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-rw-r--r--lib/feature.rb70
1 files changed, 48 insertions, 22 deletions
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