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authorhelma@in-silico.ch <helma@in-silico.ch>2018-11-06 19:01:58 +0100
committerhelma@in-silico.ch <helma@in-silico.ch>2018-11-06 19:01:58 +0100
commitcf80ed17102a0368df8d65037d113b521cdf6f0c (patch)
treef2930939673d7e5b28021351d32d92750875992b
parent3a9c9332b660d35720ad4fa1f55ee0883e53aecd (diff)
sdf export fixed
-rw-r--r--lib/dataset.rb19
-rw-r--r--lib/model.rb8
2 files changed, 15 insertions, 12 deletions
diff --git a/lib/dataset.rb b/lib/dataset.rb
index 42733e4..b09d7bf 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -199,7 +199,6 @@ module OpenTox
end
dataset.parse_table table
end
- dataset.save
dataset
end
@@ -290,7 +289,7 @@ module OpenTox
all_substances = []
table.each_with_index do |vals,i|
- original_id.name.match(/LineID$/) ? original_id_value = i+1 : original_id_value = vals.shift.strip
+ original_id.name.match(/LineID$/) ? original_id_value = i+1 : original_id_value = vals.shift.to_s.strip
identifier = vals.shift.strip
begin
case compound_format
@@ -368,13 +367,17 @@ module OpenTox
# @return [String] SDF string
def to_sdf
sdf = ""
- substances.each do |substance|
- sdf_lines = substance.sdf.sub(/\$\$\$\$\n/,"").split("\n")
- sdf_lines[0] = substance.smiles
+ compounds.each do |compound|
+ sdf_lines = compound.sdf.sub(/\$\$\$\$\n/,"").split("\n")
+ sdf_lines[0] = compound.smiles
sdf += sdf_lines.join("\n")
- features.each do |f|
- sdf += "\n> <#{f.name}>\n"
- sdf += values(substance,f).uniq.join ","
+ bioactivity_features.each do |f|
+ v = values(compound,f)
+ unless v.empty?
+ sdf += "\n> <#{f.name}>\n"
+ sdf += v.uniq.join ","
+ sdf += "\n"
+ end
end
sdf += "\n$$$$\n"
end
diff --git a/lib/model.rb b/lib/model.rb
index a0c60f0..966460b 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -481,13 +481,13 @@ module OpenTox
end
# TODO from_pubchem_aid
- def self.from_dataset training_dataset: , prediction_feature: , species: , endpoint:
+ def self.from_dataset training_dataset: , prediction_feature: , species: , endpoint: , folds: 10, repeats: 5
model_validation = Model::Validation.create species: species, endpoint: endpoint
- p "create model"
+ #p "create model"
model = Lazar.create training_dataset: training_dataset, prediction_feature: prediction_feature
model_validation[:model_id] = model.id
- p "create_crossvalidations"
- model_validation[:repeated_crossvalidation_id] = OpenTox::Validation::RepeatedCrossValidation.create(model).id # full class name required
+ #p "create_crossvalidations"
+ model_validation[:repeated_crossvalidation_id] = OpenTox::Validation::RepeatedCrossValidation.create(model,folds,repeats).id # full class name required
model_validation.save
model_validation
end