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authormr <mr@mrautenberg.de>2011-08-02 17:34:07 +0200
committermr <mr@mrautenberg.de>2011-08-02 17:34:07 +0200
commitd5742dccb894de51644c1f804693e497c8e5be66 (patch)
tree4e7ae9e8699ded1345dfa70d6224c69238744ad3
parentfeccf0995ef995a4d32119fb5582b9a37b7f9dd0 (diff)
parent91b70cba5d1d0045b0db0d9c77f867e68e61fe2e (diff)
fix merge conflicts
Diffstat
-rw-r--r--application.rb75
-rw-r--r--model.rb10
-rw-r--r--public/hamster_carcinogenicity.sdf2805
-rwxr-xr-xpublic/javascripts/toxcreate.js8
-rw-r--r--views/classification_validation.haml59
-rw-r--r--views/create.haml43
-rw-r--r--views/help.haml61
-rw-r--r--views/layout.haml18
-rw-r--r--views/model.haml12
-rw-r--r--views/style.sass1
10 files changed, 3003 insertions, 89 deletions
diff --git a/application.rb b/application.rb
index 75d4c70..328384a 100644
--- a/application.rb
+++ b/application.rb
@@ -17,11 +17,16 @@ set :lock, true
helpers do
- def error(message)
+ # message will be displayed to the user
+ # error will be raised -> taks will be set to error -> error details available via task-uri
+ def error(message, error=nil)
LOGGER.error message
@model.update :status => "Error", :error_messages => message
- flash[:notice] = message
- redirect url_for('/create')
+ if error
+ raise error
+ else
+ raise message
+ end
end
private
@@ -75,6 +80,7 @@ end
get '/models/?' do
@models = ToxCreateModel.all.sort(:order => "DESC")
+ @models.each{|m| raise "internal redis error: model is nil" unless m}
subjectstring = session[:subjectid] ? "?subjectid=#{CGI.escape(session[:subjectid])}" : ""
haml :models, :locals=>{:models=>@models, :subjectstring => subjectstring}
end
@@ -225,7 +231,7 @@ post '/models' do # create a new model
@model = ToxCreateModel.create(:name => name, :subjectid => subjectid)
@model.update :web_uri => url_for("/model/#{@model.id}", :full), :warnings => ""
- task = OpenTox::Task.create("Uploading dataset and creating lazar model",url_for("/models",:full)) do |task|
+ task = OpenTox::Task.create("Toxcreate Task - Uploading dataset and creating lazar model",url_for("/models",:full)) do |task|
task.progress(5)
@model.update :status => "Uploading and saving dataset", :task_uri => task.uri
@@ -243,14 +249,17 @@ post '/models' do # create a new model
File.rename(params[:file][:tempfile].path, excel_file) # add extension, spreadsheet does not read files without extensions
@dataset.load_spreadsheet(Excel.new excel_file, subjectid)
if @dataset.metadata[OT.Errors]
- error "Incorrect file format. Please follow the instructions for #{link_to "Excel", "/help"} or #{link_to "CSV", "/help"} formats."
+ raise "Incorrect file format. Please follow the instructions for #{link_to "Excel", "/help"} or #{link_to "CSV", "/help"} formats."
end
+ when ".sdf"
+ sdf = params[:file][:tempfile].read
+ @dataset.load_sdf(sdf, subjectid)
else
- error "#{params[:file][:filename]} has a unsupported file type."
+ raise "#{params[:file][:filename]} has an unsupported file type."
end
@dataset.save(subjectid)
rescue => e
- error "Dataset creation failed with #{e.message}"
+ error "Dataset creation failed '#{e.message}'",e
end
if @dataset.features.keys.size != 1
error "More than one feature in dataset #{params[:file][:filename]}. Please delete irrelvant columns and try again."
@@ -267,11 +276,11 @@ post '/models' do # create a new model
@model.update :warnings => @dataset.metadata[OT.Warnings] unless @dataset.metadata[OT.Warnings] and @dataset.metadata[OT.Warnings].empty?
task.progress(15)
begin
- lazar = OpenTox::Model::Lazar.create(:dataset_uri => @dataset.uri, :prediction_feature => @prediction_feature.uri, :subjectid => subjectid)
+ lazar = OpenTox::Model::Lazar.create( {:dataset_uri => @dataset.uri, :prediction_feature => @prediction_feature.uri, :subjectid => subjectid},
+ OpenTox::SubTask.new(task,15,25))
rescue => e
- error "Model creation failed with '#{e.message}'."# Please check if the input file is in a valid #{link_to "Excel", "/help"} or #{link_to "CSV", "/help"} format."
