diff options
author | Christoph Helma <helma@in-silico.ch> | 2016-10-05 14:10:25 +0200 |
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committer | Christoph Helma <helma@in-silico.ch> | 2016-10-05 14:10:25 +0200 |
commit | 016403f7db0dedf8237f29af41312b5ff2720c30 (patch) | |
tree | b276ad7bbb11ff73049b9c7cfeda15c140846436 /test/compound.rb | |
parent | 5d4e5e463c2b87241bbb56e4658e1e26c0ed084f (diff) |
compound and descriptor tests fixed
Diffstat (limited to 'test/compound.rb')
-rw-r--r-- | test/compound.rb | 21 |
1 files changed, 16 insertions, 5 deletions
diff --git a/test/compound.rb b/test/compound.rb index c9faa21..c78acb1 100644 --- a/test/compound.rb +++ b/test/compound.rb @@ -85,7 +85,13 @@ print c.sdf refute_nil c.fingerprint("MP2D") end c = d.compounds[371] - n = c.fingerprint_neighbors({:type => "FP4", :min_sim => 0.7, :dataset_id => d.id, :prediction_feature_id => d.features.first.id }) + n = c.neighbors( + descriptors: {:method => "fingerprint", :type => "FP4"}, + similarity: {:method => "Algorithm::Similarity.tanimoto", :min => 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 @@ -118,7 +124,12 @@ print c.sdf ].each do |smi| c = OpenTox::Compound.from_smiles smi types.each do |type| - neighbors = c.fingerprint_neighbors({:type => type, :dataset_id => training_dataset.id, :min_sim => min_sim, :prediction_feature_id => training_dataset.features.first.id}) + neighbors = c.fingerprint_neighbors( + descriptors: {:method => "fingerprint",:type => type}, + dataset_id: training_dataset.id, + similarity: {:method => "Algorithm::Similarity.tanimoto", :min => 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 @@ -197,8 +208,8 @@ print c.sdf def test_physchem c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C" - assert_equal PhysChem::OBDESCRIPTORS.size, c.physchem.size - assert_equal PhysChem::OBDESCRIPTORS.size, c.physchem(PhysChem.openbabel_descriptors).size - assert_equal PhysChem::unique_descriptors.size, c.physchem(PhysChem.unique_descriptors).size + assert_equal PhysChem::OBDESCRIPTORS.size, c.calculated_physchem.size + assert_equal PhysChem::OBDESCRIPTORS.size, c.calculated_physchem(PhysChem.openbabel_descriptors).size + assert_equal PhysChem::unique_descriptors.size, c.calculated_physchem(PhysChem.unique_descriptors).size end end |