rubabel 0.4.1 → 0.4.2

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -4,6 +4,8 @@ Ruby interface to the OpenBabel ruby bindings (or the openbabel gem).  The
 interface attempts to be a ruby-ish analogue of
 [pybel](http://openbabel.org/docs/current/UseTheLibrary/Python_PybelAPI.html).  Works with ruby 1.9 and 2.0.
 
+**NOTE: Lipid fragmentation code has been moved to the [msplinter](https://github.com/princelab/msplinter).**
+
 ## Examples
 
 The [Chemistry Toolkit Rosetta Wiki](http://ctr.wikia.com/wiki/Chemistry_Toolkit_Rosetta_Wiki) has a lot of examples you can check out.
@@ -23,13 +25,14 @@ serine = Rubabel::Molecule.from_string("C(C(C(=O)O)N)O")
 # also any other format openbabel supports, for example inchi
 serine = Rubabel["InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)", :inchi]
 
-# from the internet:
-mol = Rubabel[some_molecule, Rubabel.format_from_mime(some_mime_type)]
+# from an InChI Key or other id (such as LipidMaps ID) [requires internet]
+serine = Rubabel["MTCFGRXMJLQNBG-REOHCLBHSA-N", :inchikey]
 
 Find out all the formats Rubabel supports (hash is format key pointing to the description):
 
