operations.  It was a lightweight solution with a fast XS dropin that overlaps very well with the desirables for working with atomic coordinates.  Extensions that treat much larger systems will definitely benefit from the capabilities PDL. 

Any advice, tips, contribs, etc. are welcome!

Demian

[Jonathan "Duke" Leto]

Howdy,

This looks like a superb contribution to CPAN + Github. Thank you!

I am the author/maintainer of Math::GSL [0], so if you find that you need anything from there and you want help, please let me know.

[0] https://metacpan.org/module/Math::GSL

Duke

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[Demian Riccardi]

Thanks!

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[Jay Hannah]

On Sep 16, 2013, at 3:35 PM, Demian Riccardi <demianr...@gmail.com> wrote:
> I finally pushed my Perl 5, Moose library for OO molecules to GitHub:
> https://github.com/demianriccardi/HackaMol

Neato! Congrats and thanks!! :D

j
http://www.bioperl.org/wiki/Jay_Hannah

[Demian Riccardi]

Thanks Jay!  

Everyone, a HackaMol developer release with POD in progress is now on cpan/metacpan. 

One question I have is in respect to the namespace of the extensions.  I know others have thought a bit about this via blogs and whatnot, but I'm going to ask it anyway because I'm still uncertain.  I would like to follow the Moose/MooseX pattern and have the HackaMolX be the location of the extensions so there is something of a clear separation between the core, which should be easy to install and well documented and the extensions, which could pass through functional states of horror with sometimes hard to install dependencies.  Any advice?  I asked something similar on prepan.org (http://prepan.org/module/nXWJ8Y9sBtj), but haven't heard much since.

Demian