From 23ecfc6fa5ae4913e5cd17b7d58432d1f88d780c Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Mon, 10 Aug 2015 09:48:57 +0200
Subject: transfer to new git project started

---
 lib/feature.rb | 70 ++++++++++++++++++++++++++++++++++++++++------------------
 1 file changed, 48 insertions(+), 22 deletions(-)

(limited to 'lib/feature.rb')

diff --git a/lib/feature.rb b/lib/feature.rb
index 005d78f..9deb199 100644
--- a/lib/feature.rb
+++ b/lib/feature.rb
@@ -1,17 +1,16 @@
 module OpenTox
 
+  # Basic feature class
   class Feature
     field :name, as: :title, type: String
     field :nominal, type: Boolean
     field :numeric, type: Boolean
     field :measured, type: Boolean
-    field :calculated, type: Boolean
-    field :supervised, type: Boolean
-    field :source, as: :title, type: String
-    #belongs_to :dataset
   end
 
+  # Feature for categorical variables
   class NominalFeature < Feature
+    # TODO check if accept_values are still needed 
     field :accept_values, type: Array
     def initialize params
       super params
@@ -19,6 +18,7 @@ module OpenTox
     end
   end
 
+  # Feature for quantitative variables
   class NumericFeature < Feature
     def initialize params
       super params
@@ -26,43 +26,69 @@ module OpenTox
     end
   end
 
+  # Feature for SMARTS fragments
   class Smarts < NominalFeature
     field :smarts, type: String 
-    #field :name, as: :smarts, type: String # causes warnings
-    field :algorithm, type: String, default: "OpenTox::Algorithm::Descriptors.smarts_match"
-    field :parameters, type: Hash, default: {:count => false}
-    def initialize params
-      super params
-      nominal = true
-    end
   end
 
+  # Feature for supervised fragments from Fminer algorithm
   class FminerSmarts < Smarts
-    field :pValue, type: Float
+    field :p_value, type: Float
+    # TODO check if effect is used
     field :effect, type: String
     field :dataset_id 
-    def initialize params
-      super params
-      supervised = true
-    end
   end
 
+  # Feature for database fingerprints
+  # needs count for efficient retrieval (see compound.rb)
   class FingerprintSmarts < Smarts
     field :count, type: Integer
+    def self.fingerprint
+      @@fp4 ||= OpenTox::FingerprintSmarts.all
+      unless @@fp4.size == 306
+        @@fp4 = []
+        # OpenBabel FP4 fingerprints
+        # OpenBabel http://open-babel.readthedocs.org/en/latest/Fingerprints/intro.html
+        # TODO investigate other types of fingerprints (MACCS)
+        # OpenBabel http://open-babel.readthedocs.org/en/latest/Fingerprints/intro.html
+        # http://www.dalkescientific.com/writings/diary/archive/2008/06/26/fingerprint_background.html
+        # OpenBabel MNA http://openbabel.org/docs/dev/FileFormats/Multilevel_Neighborhoods_of_Atoms_(MNA).html#multilevel-neighborhoods-of-atoms-mna
+        # Morgan ECFP, FCFP
+        # http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/fingerprint/CircularFingerprinter.html
+        # http://www.rdkit.org/docs/GettingStartedInPython.html
+        # Chemfp
+        # https://chemfp.readthedocs.org/en/latest/using-tools.html
+        # CACTVS/PubChem
+
+        File.open(File.join(File.dirname(__FILE__),"SMARTS_InteLigand.txt")).each do |l| 
+          l.strip!
+          unless l.empty? or l.match /^#/
+            name,smarts = l.split(': ')
+            @@fp4 << OpenTox::FingerprintSmarts.find_or_create_by(:name => name, :smarts => smarts) unless smarts.nil?
+          end
+        end
+      end
+      @@fp4
+    end
   end
 
+  # Feature for physico-chemical descriptors
+  class PhysChemDescriptor < NumericFeature
+    field :algorithm, type: String, default: "OpenTox::Algorithm::Descriptor.physchem"
+    field :parameters, type: Hash
+    field :creator, type: String
+  end
+
+  # Feature for categorical bioassay results
   class NominalBioAssay < NominalFeature
+    # TODO: needed? move to dataset?
     field :description, type: String
   end
 
+  # Feature for quantitative bioassay results
   class NumericBioAssay < NumericFeature
+    # TODO: needed? move to dataset?
     field :description, type: String
   end
 
-  class PhysChemDescriptor < NumericFeature
-    field :algorithm, type: String, default: "OpenTox::Algorithm::Descriptor.physchem"
-    field :parameters, type: Hash
-    field :creator, type: String
-  end
-
 end
-- 
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