glycobook 0.1.0.alpha.24-java → 0.1.0.alpha.26-java

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: c57696fa2ad8b032a46281386ea028f2640043f9ee43fe1b4c6f08e225382ecf
-  data.tar.gz: 43ed043caab23d4f79af74c595e4c7d86ea91c233c3b3ec5231ce40ae3810e3a
+  metadata.gz: 85778515c6bb06cddc7c8a4585ba7b8221e5f0c128b52182c8da8892979ccd09
+  data.tar.gz: fb5da58cc677ab39d7c2fec3f0951513a07e2482862c502dcd9245deae87383e
 SHA512:
-  metadata.gz: 01a1b387ace6b56ef15b38c2d2ae87bf8dcfa32a1cfc20793a9108dd0f64cc055113a73c73af3fb23533614cf5a94bbcf4af91db76e11f8be9e37b48498a26df
-  data.tar.gz: 02be25d4e3a1f3d1535a5e2db614316cd2454a77ba51b800ad86b5ee6b1ca3609e18fba9e161d102bb1265bc1594ca296e550d7f226838f56e2e9b2562504389
+  metadata.gz: 522239fa63aa56f53ad882acc1936c4ac4ac17731a043e95ae8a6e9bdd36c41c4bd3a3b4a8fd6855311ef3853af34370320c509a4c4f1f6c9bca351e6485bac8
+  data.tar.gz: 913af58afa9769074e7a2478c03a9317edbaa4712a136bf300d5a4e17bea3d8c9574c38266f169753eab2def76e72b39a04369dbdc0d3e81cfff940439772549

data/jar.yml

@@ -24,11 +24,11 @@ libraries:
     url: "https://gitlab.com/glycoinfo/wurcsframework/-/package_files/87428121/download"
     file: "jar/wurcsframework-1.2.14.jar"
 
-  - name: wurcsframework-1.0.1
+  - name: wurcsframework-1.3.1
     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"
+    version: 1.3.1
+    url: "https://gitlab.com/glycoinfo/wurcsframework/-/package_files/127116856/download"
+    file: "jar/wurcsframework-1.3.1.jar"
 
   - name: slf4j-api
     info: "https://www.slf4j.org/index.html"
@@ -44,8 +44,8 @@ libraries:
 
   - name: subsumption
     info: "https://gitlab.glyco.info/glycosmos/subsumption/subsumption"
-    version: 0.9.9
-    url: "https://gitlab.glyco.info/glycosmos/subsumption/subsumption/-/package_files/647/download"
+    version: 0.10.0
+    url: "https://gitlab.glyco.info/glycosmos/subsumption/subsumption/-/package_files/758/download"
     file: "jar/subsumption.jar"
 
   - name: archetype

data/lib/bookinit.rb

@@ -4,18 +4,27 @@ require 'fileutils'
 require 'yaml'
 
 module BookInit
+  def self.load_settings(file_path, flag)
+    downloads = []
 
-  def self.load_settings(file_path)
+    unless Dir.exist?(ENV['HOME'] + "/.glycobook")
+      Dir.mkdir(ENV['HOME'] + "/.glycobook")
+    end
 
-    downloads = []
+    folder_path = File.dirname(__FILE__) + "/jar"
+    unless Dir.exist?(folder_path)
+      FileUtils.mkdir_p(folder_path)
+    end
 
     if File.exist?(file_path)
       downloads = YAML.load_file(file_path)
     else
-      unless Dir.exist?(ENV['HOME'] + "/.glycobook")
-        Dir.mkdir(ENV['HOME'] + "/.glycobook")
-      end
-      FileUtils.mv(File.dirname(File.expand_path(__FILE__)) + "/../jar.yml", file_path)
+      FileUtils.cp(File.dirname(File.expand_path(__FILE__)) + "/../jar.yml", file_path)
+    end
+
+    if flag
+      FileUtils.cp(File.dirname(File.expand_path(__FILE__)) + "/../jar.yml", file_path)
+      downloads = YAML.load_file(file_path)
     end
 
     downloads
@@ -23,63 +32,60 @@ module BookInit
 
   def self.run
     puts <<-EOT
-
-Would you like to resolve Java dependencies?(No/yes)
+Would you like to resolve Java dependencies? (No/yes)
     EOT
 
-  case gets.chomp
-    when "yes", "YES", "y"
-    when "no", "NO", "n"
+    case gets.chomp.downcase
+    when "yes", "y"
+      flag = true
+    when "no", "n"
       exit 1
     else
+      puts "Invalid input. Exiting..."
       exit 1
-  end
+    end
 
+    puts <<-EOT
+Set recommended Java library version? (No/yes)
+    EOT
 
-  # YAMLファイルからdownloads情報をロード
-  downloads = load_settings(ENV['HOME'] + "/.glycobook/jar.yml")
+    case gets.chomp.downcase
+    when "yes", "y"
+      flag = true
+    end
 
-  require 'open-uri'
+    downloads = load_settings(ENV['HOME'] + "/.glycobook/jar.yml", flag)
 
-  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)
+    # 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)
-    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
-        rescue StandardError => e
-        puts "Failed to save file: #{download["file"]}. Error: #{e.message}"
+
+      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
-    else
-      puts "Failed to download file: #{download["file"]}"
-    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
+        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
 end

data/lib/glycobook/mol_wurcs.rb

@@ -14,17 +14,20 @@ 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'
+java_import 'java.io.IOException'
+java_import 'java.io.StringReader'
 
 module GlycoBook
-  class MolWURCS
-    def wurcs2mol(w, format)
+class MolWURCS
+# @param [String] w String of WURCS
+# @param [String] format: smiles or sdf
+# @return [String] string with specified molecular descriptor
+    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?
 

