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authormr <mr@mrautenberg.de>2011-08-04 18:38:58 +0200
committermr <mr@mrautenberg.de>2011-08-04 18:38:58 +0200
commit6fe3a5648ad862087421081e33d5540d71856b68 (patch)
treecc1774b33379574279fe4e12a080a26175620357
parent13313d9fa8f5e4b29bbbc0ddeb0e455765b0774d (diff)
parentaa588fc87f1a892f3de903f5d60df68d4eaa6b52 (diff)
Merge branch 'release/v2.1.0'
Diffstat
-rw-r--r--.gitignore1
-rw-r--r--application.rb98
-rw-r--r--helper.rb52
-rw-r--r--model.rb10
-rw-r--r--public/EPAFHM.csv618
-rw-r--r--public/EPAFHM.xlsbin0 -> 55808 bytes
-rw-r--r--public/hamster_carcinogenicity.csv172
-rw-r--r--public/hamster_carcinogenicity.sdf2805
-rwxr-xr-xpublic/javascripts/toxcreate.js17
-rw-r--r--views/classification_validation.haml59
-rw-r--r--views/create.haml43
-rw-r--r--views/feature_table.haml12
-rw-r--r--views/help.haml81
-rw-r--r--views/layout.haml18
-rw-r--r--views/lazar.haml6
-rw-r--r--views/lazar_algorithm.haml32
-rw-r--r--views/model.haml18
-rw-r--r--views/models.haml2
-rw-r--r--views/neighbors.haml6
-rw-r--r--views/prediction.haml4
-rw-r--r--views/significant_fragments.haml2
-rw-r--r--views/style.sass1
22 files changed, 3840 insertions, 217 deletions
diff --git a/.gitignore b/.gitignore
index f138bed..079637f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,3 +3,4 @@ log/*
TODO
documentation/
*.*~
+.sass-cache
diff --git a/application.rb b/application.rb
index 8d96dbe..3b88700 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 + "\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')
@@ -350,8 +372,14 @@ post '/predict/?' do # post chemical name to model
confidence = nil
title = nil
db_activities = []
- lazar = OpenTox::Model::Lazar.new model.uri
+ lazar = OpenTox::Model::Lazar.find model.uri
prediction_dataset_uri = lazar.run({:compound_uri => @compound.uri, :subjectid => subjectid})
+ LOGGER.debug "Prediction dataset_uri: #{prediction_dataset_uri}"
+ if lazar.value_map
+ @value_map = lazar.value_map
+ else
+ @value_map = nil
+ end
prediction_dataset = OpenTox::LazarPrediction.find(prediction_dataset_uri, subjectid)
if prediction_dataset.metadata[OT.hasSource].match(/dataset/)
@predictions << {
@@ -366,12 +394,17 @@ post '/predict/?' do # post chemical name to model
:title => model.name,
:error => prediction.metadata[OT.error]
}
+ elsif prediction_dataset.value(@compound).nil?
+ @predictions << {
+ :title => model.name,
+ :error => "Not enough similar compounds in training dataset."
+ }
else
@predictions << {
:title => model.name,
:model_uri => model.uri,
- :prediction => prediction.metadata[OT.prediction],
- :confidence => prediction.metadata[OT.confidence]
+ :prediction => prediction_dataset.value(@compound),
+ :confidence => prediction_dataset.confidence(@compound)
}
end
end
@@ -385,8 +418,13 @@ post "/lazar/?" do # get detailed prediction
@page = 0
@page = params[:page].to_i if params[:page]
@model_uri = params[:model_uri]
- lazar = OpenTox::Model::Lazar.new @model_uri
+ lazar = OpenTox::Model::Lazar.find @model_uri
prediction_dataset_uri = lazar.run(:compound_uri => params[:compound_uri], :subjectid => session[:subjectid])
+ if lazar.value_map
+ @value_map = lazar.value_map
+ else
+ @value_map = nil
+ end
@prediction = OpenTox::LazarPrediction.find(prediction_dataset_uri, session[:subjectid])
@compound = OpenTox::Compound.new(params[:compound_uri])
haml :lazar
diff --git a/helper.rb b/helper.rb
index 2fe8785..698fd3e 100644
--- a/helper.rb
+++ b/helper.rb
@@ -51,23 +51,60 @@ helpers do
haml :js_link, :locals => {:name => name, :destination => destination, :method => "toggle"}, :layout => false
end
- def sort(descriptors)
+ def sort(descriptors,value_map)
features = {:activating => [], :deactivating => []}
- descriptors.each { |d| features[d[OT.effect].to_sym] << {:smarts => d[OT.smarts],:p_value => d[OT.pValue]} }
+ descriptors.each do |d|
+ if !value_map.empty?
