diff options
author | Christoph Helma <helma@in-silico.ch> | 2016-10-13 10:11:09 +0200 |
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committer | Christoph Helma <helma@in-silico.ch> | 2016-10-13 10:11:09 +0200 |
commit | 8d325866dd7cacdd04bd2306a9144a5e7300c7c8 (patch) | |
tree | 5e730f20a26e58e41cdff9c22bd5647c886ca834 /lib | |
parent | 1810b12e7faf2f0677482a3c7a8c23e0e11b8d29 (diff) |
molecular_weight fixed
Diffstat (limited to 'lib')
-rw-r--r-- | lib/compound.rb | 5 | ||||
-rw-r--r-- | lib/model.rb | 4 | ||||
-rw-r--r-- | lib/regression.rb | 1 |
3 files changed, 5 insertions, 5 deletions
diff --git a/lib/compound.rb b/lib/compound.rb index 0f178ce..ca9d5e3 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -75,9 +75,10 @@ module OpenTox fingerprints[type] end - def calculated_properties types=["OPENBABEL"] + def calculated_properties types=["PhysChem::OPENBABEL"] descriptors = [] types.each do |t| + p t descriptors += PhysChem.descriptors OpenTox.const_get(t) end # TODO: speedup java descriptors @@ -304,7 +305,7 @@ module OpenTox # @return [Float] molecular weight def molecular_weight mw_feature = PhysChem.find_or_create_by(:name => "Openbabel.MW") - calculated_physchem([mw_feature])[mw_feature.id.to_s] + calculated_properties[mw_feature.id.to_s] end private diff --git a/lib/model.rb b/lib/model.rb index f3f0603..859df8b 100644 --- a/lib/model.rb +++ b/lib/model.rb @@ -126,7 +126,8 @@ module OpenTox end model.descriptor_ids = model.fingerprints.flatten.uniq model.descriptor_ids.each do |d| - model.independent_variables << model.substance_ids.collect_with_index{|s,i| model.fingerprints[i].include? d} + # resulting model may break BSON size limit (e.g. f Kazius dataset + model.independent_variables << model.substance_ids.collect_with_index{|s,i| model.fingerprints[i].include? d} if model.algorithms[:prediction][:method].match /Caret/ end else # parse independent_variables @@ -225,7 +226,6 @@ module OpenTox else # call prediction algorithm result = Algorithm.run algorithms[:prediction][:method], dependent_variables:neighbor_dependent_variables,independent_variables:neighbor_independent_variables ,weights:neighbor_similarities, query_variables:query_descriptors - p result prediction.merge! result prediction[:neighbors] = neighbor_ids.collect_with_index{|id,i| {:id => id, :measurement => neighbor_dependent_variables[i], :similarity => neighbor_similarities[i]}} end diff --git a/lib/regression.rb b/lib/regression.rb index bed6df8..d1724fd 100644 --- a/lib/regression.rb +++ b/lib/regression.rb @@ -4,7 +4,6 @@ module OpenTox class Regression def self.weighted_average dependent_variables:, independent_variables:nil, weights:, query_variables: - #def self.weighted_average descriptors:nil, neighbors:, parameters:nil, method:nil, relevant_features:nil # TODO: prediction_interval weighted_sum = 0.0 sim_sum = 0.0 |