glycobook 0.1.0.alpha.20-java → 0.1.0.alpha.22-java

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: f9e01c7b3d2c8af82fe1925a89a2494aa4e0b7098ebbef37be92b500da566db2
+  metadata.gz: c30b663e17567babecd2deaee54be71f43e7fc30452bff1dbbd751156a5e07fb
+  data.tar.gz: 9e1c862ce6ff0b91391338d4b42953ea2e53b05265550b4bccb4b1449d8bd3d0
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+  metadata.gz: e156bf8df3954c0f29a926fe00ee122ba4ef8e3eda04fe7d9d02f624abd6b6abefd2faef729de5ad8f037ba09356a9b84fcb63c358ed3637cfd0c488cb7bd18d
+  data.tar.gz: 9a873652978c7c9bca1dcd975ad7afb6fd4f87d913973f860e46eb4499bac1dd3756cca68ccd9205210359b60d72e34daac383c7fbaae5594ebdebef5553efa8

data/jar.yml

@@ -1,24 +1,79 @@
 ---
-list:
-  - url: "https://repo1.maven.org/maven2/org/apache/xmlgraphics/batik-all/1.16/batik-all-1.16.jar"
+libraries:
+  - name: batik-all
+    info: "https://xmlgraphics.apache.org/batik/download.html"
+    version: 1.16
+    url: "https://repo1.maven.org/maven2/org/apache/xmlgraphics/batik-all/1.16/batik-all-1.16.jar"
     file: "jar/batik-all.jar"
-  - url: "https://raw.githubusercontent.com/glycoinfo/MavenRepository/master/org/eurocarbdb/glycanbuilder/glycanbuilder2/1.23.1/glycanbuilder2-1.23.1.jar"
+
+  - name: glycanbuilder2
+    info: "https://gitlab.com/glycoinfo/glycanbuilder2"
+    version: 1.23.1
+    url: "https://raw.githubusercontent.com/glycoinfo/MavenRepository/master/org/eurocarbdb/glycanbuilder/glycanbuilder2/1.23.1/glycanbuilder2-1.23.1.jar"
     file: "jar/glycanbuilder2.jar"
-  - url: "https://gitlab.com/glycoinfo/wurcsframework/-/package_files/87428121/download"
+
+  - name: wurcsframework
+    info: "https://gitlab.com/glycoinfo/wurcsframework"
+    version: 1.2.14
+    url: "https://gitlab.com/glycoinfo/wurcsframework/-/package_files/87428121/download"
     file: "jar/wurcsframework.jar"
-  - url: "https://gitlab.com/glycoinfo/wurcsframework/-/package_files/87428121/download"
+
+  - name: wurcsframework-1.2.14
+    info: "https://gitlab.com/glycoinfo/wurcsframework"
+    version: 1.2.14
+    url: "https://gitlab.com/glycoinfo/wurcsframework/-/package_files/87428121/download"
     file: "jar/wurcsframework-1.2.14.jar"
-  - url: "https://gitlab.com/glycoinfo/wurcsframework/-/package_files/70458150/download"
+
+  - name: wurcsframework-1.0.1
+    info: "https://gitlab.com/glycoinfo/wurcsframework"
+    version: 1.0.1
+    url: "https://gitlab.com/glycoinfo/wurcsframework/-/package_files/70458150/download"
     file: "jar/wurcsframework-1.0.1.jar"
-  - url: "https://repo1.maven.org/maven2/org/slf4j/slf4j-api/2.0.9/slf4j-api-2.0.9.jar"
+
+  - name: slf4j-api
+    info: "https://www.slf4j.org/index.html"
+    version: 2.0.9
+    url: https://repo1.maven.org/maven2/org/slf4j/slf4j-api/2.0.9/slf4j-api-2.0.9.jar
     file: "jar/slf4j-api.jar"
-  - url: "https://repo1.maven.org/maven2/org/slf4j/slf4j-simple/2.0.9/slf4j-simple-2.0.9.jar"
+
+  - name: slf4j-simple
+    info: "https://www.slf4j.org/index.html"
+    version: 2.0.9
+    url: "https://repo1.maven.org/maven2/org/slf4j/slf4j-simple/2.0.9/slf4j-simple-2.0.9.jar"
     file: "jar/slf4j-simple.jar"
-  - url: "https://gitlab.glyco.info/glycosmos/subsumption/subsumption/-/package_files/590/download"
+
+  - 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"
     file: "jar/subsumption.jar"
-  - url: "https://gitlab.glyco.info/glycosmos/glytoucangroup/archetype/lib/-/package_files/489/download"
+
+  - name: archetype
+    info: "https://gitlab.glyco.info/glycosmos/glytoucangroup/archetype/lib"
+    version: 0.1.4
+    url: "https://gitlab.glyco.info/glycosmos/glytoucangroup/archetype/lib/-/package_files/489/download"
     file: "jar/archetype.jar"
-  - url: "https://gitlab.com/glycoinfo/glycanformatconverter/-/package_files/81149971/download"
+
+  - name: glycanformatconverter
+    info: "https://gitlab.com/glycoinfo/glycanformatconverter"
+    version: 2.10.0
+    url: "https://gitlab.com/glycoinfo/glycanformatconverter/-/package_files/81149971/download"
     file: "jar/glycanformatconverter.jar"
-  - url: "https://raw.githubusercontent.com/glycoinfo/MavenRepository/master/org/eurocarbdb/MolecularFramework/1.0.0/MolecularFramework-1.0.0.jar"
+
+  - name: MolecularFramework
+    info: "https://github.com/glycoinfo/MolecularFramework"
+    version: 1.0.0
+    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
+    info: https://github.com/cdk/cdk
+    version: 2.9
+    url: https://github.com/cdk/cdk/releases/download/cdk-2.9/cdk-2.9.jar
+    file: jar/cdk.jar
+
+  - name: MolWURCS
+    info: https://gitlab.com/glycoinfo/molwurcs
+    version: 0.10.2
+    url: https://gitlab.com/glycoinfo/molwurcs/-/package_files/89942780/download
+    file: jar/MolWURCS.jar

