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authorChristoph Helma <helma@in-silico.ch>2015-10-08 14:10:00 +0200
committerChristoph Helma <helma@in-silico.ch>2015-10-08 14:10:00 +0200
commit596ef28dea32baa37b47fa5b82bdc4649ca69382 (patch)
tree4a21f548adeab168276d237871cc19b4dede6836 /lib/feature.rb
parent1a56148aadef031c4f487bc23fda43f4ac5b7369 (diff)
new environment variable LAZAR_ENV for databases and log levels
Diffstat (limited to 'lib/feature.rb')
-rw-r--r--lib/feature.rb35
1 files changed, 0 insertions, 35 deletions
diff --git a/lib/feature.rb b/lib/feature.rb
index 13fa6d1..a308a55 100644
--- a/lib/feature.rb
+++ b/lib/feature.rb
@@ -42,41 +42,6 @@ module OpenTox
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"