glycobook 0.1.0.alpha.21-java → 0.1.0.alpha.23-java

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 3a227432de6774f55812c86238f8d902f4828eabb6b6b43492df5039e19f0817
-  data.tar.gz: 1b78af14d379b5761825836a9c3a55ef6e51e21261982226101aa16746b8da63
+  metadata.gz: 54291cdf1cc15d9494b5f931527624edea2b22e4406b86a5e2da164c34928d6d
+  data.tar.gz: ceabbea0e098bd5d424d9d2379f1014869242517179a26b04e4d12865bc4a63d
 SHA512:
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-  data.tar.gz: baed8895eda5734856a734bc84cbe53703c8639ddf25f985ee4b734b71f968eea4e9a1c01192ee33fe8b6f4d8083a746d405b7d35c954e9c6a794f3e28146e1f
+  metadata.gz: 711e5450c4a6db15dc122620ce179a995260a1203c36d929f922e592ff6b585716ae0513ebec06dc933d7ced9d34ed1450e9853afe0e28c6e8dd6614f1031ecd
+  data.tar.gz: ab7f7c353eb54c5047cbb64b4ff6e51fade4fed1bc7fa95afa7ac597ec9bced8c007cbd9dac8ae627d940367f9ecd17830d1d6bb98f8468761420927f7060293

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

@@ -9,48 +9,95 @@ java_import 'org.openscience.cdk.interfaces.IAtomContainerSet'
 java_import 'org.openscience.cdk.io.IChemObjectWriter'
 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'
 java_import 'java.nio.file.Files'
 java_import 'java.nio.file.Paths'
 java_import 'java.io.IOException'
 java_import 'java.lang.System'
 java_import 'java.util.ArrayList'
+java_import 'java.io.StringWriter'
 
 module GlycoBook
-class MolWURCS
-
-def wurcs2mdlmol(w)
-
-  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
+  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?
 
-  return if mols.nil?
+      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
 
-  # write mol
-  string_writer = java.io.StringWriter.new
+    private
 
-  begin
-    writer = org.openscience.cdk.io.SDFWriter.new(string_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))
+    # 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
-    writer.close
-  rescue Java::OrgOpenscienceCdkException::CDKException, Java::JavaIo::IOException => e
-    e.printStackTrace()
-  end
 
-  return  string_writer.to_s
-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
 
+    # 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
+
+    # 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
+    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.21
+  version: 0.1.0.alpha.23
 platform: java
 authors:
 - Akihiro Fujita
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-11-20 00:00:00.000000000 Z
+date: 2023-11-26 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: 3.3.26
+rubygems_version: 3.4.22
 signing_key:
 specification_version: 4
 summary: Glycobook is a JRuby library for glycaninformatics