data/lib/glycobook/wurcs_frame_work.rb

@@ -3,6 +3,7 @@ require 'java'
 module GlycoBook
 
   class WurcsFrameWork
+
     require_relative  '../jar/wurcsframework.jar'
     java_import 'org.glycoinfo.WURCSFramework.util.validation.WURCSValidator'
     
@@ -18,5 +19,58 @@ module GlycoBook
             "StandardWURCS" => validator.getReport().standard_string(),
             "RESULTS" => validator.getReport().getResults() }
     end
+
+    def to_graph(w)
+      g = nil
+      wgn = WURCSGraphNormalizer.new
+      begin
+        factory = WURCSFactory.new(w)
+        g = factory.getGraph
+        wgn.start(g)
+      rescue WURCSException => e
+        e.printStackTrace
+      end
+      return g
+    end
+    
+    def get_anomeric_status(a_o_backbone)
+      a_o_backbone.get_backbone_carbons.each do |t_o_bc|
+        return "archetype_anomer" if t_o_bc.get_descriptor.get_char.chr == 'u'
+        return "archetype_anomer" if t_o_bc.get_descriptor.get_char.chr == 'U'
+      end
+      return "anomer_unknown" if a_o_backbone.get_anomeric_symbol.chr == 'x'
+      return "anomer_alpha" if a_o_backbone.get_anomeric_symbol.chr == 'a'
+      return "anomer_beta" if a_o_backbone.get_anomeric_symbol.chr == 'b'
+      return "openchain" if a_o_backbone.get_anomeric_position != 0
+      return nil
+    end
+
+    def get_ring_type(a_o_backbone)
+      a_o_backbone.get_backbone_carbons.each do |t_o_bc|
+        return "archetype_ringtype" if t_o_bc.get_descriptor.get_char.chr == 'u'
+        return "archetype_ringtype" if t_o_bc.get_descriptor.get_char.chr == 'U'
+      end
+      for edge in a_o_backbone.get_edges 
+        if edge.is_anomeric && edge.get_modification.is_ring
+          ring_start = edge.get_linkages[0].get_backbone_position
+          ring_end = edge.get_modification.get_edges[1].get_linkages[0].get_backbone_position
+          if (ring_end - ring_start) == 6
+            return "octanose"
+          elsif (ring_end - ring_start) == 5
+            return "septanose"
+          elsif (ring_end - ring_start) == 4
+            return "pyranose"
+          elsif (ring_end - ring_start) == 3
+            return "furanose"
+          elsif (ring_end - ring_start) == 2
+            return "oxetose"
+          elsif (ring_end - ring_start) == 1
+            return "oxirose"
+          end
+        end
+      end
+      return nil
+    end
+
   end
 end

data/lib/wurcsverify.rb

@@ -12,7 +12,7 @@ java_import 'org.slf4j.Logger'
 class WurcsVerify
   def initialize
       @wfw_latest_loader = self.create_custom_classloader("jar/wurcsframework-1.2.14.jar")
-      @wfw_101_loader = self.create_custom_classloader("jar/wurcsframework-1.0.1.jar")
+      @wfw_101_loader = self.create_custom_classloader("jar/wurcsframework-1.3.1.jar")
       @validator_latest = java.lang.Class.forName("org.glycoinfo.WURCSFramework.util.validation.WURCSValidator",true,@wfw_latest_loader)
       @validator_101 = java.lang.Class.forName("org.glycoinfo.WURCSFramework.util.validation.WURCSValidator", true, @wfw_101_loader)
   end
@@ -31,7 +31,7 @@ class WurcsVerify
     v_101.start(w)
 
     ret = {"1.2.14" => self.dovalidator(v_latest),
-            "1.0.1" => self.dovalidator101(v_101) }
+            "1.3.1" => self.dovalidator131(v_131) }
     return ret
   end
 
@@ -44,8 +44,8 @@ class WurcsVerify
             "StandardWURCS" => validator.getReport().standard_string(),
             "RESULTS" => validator.getReport().getResults() }
   end
-  def dovalidator101(validator)
-    reports = { "VALIDATOR" => ["WURCSFramework-1.0.1"],
+  def dovalidator131(validator)
+    reports = { "VALIDATOR" => ["WURCSFramework-1.3.1"],
                 "WARNING" => validator.getReport().hasWarning(),
                 "ERROR" => validator.getReport().hasError(),
                 "UNVERIFIABLE" => false }

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: glycobook
 version: !ruby/object:Gem::Version
-  version: 0.1.0.alpha.24
+  version: 0.1.0.alpha.26
 platform: java
 authors:
 - Akihiro Fujita
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-12-04 00:00:00.000000000 Z
+date: 2024-05-13 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
-  type: :runtime
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
@@ -44,7 +44,7 @@ files:
 - lib/wurcsverify.rb
 homepage: https://github.com/akihirof0005/glycobook/blob/main/README.md
 licenses:
-- LGPL-3.0
+- LGPL-3.0-only
 metadata:
   source_code_uri: https://github.com/akihirof0005/glycobook
   homepage_uri: https://github.com/akihirof0005/glycobook/blob/main/README.md
@@ -64,7 +64,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: 1.3.1
 requirements: []
-rubygems_version: 3.4.22
+rubygems_version: 3.3.26
 signing_key:
 specification_version: 4
 summary: Glycobook is a JRuby library for glycaninformatics