mddb 0.0.24 → 0.0.25

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Files changed (6) hide show
  1. data/lib/mddb.rb +1 -1
  2. data/lib/mddb/parser.rb +1 -1
  3. data/lib/mddb/version.rb +1 -1
  4. data/mddb.gemspec +1 -0
  5. metadata +98 -142
  6. data/config.yml.bak +0 -23
data/lib/mddb.rb CHANGED
@@ -27,7 +27,7 @@ module Mddb
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  if opts[:all]
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  frames = Frame.all
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  else
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- frames = Frame.where(:fid.gte => opts[:from], :fid.lte => opts[:to]).all
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+ frames = Frame.where(:fid.gte => opts[:from], :fid.lte => opts[:to], :pid => opts[:pid]).all
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  end
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  if frames.empty?
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  puts "There were no frames in in this range"
data/lib/mddb/parser.rb CHANGED
@@ -3,7 +3,7 @@ module Mddb
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3
 
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  class Parser
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  def initialize(file)
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- @file = File.open(file).readlines
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+ @file = File.open(file)
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  @objects = Mddb::Config.simulation['count']
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  end
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9
 
data/lib/mddb/version.rb CHANGED
@@ -1,3 +1,3 @@
1
1
  module Mddb
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- VERSION = "0.0.24"
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+ VERSION = "0.0.25"
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  end
data/mddb.gemspec CHANGED
@@ -25,5 +25,6 @@ Gem::Specification.new do |s|
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  s.add_runtime_dependency "thor"
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  s.add_runtime_dependency "micro-optparse"
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  s.add_runtime_dependency "resque"
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+ s.add_runtime_dependency "bson_ext"
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  s.add_runtime_dependency "require_all"
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  end
metadata CHANGED
@@ -1,100 +1,104 @@
1
1
  --- !ruby/object:Gem::Specification
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  name: mddb
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  version: !ruby/object:Gem::Version
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- prerelease:
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- version: 0.0.24
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+ version: 0.0.25
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+ prerelease:
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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: 2012-03-13 00:00:00.000000000 Z
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+ date: 2012-03-22 00:00:00.000000000Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rspec
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- version_requirements: &2056 !ruby/object:Gem::Requirement
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+ requirement: &70265779694900 !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: !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: '0'
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  type: :development
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+ prerelease: false
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+ version_requirements: *70265779694900
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  - !ruby/object:Gem::Dependency
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  name: mongo_mapper
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- version_requirements: &2074 !ruby/object:Gem::Requirement
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+ requirement: &70265779694480 !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: !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: '0'
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  type: :runtime
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+ prerelease: false
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+ version_requirements: *70265779694480
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  - !ruby/object:Gem::Dependency
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  name: hirb
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- version_requirements: &2092 !ruby/object:Gem::Requirement
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+ requirement: &70265779694060 !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: !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: '0'
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  type: :runtime
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+ prerelease: false
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+ version_requirements: *70265779694060
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  - !ruby/object:Gem::Dependency
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  name: thor
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- version_requirements: &2108 !ruby/object:Gem::Requirement
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+ requirement: &70265779693640 !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: !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: '0'
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  type: :runtime
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+ prerelease: false
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+ version_requirements: *70265779693640
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  - !ruby/object:Gem::Dependency
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  name: micro-optparse
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- version_requirements: &2124 !ruby/object:Gem::Requirement
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+ requirement: &70265779724180 !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: !binary |-
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- MA==
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- none: false
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- requirement: *2124
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- prerelease: false
65
+ version: '0'
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  type: :runtime
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+ prerelease: false
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+ version_requirements: *70265779724180
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  - !ruby/object:Gem::Dependency
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  name: resque
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- version_requirements: &2140 !ruby/object:Gem::Requirement
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+ requirement: &70265779723760 !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: !binary |-
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- MA==
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- none: false
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- requirement: *2140
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+ version: '0'
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+ type: :runtime
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  prerelease: false
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+ version_requirements: *70265779723760
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+ - !ruby/object:Gem::Dependency
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+ name: bson_ext
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+ requirement: &70265779723340 !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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  type: :runtime
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+ prerelease: false
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+ version_requirements: *70265779723340
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  - !ruby/object:Gem::Dependency
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  name: require_all
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- version_requirements: &2156 !ruby/object:Gem::Requirement
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+ requirement: &70265779722920 !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: !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: '0'
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  type: :runtime
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+ prerelease: false
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+ version_requirements: *70265779722920
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  description: MDDB makes analysing molecular dynamics simulations easy
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  email:
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104
