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.
Files changed (10) hide show
  1. data/bin/stat.rb +0 -0
  2. data/{config.yml → config.yml.bak} +0 -0
  3. data/lib/mddb.rb +4 -3
  4. data/lib/mddb/cli.rb +3 -0
  5. data/lib/mddb/commands/load.rb +1 -0
  6. data/lib/mddb/commands/run.rb +34 -0
  7. data/lib/mddb/config.rb +1 -0
  8. data/lib/mddb/runner.rb +53 -0
  9. data/lib/mddb/version.rb +1 -1
  10. metadata +144 -88
data/bin/stat.rb CHANGED
File without changes
data/{config.yml → config.yml.bak} RENAMED
File without changes
data/lib/mddb.rb CHANGED
@@ -4,14 +4,15 @@ require "mddb/cli"
4
4
  require "mongo_mapper"
5
5
  require "mddb/config"
6
6
  require "mddb/parser"
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+ require "mddb/runner"
7
8
 
8
9
  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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17
  require_all 'models' unless Dir.glob('models/**/*.rb').size == 0
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  end
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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12
  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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24
  require 'mddb/commands/load'
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  elsif %w{g generate}.include? ARGV.first
data/lib/mddb/commands/load.rb CHANGED
@@ -32,6 +32,7 @@ def start_console
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  end
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  end
34
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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|
data/lib/mddb/commands/run.rb ADDED
@@ -0,0 +1,34 @@
1
+ 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
21
+ 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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+
34
+
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
data/lib/mddb/runner.rb ADDED
@@ -0,0 +1,53 @@
1
+ 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
26
+ end
27
+ end
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+
29
+ def calculations(frame)
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+ @klasses.each_with_index do |k,i|
31
+ objects = Object.const_get(k).where(:fid => frame).all
32
+ object_count = objects.count
33
+ complete = 0
34
+ failed = 0
35
+ objects.each do |o|
36
+ begin
37
+ o.run
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+ complete += 1
39
+ rescue
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+ failed += 1
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+ puts " Models (#{i}/#{model_count}) => #{k} #{complete}/#{object_count} Failed: #{failed}"
42
+ end
43
+ end
44
+ end
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+ begin
46
+ puts " Running Frame Calculations"
47
+ frame.run
48
+ rescue
49
+ " Failed"
50
+ end
51
+ end
52
+ end
53
+ end
data/lib/mddb/version.rb CHANGED
@@ -1,3 +1,3 @@
1
1
  module Mddb
2
- VERSION = "0.0.12"
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+ VERSION = "0.0.14"
3
3
  end
metadata CHANGED
@@ -1,93 +1,100 @@
1
1
  --- !ruby/object:Gem::Specification
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2
  name: mddb
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3
  version: !ruby/object:Gem::Version
4
- version: 0.0.12
5
- prerelease:
4
+ prerelease:
5
+ version: 0.0.14
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  platform: ruby
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7
  authors:
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8
  - Thomas Mulvaney
9
- autorequire:
9
+ autorequire:
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10
  bindir: bin
11
11
  cert_chain: []
12
- date: 2012-03-09 00:00:00.000000000Z
12
+ date: 2012-03-13 00:00:00.000000000 Z
13
13
  dependencies:
14
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  - !ruby/object:Gem::Dependency
15
15
  name: rspec
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- requirement: &70251383669620 !ruby/object:Gem::Requirement
17
- 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
20
+ 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
27
- 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
38
- 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
46
- version_requirements: *70251383668360
49
+ type: :runtime
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  - !ruby/object:Gem::Dependency
48
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  name: thor
49