+ error "Model creation failed",e # Please check if the input file is in a valid #{link_to "Excel", "/help"} or #{link_to "CSV", "/help"} format."
end
- task.progress(25)
=begin
type = "unknown"
if lazar.metadata[RDF.type].grep(/Classification/)
@@ -285,7 +294,7 @@ post '/models' do # create a new model
if CONFIG[:services]["opentox-validation"]
@model.update :status => "Validating model"
begin
- validation = OpenTox::Crossvalidation.create( {
+ crossvalidation = OpenTox::Crossvalidation.create( {
:algorithm_uri => lazar.metadata[OT.algorithm],
:dataset_uri => lazar.parameter("dataset_uri"),
:subjectid => subjectid,
@@ -293,38 +302,51 @@ post '/models' do # create a new model
:algorithm_params => "feature_generation_uri=#{lazar.parameter("feature_generation_uri")}" },
nil, OpenTox::SubTask.new(task,25,80))
- @model.update(:validation_uri => validation.uri)
+ @model.update(:validation_uri => crossvalidation.uri)
LOGGER.debug "Validation URI: #{@model.validation_uri}"
# create summary
- validation.summary(subjectid).each do |k,v|
- begin
- eval "@model.update :#{k.to_s} => v" if v
- rescue
- eval "@model.update :#{k.to_s} => 0"
+ validation = crossvalidation.statistics(subjectid)
+ @model.update(:nr_predictions => validation.metadata[OT.numInstances].to_i - validation.metadata[OT.numUnpredicted].to_i)
+ if validation.metadata[OT.classificationStatistics]
+ @model.update(:correct_predictions => validation.metadata[OT.classificationStatistics][OT.percentCorrect].to_f)
+ @model.update(:confusion_matrix => validation.confusion_matrix.to_yaml)
+ @model.update(:weighted_area_under_roc => validation.metadata[OT.classificationStatistics][OT.weightedAreaUnderRoc].to_f)
+ validation.metadata[OT.classificationStatistics][OT.classValueStatistics].each do |m|
+ if m[OT.classValue] =~ TRUE_REGEXP
+ #HACK: estimate true feature value correctly
+ @model.update(:sensitivity => m[OT.truePositiveRate])
+ @model.update(:specificity => m[OT.trueNegativeRate])
+ break
+ end
end
+ else
+ @model.update(:r_square => validation.metadata[OT.regressionStatistics][OT.rSquare].to_f)
+ @model.update(:root_mean_squared_error => validation.metadata[OT.regressionStatistics][OT.rootMeanSquaredError].to_f)
+ @model.update(:mean_absolute_error => validation.metadata[OT.regressionStatistics][OT.meanAbsoluteError].to_f)
end
-
+ rescue => e
+ @model.update :warnings => @model.warnings.to_s+"\nModel crossvalidation failed with #{e.message}."
+ error "Model validation failed",e
+ end
+
+ begin
@model.update :status => "Creating validation report"
- validation_report_uri = validation.find_or_create_report(subjectid, OpenTox::SubTask.new(task,80,90)) #unless @model.dirty?
+ validation_report_uri = crossvalidation.find_or_create_report(subjectid, OpenTox::SubTask.new(task,80,90)) #unless @model.dirty?
@model.update :validation_report_uri => validation_report_uri, :status => "Creating QMRF report"
qmrf_report = OpenTox::Crossvalidation::QMRFReport.create(@model.uri, subjectid, OpenTox::SubTask.new(task,90,99))
@model.update(:validation_qmrf_uri => qmrf_report.uri, :status => "Completed")
-
rescue => e
- LOGGER.debug "Model validation failed with #{e.message}."
- @model.save # to avoid dirty models
- @model.update :warnings => @model.warnings.to_s+"\nModel validation failed with #{e.message}.", :status => "Error", :error_messages => e.message
+ error "Model report creation failed",e
end
-
else
@model.update(:status => "Completed") #, :warnings => @model.warnings + "\nValidation service cannot be accessed from localhost.")
- task.progress(100)
+ task.progress(99)
end
lazar.uri
end
@model.update :task_uri => task.uri
-
+ sleep 0.25 # power nap: ohm sometimes returns nil values for model.status or for model itself
flash[:notice] = "Model creation and validation started - this may last up to several hours depending on the number and size of the training compounds."
redirect url_for('/models')
@@ -352,6 +374,7 @@ post '/predict/?' do # post chemical name to model
db_activities = []
lazar = OpenTox::Model::Lazar.new model.uri
prediction_dataset_uri = lazar.run({:compound_uri => @compound.uri, :subjectid => subjectid})
+ LOGGER.debug "Prediction dataset_uri: #{prediction_dataset_uri}"
prediction_dataset = OpenTox::LazarPrediction.find(prediction_dataset_uri, subjectid)
if prediction_dataset.metadata[OT.hasSource].match(/dataset/)
@predictions << {
diff --git a/model.rb b/model.rb
index 5b1f4f5..e433893 100644
--- a/model.rb
+++ b/model.rb
@@ -27,14 +27,10 @@ class ToxCreateModel < Ohm::Model
#attributey :validation_qmrf_task_uri
attribute :validation_qmrf_uri
-
+ attribute :confusion_matrix
attribute :nr_compounds
- attribute :nr_predictions
- attribute :true_positives
- attribute :false_positives
- attribute :true_negatives
- attribute :false_negatives
- attribute :correct_predictions
+ attribute :nr_predictions
+ attribute :correct_predictions
attribute :weighted_area_under_roc
attribute :sensitivity
attribute :specificity
diff --git a/public/hamster_carcinogenicity.sdf b/public/hamster_carcinogenicity.sdf
new file mode 100644
index 0000000..df230d5
--- /dev/null
+++ b/public/hamster_carcinogenicity.sdf
@@ -0,0 +1,2805 @@
+
+
+
+ 3 2 0 0 0 0 0 0 0 0 1 V2000
+ 2.3030 -0.6656 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1515 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -0.6656 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 2 3 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 17 19 0 0 0 0 0 0 0 0 1 V2000