+ features[:activating] << {:smarts => d[OT.smarts],:p_value => d[OT.pValue]} if d[OT.effect] == 2
+ features[:deactivating] << {:smarts => d[OT.smarts],:p_value => d[OT.pValue]} if d[OT.effect] == 1
+ else
+ if d[OT.effect] =~ TRUE_REGEXP
+ features[:activating] << {:smarts => d[OT.smarts],:p_value => d[OT.pValue]}
+ elsif d[OT.effect] =~ FALSE_REGEXP
+ features[:deactivating] << {:smarts => d[OT.smarts],:p_value => d[OT.pValue]}
+ end
+ end
+ end
features
end
- def compound_image(compound,descriptors)
- haml :compound_image, :locals => {:compound => compound, :features => sort(descriptors)}, :layout => false
+ def compound_image(compound,descriptors,value_map)
+ haml :compound_image, :locals => {:compound => compound, :features => sort(descriptors,value_map)}, :layout => false
end
- def activity_markup(activity)
+ def activity_markup(activity,value_map)
+ if value_map and !value_map.empty?
+ if value_map.size == 2
+ activity = value_map.index(activity) if value_map.has_value? activity
+ if activity.to_i == 2
+ haml ".active #{value_map[activity]}", :layout => false
+ elsif activity.to_i == 1
+ haml ".inactive #{value_map[activity]}", :layout => false
+ else
+ haml ".other #{activity.to_s}", :layout => false
+ end
+ else
+ haml ".other #{activity.to_s}", :layout => false
+ end
+ elsif OpenTox::Algorithm::numeric? activity
+ haml ".other #{sprintf('%.03g', activity.to_f)}", :layout => false
+ else
+ haml ".other #{activity.to_s}", :layout => false
+ end
+=begin
case activity.class.to_s
when /Float/
haml ".other #{sprintf('%.03g', activity)}", :layout => false
when /String/
- haml ".other #{activity.to_s}", :layout => false
- else
+ case activity
+ when "true"
+ haml ".active active", :layout => false
+ when "false"
+ haml ".inactive inactive", :layout => false
+ else
+ haml ".other #{activity.to_s}", :layout => false
+ end
+ else
if activity #true
haml ".active active", :layout => false
elsif !activity # false
@@ -76,6 +113,7 @@ helpers do
haml ".other #{activity.to_s}", :layout => false
end
end
+=end
end
def neighbors_navigation
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/EPAFHM.csv b/public/EPAFHM.csv
new file mode 100644
index 0000000..9092abc
--- /dev/null
+++ b/public/EPAFHM.csv
@@ -0,0 +1,618 @@
+"STRUCTURE_SMILES","LC50_mmol"
+"C1=CC(C=O)=CC(OC)=C1OCCCCCC",1.13E-02
+"C1(OC)=C([N+]([O-])=O)C(C=O)=CC(Br)=C1O",2.66E-01
+"CCCCCCCCOC(=O)C1=CC=CC(C(=O)OCCCCCCCC)=C1",
+"C1=CC(Cl)=CC=C1OC2=C([N+](=O)[O-])C=CC=C2",7.69E-03
+"CC1=C(NC=O)C=CC=C1Cl",2.75E-01
+"CCCCOC(=O)C1=CC=CC(C(=O)OCCCC)=C1",3.23E-03
+"C(C1=CC=CC=C1)(C2=CC=CC=C2)(O)C#C",5.33E-02
+"CCCSCCSCCC",4.22E-02
+"CCCCCCCCOC(=O)C1=CC=C(C(=O)OCCCCCCCC)C=C1",
+"OCCCCOC(=O)C1=CC=CC=C1C(=O)OCCCCOC(=O)C2=CC=CC=C2C(=O)OCCCCO",
+"CCCSCCCCSCCC",1.45E-02
+"C1([N+](=O)[O-])=CC=C(C)C=C1OP(=O)(OC2=C([N+](=O)[O-])C=CC(C)=C2)OC3=C([N+]([O-])=O)C=CC(C)=C3",
+"C1=C([N+]([O-])=O)C=CC=C1P(=O)(C2=CC([N+](=O)[O-])=CC=C2)C3=CC([N+](=O)[O-])=CC=C3",
+"ClCCOC(=O)NC1CCCCC1",1.70E-01
+"O=C1C(C2=CC=CC=C2)(C(=O)NC(=O)N1)CC",2.08E+00
+"OC1=C(C=C(C=C1)[N+](=O)[O-])[N+](=O)[O-]",5.92E-02
+"NC(=O)OCC",5.88E+01
+"[O-]C(C1=CC=CC=C1O)=O.[Na+]",1.25E+01
+"C1=CC=CC=C1C(=O)N",5.46E+00
+"CC[N+](CC)(CC)CC1(=CC=CC=C1).[Cl-]",7.07E-01
+"CN(C)N",1.31E-01
+"CC(C(C(NC([O-])=N1)=O)(C1=O)CC)CCC.[Na+]",1.99E-01
+"N1C(=O)C(CC)(CCC(C)C)C(=O)NC1=O",3.77E-01
+"O=C1C2=C(N=CN2C)N(C(=O)N1C)C",7.78E-01
+"C1=CC=C2C(=C1)C(=O)C(C)=CC2=O",6.39E-04
+"OC1=C(Cl)C(Cl)=C(Cl)C=C1Cl",4.44E-03
+"OC1=CC(C)=C(Cl)C=C1",3.84E-02
+"[H]Cl.C1=CC=CC=C1CC2=NCCN2",1.80E+00
+"O=S(O)(O)=O.C1(=CC=CC=C1CC(N)C).C2=CC=CC=C2CC(N)C",7.82E-02
+"O(CC)CC",3.45E+01
+"O=C2N5[C@@]3([H])[C@@]1([H])[C@](C[C@]4([H])N(C7)CC[C@]34C6=C5C=CC=C6)([H])C7=CCO[C@]([H])1C2.O=C9N%12[C@@]%10([H])[C@@]8([H])[C@](C[C@]%11([H])N(C%14)CC[C@]%10%11C%13=C%12C=CC=C%13)([H])C%14=CCO[C@]([H])8C9.O=S(O)(O)=O",1.11E-03
+"NC1=CC=CC=C1",1.13E+00
+"O=C(OC1=C2C(=CC=C1)C=CC=C2)NC",4.35E-02
+"CCO",3.19E+02
+"C1(=NC=CC=C1C2CCCN2C).OS(O)(=O)=O",5.30E-02
+"C1(O)=CC=CC=C1C(=O)N",7.36E-01
+"O=C1NC(=O)NC=C1",
+"CCCCCC=O",1.75E-01
+"O=C1OC2=CC=CC=C2C(O)=C1CC3=C(O)C4=CC=CC=C4OC3=O",1.52E-02
+"C1(C=O)=CC=C(OC2=CC=CC=C2)C=C1",2.32E-02
+"CO",9.17E+02
+"OC(C)C",1.44E+02
+"CC(=O)C",1.23E+02
+"ClC(Cl)Cl",5.92E-01
+"CS(=O)C",4.35E+02
+"ClC(C(Cl)(Cl)Cl)(Cl)Cl",6.00E-03
+"OC1=C(C=C(C(=C1CC2=C(C(=CC(=C2Cl)Cl)Cl)O)Cl)Cl)Cl",5.16E-05