  - thom.mulvaney@gmail.com
@@ -107,119 +111,71 @@ executables:
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  extensions: []
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  extra_rdoc_files: []
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  files:
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- - !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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- UmFrZWZpbGU=
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- - !binary |-
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- YmluL2FnZ3JlZ2F0ZXI=
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- - !binary |-
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- YmluL2F2ZXJhZ2U=
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- - !binary |-
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- YmluL2Jpbm5lcg==
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- - !binary |-
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- YmluL21kZGI=
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- - !binary |-
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- YmluL3N0YXQucmI=
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- - !binary |-
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- Y29uZmlnLnltbC5iYWs=
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- - !binary |-
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- bGliL21kZGIucmI=
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- - !binary |-
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- bGliL21kZGIvYXRvbS5yYg==
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- - !binary |-
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- bGliL21kZGIvY2FsY3VsYXRpb25zLnJi
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- - !binary |-
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- bGliL21kZGIvY2xpLnJi
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- - !binary |-
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- bGliL21kZGIvY29tbWFuZHMvY29uc29sZS5yYg==
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- - !binary |-
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- bGliL21kZGIvY29tbWFuZHMvbG9hZC5yYg==
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- - !binary |-
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- bGliL21kZGIvY29tbWFuZHMvbmV3LnJi
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- - !binary |-
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- bGliL21kZGIvY29tbWFuZHMvcnVuLnJi
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- - !binary |-
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- bGliL21kZGIvY29uZmlnLnJi
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- - !binary |-
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- bGliL21kZGIvZnJhbWUucmI=
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- - !binary |-
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- bGliL21kZGIvZ2VuZXJhdG9ycy5yYg==
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- - !binary |-
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- bGliL21kZGIvZ2VuZXJhdG9ycy9hdG9tLnJi
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- - !binary |-
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- bGliL21kZGIvZ2VuZXJhdG9ycy9tb2xlY3VsZS5yYg==
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- - !binary |-
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- bGliL21kZGIvbW9sZWN1bGUucmI=
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- - !binary |-
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- bGliL21kZGIvcGFyc2VyLnJi
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- - !binary |-
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- bGliL21kZGIvcG9pbnQucmI=
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- - !binary |-
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- bGliL21kZGIvcnVubmVyLnJi
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- - !binary |-
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- bGliL21kZGIvc3BoZXJlLnJi
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- - !binary |-
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- bGliL21kZGIvdGVtcGxhdGVzL1JFQURNRS50dA==
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- - !binary |-
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- bGliL21kZGIvdGVtcGxhdGVzL2F0b20ucmIudHQ=
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- - !binary |-
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- bGliL21kZGIvdGVtcGxhdGVzL2NvbmZpZy55bWwudHQ=
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- - !binary |-
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- bGliL21kZGIvdGVtcGxhdGVzL2ZyYW1lLnJiLnR0
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- - !binary |-
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- bGliL21kZGIvdGVtcGxhdGVzL21vbGVjdWxlLnJiLnR0
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- - !binary |-
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- bGliL21kZGIvdGVtcGxhdGVzL3NwZWMvYXRvbV9zcGVjLnJiLnR0
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- - !binary |-
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- bGliL21kZGIvdGVtcGxhdGVzL3NwZWMvbW9sZWN1bGVfc3BlYy5yYi50dA==
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- - !binary |-
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- bGliL21kZGIvdmVjdG9yLnJi
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- - !binary |-
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- bGliL21kZGIvdmVyc2lvbi5yYg==
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- - !binary |-
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- bWRkYi5nZW1zcGVj
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- - !binary |-
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- cXVpY2sueHl6
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- - !binary |-
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- c3BlYy9hdG9tX3NwZWMucmI=
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- - !binary |-
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- c3BlYy9veHlnZW5fc3BlYy5yYg==
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- - !binary |-
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- c3BlYy9zcGVjX2hlbHBlci5yYg==
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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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+ - 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/commands/run.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/runner.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
192
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  homepage: ''
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  licenses: []
194
- post_install_message:
156
+ 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
161
+ none: false
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  requirements:
200
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  - - ! '>='
201
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  - !ruby/object:Gem::Version
202
- version: !binary |-
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- MA==
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- none: false
165
+ version: '0'
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  required_rubygems_version: !ruby/object:Gem::Requirement
167
+ none: false
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  requirements:
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  - - ! '>='
208
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  - !ruby/object:Gem::Version
209
- version: !binary |-
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- MA==
211
- none: false
171
+ version: '0'
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  requirements: []
213
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  rubyforge_project: mddb
214
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  rubygems_version: 1.8.15
215
- signing_key:
175
+ signing_key:
216
176
  specification_version: 3
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  summary: MDDB molecular database and framework
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  test_files:
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- - !binary |-
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- c3BlYy9hdG9tX3NwZWMucmI=
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- - !binary |-
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- c3BlYy9veHlnZW5fc3BlYy5yYg==
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- - !binary |-
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- c3BlYy9zcGVjX2hlbHBlci5yYg==
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- ...
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+ - spec/atom_spec.rb
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+ - spec/oxygen_spec.rb
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+ - spec/spec_helper.rb
data/config.yml.bak DELETED
@@ -1,23 +0,0 @@
1
- database:
2
- host:
3
- port:
4
- name: tom_test
5
-
6
- simulation:
7
- file: 'quick.xyz'
8
- dimensions: 24.669, 24.669, 24.669
9
- count: 1538
10
- objects:
11
- water:
12
- count: 512
13
- start: 1
14
- atom:
15
- - oxygen
16
- - hydrogen
17
- - hydrogen
18
- blob:
19
- count: 1
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- start: 1537
21
- atom:
22
- - phobe
23
- - phobe