add ketcher api for convert to inchi

ComPlat · Dec 2, 2021 · 287c848 · 287c848
1 parent 9c20d43
commit 287c848
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Showing 5 changed files with 31 additions and 12 deletions.
diff --git a/Gemfile b/Gemfile
@@ -10,8 +10,9 @@ gemspec
 # Git. Remember to move these dependencies to your gemspec before releasing
 # your gem to rubygems.org.
 
-gem 'mimemagic', github: 'mimemagicrb/mimemagic', ref: '01f92d86d15d85cfd0f20dabd025dcbd36a8a60f'
+gem 'openbabel', '2.4.90.3', git: 'https://github.com/ComPlat/openbabel-gem.git', branch: 'hot-fix-svg'
+gem 'inchi-gem', '1.06.1', git: 'https://github.com/ComPlat/inchi-gem.git', branch: 'main'
 
 # To use a debugger
 # gem 'byebug', group: [:development, :test]
-gem 'openbabel', '2.4.90.3', git: 'https://github.com/ComPlat/openbabel-gem.git', branch: 'hot-fix-svg'
+
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,17 +1,17 @@
+GIT
+  remote: https://github.com/ComPlat/inchi-gem.git
+  revision: 9a95669b42e18a20d2a0c2d5440670ff94e46c37
+  branch: main
+  specs:
+    inchi-gem (1.06.1)
+
 GIT
   remote: https://github.com/ComPlat/openbabel-gem.git
   revision: 3e25548fd95c2ac83c7fb5d9544ed2cf6ae1344b
   branch: hot-fix-svg
   specs:
     openbabel (2.4.90.3)
 
-GIT
-  remote: https://github.com/mimemagicrb/mimemagic.git
-  revision: 01f92d86d15d85cfd0f20dabd025dcbd36a8a60f
-  ref: 01f92d86d15d85cfd0f20dabd025dcbd36a8a60f
-  specs:
-    mimemagic (0.3.5)
-
 PATH
   remote: .
   specs:
@@ -25,9 +25,11 @@ PATH
       grape-active_model_serializers (~> 1.3.2)
       haml-rails
       httparty
+      inchi-gem
       jquery-rails
       jquery-ui-rails (~> 5.0.5)
       kaminari
+      mimemagic (>= 0.3.10)
       nokogiri (>= 1.10, < 1.13)
       openbabel
       paperclip (~> 5.2.0)
@@ -193,6 +195,9 @@ GEM
     mime-types (3.4.1)
       mime-types-data (~> 3.2015)
     mime-types-data (3.2021.1115)
+    mimemagic (0.3.10)
+      nokogiri (~> 1)
+      rake
     mini_mime (1.1.2)
     mini_portile2 (2.6.1)
     minitest (5.14.4)
@@ -290,8 +295,8 @@ DEPENDENCIES
   byebug
   grape
   grape-swagger
+  inchi-gem (= 1.06.1)!
   ketcherails!
-  mimemagic!
   openbabel (= 2.4.90.3)!
   pg
   rspec

diff --git a/app/api/ketcherails/ketcher_api.rb b/app/api/ketcherails/ketcher_api.rb
@@ -99,6 +99,18 @@ class KetcherAPI < Grape::API
           name: mol_info[:names]
         }
       end
+
+      desc 'Return Inchi from mol data'
+      params do
+        requires :moldata, type: String, desc: 'Mol data'
+      end
+      post :getinchi do
+        return_values = Inchi::ExtraInchiReturnValues.new
+        inchikey = Inchi.molfileToInchi(params[:moldata], return_values, '-Polymers -FoldCRU -NPZz -SAtZZ -LargeMolecules')
+
+        env['api.format'] = :binary
+        "Ok.\n" + inchikey
+      end
     end
   end
 end
diff --git a/app/assets/javascripts/ketcherails/ui/ui.js.erb b/app/assets/javascripts/ketcherails/ui/ui.js.erb
@@ -1711,7 +1711,7 @@ ui.buildAminoAcidsSequence = function(sequence_name, reversed = false) {
             var tool = new rnd.Editor.TemplateTool(ui.editor, data);
             ui.render.current_tool = tool;
           } else if(res.status == 404) {
-            alert("Error: can not find one of items in sequnce. Some items are not known.");
+            alert("Error: block unknown: cannot find one of the block from the sequence.");
           }
           else if (res.responseText.startsWith('Error.')) {
             alert(res.responseText.split('\n')[1]);

diff --git a/ketcherails.gemspec b/ketcherails.gemspec
@@ -34,7 +34,8 @@ Gem::Specification.new do |s|
   s.add_dependency 'grape-active_model_serializers', '~> 1.3.2'
   s.add_dependency 'active_model_serializers', '< 0.10.0'
   s.add_dependency 'openbabel'
-
+  s.add_dependency 'mimemagic', '>= 0.3.10'
+  s.add_dependency 'inchi-gem'
 
 
   # s.add_dependency 'openbabel', '~> 2.4.90.1'#, git: 'https://github.com/ComPlat/openbabel-gem'