+"C1=CC(=CC=C1N)C(=O)CC",9.79E-01
+"OCCC",7.57E+01
+"CCCCO",2.33E+01
+"CCCCCO",5.36E+00
+"C1=CC=CC=C1",2.25E-01
+"CC(Cl)(Cl)Cl",3.55E-01
+"[S-]C1=NC(C(C(C)CCC)(CC)C(N1)=O)=O.[Na+]",9.91E-02
+"CC#N",4.01E+01
+"CC=O",7.67E-01
+"ClCCl",3.89E+00
+"IC(I)I",7.42E-03
+"[N+](C)(C)(C)C.[Cl-]",4.22E+00
+"CC(C)(C)O",8.65E+01
+"C(F)(F)(F)CO",1.19E+00
+"CC(=O)C(C)(C)C",8.69E-01
+"ClC(C(Cl)Cl)(Cl)Cl",3.72E-02
+"CC1(C)NC(=O)NC1=O",1.29E+02
+"CCC(O)(C)CC",6.58E+00
+"C#CC(O)(C)CC",1.24E+01
+"C1CCCC(C#C)(O)C1",2.06E+00
+"CCCCOCCOP(=O)(OCCOCCCC)OCCOCCCC",2.81E-02
+"OCC(C)C",1.93E+01
+"CC(Cl)CCl",1.12E+00
+"NCC(N)C",1.36E+01
+"CC(O)CC",4.95E+01
+"CCC(=O)C",4.47E+01
+"OC(C)CN",3.36E+01
+"ClC(CCl)Cl",6.12E-01
+"ClC(=CCl)Cl",3.36E-01
+"CC(=O)OC",4.82E+00
+"ClC(C(Cl)Cl)Cl",1.21E-01
+"C1(C)(C)CCCC(C)=C1C=CC(C)=O",2.65E-02
+"ClC1=C(O)C(Cl)=CC(=C1)C(C2=CC(Cl)=C(O)C(=C2)Cl)(C)C",3.63E-03
+"C(C1C=CC(=CC=1)O)(CC)(C)C",1.58E-02
+"C1CC(CCC1(N)C)C(C)(N)C",3.83E-01
+"ClC(Cl)C1=C(Cl)C=CC=C1Cl",4.22E-03
+"C1=CC=C2C=CC=C3C2=C1CC3",1.12E-02
+"CC1=CNC2=C1C=CC=C2",6.74E-02
+"O=C([C@](C(C=C4OC)=C(C=C4OC)OC3)([H])[C@]3([H])O2)C(C=C5)=C2C1=C5O[C@@H]([C@@](C)=C)C1",1.32E-05
+"O=C2C1=NC3=C(C=C(C)C(C)=C3)N(C[C@H](O)[C@H](O)[C@H](O)CO)C1=NC(N2)=O",
+"C1=CC=CC=C1OC(=O)C2=CC=CC=C2C(=O)OC3=CC=CC=C3",2.51E-04
+"O=C1C2=C(C=CC=C2)C(=O)C3=C1C=CC=C3",
+"CCOC(=O)C1=CC=CC=C1C(=O)OCC",1.43E-01
+"C1=CC=C(C(=O)OCCCC)C(=C1)C(=O)OCCCC",3.5900E-03
+"CCC1=C(Br)C(Br)=C(Br)C(Br)=C1Br",
+"O=C1C2=C(C=CC=C2)N=NN1CSP(=S)(OC)OC",2.02E-04
+"C1=CC=CC=C1NC(=O)C2=C(O)C=CC=C2",1.85E-02
+"Cl\C(Cl)=C(Cl)/C(Cl)=C(Cl)\Cl",3.45E-04
+"OC1=C(C(=C(C(=C1Cl)Cl)Cl)Cl)Cl",9.12E-04
+"OC1=C(C=C(C=C1Cl)Cl)Cl",2.48E-02
+"OC1=CC(C(F)(F)F)=C([N+]([O-])=O)C=C1",4.41E-02
+"C1(N)=CC=CC=C1C(=O)N",2.90E+00
+"OC1=C([N+]([O-])=O)C=CC=C1",1.15E+00
+"OC1=C(C=C(C=C1C(CC)C)[N+](=O)[O-])[N+](=O)[O-]",2.23E-03
+"O=CC1=CC=CC=C1O",1.88E-02
+"OC1=CC=CC2=CC=CC=C12",3.21E-02
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diff --git a/public/EPAFHM.xls b/public/EPAFHM.xls
new file mode 100644
index 0000000..fbfb016
--- /dev/null
+++ b/public/EPAFHM.xls
Binary files differ
diff --git a/public/hamster_carcinogenicity.csv b/public/hamster_carcinogenicity.csv
index f087233..52d89a3 100644
--- a/public/hamster_carcinogenicity.csv
+++ b/public/hamster_carcinogenicity.csv
@@ -1,86 +1,86 @@
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+OCC1CO1,true
+O=C2C1=C(OC)C=C(OC)C(Cl)=C1O[C@]32C(OC)=CC(C[C@@](C)3[H])=O,false
+ClC1=C(C(=C(C(=C1Cl)Cl)Cl)Cl)Cl,true
+NN,true
+OS(=O)(=O)O.NN,true
+CC(=O)N(O)C1=CC2=C(C=C1)C3=CC=CC=C3C2,true
+OCCNN,false
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+OC(=O)C1=CC=NC=C1,false
+O=C(NC1=CC=CC(=C1)Cl)OC(C)C,false
+O=C(NC1=CC=CC=C1)OC(C)C,false
+[O-]C(C)=O.[O-]C(C)=O.[Pb+2].[OH-].[OH-].[Pb+2].[OH-].[OH-].[Pb+2],false
+CN(C)CCN(CC2=CC=CS2)C1=NC=CC=C1.Cl,false
+NC1=C2C(=NC(=N1)N)N=CC(=N2)CN(C3=CC=C(C=C3)C(=O)N[C@@H](CCC(=O)O)C(=O)O)C,false
+CN(N)C=O,true
+O=C(C(=C)C)OC,false
+CNN,true
+O=C(C1=CC=CN=C1)CCCN(N=O)C,false
+CC1=CC(=O)NC(=S)N1,true
+CC(C(O)=O)(OC1=CC=C(C=C1)C2CCCC3=C2C=CC=C3)C,false
+O=N[O-].[Na+],false
+[O-][N+](C1=CC=C(C2=CSC(NC(C)=O)=N2)O1)=O,true
+[O-][N+](=O)C1=CC=C(O1)C2=CSC(=N2)NC=O,true
+O=[N+](C1=CC=C2C3=C1C=CC=C3CC2)[O-],false
+N(CC(CO)O)(CC(O)C)N=O,true
+N(CC(CO)O)(CC(C)=O)N=O,true
+N(CC(CO)O)(CCO)N=O,false
+O=C(C)CN(N=O)CCO,true
+C1C(N(C(CN1N=O)C)C)C,true
+N(CC(C)=O)(CC=C)N=O,true
+N(CC(CO)O)(C)N=O,true
+O=NN1CCOCC1,true
+N1C=CC=C(C=1)C2N(N=O)CCC2,true
+C1=CC=C(C=[N+]1[O-])C2CCCN2N=O,false
+O=NN1CCCCC1,true
+O=NN1CCCC1,true
+O=C(N(CC(C)=O)N=O)NCCCl,true
+N(C(=O)N)(N=O)CC(C)=O,true
+C1(CCN=C=S)=CC=CC=C1,false
+O=C1C(C2=CC=CC=C2)(C(=O)NC(=O)N1)CC,false
+C1=C2C(=CC=C1NC3=CC=CC=C3)C=CC=C2,false
+O=C1N2C(C3=C(C=CC=C3)CC2)CN(C1)C(=O)C4CCCCC4,false
+C1(=CC(=C(O)C=C1)O)C(O)=O,false
+O=C1C2=C(C=C(C=C2O)O)O/C(=C\1O)C3=CC(=C(C=C3)O)O.O.O,false
+C1=C(C=CC(=C1)C(C2=CC=C(N)C(=C2)C)=C3C=CC(=N)C=C3)N.[H]Cl,false
+C(C1=CC=C(C=C1)N)(C2=CC=C(C=C2)N)=C3C=CC(C=C3)=N.[H]Cl,false
+OC2=CC1=C(C(O)=C2)C(C(O[C@@H]4O[C@@H]([C@H]([C@H](O)[C@H]4O)O)CO[C@H]3[C@H](O)[C@H](O)[C@H]([C@H](C)O3)O)=C(C5=CC(O)=C(C=C5)O)O1)=O,false
+ClC(=CCl)Cl,false
+NC(=O)OCC,true
+C=CCl,true
+N#[N+]C1=CC=CC=C1.F[B-](F)(F)F,false
+C1(CN(CC(N1N=O)C)N=O)C,true
+N(CCN(C)C)(C)N=O,true
+C1(CN(N=O)CC(O1)C)C,true
+O1C(N(CC1C)N=O)=O,true
+CCOC(=O)N(C)N=O,true
