diff options
Diffstat (limited to 'lib/compound.rb')
| -rw-r--r-- | lib/compound.rb | 40 |
1 files changed, 5 insertions, 35 deletions
diff --git a/lib/compound.rb b/lib/compound.rb index 4e29938..3ba1670 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -11,32 +11,6 @@ module OpenTox class Compound include OpenTox - # OpenBabel FP4 fingerprints - # OpenBabel http://open-babel.readthedocs.org/en/latest/Fingerprints/intro.html - fp4 = FingerprintSmarts.all - unless fp4 - fp4 = [] - 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 = fp4 - - # 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 - field :inchi, type: String attr_readonly :inchi field :smiles, type: String @@ -48,21 +22,17 @@ module OpenTox field :sdf_id, type: BSON::ObjectId field :fp4, type: Array field :fp4_size, type: Integer - #belongs_to :dataset - #belongs_to :data_entry - - #def == compound - #self.inchi == compound.inchi - #end + # Overwrites standard Mongoid method to create fingerprints before database insertion def self.find_or_create_by params compound = self.find_or_initialize_by params - unless compound.fp4 + unless compound.fp4 and !compound.fp4.empty? compound.fp4_size = 0 compound.fp4 = [] - Algorithm::Descriptor.smarts_match(compound, FP4.collect{|f| f.smarts}).each_with_index do |m,i| + fingerprint = FingerprintSmarts.fingerprint + Algorithm::Descriptor.smarts_match(compound, fingerprint).each_with_index do |m,i| if m > 0 - compound.fp4 << FP4[i].id + compound.fp4 << fingerprint[i].id compound.fp4_size += 1 end end |