glycobook 0.1.0.alpha.22-java → 0.1.0.alpha.24-java

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 9e1c862ce6ff0b91391338d4b42953ea2e53b05265550b4bccb4b1449d8bd3d0
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+  data.tar.gz: 43ed043caab23d4f79af74c595e4c7d86ea91c233c3b3ec5231ce40ae3810e3a
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+  data.tar.gz: 02be25d4e3a1f3d1535a5e2db614316cd2454a77ba51b800ad86b5ee6b1ca3609e18fba9e161d102bb1265bc1594ca296e550d7f226838f56e2e9b2562504389

data/jar.yml

@@ -44,8 +44,8 @@ libraries:
 
   - name: subsumption
     info: "https://gitlab.glyco.info/glycosmos/subsumption/subsumption"
-    version: 0.9.6
-    url: "https://gitlab.glyco.info/glycosmos/subsumption/subsumption/-/package_files/590/download"
+    version: 0.9.9
+    url: "https://gitlab.glyco.info/glycosmos/subsumption/subsumption/-/package_files/647/download"
     file: "jar/subsumption.jar"
 
   - name: archetype
@@ -66,7 +66,7 @@ libraries:
     url: "https://raw.githubusercontent.com/glycoinfo/MavenRepository/master/org/eurocarbdb/MolecularFramework/1.0.0/MolecularFramework-1.0.0.jar"
     file: "jar/MolecularFramework.jar"
   
-  - name: The Chemistry Development Kit
+  - name: TheChemistryDevelopmentKit
     info: https://github.com/cdk/cdk
     version: 2.9
     url: https://github.com/cdk/cdk/releases/download/cdk-2.9/cdk-2.9.jar
@@ -76,4 +76,4 @@ libraries:
     info: https://gitlab.com/glycoinfo/molwurcs
     version: 0.10.2
     url: https://gitlab.com/glycoinfo/molwurcs/-/package_files/89942780/download
-    file: jar/MolWURCS.jar
+    file: jar/MolWURCS.jar

data/lib/glycobook/Loggerinit.rb

@@ -10,18 +10,18 @@ class JRubySLF4JLogger < Logger
     super(STDOUT)  # STDOUT is dummy
     @java_logger = LoggerFactory.getLogger(name)
   end
-  def add(severity, progname ,  message, &block)
+  def add(severity, message, progname, &block)
 
   message = block.call if block
   message = message.to_s
 
   case severity
     when 0  # Logger::DEBUG
-      @java_logger.debug(message)
+      @java_logger.info(message)
     when 1  # Logger::INFO
       @java_logger.info(message)
     when 2  # Logger::WARN
-      @java_logger.warn(message)
+      @java_logger.info(message)
     when 3, 4# Logger::ERROR, Logger::FATAL
       @java_logger.error(message)
     else

data/lib/glycobook/mol_wurcs.rb

@@ -11,6 +11,7 @@ java_import 'org.openscience.cdk.io.ISimpleChemObjectReader'
 java_import 'org.openscience.cdk.silent.AtomContainerSet'
 java_import 'org.openscience.cdk.DefaultChemObjectBuilder'
 java_import 'org.openscience.cdk.io.SDFWriter'
+java_import 'org.openscience.cdk.smiles.SmiFlavor'
 java_import 'org.openscience.cdk.smiles.SmilesGenerator'
 java_import 'org.openscience.cdk.silent.SilentChemObjectBuilder'
 java_import 'java.io.StringReader'
@@ -22,60 +23,81 @@ java_import 'java.util.ArrayList'
 java_import 'java.io.StringWriter'
 
 module GlycoBook
-class MolWURCS
+  class MolWURCS
+    def wurcs2mol(w, format)
+      mols = read_wurcs(w)
+      return {"flag": false,"wurcs": w, "message": "WURCS strings that could not be parsed to the atomic level"} if mols.nil?
 