+ 5.7640 -1.7698 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.0213 -1.3540 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.8046 -2.4275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 9.1296 -2.2921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 9.6712 -1.0735 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 8.8878 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.5629 -0.1451 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.0213 -3.5106 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.7640 -3.0948 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6035 -3.7621 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.4526 -3.0948 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.4526 -1.7698 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6035 -1.1025 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.3017 -3.7621 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1509 -3.0948 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -3.7621 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1509 -1.7698 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 1 9 1 0 0 0 0
+ 1 13 2 0 0 0 0
+ 2 3 2 0 0 0 0
+ 2 7 1 0 0 0 0
+ 3 4 1 0 0 0 0
+ 3 8 1 0 0 0 0
+ 4 5 2 0 0 0 0
+ 5 6 1 0 0 0 0
+ 6 7 2 0 0 0 0
+ 8 9 1 0 0 0 0
+ 9 10 2 0 0 0 0
+ 10 11 1 0 0 0 0
+ 11 12 2 0 0 0 0
+ 11 14 1 0 0 0 0
+ 12 13 1 0 0 0 0
+ 14 15 1 0 0 0 0
+ 15 16 1 0 0 0 0
+ 15 17 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 18 19 0 0 0 0 0 0 0 0 2 V2000
+ 3.2537 -3.5906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.2537 -2.2607 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.4062 -1.5958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.4062 -4.2555 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.1011 -4.2555 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.9682 -0.2748 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.6649 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.1011 -1.5958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -1.1525 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.8866 -2.1366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.7006 -3.5817 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.0038 -3.8654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.5587 -2.2607 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.6687 -2.7129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 6.7733 -1.7199 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.5446 -5.0800 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
+ 6.7644 -6.1527 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
+ 8.8656 -5.2130 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 1 5 1 0 0 0 0
+ 1 4 2 0 0 0 0
+ 2 3 2 0 0 0 0
+ 2 8 1 0 0 0 0
+ 3 13 1 0 0 0 0
+ 6 7 1 0 0 0 0
+ 6 8 1 0 0 0 0
+ 7 9 2 0 0 0 0
+ 8 10 2 0 0 0 0
+ 9 10 1 0 0 0 0
+ 11 12 1 0 0 0 0
+ 11 13 1 0 0 0 0
+ 12 14 2 0 0 0 0
+ 12 16 1 0 0 0 0
+ 13 15 2 0 0 0 0
+ 14 15 1 0 0 0 0
+ 16 17 1 0 0 0 0
+ 16 18 2 0 0 0 0
+M CHG 2 16 1 17 -1
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 6 6 0 0 0 0 0 0 0 0 1 V2000
+ 1.3304 -1.0738 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.1104 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.3767 -0.4086 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.3767 -1.7390 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.1104 -2.1509 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -1.0738 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 1 5 2 0 0 0 0
+ 1 6 1 0 0 0 0
+ 2 3 2 0 0 0 0
+ 3 4 1 0 0 0 0
+ 4 5 1 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+inactive
+
+$$$$
+
+
+
+ 13 13 0 0 0 0 0 0 0 0 1 V2000
+ 1.1541 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.3012 -0.6703 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.4553 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6094 -0.6703 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6094 -1.9972 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.4553 -2.6606 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.3012 -1.9972 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1541 -2.6606 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.4837 -1.5134 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.8175 -3.8147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -3.3309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.7566 -2.6606 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 6.9107 -1.9972 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 2 3 2 0 0 0 0
+ 2 7 1 0 0 0 0
+ 3 4 1 0 0 0 0
+ 4 5 2 0 0 0 0
+ 5 6 1 0 0 0 0
+ 5 12 1 0 0 0 0
+ 6 7 2 0 0 0 0
+ 7 8 1 0 0 0 0
+ 8 9 1 0 0 0 0
+ 8 10 1 0 0 0 0
+ 8 11 1 0 0 0 0
+ 12 13 1 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+inactive
+
+$$$$
+
+
+
+ 3 0 0 0 0 0 0 0 0 0 2 V2000
+ 10.0000 -0.0700 0.0000 Cl 0 5 0 0 0 0 0 0 0 0 0 0
+ 4.5200 0.0000 0.0000 Cd 0 2 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -0.3400 0.0000 Cl 0 5 0 0 0 0 0 0 0 0 0 0
+M CHG 3 1 -1 2 2 3 -1
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+inactive
+
+$$$$
+
+
+
+ 6 4 0 0 0 0 0 0 0 0 2 V2000
+ 2.6600 -2.6600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.6600 -1.3320 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.6600 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.3280 -1.3320 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
+ 3.9880 -1.3320 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -1.3320 0.0000 Cd 0 2 0 0 0 0 0 0 0 0 0 0
+ 1 2 2 0 0 0 0
+ 2 3 2 0 0 0 0
+ 2 4 1 0 0 0 0
+ 2 5 1 0 0 0 0
+M CHG 3 4 -1 5 -1 6 2
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+inactive
+
+$$$$
+
+
+
+ 0 0 0 0 0 0 0 0 0 0 1 V2000
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+inactive
+
+$$$$
+
+
+
+ 21 22 0 0 0 0 0 0 0 0 1 V2000
