glydevkit 0.2.0.pre.beta.4-java → 0.2.0.pre.beta.6-java

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: a639692f34e5d2c99fc18967dc3f1f3d02790584b272e737df1cbe69d6dbfad1
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+  data.tar.gz: 52316bec1211005dd3f8809d2e393fe8de9ac3c1daf2c72c16e60fbeffeb579f
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+  data.tar.gz: 38e76b7317d36f85bac5e144ce0ebfa4c4d7aa6412df2d03e5b884e2f73d745c02b25be194b0606acbbff58e32afddcc78c88699681c659b8f51717ee553b53d

data/jar.yml

@@ -92,6 +92,6 @@ libraries:
 
   - name: MolWURCS
     info: https://gitlab.com/glycoinfo/molwurcs
-    version: 0.10.2
-    url: https://gitlab.com/glycoinfo/molwurcs/-/package_files/89942780/download
+    version: 0.11.0
+    url: https://gitlab.com/glycoinfo/molwurcs/-/package_files/106726568/download
     file: jar/MolWURCS.jar

data/lib/glydevkit/cdk.rb

@@ -0,0 +1,64 @@
+require "java"
+
+require_relative '../jar/cdk.jar'
+
+java_import 'org.openscience.cdk.similarity.Tanimoto'
+java_import 'org.openscience.cdk.DefaultChemObjectBuilder'
+java_import 'org.openscience.cdk.smiles.SmilesParser'
+java_import 'org.openscience.cdk.fingerprint.CircularFingerprinter'
+java_import 'org.openscience.cdk.layout.StructureDiagramGenerator'
+java_import 'org.openscience.cdk.depict.DepictionGenerator'
+
+module GlyDevKit
+  class CDK
+    
+    def sim(seq1,seq2,format)
+      if format == "wurcs"
+          Tanimoto.calculate(w2bit(seq1), w2bit(seq2))
+      elsif format == "smiles"
+          Tanimoto.calculate(smiles2bit(seq1), smiles2bit(seq2))
+      end
+    end 
+
+    def mol2svg(smiles)
+      
+      begin
+        sp = SmilesParser.new(DefaultChemObjectBuilder.getInstance)
+        molecule = sp.parseSmiles(smiles)
+
+        sdg = StructureDiagramGenerator.new(molecule)
+        sdg.generateCoordinates
+        molecule = sdg.molecule
+          
+        depiction_gen = DepictionGenerator.new
+        return depiction_gen.withSize(30, 30).depict(molecule).toSvgStr
+      
+      rescue => e
+        puts e.message
+      end
+    end
+
+    private
+    
+    def w2bit(w)
+      mw = GlyDevKit::MolWURCS.new
+      smiles =  mw.wurcs2mol(w,"smiles")[:smiles]
+    
+      sp = SmilesParser.new(DefaultChemObjectBuilder.getInstance())
+      molecule = sp.parseSmiles(smiles)
+      fingerprinter = CircularFingerprinter.new
+      fingerprinter.calculate(molecule)
+      return fingerprinter.getBitFingerprint(molecule).asBitSet()
+    end
+    
+    def smiles2bit(s)
+    
+      sp = SmilesParser.new(DefaultChemObjectBuilder.getInstance())
+      molecule = sp.parseSmiles(s)
+      fingerprinter = CircularFingerprinter.new
+      fingerprinter.calculate(molecule)
+      return fingerprinter.getBitFingerprint(molecule).asBitSet()
+    end
+
+  end
+end

data/lib/glydevkit.rb

@@ -5,6 +5,7 @@ require 'glydevkit/Loggerinit'
 require 'glydevkit/glycan_builder'
 require 'glydevkit/glycan_format_converter'
 require 'glydevkit/gly_tou_can'
+require 'glydevkit/cdk'
 require 'glydevkit/glytoucan_data_handler'
 require 'glydevkit/subsumption'
 require 'glydevkit/wurcs_frame_work'

data/lib/init.rb

@@ -4,6 +4,7 @@ require 'fileutils'
 require 'yaml'
 require 'digest'
 require 'fileutils'
+require 'terminal-table'
 
 
 module Init
@@ -89,7 +90,7 @@ Set recommended Java library version? (No/yes)
     end
   end
 
-  def self.check_WFW_version()
+  def self.show_WFW_version()
     target_file_path = File.dirname(__FILE__) + '/jar/wurcsframework.jar'  
     folder_path = File.dirname(__FILE__) + '/jar' 
   
@@ -107,6 +108,17 @@ Set recommended Java library version? (No/yes)
     end
   end
 
+  def self.show_dependencies
+    yaml_data = File.read(Dir.home+'/.glycobook/jar.yml')
+    parsed_data = YAML.load(yaml_data)
+    rows = []
+    rows.push(["name","version","Link"])
+    parsed_data["libraries"].each{|item|
+      rows.push([item["name"].to_s , item["version"].to_s , item["info"].to_s ])
+    }
+    puts Terminal::Table.new rows: rows
+end
+
   private
   # Loads the settings from a YAML file and prepares the environment.
   #

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: glydevkit
 version: !ruby/object:Gem::Version
-  version: 0.2.0.pre.beta.4
+  version: 0.2.0.pre.beta.6
 platform: java
 authors:
 - Akihiro Fujita
@@ -11,19 +11,47 @@ cert_chain: []
 date: 2024-10-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: java
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 0.0.2
-  type: :runtime
+  name: java
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 0.0.2
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  name: yaml
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  name: terminal-table
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 description: The Glycoscience Development Kit (GlyDevKit) is a JRuby library for glyco-informatics
 email:
 - akihirof0005@gmail.com
@@ -34,6 +62,7 @@ files:
 - jar.yml
 - lib/glydevkit.rb
 - lib/glydevkit/Loggerinit.rb
+- lib/glydevkit/cdk.rb
 - lib/glydevkit/gly_tou_can.rb
 - lib/glydevkit/glycan_builder.rb
 - lib/glydevkit/glycan_format_converter.rb
@@ -62,11 +91,11 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - ">"
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.3.1
 requirements: []
-rubygems_version: 3.5.22
+rubygems_version: 3.3.26
 signing_key:
 specification_version: 4
 summary: The Glycoscience Development Kit (GlyDevKit) is a JRuby library for glyco-informatics