-def wurcs2mol(w,format)
+      case format
+      when "sdf"
+        {"wurcs": w}.merge(export_to_sdf(mols))
+      when "smiles"
+        {"wurcs": w}.merge(export_to_smiles(mols))
+      else
+        {"flag": false,"wurcs": w, "#{format}": "", "message": "Undefined format"}
+      end
+    end
 
-  begin
-    reader = ChemFormatType::WURCS.createReader
-    reader.setReader(StringReader.new(w))
-    return unless reader.accepts(AtomContainerSet.java_class)
-    mols = AtomContainerSet.new
-    mols = reader.read(mols)
-    reader.close
-  rescue CDKException, IOException => e
-    e.printStackTrace()
-  end
+    private
+
+    # Reads WURCS and returns a molecule set
+    def read_wurcs(w)
+      begin
+        reader = ChemFormatType::WURCS.createReader
+        reader.setReader(StringReader.new(w))
+        return nil unless reader.accepts(AtomContainerSet.java_class)
+        mols = reader.read(AtomContainerSet.new)
+        reader.close
+        mols
+      rescue CDKException, IOException => e
+        e.printStackTrace
+        nil
+      end
+    end
+
+    # Exports molecule set to SDF format
+    def export_to_sdf(mols)
+      string_writer = StringWriter.new
+      begin
+        writer = SDFWriter.new(string_writer)
+        write_molecule_set(mols, writer)
+        {"sdf": string_writer.to_s}
+      rescue CDKException, IOException => e
+        e.printStackTrace
+        {"flag": false,"sdf": "", "message": e.message}
+      end
+    end
 
-  return if mols.nil?
-  if format == "sdf"
-    # write mol
-    string_writer = java.io.StringWriter.new
+    # Exports molecule set to SMILES format
+    def export_to_smiles(mols)
+      smiles_gen = SmilesGenerator.new(SmiFlavor::Isomeric)
+      string_writer = StringWriter.new
+      begin
+        mols.atomContainers.each do |mol|
+          smiles = smiles_gen.create(mol)
+          string_writer.write(smiles)
+        end
+        smiles = string_writer.toString
+        if (smiles == "")
+          {"flag": false,"smiles": smiles, "message": "the case of successfully converted to empty characters in the library"} 
+        else
+          {"flag": true,"smiles": smiles} 
+        end
+      rescue CDKException, IOException => e
+        e.printStackTrace
+        {"flag": false,"smiles": "", "message": e.message}
+      end
+    end
 
-    begin
-      writer = org.openscience.cdk.io.SDFWriter.new(string_writer)
+    # Writes molecule set using provided writer
+    def write_molecule_set(mols, writer)
       if writer.accepts(mols.java_class)
         writer.write(mols)
       elsif writer.accepts(mols.get_atom_container(0).java_class)
         writer.write(mols.get_atom_container(0))
       end
       writer.close
-    rescue Java::OrgOpenscienceCdkException::CDKException, Java::JavaIo::IOException => e
-      e.printStackTrace()
     end
 
-    return  string_writer.to_s
-
-  elsif format == "smiles"
-    # SMILESジェネレータの生成
-    smiles_gen = SmilesGenerator.absolute()
-
-    string_writer = java.io.StringWriter.new
-
-    begin
-      mols.atomContainers.each do |mol|
-        # 各分子に対してSMILES表現の生成
-        smiles = smiles_gen.createSMILES(mol)
-        string_writer.write(smiles + "\n")
-      end
-
-      # 生成したSMILESの出力
-      return string_writer.toString
-    rescue Java::OrgOpenscienceCdkException::CDKException, Java::JavaIo::IOException => e
-      e.printStackTrace()
-      return ""
-    end
   end
 end
-end
-end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: glycobook
 version: !ruby/object:Gem::Version
-  version: 0.1.0.alpha.22
+  version: 0.1.0.alpha.24
 platform: java
 authors:
 - Akihiro Fujita
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-11-21 00:00:00.000000000 Z
+date: 2023-12-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
@@ -17,8 +17,8 @@ dependencies:
       - !ruby/object:Gem::Version
         version: 0.0.2
   name: java
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
@@ -64,7 +64,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: 1.3.1
 requirements: []
-rubygems_version: 3.2.33
+rubygems_version: 3.4.22
 signing_key:
 specification_version: 4
 summary: Glycobook is a JRuby library for glycaninformatics