+ 5.7698 0.0000 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.7698 -1.3315 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 6.9111 -2.0036 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 6.9111 -3.3351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.7698 -3.9945 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6158 -3.3351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6158 -2.0036 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.4619 -3.9945 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.3079 -3.3351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1540 -3.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1540 -5.3260 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -3.3351 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 8.0650 -3.9945 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 9.2190 -3.3351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 9.2190 -2.0036 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 10.3730 -1.3315 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 11.5269 -2.0036 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 11.5269 -3.3351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 10.3730 -3.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 10.3730 -5.3260 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 12.6809 -3.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 2 3 2 0 0 0 0
+ 2 7 1 0 0 0 0
+ 3 4 1 0 0 0 0
+ 4 5 2 0 0 0 0
+ 4 13 1 0 0 0 0
+ 5 6 1 0 0 0 0
+ 6 7 2 0 0 0 0
+ 6 8 1 0 0 0 0
+ 8 9 1 0 0 0 0
+ 9 10 1 0 0 0 0
+ 10 11 2 0 0 0 0
+ 10 12 1 0 0 0 0
+ 13 14 1 0 0 0 0
+ 14 15 2 0 0 0 0
+ 14 19 1 0 0 0 0
+ 15 16 1 0 0 0 0
+ 16 17 2 0 0 0 0
+ 17 18 1 0 0 0 0
+ 18 19 2 0 0 0 0
+ 18 21 1 0 0 0 0
+ 19 20 1 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+inactive
+
+$$$$
+
+
+
+ 4 3 0 0 0 0 0 0 0 0 1 V2000
+ 3.4575 0.0000 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.3061 -0.6638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1513 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -0.6638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 1 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 5 4 0 0 0 0 0 0 0 0 1 V2000
+ 2.2415 -0.6520 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1191 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.3606 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -0.6520 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.2415 -2.0836 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 1 3 2 0 0 0 0
+ 1 5 1 0 0 0 0
+ 2 4 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+inactive
+
+$$$$
+
+
+
+ 21 22 0 0 0 0 0 0 0 0 1 V2000
+ 12.5806 -1.3138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 11.2668 -1.3138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 9.9397 -1.3138 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.3083 -2.4683 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.9945 -2.4683 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 13.2574 -0.1592 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.3177 -1.3138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.9718 -1.3138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.3177 -3.6229 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.9585 -3.6229 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 13.2707 -2.4683 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 9.2762 -2.4683 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.3403 -2.4683 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.9359 -2.4683 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.9906 -1.3138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.9906 -3.6229 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.2989 -3.6229 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.2989 -1.3138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -2.4683 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
+ 11.2668 -2.6674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 11.2668 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 1 6 2 0 0 0 0
+ 1 11 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 2 20 1 0 0 0 0
+ 2 21 1 0 0 0 0
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+ 8.0580 -3.9908 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 10.3668 -3.9908 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 8.0580 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.7644 -1.3303 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.4556 -5.3210 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.4556 -3.9908 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.3088 -5.9785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.3088 -7.3088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1468 -7.9815 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1468 -5.3210 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.4556 -11.9723 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.4556 -13.3026 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.3088 -13.9600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1468 -13.3026 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -13.9600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1468 -11.9723 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.3088 -11.2995 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.3088 -15.2903 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 2 0 0 0 0
+ 1 10 1 0 0 0 0
+ 1 36 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 2 14 1 0 0 0 0
+ 3 4 1 0 0 0 0
+ 3 13 2 0 0 0 0
+ 4 5 1 0 0 0 0
+ 4 9 2 0 0 0 0
+ 5 6 2 0 0 0 0
+ 5 12 1 0 0 0 0
+ 6 7 1 0 0 0 0
+ 7 8 2 0 0 0 0
+ 7 11 1 0 0 0 0
+ 8 9 1 0 0 0 0
+ 9 10 1 0 0 0 0
+ 15 14 1 1 0 0 0
+ 15 16 1 0 0 0 0
+ 15 33 1 0 0 0 0
+ 16 17 1 0 0 0 0
+ 17 18 1 1 0 0 0
+ 17 30 1 0 0 0 0
+ 18 19 1 0 0 0 0
+ 20 19 1 1 0 0 0
+ 20 21 1 0 0 0 0
+ 20 26 1 0 0 0 0
+ 21 22 1 0 0 0 0
+ 21 29 1 6 0 0 0
