rubabel 0.1.0 → 0.1.1

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Files changed (28) hide show
  1. data/README.rdoc +13 -9
  2. data/Rakefile +10 -2
  3. data/VERSION +1 -1
  4. data/bin/rubabel +229 -0
  5. data/lib/rubabel.rb +46 -14
  6. data/lib/rubabel/atom.rb +78 -0
  7. data/lib/rubabel/bond.rb +18 -0
  8. data/lib/rubabel/molecule.rb +187 -59
  9. data/lib/rubabel/molecule/fragmentable.rb +209 -0
  10. data/lib/rubabel/molecule_data.rb +89 -0
  11. data/reference/arity_method_list.txt +1564 -1294
  12. data/rubabel.gemspec +100 -0
  13. data/spec/chemistry_toolkit_rosetta/README.txt +1 -0
  14. data/spec/chemistry_toolkit_rosetta/benzodiazepine.sdf.gz +0 -0
  15. data/spec/chemistry_toolkit_rosetta/benzodiazepine.smi.gz +0 -0
  16. data/spec/chemistry_toolkit_rosetta/chemistry_toolkit_rosetta_spec.rb +225 -0
  17. data/spec/chemistry_toolkit_rosetta/key/benzodiazepine_heavy_atom_counts.output.10.txt +10 -0
  18. data/spec/chemistry_toolkit_rosetta/key/benzodiazepine_ring_counts.output.10.txt +10 -0
  19. data/spec/chemistry_toolkit_rosetta/key/rule5.10.sdf +1924 -0
  20. data/spec/rubabel/atom_spec.rb +35 -0
  21. data/spec/rubabel/molecule/fragmentable_spec.rb +51 -0
  22. data/spec/rubabel/molecule_data_spec.rb +76 -0
  23. data/spec/rubabel/molecule_spec.rb +131 -1
  24. data/spec/rubabel_spec.rb +33 -3
  25. data/spec/spec_helper.rb +24 -0
  26. data/spec/testfiles/Samples.sdf.gz +0 -0
  27. metadata +65 -4
  28. data/lib/rubabel/fragmentation.rb +0 -23
data/spec/testfiles/Samples.sdf.gz ADDED
Binary file
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !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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+ version: 0.1.1
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  prerelease:
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  platform: ruby
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  authors:
@@ -9,8 +9,56 @@ authors:
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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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+ date: 2012-05-31 00:00:00.000000000 Z
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  dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: openbabel
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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: 2.3.1.2
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+ type: :runtime
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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: 2.3.1.2
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+ - !ruby/object:Gem::Dependency
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+ name: commander
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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: 4.1.2
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+ type: :runtime
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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: 4.1.2
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+ - !ruby/object:Gem::Dependency
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+ name: andand
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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: 1.3.3
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+ type: :runtime
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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: 1.3.3
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  - !ruby/object:Gem::Dependency
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  name: rspec
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  requirement: !ruby/object:Gem::Requirement
@@ -63,7 +111,8 @@ description: ! 'Ruby interface to the openbabel ruby bindings (or the openbabel
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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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+ executables:
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+ - rubabel
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  extensions: []
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  extra_rdoc_files:
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  - LICENSE
@@ -75,12 +124,13 @@ files:
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  - README.rdoc
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  - Rakefile
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  - VERSION
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+ - bin/rubabel
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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/fragmentable.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
@@ -91,14 +141,25 @@ files:
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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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+ - rubabel.gemspec
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+ - spec/chemistry_toolkit_rosetta/README.txt
146
+ - spec/chemistry_toolkit_rosetta/benzodiazepine.sdf.gz
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+ - spec/chemistry_toolkit_rosetta/benzodiazepine.smi.gz
148
+ - spec/chemistry_toolkit_rosetta/chemistry_toolkit_rosetta_spec.rb
149
+ - spec/chemistry_toolkit_rosetta/key/benzodiazepine_heavy_atom_counts.output.10.txt
150
+ - spec/chemistry_toolkit_rosetta/key/benzodiazepine_ring_counts.output.10.txt
151
+ - spec/chemistry_toolkit_rosetta/key/rule5.10.sdf
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  - spec/rubabel/atom_spec.rb
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153
  - spec/rubabel/bond_spec.rb
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+ - spec/rubabel/molecule/fragmentable_spec.rb
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+ - spec/rubabel/molecule_data_spec.rb
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  - spec/rubabel/molecule_spec.rb
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  - spec/rubabel_spec.rb
98
158
  - 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/Samples.sdf.gz
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  - spec/testfiles/cholesterol.mol
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164
  - spec/testfiles/cholesterol.sdf
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165
  - spec/testfiles/two.sdf
data/lib/rubabel/fragmentation.rb DELETED
@@ -1,23 +0,0 @@
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-
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- module Rubabel
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- class Fragmentation
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-
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- ADDUCTS = [:lioh, :nh4cl, :nh4oh]
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-
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- DEFAULTS = {
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- ph: 7.4,
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- adducts: [],
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- }
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-
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- def initialize(mol, options)
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- @mol = mol
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- @options = options
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- end
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-
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- def fragment(rules=[:co])
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- end
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-
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-
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-
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- end
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- end