mddb 0.0.12 → 0.0.14

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
File without changes
File without changes
@@ -4,14 +4,15 @@ require "mddb/cli"
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  require "mongo_mapper"
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  require "mddb/config"
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  require "mddb/parser"
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+ require "mddb/runner"
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  if File.exists? "config.yml"
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  Mddb::Config.config = "config.yml"
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- require "mddb/point"
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- require "mddb/vector"
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- require "mddb/frame"
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  require "mddb/atom"
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  require "mddb/molecule"
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+ require "mddb/frame"
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+ require "mddb/point"
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+ require "mddb/vector"
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  require "require_all"
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  require_all 'models' unless Dir.glob('models/**/*.rb').size == 0
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  end
@@ -10,6 +10,7 @@ require 'mddb/version'
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  puts " Leave blank for list of available "
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  puts " models"
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  puts " console Starts an interactice MDDB console"
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+ puts " run Run calculation"
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  elsif %w{-v --version --v}.include? ARGV.first
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  puts Mddb::VERSION
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  elsif ARGV.first == 'new'
@@ -17,6 +18,8 @@ require 'mddb/version'
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  require 'mddb/commands/new'
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  elsif ARGV.first == 'console'
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  require 'mddb/commands/console'
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+ elsif ARGV.first == 'run'
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+ require 'mddb/commands/run'
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  elsif ARGV.first == 'load'
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  require 'mddb/commands/load'
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  elsif %w{g generate}.include? ARGV.first
@@ -32,6 +32,7 @@ def start_console
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  end
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  end
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  end
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+ puts "parsing"
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  p = Mddb::Parser::Parser.new file
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  fid = 1 + last_frame
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  p.each_frame do |f|
@@ -0,0 +1,34 @@
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+ module Mddb::Commands
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+ class Run
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+ def initialize
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+ puts "Started Runner"
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+ end
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+
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+ def resque
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+ puts "Running Jobs Using Resque"
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+ puts "Booting up workers..."
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+ end
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+
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+ def qsub
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+ puts "Submitting multiple QSUB jobs"
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+ end
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+
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+ def local
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+ puts "Running locally..."
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+ x = Mddb::Runner.new
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+ x.run(1,2)
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+ end
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+ end
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+ ARGV.shift
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+ options = ['local', 'qsub','resque']
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+ unless options.include? ARGV.first
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+ puts "Please specify an option for run"
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+ options.each do |o|
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+ puts o
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+ end
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+ else
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+ Run.new.send(ARGV.first)
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+ end
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+ end
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+
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+
@@ -13,6 +13,7 @@ module Mddb
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  config['database']['host'] = 'localhost' if config['database']['host'].nil?
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  config['database']['port'] = 27017 if config['database']['port'].nil?
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  raise "bad config file: database name needs to be defined" if config['database']['name'].nil?
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+ raise "bad config file: rcut needs to be defined" if config['simulation']['rcut'].nil?
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  config['simulation']['dimensions'] = config['simulation']['dimensions'].split(',').collect {|a| a.to_f}
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  @@config = config
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  self.connect
@@ -0,0 +1,53 @@
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+ module Mddb
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+ class Runner
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+ def initialize
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+ begin
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+ @klasses = Frame.associations.keys.map {|k| t.to_s.classify}
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+ rescue
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+ @klasses = []
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+ end
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+ end
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+
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+ def fine?
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+ if @klasses.empty?
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+ puts "No models belong to frame, aborting."
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+ false
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+ else
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+ true
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+ end
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+ end
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+
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+ def run (start, finish)
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+ if self.fine?
