glydevkit 0.2.0.pre.beta.5-java → 0.2.0.pre.beta.7-java

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/glydevkit/cdk.rb

@@ -0,0 +1,64 @@
+require "java"
+
+require_relative '../jar/cdk.jar'
+
+java_import 'org.openscience.cdk.similarity.Tanimoto'
+java_import 'org.openscience.cdk.DefaultChemObjectBuilder'
+java_import 'org.openscience.cdk.smiles.SmilesParser'
+java_import 'org.openscience.cdk.fingerprint.CircularFingerprinter'
+java_import 'org.openscience.cdk.layout.StructureDiagramGenerator'
+java_import 'org.openscience.cdk.depict.DepictionGenerator'
+
+module GlyDevKit
+  class CDK
+    
+    def sim(seq1,seq2,format)
+      if format == "wurcs"
+          Tanimoto.calculate(w2bit(seq1), w2bit(seq2))
+      elsif format == "smiles"
+          Tanimoto.calculate(smiles2bit(seq1), smiles2bit(seq2))
+      end
+    end 
+
+    def mol2svg(smiles)
+      
+      begin
+        sp = SmilesParser.new(DefaultChemObjectBuilder.getInstance)
+        molecule = sp.parseSmiles(smiles)
+
+        sdg = StructureDiagramGenerator.new(molecule)
+        sdg.generateCoordinates
+        molecule = sdg.molecule
+          
+        depiction_gen = DepictionGenerator.new
+        return depiction_gen.withSize(30, 30).depict(molecule).toSvgStr
+      
+      rescue => e
+        puts e.message
+      end
+    end
+
+    private
+    
+    def w2bit(w)
+      mw = GlyDevKit::MolWURCS.new
+      smiles =  mw.wurcs2mol(w,"smiles")[:smiles]
+    
+      sp = SmilesParser.new(DefaultChemObjectBuilder.getInstance())
+      molecule = sp.parseSmiles(smiles)
+      fingerprinter = CircularFingerprinter.new
+      fingerprinter.calculate(molecule)
+      return fingerprinter.getBitFingerprint(molecule).asBitSet()
+    end
+    
+    def smiles2bit(s)
+    
+      sp = SmilesParser.new(DefaultChemObjectBuilder.getInstance())
+      molecule = sp.parseSmiles(s)
+      fingerprinter = CircularFingerprinter.new
+      fingerprinter.calculate(molecule)
+      return fingerprinter.getBitFingerprint(molecule).asBitSet()
+    end
+
+  end
+end

data/lib/glydevkit/mol_wurcs.rb

@@ -21,6 +21,12 @@ java_import 'java.util.ArrayList'
 java_import 'java.io.StringWriter'
 java_import 'java.io.IOException'
 java_import 'java.io.StringReader'
+java_import "org.openscience.cdk.interfaces.IAtomContainer"
+java_import "org.openscience.cdk.smiles.SmilesParser"
+java_import "org.glycoinfo.MolWURCS.exchange.toWURCS.MoleculeToWURCSGraph"
+java_import "org.glycoinfo.WURCSFramework.util.WURCSFactory"
+java_import "org.glycoinfo.WURCSFramework.wurcs.graph.WURCSGraph"
+java_import "org.openscience.cdk.interfaces.IAtomContainer"
 
 module GlyDevKit
 class MolWURCS
@@ -41,6 +47,19 @@ class MolWURCS
       end
     end
 
+    def mol2wurcs(smiles)
+      parser = SmilesParser.new(DefaultChemObjectBuilder.getInstance)
+      molecule = parser.parseSmiles(smiles)
+      begin
+        graphs = MoleculeToWURCSGraph.new.start(molecule)
+      rescue StandardError => e
+        puts "An error occurred: #{e.message}"
+        puts "This method currently only supports up to WURCSFramework version 1.2.16. You need to downgrade the WURCSFramework using the command: `ruby -r init -e \'Init.switch_WFW_version(\"1.2.16\")\'`."
+        raise
+      end
+      factory = WURCSFactory.new(graphs[0])
+      return {"wurcs": factory.getWURCS(), "input": smiles} 
+    end
     private
 
     # Reads WURCS and returns a molecule set

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: glydevkit
 version: !ruby/object:Gem::Version
-  version: 0.2.0.pre.beta.5
+  version: 0.2.0.pre.beta.7
 platform: java
 authors:
 - Akihiro Fujita
@@ -62,6 +62,7 @@ files:
 - jar.yml
 - lib/glydevkit.rb
 - lib/glydevkit/Loggerinit.rb
+- lib/glydevkit/cdk.rb
 - lib/glydevkit/gly_tou_can.rb
 - lib/glydevkit/glycan_builder.rb
 - lib/glydevkit/glycan_format_converter.rb