+C1N(COC1)N=O,true
+O=C(N(CCC1=CC=CC=C1)N=O)N,true
+O=NN1CCC1,true
+F[B-](F)(F)F.[Na+],false
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
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+ 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
+
+$$$$
+
+
+
+ 17 19 0 0 0 0 0 0 0 0 1 V2000
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+ 15 16 1 0 0 0 0
+ 15 17 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 18 19 0 0 0 0 0 0 0 0 2 V2000
+ 3.2537 -3.5906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 16 17 1 0 0 0 0
+ 16 18 2 0 0 0 0
+M CHG 2 16 1 17 -1
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 6 6 0 0 0 0 0 0 0 0 1 V2000
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+ 3 4 1 0 0 0 0
+ 4 5 1 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+inactive
+
+$$$$
+
+
+
+ 13 13 0 0 0 0 0 0 0 0 1 V2000
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+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+inactive
+
+$$$$
+
+
+
+ 3 0 0 0 0 0 0 0 0 0 2 V2000
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+ 0.0000 -0.3400 0.0000 Cl 0 5 0 0 0 0 0 0 0 0 0 0
+M CHG 3 1 -1 2 2 3 -1
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+inactive
+
+$$$$
+
+
+
+ 6 4 0 0 0 0 0 0 0 0 2 V2000
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+ 2 4 1 0 0 0 0
+ 2 5 1 0 0 0 0
+M CHG 3 4 -1 5 -1 6 2
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+inactive
+
+$$$$
+
+
+
+ 0 0 0 0 0 0 0 0 0 0 1 V2000
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+inactive
+
+$$$$
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+ 21 22 0 0 0 0 0 0 0 0 1 V2000
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+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+inactive
+
+$$$$
+
+
+
+ 4 3 0 0 0 0 0 0 0 0 1 V2000
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+ 3 4 1 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 5 4 0 0 0 0 0 0 0 0 1 V2000
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+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+inactive
+
+$$$$
+
+
+
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+ 14 18 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+inactive
+
+$$$$
+
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+
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+ 10 11 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+inactive
+
+$$$$
+
+
+
+ 18 19 0 0 0 0 0 0 0 0 1 V2000
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+ 15 16 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 19 20 0 0 0 0 0 0 0 0 1 V2000
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+
+ 3 2 0 0 0 0 0 0 0 0 1 V2000
+ 2.3030 -0.6656 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1515 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -0.6656 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 2 0 0 0 0
+ 2 3 1 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 13 12 0 0 0 0 0 0 0 0 2 V2000
+ 0.0000 -1.1513 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.3274 -1.1513 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
+ 2.6611 -1.1513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.3217 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6554 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.3159 -1.1513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6554 -2.3025 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.3217 -2.3025 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.6611 -6.2911 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.6611 -4.9636 0.0000 B 0 5 0 0 0 0 0 0 0 0 0 0
+ 1.3274 -4.9636 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.6611 -3.6299 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.9885 -4.9636 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 3 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 2 0 0 0 0
+ 3 8 1 0 0 0 0
+ 4 5 1 0 0 0 0
+ 5 6 2 0 0 0 0
+ 6 7 1 0 0 0 0
+ 7 8 2 0 0 0 0
+ 9 10 1 0 0 0 0
+ 10 11 1 0 0 0 0
+ 10 12 1 0 0 0 0
+ 10 13 1 0 0 0 0
+M CHG 2 2 1 10 -1
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+inactive
+
+$$$$
+
+
+
+ 12 12 0 0 0 0 0 0 0 0 1 V2000