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+ (start..finish).each do |f|
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+ puts "Running => Frame 1"
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+ self.calculations(f)
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+ end
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+ end
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+ end
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+
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+ def calculations(frame)
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+ @klasses.each_with_index do |k,i|
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+ objects = Object.const_get(k).where(:fid => frame).all
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+ object_count = objects.count
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+ complete = 0
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+ failed = 0
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+ objects.each do |o|
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+ begin
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+ o.run
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+ complete += 1
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+ rescue
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+ failed += 1
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+ puts " Models (#{i}/#{model_count}) => #{k} #{complete}/#{object_count} Failed: #{failed}"
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+ end
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+ end
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+ end
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+ begin
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+ puts " Running Frame Calculations"
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+ frame.run
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+ rescue
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+ " Failed"
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+ end
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+ end
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+ end
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+ end
@@ -1,3 +1,3 @@
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  module Mddb
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- VERSION = "0.0.12"
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+ VERSION = "0.0.14"
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  end
metadata CHANGED
@@ -1,93 +1,100 @@
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  --- !ruby/object:Gem::Specification
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  name: mddb
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  version: !ruby/object:Gem::Version
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- version: 0.0.12
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- prerelease:
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+ prerelease:
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+ version: 0.0.14
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  platform: ruby
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  authors:
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  - Thomas Mulvaney
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- autorequire:
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+ autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2012-03-09 00:00:00.000000000Z
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+ date: 2012-03-13 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rspec
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- requirement: &70251383669620 !ruby/object:Gem::Requirement
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- none: false
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+ version_requirements: &2056 !ruby/object:Gem::Requirement
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  requirements:
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  - - ! '>='
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  - !ruby/object:Gem::Version
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- version: '0'
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- type: :development
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+ version: !binary |-
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+ MA==
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+ none: false
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+ requirement: *2056
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  prerelease: false
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- version_requirements: *70251383669620
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+ type: :development
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  - !ruby/object:Gem::Dependency
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  name: mongo_mapper
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- requirement: &70251383668980 !ruby/object:Gem::Requirement
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- none: false
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+ version_requirements: &2074 !ruby/object:Gem::Requirement
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  requirements:
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  - - ! '>='
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  - !ruby/object:Gem::Version
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- version: '0'
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- type: :runtime
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+ version: !binary |-
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+ MA==
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+ none: false
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+ requirement: *2074
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  prerelease: false
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- version_requirements: *70251383668980
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+ type: :runtime
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  - !ruby/object:Gem::Dependency
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  name: hirb
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- requirement: &70251383668360 !ruby/object:Gem::Requirement
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- none: false
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+ version_requirements: &2092 !ruby/object:Gem::Requirement
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  requirements:
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  - - ! '>='
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  - !ruby/object:Gem::Version
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- version: '0'
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- type: :runtime
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+ version: !binary |-
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+ MA==
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+ none: false
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+ requirement: *2092
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  prerelease: false
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- version_requirements: *70251383668360
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+ type: :runtime
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  - !ruby/object:Gem::Dependency
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  name: thor
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- requirement: &70251383667680 !ruby/object:Gem::Requirement
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- none: false
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+ version_requirements: &2108 !ruby/object:Gem::Requirement
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  requirements:
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  - - ! '>='
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  - !ruby/object:Gem::Version
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- version: '0'
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- type: :runtime
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+ version: !binary |-
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+ MA==
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+ none: false
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+ requirement: *2108
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  prerelease: false
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- version_requirements: *70251383667680
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+ type: :runtime
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  - !ruby/object:Gem::Dependency
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  name: micro-optparse
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- requirement: &70251383666960 !ruby/object:Gem::Requirement
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- none: false
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+ version_requirements: &2124 !ruby/object:Gem::Requirement
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  requirements:
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  - - ! '>='
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  - !ruby/object:Gem::Version
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- version: '0'
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- type: :runtime
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+ version: !binary |-
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+ MA==
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+ none: false
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+ requirement: *2124
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  prerelease: false
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- version_requirements: *70251383666960
