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authorChristoph Helma <helma@in-silico.ch>2015-10-08 10:43:43 +0200
committerChristoph Helma <helma@in-silico.ch>2015-10-08 10:43:43 +0200
commit1a56148aadef031c4f487bc23fda43f4ac5b7369 (patch)
tree3555c5883ed0c292b105c40c185ebba3e5bd4e3e /lib/feature.rb
parent394d564699756288569169ff3e198d6d7702f092 (diff)
parente3217075b602a950a0ee995fcfa731d97b5ba3eb (diff)
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+module OpenTox
+
+ # Basic feature class
+ class Feature
+ field :nominal, type: Boolean
+ field :numeric, type: Boolean
+ field :measured, type: Boolean
+ 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
+ nominal = true
+ end
+ end
+
+ # Feature for quantitative variables
+ class NumericFeature < Feature
+ def initialize params
+ super params
+ numeric = true
+ end
+ end
+
+ # Feature for SMARTS fragments
+ class Smarts < NominalFeature
+ field :smarts, type: String
+ index "smarts" => 1
+ def self.from_smarts smarts
+ self.find_or_create_by :smarts => smarts
+ end
+ end
+
+ # Feature for supervised fragments from Fminer algorithm
+ class FminerSmarts < Smarts
+ field :p_value, type: Float
+ # TODO check if effect is used
+ field :effect, type: String
+ field :dataset_id
+ end
+
+ # Feature for database fingerprints
+ # needs count for efficient retrieval (see compound.rb)
+ class FingerprintSmarts < Smarts
+ field :count, type: Integer
+ def self.fingerprint
+=begin
+ @@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
+ 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
+ end
+
+ # Feature for quantitative bioassay results
+ class NumericBioAssay < NumericFeature
+ end
+
+end