+ 3.4560 -1.3271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6103 -1.9906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6103 -3.3247 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.4560 -3.9882 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.3017 -3.3247 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.3017 -1.9906 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1543 -1.3271 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -1.9906 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1543 -3.9882 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.7577 -3.9882 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 6.9120 -3.3247 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.4560 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 1 6 1 0 0 0 0
+ 1 12 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 1 0 0 0 0
+ 3 10 1 0 0 0 0
+ 4 5 1 0 0 0 0
+ 5 6 1 0 0 0 0
+ 5 9 1 0 0 0 0
+ 6 7 1 0 0 0 0
+ 7 8 2 0 0 0 0
+ 10 11 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 9 8 0 0 0 0 0 0 0 0 1 V2000
+ 4.6053 -1.9954 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.4522 -1.3257 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.2992 -1.9954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1530 -1.3257 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -1.9954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1530 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6053 -3.3210 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.7514 -1.3257 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 6.9045 -1.9954 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 1 7 1 0 0 0 0
+ 1 8 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 1 0 0 0 0
+ 4 5 1 0 0 0 0
+ 4 6 1 0 0 0 0
+ 8 9 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 10 10 0 0 0 0 0 0 0 0 1 V2000
+ 0.6656 -1.1543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.9968 -1.1543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.6577 -2.3040 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.9889 -2.3040 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6545 -1.1543 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.9968 -3.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.6656 -3.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -2.3040 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -4.6079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 1 8 1 0 0 0 0
+ 1 10 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 1 0 0 0 0
+ 3 6 1 0 0 0 0
+ 4 5 2 0 0 0 0
+ 6 7 1 0 0 0 0
+ 7 8 1 0 0 0 0
+ 7 9 1 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 9 9 0 0 0 0 0 0 0 0 1 V2000
+ 2.1136 -0.3740 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.3772 -0.7820 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.3772 -2.1136 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.1136 -2.5272 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.3316 -1.4506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -1.4506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.4538 -2.8956 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.6665 -2.3572 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.4538 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 1 5 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 2 9 2 0 0 0 0
+ 3 4 1 0 0 0 0
+ 3 7 1 0 0 0 0
+ 4 5 1 0 0 0 0
+ 5 6 1 0 0 0 0
+ 7 8 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 9 8 0 0 0 0 0 0 0 0 1 V2000
+ 0.0000 -1.1552 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.6644 -2.3044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.9932 -2.3044 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.6576 -1.1552 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.9932 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.9924 -1.1552 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6568 -2.3044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.6568 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.9855 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 1 0 0 0 0
+ 4 5 2 0 0 0 0
+ 4 6 1 0 0 0 0
+ 6 7 1 0 0 0 0
+ 6 8 1 0 0 0 0
+ 8 9 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 7 7 0 0 0 0 0 0 0 0 1 V2000
+ 3.5169 -2.1419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.3050 -1.5998 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.4416 -0.2777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.7417 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.4072 -1.1547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1503 -2.2653 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -1.5998 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 1 5 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 2 6 1 0 0 0 0