+ 22 23 1 0 0 0 0
+ 22 28 1 6 0 0 0
+ 23 24 1 1 0 0 0
+ 23 25 1 0 0 0 0
+ 25 26 1 0 0 0 0
+ 25 27 1 6 0 0 0
+ 30 31 1 6 0 0 0
+ 30 32 1 0 0 0 0
+ 32 33 1 0 0 0 0
+ 32 35 1 1 0 0 0
+ 33 34 1 6 0 0 0
+ 36 37 2 0 0 0 0
+ 36 42 1 0 0 0 0
+ 37 38 1 0 0 0 0
+ 38 39 2 0 0 0 0
+ 38 43 1 0 0 0 0
+ 39 40 1 0 0 0 0
+ 39 41 1 0 0 0 0
+ 41 42 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+inactive
+
+$$$$
+
+
+
+ 5 4 0 0 0 0 0 0 0 0 1 V2000
+ 3.4567 -1.9945 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.3056 -1.3308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1511 -1.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -1.3308 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.3056 0.0000 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 2 3 2 0 0 0 0
+ 2 5 1 0 0 0 0
+ 3 4 1 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+inactive
+
+$$$$
+
+
+
+ 6 5 0 0 0 0 0 0 0 0 1 V2000
+ 4.6084 -1.9954 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.4563 -1.3318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.4563 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.3042 -1.9954 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1521 -1.3318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -1.9954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 2 3 2 0 0 0 0
+ 2 4 1 0 0 0 0
+ 4 5 1 0 0 0 0
+ 5 6 1 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 3 2 0 0 0 0 0 0 0 0 1 V2000
+ 2.3030 -0.6656 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1515 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -0.6656 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 2 0 0 0 0
+ 2 3 1 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 13 12 0 0 0 0 0 0 0 0 2 V2000
+ 0.0000 -1.1513 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.3274 -1.1513 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
+ 2.6611 -1.1513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.3217 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6554 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.3159 -1.1513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6554 -2.3025 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.3217 -2.3025 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.6611 -6.2911 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.6611 -4.9636 0.0000 B 0 5 0 0 0 0 0 0 0 0 0 0
+ 1.3274 -4.9636 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.6611 -3.6299 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.9885 -4.9636 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 3 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 2 0 0 0 0
+ 3 8 1 0 0 0 0
+ 4 5 1 0 0 0 0
+ 5 6 2 0 0 0 0
+ 6 7 1 0 0 0 0
+ 7 8 2 0 0 0 0
+ 9 10 1 0 0 0 0
+ 10 11 1 0 0 0 0
+ 10 12 1 0 0 0 0
+ 10 13 1 0 0 0 0
+M CHG 2 2 1 10 -1
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+inactive
+
+$$$$
+
+
+
+ 12 12 0 0 0 0 0 0 0 0 1 V2000
+ 3.4560 -1.3271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6103 -1.9906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6103 -3.3247 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.4560 -3.9882 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.3017 -3.3247 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.3017 -1.9906 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1543 -1.3271 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -1.9906 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1543 -3.9882 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.7577 -3.9882 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 6.9120 -3.3247 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.4560 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 1 6 1 0 0 0 0
+ 1 12 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 1 0 0 0 0
+ 3 10 1 0 0 0 0
+ 4 5 1 0 0 0 0
+ 5 6 1 0 0 0 0
+ 5 9 1 0 0 0 0
+ 6 7 1 0 0 0 0
+ 7 8 2 0 0 0 0
+ 10 11 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 9 8 0 0 0 0 0 0 0 0 1 V2000
+ 4.6053 -1.9954 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.4522 -1.3257 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.2992 -1.9954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1530 -1.3257 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -1.9954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1530 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6053 -3.3210 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.7514 -1.3257 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 6.9045 -1.9954 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 1 7 1 0 0 0 0
+ 1 8 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 1 0 0 0 0
+ 4 5 1 0 0 0 0
+ 4 6 1 0 0 0 0
+ 8 9 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 10 10 0 0 0 0 0 0 0 0 1 V2000
+ 0.6656 -1.1543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.9968 -1.1543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.6577 -2.3040 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.9889 -2.3040 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6545 -1.1543 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.9968 -3.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.6656 -3.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -2.3040 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -4.6079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 1 8 1 0 0 0 0
+ 1 10 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 1 0 0 0 0
+ 3 6 1 0 0 0 0
+ 4 5 2 0 0 0 0
+ 6 7 1 0 0 0 0
+ 7 8 1 0 0 0 0
+ 7 9 1 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 9 9 0 0 0 0 0 0 0 0 1 V2000