 hash = Rubabel.in_formats
 hash = Rubabel.out_formats
+hash = Rubabel.id_formats # molecule retrieved by web-lookup
 ```
 
 #### From a file

data/lib/rubabel.rb

@@ -25,8 +25,16 @@ module Rubabel
 
   class << self
 
+    # accepts a string specifying the molecule (calling Rubabel::Molecule.from_string) 
+    # or an id (calls Rubabel::Molecule.from_id)
     def [](string, type=Rubabel::Molecule::DEFAULT_IN_TYPE)
-      Rubabel::Molecule.from_string(string, type)
+      methd = 
+        if type && Rubabel::Molecule::ID_TYPE_KEYS.include?(type)
+          :from_id
+        else
+          :from_string
+        end
+      Rubabel::Molecule.send(methd, string, type)
     end
 
     def force_field(type=DEFAULT_FORCEFIELD)
@@ -45,6 +53,11 @@ module Rubabel
       @out_formats ||= formats_to_hash(OpenBabel::OBConversion.new.get_supported_output_format)
     end
 
+    # returns the formats retrievable by url lookup of the id or key
+    def id_formats
+      Rubabel::Molecule::ID_TYPES
+    end
+
     # returns the format Symbol that can be used for conversion, or nil if
     # the extension is not recognized.
     def format_from_ext(filename)

data/lib/rubabel/molecule.rb

@@ -1,3 +1,5 @@
+require 'open-uri'
+require 'rexml/document'
 require 'openbabel'
 require 'rubabel'
 require 'rubabel/atom'
@@ -76,6 +78,12 @@ module Rubabel
     DEFAULT_FINGERPRINT = "FP2"
     DEFAULT_OUT_TYPE = :can
     DEFAULT_IN_TYPE = :smi
+    DEFAULT_ID_TYPE = :pubchem
+    ID_TYPES = {
+      inchikey: "InChI key",
+      lmid: "LipidMaps ID"
+    }
+    ID_TYPE_KEYS = ID_TYPES.keys
 
     # the OpenBabel::OBmol object
     attr_accessor :ob
@@ -92,6 +100,9 @@ module Rubabel
       end
 
       def from_string(string, type=DEFAULT_IN_TYPE)
+        if type == :inchi
+          string.prepend("InChI=") unless string[/^InChI=/]
+        end
         obmol = OpenBabel::OBMol.new
         obconv = OpenBabel::OBConversion.new
         obconv.set_in_format(type.to_s) || raise(ArgumentError, "invalid format #{type}")
@@ -99,6 +110,34 @@ module Rubabel
         self.new(obmol)
       end
 
+      def retrieve_info_from_url(url)
+        begin
+          info = open(url) {|io| io.read }
+        rescue => e
+          puts "Some kind of internet connectivity error. Check your connection!"
+          raise e
+        end
+        info
+      end
+
+      # requires an internet connection
+      def from_id(id, type=DEFAULT_ID_TYPE)
+          case type
+          when :inchikey
+            url = "http://www.chemspider.com/InChI.asmx/InChIKeyToInChI?inchi_key=" + URI::encode(id)
+            doc_string = retrieve_info_from_url(url)
+            doc = REXML::Document.new( doc_string )
+            inchi_string = doc.root.children.first.to_s
+            raise(ArgumentError, "did not retrieve a valid inchi string") unless inchi_string[/^InChI=/]
+            from_string(inchi_string, :inchi)
+          when :lmid # lipidmaps id
+            url = "http://www.lipidmaps.org/data/LMSDRecord.php?OutputType=SDF&Mode=File&LMID=" + id
+            doc_string = retrieve_info_from_url(url)
+            from_string(doc_string, :sdf)
+          end
+      end
+      alias_method :from_key, :from_id
+
       def from_atoms_and_bonds(atoms=[], bonds=[])
         obj = self.new( OpenBabel::OBMol.new )
         atoms.each {|atom| obj.add_atom(atom) }

data/lib/rubabel/version.rb

@@ -1,3 +1,3 @@
 module Rubabel
-  VERSION = "0.4.1"
+  VERSION = "0.4.2"
 end

data/rubabel.gemspec

@@ -30,7 +30,6 @@ interface attempts to be a ruby-ish analogue of pybel.}
     ["bundler", "~> 1.3"],
     ["rspec", "~> 2.13.0"], 
     ["rdoc", "~> 3.12"], 
-    ["jeweler", "~> 1.8.3"],
     ["simplecov"],
     ["rake"]
   ].each do |args|

data/spec/rubabel/molecule_spec.rb

@@ -4,6 +4,12 @@ require 'rubabel/molecule'
 
 describe Rubabel::Molecule do
   describe 'creation' do
+    it 'can be made from scratch' do
+      mol = Rubabel::Molecule.new
+      mol.atoms.size == 0
+      mol.title.should == ''
+    end
+
     it 'can be made with Rubabel[]' do
       mol = Rubabel["CC(O)O"]
       mol.csmiles.should == "CC(O)O"
@@ -14,11 +20,45 @@ describe Rubabel::Molecule do
       mol_dup = Rubabel::Molecule.new(mol.ob)
     end
 
-    it 'can be made fresh' do
-      mol = Rubabel::Molecule.new
-      mol.atoms.size == 0
-      mol.title.should == ''
+    describe 'creation from different input strings' do
+      before(:all) do
+        @exp = Rubabel["CC(=O)O"]
+      end
+
+      # same as Rubabel::Molecule.from_string *args
+      specify 'smiles' do
+        Rubabel["CC(=O)O"].should == @exp
+      end
+
+      specify 'inchi' do
+        Rubabel["InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)", :inchi].should == @exp
+      end
+
+      specify 'inchi with no InChI= leader okay!' do
+        Rubabel["1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)", :inchi].should == @exp
+      end
+
+      describe 'creation with web lookup of ID or keys' do
+        before(:all) do
+          @exp = Rubabel["CC(=O)O"]
+        end
+
+        specify 'inchi key' do
+          Rubabel::Molecule.from_id( 'QTBSBXVTEAMEQO-UHFFFAOYSA-N', :inchikey ).should == @exp
+          Rubabel['QTBSBXVTEAMEQO-UHFFFAOYSA-N', :inchikey].should == @exp
+        end
+
+        specify 'lipidmaps id' do
+          Rubabel::Molecule.from_id( 'LMFA01010002', :lmid ).should == @exp
+          Rubabel['LMFA01010002', :lmid].should == @exp
+        end
+
+        specify 'pubchem id'
+
+      end
+
     end
+
   end
 
   #xit 'can add a hydrogen to the formula' do

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rubabel
 version: !ruby/object:Gem::Version
-  version: 0.4.1
+  version: 0.4.2
 platform: ruby
 authors:
 - John T. Prince
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-06-18 00:00:00.000000000 Z
+date: 2013-07-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: openbabel
@@ -94,20 +94,6 @@ dependencies:
     - - ~>
       - !ruby/object:Gem::Version
         version: '3.12'
-- !ruby/object:Gem::Dependency
-  name: jeweler
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: 1.8.3
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: 1.8.3
 - !ruby/object:Gem::Dependency
   name: simplecov
   requirement: !ruby/object:Gem::Requirement
@@ -150,7 +136,6 @@ files:
 - LICENSE
 - README.md
 - Rakefile
-- VERSION
 - lib/rubabel.rb
 - lib/rubabel/atom.rb
 - lib/rubabel/bond.rb
@@ -214,7 +199,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.2
+rubygems_version: 2.0.3
 signing_key: 
 specification_version: 4
 summary: Ruby interface to the openbabel ruby bindings (or the openbabel gem).  The
@@ -243,4 +228,3 @@ test_files:
 - spec/testfiles/cholesterol.mol
 - spec/testfiles/cholesterol.sdf
 - spec/testfiles/two.sdf
-has_rdoc: 

data/VERSION

@@ -1 +0,0 @@
-0.3.1