+ 3 4 1 0 0 0 0
+ 4 5 1 0 0 0 0
+ 6 7 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 14 14 0 0 0 0 0 0 0 0 1 V2000
+ 1.9935 -3.4527 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.3316 -2.3044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.9935 -1.1482 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.3251 -1.1482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.9869 -2.3044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.3186 -2.3044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.9804 -1.1482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.3120 -1.1482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.9739 -2.3044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.3120 -3.4527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.9804 -3.4527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.3316 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -2.3044 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 2 0 0 0 0
+ 2 3 1 0 0 0 0
+ 2 14 1 0 0 0 0
+ 3 4 1 0 0 0 0
+ 3 12 1 0 0 0 0
+ 4 5 1 0 0 0 0
+ 5 6 1 0 0 0 0
+ 6 7 2 0 0 0 0
+ 6 11 1 0 0 0 0
+ 7 8 1 0 0 0 0
+ 8 9 2 0 0 0 0
+ 9 10 1 0 0 0 0
+ 10 11 2 0 0 0 0
+ 12 13 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 6 6 0 0 0 0 0 0 0 0 1 V2000
+ 2.2694 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.2694 -1.3318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.9376 -1.3318 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -2.2694 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.3409 -3.5516 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.9376 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 1 6 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 1 0 0 0 0
+ 3 6 1 0 0 0 0
+ 4 5 2 0 0 0 0
+M END
+> <ActivityOutcome_CPDBAS_Hamster>
+active
+
+$$$$
+
+
+
+ 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 d9946c4..91789f8 100755
--- a/public/javascripts/toxcreate.js
+++ b/public/javascripts/toxcreate.js
@@ -4,10 +4,10 @@ $(function() {
var id = id;
this.bind("click", function() {
if($("a#show_model_" + id + "_warnings").html()=="show") {
- $("dd#model_" + id + "_warnings").slideDown("slow");
+ $("div#model_" + id + "_warnings").slideDown("slow");
$("a#show_model_" + id + "_warnings").html("hide");
}else{
- $("dd#model_" + id + "_warnings").slideUp("slow");
+ $("div#model_" + id + "_warnings").slideUp("slow");
$("a#show_model_" + id + "_warnings").html("show");
}
return false;
@@ -50,7 +50,7 @@ $(function() {
if( status_before != status_after) {
$("span#model_" + id + "_status").html(data);
loadModel(id, 'model');
- if (status_after == "Completed") id = -1;
+ if (status_after == "Completed" || status_after == "Error") id = -1;
}
},
error: function(data) {
@@ -77,8 +77,7 @@ $(function() {
if (progress == "100") return -1;
$("div#model_" + id + "_progress").progressbar("value", parseInt(progress));
- $("div#model_" + id + "_progress").attr({title: parseInt(progress) + "%", alt: parseInt(progress) + "%"});
- //$("div#model_" + id + "_progress").attr("alt", parseInt(progress) + "%");
+ $("div#model_" + id + "_progress").attr({title: parseInt(progress) + "%"});
},
error: function(data) {
id = -1;
@@ -101,6 +100,7 @@ $(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 +228,10 @@ 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 +240,4 @@ $(document).ready(function() {
window.open($(this).attr('href'));
return false;
});
-});
-
+};
diff --git a/views/classification_validation.haml b/views/classification_validation.haml
index 41362ba..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", :target => "_blank"} 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", :target => "_blank"} 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", :target => "_blank"} 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", :target => "_blank"} 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/feature_table.haml b/views/feature_table.haml
index a8a153f..7c57331 100644
--- a/views/feature_table.haml
+++ b/views/feature_table.haml
@@ -2,7 +2,11 @@
- unless features[:activating].empty?