+ 2.1136 -0.3740 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.3772 -0.7820 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.3772 -2.1136 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.1136 -2.5272 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.3316 -1.4506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -1.4506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.4538 -2.8956 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.6665 -2.3572 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.4538 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 1 5 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 2 9 2 0 0 0 0
+ 3 4 1 0 0 0 0
+ 3 7 1 0 0 0 0
+ 4 5 1 0 0 0 0
+ 5 6 1 0 0 0 0
+ 7 8 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 9 8 0 0 0 0 0 0 0 0 1 V2000
+ 0.0000 -1.1552 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.6644 -2.3044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.9932 -2.3044 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.6576 -1.1552 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.9932 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.9924 -1.1552 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6568 -2.3044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6568 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.9855 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 1 0 0 0 0
+ 4 5 2 0 0 0 0
+ 4 6 1 0 0 0 0
+ 6 7 1 0 0 0 0
+ 6 8 1 0 0 0 0
+ 8 9 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 7 7 0 0 0 0 0 0 0 0 1 V2000
+ 3.5169 -2.1419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.3050 -1.5998 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.4416 -0.2777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.7417 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.4072 -1.1547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1503 -2.2653 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -1.5998 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 1 5 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 2 6 1 0 0 0 0
+ 3 4 1 0 0 0 0
+ 4 5 1 0 0 0 0
+ 6 7 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 14 14 0 0 0 0 0 0 0 0 1 V2000
+ 1.9935 -3.4527 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.3316 -2.3044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.9935 -1.1482 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.3251 -1.1482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.9869 -2.3044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.3186 -2.3044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.9804 -1.1482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.3120 -1.1482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.9739 -2.3044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.3120 -3.4527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.9804 -3.4527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.3316 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -2.3044 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 2 0 0 0 0
+ 2 3 1 0 0 0 0
+ 2 14 1 0 0 0 0
+ 3 4 1 0 0 0 0
+ 3 12 1 0 0 0 0
+ 4 5 1 0 0 0 0
+ 5 6 1 0 0 0 0
+ 6 7 2 0 0 0 0
+ 6 11 1 0 0 0 0
+ 7 8 1 0 0 0 0
+ 8 9 2 0 0 0 0
+ 9 10 1 0 0 0 0
+ 10 11 2 0 0 0 0
+ 12 13 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 6 6 0 0 0 0 0 0 0 0 1 V2000
+ 2.2694 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.2694 -1.3318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.9376 -1.3318 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -2.2694 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.3409 -3.5516 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.9376 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 1 6 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 1 0 0 0 0
+ 3 6 1 0 0 0 0
+ 4 5 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 6 4 0 0 0 0 0 0 0 0 2 V2000
+ 2.6600 -2.6600 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.6600 -1.3320 0.0000 B 0 5 0 0 0 0 0 0 0 0 0 0
+ 1.3280 -1.3320 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.6600 0.0000 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.9880 -1.3320 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -1.3320 0.0000 Na 0 3 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 2 4 1 0 0 0 0
+ 2 5 1 0 0 0 0
+M CHG 2 2 -1 6 1
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+inactive
+
diff --git a/public/javascripts/toxcreate.js b/public/javascripts/toxcreate.js
index 68cd769..a5dc44c 100755
--- a/public/javascripts/toxcreate.js
+++ b/public/javascripts/toxcreate.js
@@ -101,6 +101,7 @@ $(function() {
success: function(data) {
if (view == "model") $("div#model_" + id).html(data);
if (view.match(/validation/)) $("dl#model_validation_" + id).html(data);
+ addExternalLinks();
},
error: function(data) {
//alert("loadModel error");
@@ -228,6 +229,10 @@ jQuery.fn.deleteModel = function(type, options) {
};
$(document).ready(function() {
+ addExternalLinks();
+});
+
+addExternalLinks = function() {
$('A[rel="external"]').each(function() {
$(this).attr('alt', 'Link opens in new window.');
$(this).attr('title', 'Link opens in new window.');
@@ -236,5 +241,4 @@ $(document).ready(function() {
window.open($(this).attr('href'));
return false;
});
-});
-
+};
diff --git a/views/classification_validation.haml b/views/classification_validation.haml
index 5649d7f..f25a321 100644
--- a/views/classification_validation.haml
+++ b/views/classification_validation.haml
@@ -1,33 +1,44 @@
%dt Correct predictions:
%dd
- = sprintf("%.2f", model.correct_predictions.to_f) if model.correct_predictions
- = '%'
+ = sprintf("%.2f", model.correct_predictions.to_f) if model.correct_predictions
+ = '%'
%dt
- %a{:href => "http://en.wikipedia.org/wiki/Receiver_operating_characteristic", :rel => "external"} Weighted area under ROC:
