rubabel 0.1.0

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Files changed (34) hide show
  1. data/.document +5 -0
  2. data/.rspec +1 -0
  3. data/LICENSE +21 -0
  4. data/README.rdoc +52 -0
  5. data/Rakefile +43 -0
  6. data/VERSION +1 -0
  7. data/lib/rubabel.rb +116 -0
  8. data/lib/rubabel/atom.rb +143 -0
  9. data/lib/rubabel/bond.rb +47 -0
  10. data/lib/rubabel/fingerprint.rb +0 -0
  11. data/lib/rubabel/fragmentation.rb +23 -0
  12. data/lib/rubabel/molecule.rb +305 -0
  13. data/lib/rubabel/molecule_data.rb +0 -0
  14. data/lib/rubabel/pm.rb +38 -0
  15. data/lib/rubabel/smarts.rb +27 -0
  16. data/reference/OBConversion_methods.txt +47 -0
  17. data/reference/arity_method_list.txt +3553 -0
  18. data/reference/arity_method_list_CLASS.txt +337 -0
  19. data/reference/atom_methods.txt +145 -0
  20. data/reference/bond_methods.txt +79 -0
  21. data/reference/get_methods.rb +52 -0
  22. data/reference/mol_methods.txt +183 -0
  23. data/spec/rubabel/atom_spec.rb +49 -0
  24. data/spec/rubabel/bond_spec.rb +19 -0
  25. data/spec/rubabel/molecule_spec.rb +91 -0
  26. data/spec/rubabel_spec.rb +67 -0
  27. data/spec/spec_helper.rb +12 -0
  28. data/spec/testfiles/7-oxocholesterol-d7.mol +97 -0
  29. data/spec/testfiles/7-oxocholesterol-d7.sdf +155 -0
  30. data/spec/testfiles/Samples.sdf +2441 -0
  31. data/spec/testfiles/cholesterol.mol +74 -0
  32. data/spec/testfiles/cholesterol.sdf +132 -0
  33. data/spec/testfiles/two.sdf +287 -0
  34. metadata +130 -0
metadata ADDED
@@ -0,0 +1,130 @@
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+ --- !ruby/object:Gem::Specification
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+ name: rubabel
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+ version: !ruby/object:Gem::Version
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+ version: 0.1.0
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+ prerelease:
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+ platform: ruby
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+ authors:
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+ - John T. Prince
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+ autorequire:
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+ bindir: bin
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+ cert_chain: []
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+ date: 2012-05-10 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: !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: 2.8.0
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+ type: :development
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+ prerelease: false
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+ version_requirements: !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: 2.8.0
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+ - !ruby/object:Gem::Dependency
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+ name: rdoc
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+ requirement: !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: '3.12'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !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: '3.12'
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+ - !ruby/object:Gem::Dependency
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+ name: jeweler
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+ requirement: !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: 1.8.3
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+ type: :development
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+ prerelease: false
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+ version_requirements: !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: 1.8.3
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+ description: ! 'Ruby interface to the openbabel ruby bindings (or the openbabel gem). The
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+
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+ interface attempts to be a ruby-ish analogue of pybel.'
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+ email: jtprince@gmail.com
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+ executables: []
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+ extensions: []
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+ extra_rdoc_files:
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+ - LICENSE
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+ - README.rdoc
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+ files:
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+ - .document
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+ - .rspec
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+ - LICENSE
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+ - README.rdoc
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+ - Rakefile
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+ - VERSION
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+ - lib/rubabel.rb
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+ - lib/rubabel/atom.rb
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+ - lib/rubabel/bond.rb
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+ - lib/rubabel/fingerprint.rb
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+ - lib/rubabel/fragmentation.rb
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+ - lib/rubabel/molecule.rb
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+ - lib/rubabel/molecule_data.rb
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+ - lib/rubabel/pm.rb
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+ - lib/rubabel/smarts.rb
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+ - reference/OBConversion_methods.txt
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+ - reference/arity_method_list.txt
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+ - reference/arity_method_list_CLASS.txt
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+ - reference/atom_methods.txt
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+ - reference/bond_methods.txt
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+ - reference/get_methods.rb
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+ - reference/mol_methods.txt
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+ - spec/rubabel/atom_spec.rb
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+ - spec/rubabel/bond_spec.rb
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+ - spec/rubabel/molecule_spec.rb
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+ - spec/rubabel_spec.rb
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+ - spec/spec_helper.rb
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+ - spec/testfiles/7-oxocholesterol-d7.mol
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+ - spec/testfiles/7-oxocholesterol-d7.sdf
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+ - spec/testfiles/Samples.sdf
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+ - spec/testfiles/cholesterol.mol
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+ - spec/testfiles/cholesterol.sdf
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+ - spec/testfiles/two.sdf
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+ homepage: http://github.com/princelab/rubabel
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+ licenses:
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+ - MIT
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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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+ 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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+ requirements: []
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+ rubyforge_project:
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+ rubygems_version: 1.8.18
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+ signing_key:
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+ specification_version: 3
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+ summary: Ruby interface to the OpenBabel ruby bindings similar to pybel
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+ test_files: []