- 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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  - - ! '>='
53
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  - !ruby/object:Gem::Version
54
- version: '0'
55
- type: :runtime
56
+ version: !binary |-
57
+ MA==
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+ none: false
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+ requirement: *2108
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60
  prerelease: false
57
- version_requirements: *70251383667680
61
+ type: :runtime
58
62
  - !ruby/object:Gem::Dependency
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63
  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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  - - ! '>='
64
67
  - !ruby/object:Gem::Version
65
- version: '0'
66
- type: :runtime
68
+ version: !binary |-
69
+ MA==
70
+ none: false
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+ requirement: *2124
67
72
  prerelease: false
68
- version_requirements: *70251383666960
73
+ type: :runtime
69
74
  - !ruby/object:Gem::Dependency
70
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  name: resque
71
- requirement: &70251383666240 !ruby/object:Gem::Requirement
72
- none: false
76
+ version_requirements: &2140 !ruby/object:Gem::Requirement
73
77
  requirements:
74
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  - - ! '>='
75
79
  - !ruby/object:Gem::Version
76
- version: '0'
77
- type: :runtime
80
+ version: !binary |-
81
+ MA==
82
+ none: false
83
+ requirement: *2140
78
84
  prerelease: false
79
- version_requirements: *70251383666240
85
+ type: :runtime
80
86
  - !ruby/object:Gem::Dependency
81
87
  name: require_all
82
- requirement: &70251383665540 !ruby/object:Gem::Requirement
83
- none: false
88
+ version_requirements: &2156 !ruby/object:Gem::Requirement
84
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  requirements:
85
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  - - ! '>='
86
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  - !ruby/object:Gem::Version
87
- version: '0'
88
- type: :runtime
92
+ version: !binary |-
93
+ MA==
94
+ none: false
95
+ requirement: *2156
89
96
  prerelease: false
90
- version_requirements: *70251383665540
97
+ type: :runtime
91
98
  description: MDDB makes analysing molecular dynamics simulations easy
92
99
  email:
93
100
  - thom.mulvaney@gmail.com
@@ -100,70 +107,119 @@ executables:
100
107
  extensions: []
101
108
  extra_rdoc_files: []
102
109
  files:
103
- - .gitignore
104
- - Gemfile
105
- - Rakefile
106
- - bin/aggregater
107
- - bin/average
108
- - bin/binner
109
- - bin/mddb
110
- - bin/stat.rb
111
- - config.yml
112
- - lib/mddb.rb
113
- - lib/mddb/atom.rb
114
- - lib/mddb/calculations.rb
115
- - lib/mddb/cli.rb
116
- - lib/mddb/commands/console.rb
117
- - lib/mddb/commands/load.rb
118
- - lib/mddb/commands/new.rb
119
- - lib/mddb/config.rb
120
- - lib/mddb/frame.rb
121
- - lib/mddb/generators.rb
122
- - lib/mddb/generators/atom.rb
123
- - lib/mddb/generators/molecule.rb
124
- - lib/mddb/molecule.rb
125
- - lib/mddb/parser.rb
126
- - lib/mddb/point.rb
127
- - lib/mddb/sphere.rb
128
- - lib/mddb/templates/README.tt
129
- - lib/mddb/templates/atom.rb.tt
130
- - lib/mddb/templates/config.yml.tt
131
- - lib/mddb/templates/frame.rb.tt
132
- - lib/mddb/templates/molecule.rb.tt
133
- - lib/mddb/templates/spec/atom_spec.rb.tt
134
- - lib/mddb/templates/spec/molecule_spec.rb.tt
135
- - lib/mddb/vector.rb
136
- - lib/mddb/version.rb
137
- - mddb.gemspec
138
- - quick.xyz
139
- - spec/atom_spec.rb
140
- - spec/oxygen_spec.rb
141
- - spec/spec_helper.rb
110
+ - !binary |-
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+ LmdpdGlnbm9yZQ==
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+ - !binary |-
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+ R2VtZmlsZQ==
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+ - !binary |-
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+ 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: '0'
154
- required_rubygems_version: !ruby/object:Gem::Requirement
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: '0'
209
+ version: !binary |-
210
+ MA==
211
+ none: false
160
212
  requirements: []
161
213
  rubyforge_project: mddb
162
- rubygems_version: 1.8.10
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
- - spec/atom_spec.rb
168
- - spec/oxygen_spec.rb
169
- - spec/spec_helper.rb
219
+ - !binary |-
220
+ c3BlYy9hdG9tX3NwZWMucmI=
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+ ...