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| author | gebele <gebele@in-silico.ch> | 2015-09-18 13:31:13 +0200 |
|---|---|---|
| committer | gebele <gebele@in-silico.ch> | 2015-09-18 13:31:13 +0200 |
| commit | 1255775bca9bcb9ca9100c38504e42541249865d (patch) | |
| tree | 0f332a14a915ac2f8d63bad4d2c6b6c8d8fcb1e8 /lib/neighbor.rb | |
| parent | 9bf81bcafaf958c02a448d3ff3410220dd791d40 (diff) | |
| parent | 33989261450bba279b4e002e5e4ea0475d742abb (diff) | |
Merge branch 'development' of github.com:opentox/lazar into development
Diffstat (limited to 'lib/neighbor.rb')
| -rw-r--r-- | lib/neighbor.rb | 25 |
1 files changed, 0 insertions, 25 deletions
diff --git a/lib/neighbor.rb b/lib/neighbor.rb deleted file mode 100644 index d849cbf..0000000 --- a/lib/neighbor.rb +++ /dev/null @@ -1,25 +0,0 @@ -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) - 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 |