%tr
%th
- activating
+ - if @value_map.empty?
+ activating
+ - else
+ predominatly in compounds with activity
+ = "\"#{@value_map[@value_map.keys.sort.last]}\""
(
%a{:href => "http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html", :rel => "external"} SMARTS
)
@@ -15,7 +19,11 @@
- unless features[:deactivating].empty?
%tr
%th
- deactivating
+ - if @value_map.empty?
+ deactivating
+ - else
+ predominatly in compounds with activity
+ = "\"#{@value_map[@value_map.keys.sort.first]}\""
(
%a{:href => "http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html", :rel => "external"} SMARTS
)
diff --git a/views/help.haml b/views/help.haml
index 3d39641..f602dff 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
@@ -85,26 +86,76 @@
%td 0
%p
- Excel example file for download:
- = link_to "hamster_carcinogenicity.xls", "/hamster_carcinogenicity.xls"
+ Excel examples for download:
+%ul
+ %li
+ = link_to "hamster_carcinogenicity.xls", "/hamster_carcinogenicity.xls"
+ (classification)
+ %li
+ = link_to "EPAFHM.xls", "/EPAFHM.xls"
+ (regression)
%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 example for download:
- = link_to "hamster_carcinogenicity.csv", "/hamster_carcinogenicity.csv"
+ CSV examples for download:
+%ul
+ %li
+ = link_to "hamster_carcinogenicity.csv", "/hamster_carcinogenicity.csv"
+ (classification)
+ %li
+ = link_to "EPAFHM.csv", "/EPAFHM.csv"
+ (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/lazar.haml b/views/lazar.haml
index 3f1d030..870fcab 100644
--- a/views/lazar.haml
+++ b/views/lazar.haml
@@ -18,8 +18,8 @@
%th Supporting information
%tr
- %td.image= compound_image(@compound,@prediction.descriptors(@compound))
- %td= activity_markup(@prediction.value(@compound))
+ %td.image= compound_image(@compound,@prediction.descriptors(@compound),@value_map)
+ %td= activity_markup(@prediction.value(@compound), @value_map)
%td= sprintf('%.03g', @prediction.confidence(@compound))
%td
%ul
@@ -40,7 +40,7 @@
%tr#fragments{ :style => "display: none;" }
%td{:colspan => '4'}
= hide_link('#fragments')
- = haml :feature_table, :locals => {:features => sort(@prediction.descriptors(@compound))}, :layout => false
+ = haml :feature_table, :locals => {:features => sort(@prediction.descriptors(@compound),@value_map)}, :layout => false
%tbody#neighbors
= haml :neighbors, :locals => {:neighbors => @prediction.neighbors(@compound), :page => @page}, :layout => false
diff --git a/views/lazar_algorithm.haml b/views/lazar_algorithm.haml
index 85823b5..76a993b 100644
--- a/views/lazar_algorithm.haml
+++ b/views/lazar_algorithm.haml
@@ -32,15 +32,29 @@
%p
= toggle_link "#significant_fragments", "Significant fragments"
are highlighted in the structure display as follows:
- %ul
- %li
- .active activating fragments
- %li
- .inactive deactivating fragments
- %li
- .inconclusive regions, where activating and deactivating fragments overlap
- %li
- .other inert parts
+ - if @value_map.empty?
+ %ul
+ %li
+ .active activating fragments
+ %li
+ .inactive deactivating fragments
+ %li
+ .inconclusive regions, where activating and deactivating fragments overlap
+ %li
+ .other inert parts
+ - else
+ %ul
+ %li
+ .active= "features that occur predominately in compounds with activity: \"#{@value_map[@value_map.keys.sort.last]}\""
+ %li
+ .inactive= "features that occur predominately in compounds with activity: \"#{@value_map[@value_map.keys.sort.first]}\""
+ %li
+ .inconclusive regions, where fragments from different classes overlap
+ %li
+ .other inert parts
+ - if @value_map.size > 2
+ .notice Incomplete implementation of feature highlighting and display of significant fragments. Only features for 2 classes are shown!
