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author | Christoph Helma <helma@in-silico.ch> | 2015-08-10 13:26:06 +0200 |
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committer | Christoph Helma <helma@in-silico.ch> | 2015-08-10 13:26:06 +0200 |
commit | b7cd3ebbb858a8891c35c45896f1bdd525f3534e (patch) | |
tree | a9df6b1f4fc15f2f953e9a23c6dd00b74a967754 /lib/neighbor.rb | |
parent | 23ecfc6fa5ae4913e5cd17b7d58432d1f88d780c (diff) |
algorithm libraries added, fminer tests pass
Diffstat (limited to 'lib/neighbor.rb')
-rw-r--r-- | lib/neighbor.rb | 25 |
1 files changed, 25 insertions, 0 deletions
diff --git a/lib/neighbor.rb b/lib/neighbor.rb new file mode 100644 index 0000000..a2c28d4 --- /dev/null +++ b/lib/neighbor.rb @@ -0,0 +1,25 @@ +module OpenTox + module Algorithm + class Neighbor + + def self.fingerprint_similarity compound, params={} + compound.neighbors params[:min_sim] + end + + def self.fminer_similarity compound, params + feature_dataset = Dataset.find params[:feature_dataset_id] + query_fingerprint = Algorithm::Descriptor.smarts_match(compound, feature_dataset.features.collect{|f| f.smarts} ) + neighbors = [] + + # find neighbors + feature_dataset.data_entries.each_with_index do |fingerprint, i| + sim = Algorithm::Similarity.tanimoto fingerprint, query_fingerprint + if sim > params[:min_sim] + neighbors << [feature_dataset.compound_ids[i],sim] # use compound_ids, instantiation of Compounds is too time consuming + end + end + neighbors + end + end + end +end |