+ %a{:href => "http://en.wikipedia.org/wiki/Receiver_operating_characteristic", :rel => "external"} Weighted area under ROC:
%dd
- = sprintf("%.3f", model.weighted_area_under_roc.to_f) if model.weighted_area_under_roc
+ = sprintf("%.3f", model.weighted_area_under_roc.to_f) if model.weighted_area_under_roc
%dt
- %a{:href => "http://en.wikipedia.org/wiki/Sensitivity_and_specificity", :rel => "external"} Specificity:
+ %a{:href => "http://en.wikipedia.org/wiki/Sensitivity_and_specificity", :rel => "external"} Specificity:
%dd= sprintf("%.3f", model.specificity.to_f) if model.specificity
%dt
- %a{:href => "http://en.wikipedia.org/wiki/Sensitivity_and_specificity", :rel => "external"} Sensitivity:
+ %a{:href => "http://en.wikipedia.org/wiki/Sensitivity_and_specificity", :rel => "external"} Sensitivity:
%dd= sprintf("%.3f", model.sensitivity.to_f) if model.sensitivity
%dt
- %a{:href => "http://en.wikipedia.org/wiki/Confusion_matrix", :rel => "external"} Confusion Matrix:
-%dd
- %table
- %tr
- %td{:colspan => 2, :rowspan => 2}
- %th{:colspan => 2} Measured
- %tr
- %th{:bgcolor => "#CCD2DC"} active
- %th{:bgcolor => "#CCD2DC"} inactive
- %tr
- %th{:rowspan => 2} Predicted
- %th{:bgcolor => "#CCD2DC"} active
- %td= model.true_positives if model.true_positives
- %td= model.false_positives if model.false_positives
- %tr
- %th{:bgcolor => "#CCD2DC"} inactive
- %td= model.false_negatives if model.false_negatives
- %td= model.true_negatives if model.true_negatives
+ %a{:href => "http://en.wikipedia.org/wiki/Confusion_matrix", :rel => "external"} Confusion Matrix:
+- if model.confusion_matrix
+ - cm = YAML.load(model.confusion_matrix)
+ %dd
+ %table
+ %tr
+ %td{:colspan => 2, :rowspan => 2}
+ %th{:colspan => (cm.size - 1)} Measured
+ %tr
+ - (1..cm[0].size-1).each do |i|
+ %th{:bgcolor => "#CCD2DC"}
+ = cm[0][i]
+ %tr
+ %th{:rowspan => (cm.size - 1)} Predicted
+ - (0..cm[1].size-1).each do |i|
+ - if i == 0
+ %th{:bgcolor => "#CCD2DC"}
+ = cm[1][i]
+ - else
+ %td= cm[1][i]
+ - if cm.size > 2
+ - (2..cm.size-1).each do |i|
+ %tr
+ - (0..cm[i].size-1).each do |j|
+ - if j == 0
+ %th{:bgcolor => "#CCD2DC"}
+ = cm[i][j]
+ - else
+ %td= cm[i][j]
diff --git a/views/create.haml b/views/create.haml
index 757adc2..b706484 100644
--- a/views/create.haml
+++ b/views/create.haml
@@ -1,19 +1,13 @@
.input
- This service creates
- %ul
- %li
- = toggle_link("#lazar_description","lazar")
- %em= toggle_link("#classification","classification")
- models and
- %li
- = toggle_link("#lazar_description","lazar")
- %em= toggle_link("#regression","regression")
- models (experimental)
- from your uploaded datasets. Further modelling algorithms will be added in future versions.
-
%p
- Please read the
+ You will need to upload training data that includes chemical structures and their measured toxicity values, in
+ = link_to "Excel", '/help'
+ ,
+ = link_to "CSV", '/help'
+ or
+ = link_to "SDF", '/help'
+ file formats to create a prediction model. Please read the
= link_to "instructions for creating training datasets", '/help'
before submitting.
@@ -24,8 +18,10 @@
%label{:for => 'file'}
Upload training data in
= link_to "Excel", '/help'
- or
+ ,
= link_to "CSV", '/help'
+ or
+ = link_to "SDF", '/help'
format:
%input{:type => 'file', :name => 'file', :id => 'file', :size => '41'}
%input{ :type => "submit", :value => "Create model"}
@@ -43,6 +39,25 @@
= haml :endpoint, :layout => false
= haml :unit, :layout => false
+ %p
+ This service creates and validates new
+ %em= toggle_link("#classification","classification")
+ and
+ %em= toggle_link("#regression","regression")
+ structure-activity models from your experimental data. The models can be used to predict toxicity of new chemicals (e.g. for
+ %a{:href => "http://ec.europa.eu/environment/chemicals/reach/reach_intro.htm", :rel => "external"} REACH
+ purposes) and to reduce the need for animal testing. The following methods are currently available:
+ %ul
+ %li
+ = toggle_link("#lazar_description","lazar")
+ %em= toggle_link("#classification","classification")
+ models and
+ %li
+ = toggle_link("#lazar_description","lazar")
+ %em= toggle_link("#regression","regression")
+ models (experimental)
+ Further modelling algorithms may be added in future versions.
+
.login_notice
- if session[:username] == "guest"
diff --git a/views/help.haml b/views/help.haml
index 4882380..2b39d6c 100644
--- a/views/help.haml
+++ b/views/help.haml
@@ -1,4 +1,5 @@
= link_to "Back to model creation", '/create'
+%h2 Spreadsheets (Excel, CSV)
%p
Input files have two columns. Enter in the first column the chemical structure in
%a{:href => "http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification", :rel => "external"} SMILES
@@ -97,17 +98,18 @@
%h3 CSV example
.code
- %code
- %br SMILES, Hamster Carcinogenicity
- %br CC(=O)Nc1ccc(O)cc1, 1
- %br O=c1[nH]cnc2[nH]ncc12, 1
- %br CCCCNc1cc(cc(c1Oc2ccccc2)S(=O)(=O)N)C(=O)O, 1
- %br CC(C)(C)NCC(O)COc1cccc2NC(=O)CCc12, 1
- %br CN(C)CCCC1(OCc2cc(C#N)ccc21)c3ccc(F)cc3, 1
- %br CCC(CC)CCN1C(=O)CN=C(C2CCCCC2F)c3cc(Cl)ccc13, 0
- %br CCN(CC)CC(=O)Nc1c(C)cccc1C, 0
- %br CC(C)(C)NCC(O)COc1cccc2CC(O)C(O)Cc12, 0
- %br CN1CCCC1c2cccnc2, 0
+ %pre
+ :preserve
+ SMILES, Hamster Carcinogenicity
+ CC(=O)Nc1ccc(O)cc1, 1
+ O=c1[nH]cnc2[nH]ncc12, 1
+ CCCCNc1cc(cc(c1Oc2ccccc2)S(=O)(=O)N)C(=O)O, 1
+ CC(C)(C)NCC(O)COc1cccc2NC(=O)CCc12, 1
+ CN(C)CCCC1(OCc2cc(C#N)ccc21)c3ccc(F)cc3, 1
+ CCC(CC)CCN1C(=O)CN=C(C2CCCCC2F)c3cc(Cl)ccc13, 0
+ CCN(CC)CC(=O)Nc1c(C)cccc1C, 0
+ CC(C)(C)NCC(O)COc1cccc2CC(O)C(O)Cc12, 0
+ CN1CCCC1c2cccnc2, 0
%p
CSV examples for download:
@@ -120,3 +122,40 @@
(regression)
%p You can create CSV files in Excel: Create a sheet with two columns and export them as CSV file with the "Save As" option from the menu, selecting the CSV (comma delimited) format.