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+ type: :runtime
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  - !ruby/object:Gem::Dependency
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  name: resque
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- requirement: &70251383666240 !ruby/object:Gem::Requirement
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- none: false
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+ version_requirements: &2140 !ruby/object:Gem::Requirement
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  requirements:
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  - - ! '>='
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  - !ruby/object:Gem::Version
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- version: '0'
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- type: :runtime
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+ version: !binary |-
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+ MA==
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+ none: false
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+ requirement: *2140
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  prerelease: false
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- version_requirements: *70251383666240
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+ type: :runtime
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  - !ruby/object:Gem::Dependency
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  name: require_all
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- requirement: &70251383665540 !ruby/object:Gem::Requirement
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- none: false
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+ version_requirements: &2156 !ruby/object:Gem::Requirement
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  requirements:
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  - - ! '>='
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  - !ruby/object:Gem::Version
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- version: '0'
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- type: :runtime
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+ version: !binary |-
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+ MA==
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+ none: false
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+ requirement: *2156
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  prerelease: false
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- version_requirements: *70251383665540
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+ type: :runtime
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  description: MDDB makes analysing molecular dynamics simulations easy
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  email:
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  - thom.mulvaney@gmail.com
@@ -100,70 +107,119 @@ executables:
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  extensions: []
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  extra_rdoc_files: []
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  files:
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- - .gitignore
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- - Gemfile
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- - Rakefile
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- - bin/aggregater
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- - bin/average
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- - bin/binner
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- - bin/mddb
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- - bin/stat.rb
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- - config.yml
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- - lib/mddb.rb
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- - lib/mddb/atom.rb
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- - lib/mddb/calculations.rb
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- - lib/mddb/cli.rb
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- - lib/mddb/commands/console.rb
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- - lib/mddb/commands/load.rb
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- - lib/mddb/commands/new.rb
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- - lib/mddb/config.rb
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- - lib/mddb/frame.rb
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- - lib/mddb/generators.rb
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- - lib/mddb/generators/atom.rb
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- - lib/mddb/generators/molecule.rb
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- - lib/mddb/molecule.rb
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- - lib/mddb/parser.rb
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- - lib/mddb/point.rb
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- - lib/mddb/sphere.rb
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- - lib/mddb/templates/README.tt
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- - lib/mddb/templates/atom.rb.tt
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- - lib/mddb/templates/config.yml.tt
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- - lib/mddb/templates/frame.rb.tt
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- - lib/mddb/templates/molecule.rb.tt
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- - lib/mddb/templates/spec/atom_spec.rb.tt
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- - lib/mddb/templates/spec/molecule_spec.rb.tt
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- - lib/mddb/vector.rb
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- - lib/mddb/version.rb
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- - mddb.gemspec
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- - quick.xyz
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- - spec/atom_spec.rb
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- - spec/oxygen_spec.rb
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- - spec/spec_helper.rb
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+ - !binary |-
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+ LmdpdGlnbm9yZQ==
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+ - !binary |-
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+ bWRkYi5nZW1zcGVj
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+ cXVpY2sueHl6
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+ - !binary |-
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+ - !binary |-
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+ c3BlYy9veHlnZW5fc3BlYy5yYg==
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+ - !binary |-
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+ c3BlYy9zcGVjX2hlbHBlci5yYg==
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  homepage: ''
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  licenses: []
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- post_install_message:
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+ post_install_message:
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  rdoc_options: []
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  require_paths:
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  - lib
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  required_ruby_version: !ruby/object:Gem::Requirement
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- none: false
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  requirements:
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  - - ! '>='
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  - !ruby/object:Gem::Version
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- version: '0'
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- required_rubygems_version: !ruby/object:Gem::Requirement
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+ version: !binary |-
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+ MA==
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  none: false
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+ required_rubygems_version: !ruby/object:Gem::Requirement
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  requirements:
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  - - ! '>='
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  - !ruby/object:Gem::Version
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- version: '0'
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+ version: !binary |-
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+ MA==
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+ none: false
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  requirements: []
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  rubyforge_project: mddb
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- rubygems_version: 1.8.10
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- signing_key:
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+ rubygems_version: 1.8.15
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+ signing_key:
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  specification_version: 3
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  summary: MDDB molecular database and framework
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  test_files:
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- - spec/atom_spec.rb
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- - spec/oxygen_spec.rb
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- - spec/spec_helper.rb
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+ - !binary |-
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+ c3BlYy9hdG9tX3NwZWMucmI=
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+ c3BlYy9zcGVjX2hlbHBlci5yYg==
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+ ...