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.
- data/bin/stat.rb +0 -0
- data/{config.yml → config.yml.bak} +0 -0
- data/lib/mddb.rb +4 -3
- data/lib/mddb/cli.rb +3 -0
- data/lib/mddb/commands/load.rb +1 -0
- data/lib/mddb/commands/run.rb +34 -0
- data/lib/mddb/config.rb +1 -0
- data/lib/mddb/runner.rb +53 -0
- data/lib/mddb/version.rb +1 -1
- metadata +144 -88
data/bin/stat.rb
CHANGED
File without changes
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File without changes
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data/lib/mddb.rb
CHANGED
@@ -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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7
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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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10
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-
require "mddb/point"
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-
require "mddb/vector"
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12
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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
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data/lib/mddb/cli.rb
CHANGED
@@ -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'
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@@ -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
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data/lib/mddb/commands/load.rb
CHANGED
@@ -0,0 +1,34 @@
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1
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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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6
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+
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7
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def resque
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8
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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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def qsub
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puts "Submitting multiple QSUB jobs"
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end
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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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data/lib/mddb/config.rb
CHANGED
@@ -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
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data/lib/mddb/runner.rb
ADDED
@@ -0,0 +1,53 @@
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1
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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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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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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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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
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data/lib/mddb/version.rb
CHANGED
metadata
CHANGED
@@ -1,93 +1,100 @@
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1
1
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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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-
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-
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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-
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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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-
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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:
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-
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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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-
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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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-
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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:
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-
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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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-
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type: :runtime
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- !ruby/object:Gem::Dependency
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name: hirb
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-
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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:
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-
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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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-
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type: :runtime
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- !ruby/object:Gem::Dependency
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name: thor
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-
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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:
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-
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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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-
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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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-
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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:
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version: !binary |-
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none: false
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requirement: *2124
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prerelease: false
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-
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type: :runtime
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name: resque
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-
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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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version:
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-
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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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-
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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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-
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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:
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-
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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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-
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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
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extensions: []
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extra_rdoc_files: []
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files:
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|
+
bGliL21kZGIvdmVjdG9yLnJi
|
180
|
+
- !binary |-
|
181
|
+
bGliL21kZGIvdmVyc2lvbi5yYg==
|
182
|
+
- !binary |-
|
183
|
+
bWRkYi5nZW1zcGVj
|
184
|
+
- !binary |-
|
185
|
+
cXVpY2sueHl6
|
186
|
+
- !binary |-
|
187
|
+
c3BlYy9hdG9tX3NwZWMucmI=
|
188
|
+
- !binary |-
|
189
|
+
c3BlYy9veHlnZW5fc3BlYy5yYg==
|
190
|
+
- !binary |-
|
191
|
+
c3BlYy9zcGVjX2hlbHBlci5yYg==
|
142
192
|
homepage: ''
|
143
193
|
licenses: []
|
144
|
-
post_install_message:
|
194
|
+
post_install_message:
|
145
195
|
rdoc_options: []
|
146
196
|
require_paths:
|
147
197
|
- lib
|
148
198
|
required_ruby_version: !ruby/object:Gem::Requirement
|
149
|
-
none: false
|
150
199
|
requirements:
|
151
200
|
- - ! '>='
|
152
201
|
- !ruby/object:Gem::Version
|
153
|
-
version:
|
154
|
-
|
202
|
+
version: !binary |-
|
203
|
+
MA==
|
155
204
|
none: false
|
205
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
156
206
|
requirements:
|
157
207
|
- - ! '>='
|
158
208
|
- !ruby/object:Gem::Version
|
159
|
-
version:
|
209
|
+
version: !binary |-
|
210
|
+
MA==
|
211
|
+
none: false
|
160
212
|
requirements: []
|
161
213
|
rubyforge_project: mddb
|
162
|
-
rubygems_version: 1.8.
|
163
|
-
signing_key:
|
214
|
+
rubygems_version: 1.8.15
|
215
|
+
signing_key:
|
164
216
|
specification_version: 3
|
165
217
|
summary: MDDB molecular database and framework
|
166
218
|
test_files:
|
167
|
-
-
|
168
|
-
|
169
|
-
-
|
219
|
+
- !binary |-
|
220
|
+
c3BlYy9hdG9tX3NwZWMucmI=
|
221
|
+
- !binary |-
|
222
|
+
c3BlYy9veHlnZW5fc3BlYy5yYg==
|
223
|
+
- !binary |-
|
224
|
+
c3BlYy9zcGVjX2hlbHBlci5yYg==
|
225
|
+
...
|