jo-sm / dcd

CHARMM and X-PLOR binary trajectory file parser in Ruby

DCD

DCD is a Ruby library for processing CHARMM and X-PLOR style binary trajectory files, aka DCD files. Based on the matdcd and VMD DCD plugin, DCD parses and allows access to various metadata and atom information for use in scripts and automated environments where the numeric positions of the atoms is useful.

Installation

Add this line to your application's Gemfile:

gem 'dcd'

And then execute:

$ bundle

Or install it yourself as:

$ gem install dcd

Usage

DCD requires an io pointer to a binary DCD file upon initialization, and can be used in two ways: instant loading and lazy loading. The difference between instant and lazy loading is passing in an optional second argument upon initialization.

> require('dcd')
=> true
> dcd_pointer = File.read('1407.dcd')
=> #<File:./1407.dcd>
> lazy_load = false
=> false
> my_dcd = DCD.new(dcd_pointer, lazy_load)
=> ... 

Once loaded, you have access to the metadata, including the nstep, nset, and step, the title, and the frames with atom coordinates in x, y, z, and w if using a 4th dimensional DCD.

TODO

1. Currently test coverage on this library is limited, especially around fixed atoms and CHARMM 4th dimensional parameters. If you DCDs, especially those with the aforementioned features, please make a pull request or an issue with the necessary files attached.
2. Examples.

License

MIT. See LICENSE for more information.