+
+%h2 SDF
+
+%p
+ Currently ToxCreate supports
+ %a{:href => "http://en.wikipedia.org/wiki/Chemical_table_file#SDF", :rel => "external"} SDF
+ files with a single data item as shown below (multiple data items will raise an error). You can also download an example SDF file:
+ = link_to "hamster_carcinogenicity.sdf", "/hamster_carcinogenicity.sdf"
+
+.code
+ %pre
+ -# keep empty lines -they are required by SDF
+ :preserve
+
+
+
+
+ 6 6 0 0 0 0 0 0 0 0 1 V2000
+ 1.3304 -1.0738 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.1104 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.3767 -0.4086 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.3767 -1.7390 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.1104 -2.1509 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -1.0738 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 1 5 2 0 0 0 0
+ 1 6 1 0 0 0 0
+ 2 3 2 0 0 0 0
+ 3 4 1 0 0 0 0
+ 4 5 1 0 0 0 0
+ M END
+ &gt; &lt;ActivityOutcome_CPDBAS_Hamster&gt;
+ inactive
+
+ $$$$
+
+
diff --git a/views/layout.haml b/views/layout.haml
index 174db9f..c76396d 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -14,7 +14,7 @@
.logo
%img{:src => "ToxCreate_rgb_72.png", :alt => 'ToxCreate', :align => 'right'}/
%br
- Create and evaluate models to predict toxicity
+ Creates computational models to predict toxicity
.index
%ul
%li{:class => ("selected" if /\/create|echa|ambit|feature/ =~ request.path )}
@@ -31,8 +31,9 @@
.content
.login_info
- User:
- %b= session[:username]
+ - if session[:username].size > 0
+ User:
+ %b= session[:username]
- if `hostname`.match(/ot-test/)
.notice
@@ -47,7 +48,18 @@
= yield
.footer
+ Disclaimer: ToxCreate uses state-of-the-art published and tested algorithms and methodologies with full validation information. However, just as with experimental measurements, computational predictions are subject to varying degrees of accuracy and uncertainty, so please read the full report carefully, particularly the validation information. No liability is accepted for any inaccuracy in predictions.
+ %p
+ - tag = `git tag`.split("\n").last
+ - tagdate = `git show #{tag}|grep Date`.chomp
+ Version:
+ = tag
+ ,
+ = tagdate
&copy;
%a{:href => 'http://www.in-silico.ch', :rel => "external"} in silico toxicology
2009-2011, powered by
%a{:href => 'http://www.opentox.org', :rel => "external"} <span style="color:#5D308A;font-family:arial,sans-serif,helvetica;letter-spacing:-1px;">Open</span><span style="color:#000;font-family:arial,sans-serif,helvetica;font-weight:bold;letter-spacing:-1px;">Tox</span>
+ (a project funded by the
+ %a{:href => "http://cordis.europa.eu/fp7/", :rel => "external"} 7th Framework Programme
+ of the European Commission)
diff --git a/views/model.haml b/views/model.haml
index e9d3b95..fe43a1f 100644
--- a/views/model.haml
+++ b/views/model.haml
@@ -43,10 +43,14 @@
- if model.error_messages
%dt Errors:
%dd= model.error_messages
+ - if CONFIG[:logger]=="debug"
+ %dt Task:
+ %dd
+ %a{:href => "#{model.task_uri}", :rel => "external"}
+ = model.task_uri
- if model.warnings
%dt Warnings:
-
- %dd
+ %dd
%a{:href => "#", :id => "show_model_#{model.id}_warnings"} show
%div{:id => "model_#{model.id}_warnings", :style => "display: none;"}= model.warnings
%dt Algorithm:
@@ -67,6 +71,8 @@
,
-#%a{:href => "#{model.training_dataset}.rdf"} RDF/XML
-#%em (experts) ,
+ %a{:href => "#{model.training_dataset}.sdf#{subjectstring}" } SDF
+ ,
%a{:href => "#{model.training_dataset}.yaml#{subjectstring}" } YAML
%em (experts)
- if model.feature_dataset
@@ -76,6 +82,8 @@
-#,
%a{:href => "#{model.feature_dataset}.xls#{subjectstring}"} Excel sheet
,
+ %a{:href => "#{model.feature_dataset}.sdf#{subjectstring}"} SDF
+ ,
%a{:href => "#{model.feature_dataset}.yaml#{subjectstring}"} YAML
%em (experts)
- if model.uri
diff --git a/views/style.sass b/views/style.sass
index ffae6a5..15ae256 100644
--- a/views/style.sass
+++ b/views/style.sass
@@ -220,6 +220,7 @@ body
.footer
margin: 0.5em
padding: 0.5em
+ font-size: small
.active
color: red
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-18 18:14:48 +0000