diff options
Diffstat (limited to 'lib/compound.rb')
| -rw-r--r-- | lib/compound.rb | 59 |
1 files changed, 30 insertions, 29 deletions
diff --git a/lib/compound.rb b/lib/compound.rb index 4d292f1..4e29938 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -11,32 +11,31 @@ module OpenTox class Compound include OpenTox -# OpenBabel FP4 fingerprints -# OpenBabel http://open-babel.readthedocs.org/en/latest/Fingerprints/intro.html -# TODO store in DB -fp4 = FingerprintSmarts.find -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? + # 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 - 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 + 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 @@ -170,15 +169,16 @@ FP4 = fp4 self["chemblid"] end - def neighbors threshold=0.3 + def neighbors threshold=0.7 # from http://blog.matt-swain.com/post/87093745652/chemical-similarity-search-in-mongodb qn = fp4.size - qmin = qn * threshold - qmax = qn / threshold + #qmin = qn * threshold + #qmax = qn / threshold #not sure if it is worth the effort of keeping feature counts up to date (compound deletions, additions, ...) #reqbits = [count['_id'] for count in db.mfp_counts.find({'_id': {'$in': qfp}}).sort('count', 1).limit(qn - qmin + 1)] aggregate = [ #{'$match': {'mfp.count': {'$gte': qmin, '$lte': qmax}, 'mfp.bits': {'$in': reqbits}}}, + {'$match': {'_id': {'$ne': self.id}}}, # remove self {'$project': { 'tanimoto': {'$let': { 'vars': {'common': {'$size': {'$setIntersection': ['$fp4', fp4]}}}, @@ -190,7 +190,8 @@ FP4 = fp4 {'$sort': {'tanimoto': -1}} ] - $mongo["compounds"].aggregate(aggregate).collect { |r| [Compound.find(r["_id"]), r["tanimoto"]]} + $mongo["compounds"].aggregate(aggregate).collect{ |r| [r["_id"], r["tanimoto"]] } + end private |