data/lib/bookinit.rb

@@ -36,35 +36,49 @@ Would you like to resolve Java dependencies?(No/yes)
   end
 
 
-    # YAMLファイルからdownloads情報をロード
-    downloads = load_settings(ENV['HOME'] + "/.glycobook/jar.yml")
-  
-    require 'open-uri'
+  # YAMLファイルからdownloads情報をロード
+  downloads = load_settings(ENV['HOME'] + "/.glycobook/jar.yml")
 
-    folder_path = File.dirname(__FILE__)+"/jar"
-    unless Dir.exist?(folder_path)
-      FileUtils.mkdir_p(folder_path)
-      puts "Folder created: #{folder_path}"
-    else
-      puts "Folder already exists: #{folder_path}"
-    end
-    # ダウンロードを実行する
-    downloads["list"].each do |download|
+  require 'open-uri'
 
-      uri = URI(download["url"])
-      response = Net::HTTP.get_response(uri)
-      if response.is_a?(Net::HTTPSuccess)
-        begin
-          File.open(File.dirname(__FILE__)+"/"+download["file"], 'wb') do |file|
-            file.write(response.body)
-            puts "Installed " + download["file"]
-          end
-          rescue StandardError => e
-          puts "Failed to save file: #{download["file"]}. Error: #{e.message}"
+  folder_path = File.dirname(__FILE__)+"/jar"
+  unless Dir.exist?(folder_path)
+    FileUtils.mkdir_p(folder_path)
+    puts "Folder created: #{folder_path}"
+  else
+    puts "Folder already exists: #{folder_path}"
+  end
+  # ダウンロードを実行する
+  downloads["libraries"].each do |download|
+
+    url = URI(download["url"])
+    http = Net::HTTP.new(url.host, url.port)
+    http.use_ssl = (url.scheme == 'https')
+  
+    request = Net::HTTP::Get.new(url.request_uri)
+    response = http.request(request)
+  
+    if response.code.to_i == 302
+      new_location = response['Location']
+      url = URI.parse(new_location)
+      http = Net::HTTP.new(url.host, url.port)
+      http.use_ssl = (url.scheme == 'https')
+      request = Net::HTTP::Get.new(url.request_uri)
+      response = http.request(request)
+    end
+  
+    if response.code.to_i == 200
+      begin
+        File.open(File.dirname(__FILE__)+"/"+download["file"], 'wb') do |file|
+          file.write(response.body)
+          puts "Installed " + download["file"]
         end
-      else
-        puts "Failed to download file: #{download["file"]}"
+        rescue StandardError => e
+        puts "Failed to save file: #{download["file"]}. Error: #{e.message}"
       end
+    else
+      puts "Failed to download file: #{download["file"]}"
+    end
 
     end
   end

data/lib/glycobook/mol_wurcs.rb

@@ -0,0 +1,81 @@
+require "java"
+
+require_relative '../jar/cdk.jar'
+require_relative '../jar/MolWURCS.jar'
+
+java_import 'org.glycoinfo.MolWURCS.io.formats.ChemFormatType'
+java_import 'org.openscience.cdk.exception.CDKException'
+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 wurcs2mol(w,format)
+
+  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
+
+  return if mols.nil?
+  if format == "sdf"
+    # 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
+
+    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

data/lib/glycobook.rb

@@ -7,6 +7,7 @@ require 'glycobook/glycan_format_converter'
 require 'glycobook/gly_tou_can'
 require 'glycobook/subsumption'
 require 'glycobook/wurcs_frame_work'
+require 'glycobook/mol_wurcs'
 require 'open-uri'
 require 'net/http'
 require 'fileutils'

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: glycobook
 version: !ruby/object:Gem::Version
-  version: 0.1.0.alpha.20
+  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
@@ -38,6 +38,7 @@ files:
 - lib/glycobook/gly_tou_can.rb
 - lib/glycobook/glycan_builder.rb
 - lib/glycobook/glycan_format_converter.rb
+- lib/glycobook/mol_wurcs.rb
 - lib/glycobook/subsumption.rb
 - lib/glycobook/wurcs_frame_work.rb
 - lib/wurcsverify.rb