From 9e99495ecbff147218023c136bade9e56a502fed Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Thu, 13 Oct 2016 14:39:04 +0200 Subject: descriptor tests fixed --- test/compound.rb | 4 ++-- test/descriptor.rb | 47 +++++++++++++++++++++-------------------------- test/model.rb | 2 +- test/regression.rb | 2 +- 4 files changed, 25 insertions(+), 30 deletions(-) (limited to 'test') diff --git a/test/compound.rb b/test/compound.rb index d1cfb3d..19f51fd 100644 --- a/test/compound.rb +++ b/test/compound.rb @@ -124,7 +124,7 @@ print c.sdf def test_physchem c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C" - assert_equal PhysChem::OPENBABEL.size, c.calculated_properties.size - assert_equal PhysChem::OPENBABEL.size, c.calculated_properties(["PhysChem::OPENBABEL"]).size + assert_equal PhysChem::OPENBABEL.size, c.properties.size + assert_equal PhysChem::OPENBABEL.size, c.properties([PhysChem::OPENBABEL]).size end end diff --git a/test/descriptor.rb b/test/descriptor.rb index 2a5be60..911f5c3 100644 --- a/test/descriptor.rb +++ b/test/descriptor.rb @@ -27,57 +27,52 @@ class DescriptorTest < MiniTest::Test def test_compound_openbabel_single c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N" PhysChem.openbabel_descriptors # required for descriptor initialisation, TODO: move into libs - PhysChem.find_or_create_by(:name => "Openbabel.logP") - result = c.calculated_physchem [PhysChem.find_or_create_by(:name => "Openbabel.logP")] - assert_equal 1.12518, result.first.last.round(5) + feature = PhysChem.find_or_create_by(:name => "Openbabel.logP") + result = c.calculate_properties([feature]) + assert_equal 1.12518, result.first.round(5) + assert_equal 1.12518, c.properties[feature.id.to_s].round(5) end def test_compound_cdk_single PhysChem.cdk_descriptors # required for descriptor initialisation, TODO: move into libs c = OpenTox::Compound.from_smiles "c1ccccc1" - result = c.calculated_physchem [PhysChem.find_or_create_by(:name => "Cdk.AtomCount.nAtom")] - assert_equal 12, result.first.last + feature = PhysChem.find_or_create_by(:name => "Cdk.AtomCount.nAtom") + result = c.calculate_properties([feature]) + assert_equal 12, result.first c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N" - result = c.calculated_physchem [PhysChem.find_or_create_by(:name => "Cdk.AtomCount.nAtom")] - assert_equal 17, result.first.last + feature = PhysChem.find_or_create_by(:name => "Cdk.AtomCount.nAtom") + result = c.calculate_properties([feature]) + assert_equal 17, result.first c_types = {"Cdk.CarbonTypes.C1SP1"=>1, "Cdk.CarbonTypes.C2SP1"=>0, "Cdk.CarbonTypes.C1SP2"=>0, "Cdk.CarbonTypes.C2SP2"=>1, "Cdk.CarbonTypes.C3SP2"=>0, "Cdk.CarbonTypes.C1SP3"=>2, "Cdk.CarbonTypes.C2SP3"=>1, "Cdk.CarbonTypes.C3SP3"=>1, "Cdk.CarbonTypes.C4SP3"=>0} physchem_features = c_types.collect{|t,nr| PhysChem.find_or_create_by(:name => t)} - result = c.calculated_physchem physchem_features - assert_equal [1, 0, 0, 1, 0, 2, 1, 1, 0], result.values + result = c.calculate_properties physchem_features + assert_equal [1, 0, 0, 1, 0, 2, 1, 1, 0], result end def test_compound_joelib_single PhysChem.joelib_descriptors # required for descriptor initialisation, TODO: move into libs c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N" - result = c.calculated_physchem [PhysChem.find_or_create_by(:name => "Joelib.LogP")] - assert_equal 2.65908, result.first.last + result = c.calculate_properties [PhysChem.find_or_create_by(:name => "Joelib.LogP")] + assert_equal 2.65908, result.first end def test_compound_all c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N" - result = c.calculated_physchem PhysChem.descriptors amr = PhysChem.find_or_create_by(:name => "Cdk.ALOGP.AMR", :library => "Cdk") sbonds = PhysChem.find_by(:name => "Openbabel.sbonds") - assert_equal 30.8723, result[amr.id.to_s] - assert_equal 5, result[sbonds.id.to_s] + result = c.calculate_properties([amr,sbonds]) + assert_equal 30.8723, result[0] + assert_equal 5, result[1] end def test_compound_descriptor_parameters PhysChem.descriptors c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N" - result = c.calculated_physchem [ "Openbabel.logP", "Cdk.AtomCount.nAtom", "Joelib.LogP" ].collect{|d| PhysChem.find_or_create_by(:name => d)} + result = c.calculate_properties [ "Openbabel.logP", "Cdk.AtomCount.nAtom", "Joelib.LogP" ].collect{|d| PhysChem.find_or_create_by(:name => d)} assert_equal 3, result.size - result.each do |fid,v| - feature = Feature.find(fid) - case feature.name - when "Openbabel.logP" - assert_equal 1.12518, v.round(5) - when "Cdk.AtomCount.nAtom" - assert_equal 17.0, v.round(5) - when "Joelib.LogP" - assert_equal 2.65908, v.round(5) - end - end + assert_equal 1.12518, result[0].round(5) + assert_equal 17.0, result[1].round(5) + assert_equal 2.65908, result[2].round(5) end end diff --git a/test/model.rb b/test/model.rb index 017ce10..322ad90 100644 --- a/test/model.rb +++ b/test/model.rb @@ -49,7 +49,7 @@ class ModelTest < MiniTest::Test def test_physchem_regression algorithms = { - :descriptors => ["PhysChem::OPENBABEL"], + :descriptors => [PhysChem::OPENBABEL], :similarity => { :method => "Algorithm::Similarity.cosine", } diff --git a/test/regression.rb b/test/regression.rb index b1051f1..cdbac4b 100644 --- a/test/regression.rb +++ b/test/regression.rb @@ -44,7 +44,7 @@ class LazarRegressionTest < MiniTest::Test def test_local_physchem_regression training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv" algorithms = { - :descriptors => ["PhysChem::OPENBABEL"], + :descriptors => [PhysChem::OPENBABEL], :similarity => { :method => "Algorithm::Similarity.weighted_cosine", :min => 0.5 -- cgit v1.2.3