diff options
Diffstat (limited to 'lib/compound.rb')
| -rw-r--r-- | lib/compound.rb | 71 |
1 files changed, 70 insertions, 1 deletions
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) |