+
%p
Please keep in mind that predictions are based on the measured activities of neighbors.
diff --git a/views/model.haml b/views/model.haml
index b4b3c59..e688ae9 100644
--- a/views/model.haml
+++ b/views/model.haml
@@ -24,7 +24,7 @@
#{js}
});
- %div{:id => "model_#{model.id}_progress", :class => "model_progress", :title => "#{percentage_completed}%", :alt => "#{percentage_completed}%"}
+ %div{:id => "model_#{model.id}_progress", :class => "model_progress", :title => "#{percentage_completed}%"}
//= haml :model_progress, :locals=>{:percentage_completed=>percentage_completed}, :layout => false
- if is_authorized(model.web_uri, "DELETE")
%a{:href => url_for("/model/#{model.id}"), :id => "delete_#{model.id}", :class => 'delete_link'}
@@ -36,17 +36,23 @@
%br
%dt Started:
- %dd= Time.parse(model.created_at.to_s).strftime("%m/%d/%Y - %I:%M:%S%p") if model.created_at
+ %dd= Time.parse(model.created_at.to_s).strftime("%m/%d/%Y - %I:%M:%S%p %Z") if model.created_at
- if model.nr_compounds
%dt Training compounds:
%dd= model.nr_compounds
- if model.error_messages
%dt Errors:
%dd= model.error_messages
+ - if CONFIG[:logger]=="debug"
+ %dt Task:
+ %dd
+ %a{:href => "#{model.task_uri}", :id => "model_#{model.id}_task_link", :rel => "external"}
+ = model.task_uri
- if model.warnings
%dt Warnings:
- %a{:href => "#", :id => "show_model_#{model.id}_warnings"} show
- %dd{:id => "model_#{model.id}_warnings", :style => "display: none;"}= model.warnings
+ %dd
+ %a{:href => "#", :id => "show_model_#{model.id}_warnings"} show
+ %div{:id => "model_#{model.id}_warnings", :style => "display: none;"}= model.warnings
%dt Algorithm:
%dd= toggle_link("#lazar_description","lazar")
- if model.type
@@ -65,6 +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
@@ -74,6 +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/models.haml b/views/models.haml
index 6724807..9ab2858 100644
--- a/views/models.haml
+++ b/views/models.haml
@@ -21,3 +21,5 @@
- if @models
- @models.each do |model|
= haml :model, :locals=>{:model=>model,:subjectstring=>subjectstring}, :layout => false
+-if @models.size == 0
+ .notice There are currently no models. You have to create a model first.
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 2df9230..e2d65fa 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -13,8 +13,8 @@
- neighbor_id += 1
- compound = OpenTox::Compound.new(neighbor[OT.compound])
%tr
- %td.image= compound_image(compound,@prediction.descriptors(compound))
- %td= activity_markup(neighbor[OT.measuredActivity])
+ %td.image= compound_image(compound,@prediction.descriptors(compound),@value_map)
+ %td= activity_markup(neighbor[OT.measuredActivity], @value_map)
%td= sprintf('%.03g', neighbor[OT.similarity])
%td
%ul
@@ -39,5 +39,5 @@
%tr{:id => "fragments#{neighbor_id}", :style => "display: none;" }
%td{:colspan => '4'}
= hide_link("#fragments#{neighbor_id}")
- = haml :feature_table, :locals => {:features => sort(@prediction.descriptors(compound))}, :layout => false
+ = haml :feature_table, :locals => {:features => sort(@prediction.descriptors(compound),@value_map)}, :layout => false
diff --git a/views/prediction.haml b/views/prediction.haml
index 9bb3f76..682b979 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -16,7 +16,7 @@
- if p[:measured_activities]
%br
- p[:measured_activities].each do |a|
- = activity_markup(a)
+ = activity_markup(a, @value_map)
%br
(
%a{:href => "#", :id => "linkTrainingData#{p.object_id}"} Measured activity
@@ -29,7 +29,7 @@
- elsif p[:error]
%br= p[:error]
- else
- = activity_markup(p[:prediction])
+ = activity_markup(p[:prediction], @value_map)
- if p[:confidence]
%br
(
diff --git a/views/significant_fragments.haml b/views/significant_fragments.haml
index bd39826..8cddf43 100644
--- a/views/significant_fragments.haml
+++ b/views/significant_fragments.haml
@@ -5,6 +5,6 @@
= hide_link "#significant_fragments"
)
%dd
- Substructures that occur (statistically significant) more frequently in active or inactive compounds. Substuctures can take any shape (without cycles) and are determined with the
+ Substructures that occur (statistically significant) more frequently in one of the toxicity classes or correlate with quantitative toxicity values. Substuctures can take any shape (without cycles) and are determined with the
%a{:href => "http://www.maunz.de/libfminer2-bbrc-doc/", :rel => "external"} fminer
algorithm.
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 2024-05-04 17:27:10 +0000