From 596ef28dea32baa37b47fa5b82bdc4649ca69382 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Thu, 8 Oct 2015 14:10:00 +0200 Subject: new environment variable LAZAR_ENV for databases and log levels --- lib/feature.rb | 35 ----------------------------------- 1 file changed, 35 deletions(-) (limited to 'lib/feature.rb') 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" -- cgit v1.2.3