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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
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