glycobook 0.1.0.alpha.21-java → 0.1.0.alpha.22-java

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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+  metadata.gz: c30b663e17567babecd2deaee54be71f43e7fc30452bff1dbbd751156a5e07fb
+  data.tar.gz: 9e1c862ce6ff0b91391338d4b42953ea2e53b05265550b4bccb4b1449d8bd3d0
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data/lib/glycobook/mol_wurcs.rb

@@ -9,17 +9,22 @@ 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.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)
+def wurcs2mol(w,format)
 
   begin
     reader = ChemFormatType::WURCS.createReader
@@ -33,24 +38,44 @@ def wurcs2mdlmol(w)
   end
 
   return if mols.nil?
+  if format == "sdf"
+    # write mol
+    string_writer = java.io.StringWriter.new
 
-  # write mol
-  string_writer = java.io.StringWriter.new
+    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))
+      end
+      writer.close
+    rescue Java::OrgOpenscienceCdkException::CDKException, Java::JavaIo::IOException => e
+      e.printStackTrace()
+    end
 
-  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))
+    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
-    writer.close
-  rescue Java::OrgOpenscienceCdkException::CDKException, Java::JavaIo::IOException => e
-    e.printStackTrace()
   end
-
-  return  string_writer.to_s
 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.22
 platform: java
 authors:
 - Akihiro Fujita
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-11-20 00:00:00.000000000 Z
+date: 2023-11-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
@@ -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: 3.2.33
 signing_key:
 specification_version: 4
 summary: Glycobook is a JRuby library for glycaninformatics