diff options
Diffstat (limited to 'algorithm.rb')
| -rw-r--r-- | algorithm.rb | 115 |
1 files changed, 0 insertions, 115 deletions
diff --git a/algorithm.rb b/algorithm.rb index 9f56387..6c6ba73 100644 --- a/algorithm.rb +++ b/algorithm.rb @@ -24,121 +24,6 @@ class AlgorithmTest < Test::Unit::TestCase end end - def test_p_sum_support - params = {} - params[:compound_features_hits] = { "c:c" => 10, "c:c:c" => 5, "O:N" => 2} - params[:training_compound] = "http://localhost/compound/InChI=1S/CH2O/c1-2/h1H2" - params[:training_compound_features_hits] = {"c:c" => 6, "c:c:c" => 3, "O:O" => 2} - params[:weights] = { "c:c" => 0.95, "c:c:c" => 0.96, "O:N" => 0.97, "O:O" => 0.98} - params[:features] = (params[:compound_features_hits].keys + params[:training_compound_features_hits].keys).uniq - 2.times{ - params[:mode] = "min" - assert_in_delta OpenTox::Algorithm.p_sum_support(params), 12.8762796504849, 0.00001 - params[:mode] = "max" - assert_in_delta OpenTox::Algorithm.p_sum_support(params), 18.8034091184372, 0.00001 - } - end - - def test_tanimoto - params = {} - params[:training_compound] = "http://localhost/compound/InChI=1S/CH2O/c1-2/h1H2" - weights = { "c:c" => 0.95, "c:c:c" => 0.96, "O:N" => 0.97, "O:O" => 0.98} - params[:compound_features_hits] = { "c:c" => 10, "c:c:c" => 5, "O:N" => 2} - features_a = params[:compound_features_hits].keys - params[:training_compound_features_hits] = {"c:c" => 6, "c:c:c" => 3, "O:O" => 2} - features_b = params[:training_compound_features_hits].keys - 2.times{ - params[:nr_hits] = false - #test without weights - assert_in_delta OpenTox::Algorithm::Similarity.tanimoto(features_a, features_b, nil, params), 0.5, 0.000001 - - #test with weights - assert_in_delta OpenTox::Algorithm::Similarity.tanimoto(features_a, features_b, weights, params), 0.498056105472291, 0.000001 - - #test with weights and nr_hits true - params[:nr_hits] = true - assert_in_delta OpenTox::Algorithm::Similarity.tanimoto(features_a, features_b, weights, params), 0.472823526091916, 0.000001 - } - - params[:training_compound_features_hits] = {"c:c" => 2, "O:N" => 2} - features_c = params[:training_compound_features_hits].keys - - 2.times{ - params[:nr_hits] = false - #test without weights - assert_in_delta OpenTox::Algorithm::Similarity.tanimoto(features_a, features_c, nil, params), 0.666666666666667, 0.000001 - - #test with weights - assert_in_delta OpenTox::Algorithm::Similarity.tanimoto(features_a, features_c, weights, params), 0.666545393630348, 0.000001 - - #test with weights and nr_hits true - params[:nr_hits] = true - assert_in_delta OpenTox::Algorithm::Similarity.tanimoto(features_a, features_c, weights, params), 0.235749338271022, 0.000001 - } - end - - def test_mlr - n_prop = [ [ -2.0, -2.0 ], - [ -1.0, -1.0 ], - [ 0.0, 0.0 ], - [ 1.0, 1.0 ], - [ 2.0, 2.0 ] ] - - q_prop = [ 1.0, 1.0 ] - - #acts = [ -2.0, - # -1.0, - # 0.0, - # 1.0, - # 2.0 ] - - acts = [ 0.0, - 0.5, - 1.0, - 1.5, - 2.0 ] - - maxcols = 2 - res1 = OpenTox::Algorithm::Neighbors::mlr(:n_prop => n_prop, :q_prop => q_prop, :acts => acts, :maxcols => maxcols) - maxcols = 1 - res2 = OpenTox::Algorithm::Neighbors::mlr(:n_prop => n_prop, :q_prop => q_prop, :acts => acts, :maxcols => maxcols) - assert_in_delta res1, 1.4958008960423, 10E-06 - assert_equal res1, res2 - end - - def test_pcr - n_prop = [ [ -2.0, -2.0 ], - [ -1.0, -1.0 ], - [ 0.0, 0.0 ], - [ 1.0, 1.0 ], - [ 2.0, 2.0 ] ] - - q_prop = [ 1.0, 1.0 ] - - #acts = [ -2.0, - # -1.0, - # 0.0, - # 1.0, - # 2.0 ] - - acts = [ 0.0, - 0.5, - 1.0, - 1.5, - 2.0 ] - - maxcols = 2 - res1 = OpenTox::Algorithm::Neighbors::pcr(:n_prop => n_prop, :q_prop => q_prop, :acts => acts, :maxcols => maxcols) - - maxcols = 1 - res2 = OpenTox::Algorithm::Neighbors::pcr(:n_prop => n_prop, :q_prop => q_prop, :acts => acts, :maxcols => maxcols) - - assert_in_delta res1, 1.4958008960423, 10E-06 - assert_equal res1, res2 - end - - - =begin def test_clustering # Parameters |