From 04af01b8135ea147e9ce253e5526e3ee3adcc675 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Fri, 7 Aug 2015 19:50:09 +0200
Subject: initial k-nn weighted average implementation

---
 lib/compound.rb | 71 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 70 insertions(+), 1 deletion(-)

(limited to 'lib/compound.rb')

diff --git a/lib/compound.rb b/lib/compound.rb
index 0c27553..4d292f1 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -1,7 +1,7 @@
 # TODO: check
 # *** Open Babel Error  in ParseFile
 #    Could not find contribution data file.
-# 3d creation??
+
 CACTUS_URI="http://cactus.nci.nih.gov/chemical/structure/"
 require 'openbabel'
 require "base64"
@@ -9,6 +9,34 @@ require "base64"
 module OpenTox
 
   class Compound
+    include OpenTox
+
+# OpenBabel FP4 fingerprints
+# OpenBabel http://open-babel.readthedocs.org/en/latest/Fingerprints/intro.html
+# TODO store in DB
+fp4 = FingerprintSmarts.find
+unless fp4
+  fp4 = []
+  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 = fp4
+
+# 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
 
     field :inchi, type: String
     attr_readonly :inchi
@@ -19,6 +47,8 @@ module OpenTox
     field :chemblid, type: String
     field :image_id, type: BSON::ObjectId
     field :sdf_id, type: BSON::ObjectId
+    field :fp4, type: Array
+    field :fp4_size, type: Integer
     #belongs_to :dataset
     #belongs_to :data_entry
 
@@ -26,6 +56,22 @@ module OpenTox
       #self.inchi == compound.inchi
     #end
 
+    def self.find_or_create_by params
+      compound = self.find_or_initialize_by params
+      unless compound.fp4
+        compound.fp4_size = 0
+        compound.fp4 = []
+        Algorithm::Descriptor.smarts_match(compound, FP4.collect{|f| f.smarts}).each_with_index do |m,i|
+          if m > 0
+            compound.fp4 << FP4[i].id
+            compound.fp4_size += 1
+          end
+        end
+      end
+      compound.save
+      compound
+    end
+
     # Create a compound from smiles string
     # @example
     #   compound = OpenTox::Compound.from_smiles("c1ccccc1")
@@ -124,6 +170,29 @@ module OpenTox
       self["chemblid"]
     end
 
+    def neighbors threshold=0.3
+      # from http://blog.matt-swain.com/post/87093745652/chemical-similarity-search-in-mongodb
+      qn = fp4.size
+      qmin = qn * threshold
+      qmax = qn / threshold
+      #not sure if it is worth the effort of keeping feature counts up to date (compound deletions, additions, ...)
+      #reqbits = [count['_id'] for count in db.mfp_counts.find({'_id': {'$in': qfp}}).sort('count', 1).limit(qn - qmin + 1)]
+      aggregate = [
+        #{'$match': {'mfp.count': {'$gte': qmin, '$lte': qmax}, 'mfp.bits': {'$in': reqbits}}},
+        {'$project': {
+          'tanimoto': {'$let': {
+            'vars': {'common': {'$size': {'$setIntersection': ['$fp4', fp4]}}},
+            'in': {'$divide': ['$$common', {'$subtract': [{'$add': [qn, '$fp4_size']}, '$$common']}]}
+          }},
+          '_id': 1
+        }},
+        {'$match':  {'tanimoto': {'$gte': threshold}}},
+        {'$sort': {'tanimoto': -1}}
+      ]
+      
+      $mongo["compounds"].aggregate(aggregate).collect { |r| [Compound.find(r["_id"]), r["tanimoto"]]}
+    end
+
     private
 
     def self.obconversion(identifier,input_format,output_format,option=nil)
-- 
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