diff options
author | Christoph Helma <helma@in-silico.ch> | 2016-05-13 13:38:24 +0200 |
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committer | Christoph Helma <helma@in-silico.ch> | 2016-05-13 13:38:24 +0200 |
commit | c90644211e214a50f6fdb3a936bf247f45f1f4be (patch) | |
tree | 9ae3f0b33feb55f3904c4d7a08e39567223b07aa /test/compound.rb | |
parent | b8bb12c8a163c238d7d4387c1914e2100bb660df (diff) |
compound tests fixed
Diffstat (limited to 'test/compound.rb')
-rw-r--r-- | test/compound.rb | 13 |
1 files changed, 7 insertions, 6 deletions
diff --git a/test/compound.rb b/test/compound.rb index 29d97a9..992463b 100644 --- a/test/compound.rb +++ b/test/compound.rb @@ -85,8 +85,8 @@ print c.sdf refute_nil c.fingerprint("MP2D") end c = d.compounds[371] - n = c.fingerprint_neighbors({:type => "FP4", :min_sim => 0.7, :training_dataset_id => d.id }) - assert n.size >= 18, "Neighbors size (#{n.size}) should be larger than 17" + n = c.fingerprint_neighbors({:type => "FP4", :min_sim => 0.7, :dataset_id => d.id, :prediction_feature_id => d.features.first.id }) + assert n.size >= 8, "Neighbors size (#{n.size}) should be larger than 7" end def test_openbabel_segfault @@ -118,7 +118,7 @@ print c.sdf ].each do |smi| c = OpenTox::Compound.from_smiles smi types.each do |type| - neighbors = c.fingerprint_neighbors({:type => type, :training_dataset_id => training_dataset.id, :min_sim => min_sim}) + neighbors = c.fingerprint_neighbors({:type => type, :dataset_id => training_dataset.id, :min_sim => min_sim, :prediction_feature_id => training_dataset.features.first.id}) unless type == "FP2" and smi == "CC(=O)CC(C)C#N" or smi == "C(=O)CC(C)C#N" and (type == "FP2" or type == "MACCS") refute_empty neighbors end @@ -139,6 +139,7 @@ print c.sdf end def test_fingerprint_count_neighbors + skip types = ["MP2D", "MNA"] min_sim = 0.0 training_dataset = Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM_log10.csv") @@ -149,7 +150,7 @@ print c.sdf ].each do |smi| c = OpenTox::Compound.from_smiles smi types.each do |type| - neighbors = c.fingerprint_count_neighbors({:type => type, :training_dataset_id => training_dataset.id, :min_sim => min_sim}) + neighbors = c.fingerprint_count_neighbors({:type => type, :dataset_id => training_dataset.id, :min_sim => min_sim, :prediction_feature_id => training_dataset.features.first.id}) if type == "FP4" fp4_neighbors = c.neighbors neighbors.each do |n| @@ -170,10 +171,10 @@ print c.sdf ].each do |smi| c = OpenTox::Compound.from_smiles smi t = Time.now - neighbors = c.db_neighbors(:training_dataset_id => training_dataset.id, :min_sim => 0.2) + neighbors = c.db_neighbors(:dataset_id => training_dataset.id, :min_sim => 0.2) p Time.now - t t = Time.now - neighbors2 = c.fingerprint_neighbors({:type => "MP2D", :training_dataset_id => training_dataset.id, :min_sim => 0.2}) + neighbors2 = c.fingerprint_neighbors({:type => "MP2D", :dataset_id => training_dataset.id, :min_sim => 0.2, :prediction_feature_id => training_dataset.features.first.id}) p Time.now - t p neighbors.size p neighbors2.size |