added mg/kg_bw/day

4 files changed, 14 insertions, 9 deletions

diff --git a/application.rb b/application.rb
index 229f3a1..1763e3a 100644
--- a/application.rb
+++ b/application.rb
@@ -202,14 +202,16 @@ get '/predict/?:csv?' do
       model = array[0]
       prediction = array[1]
       compound = key.smiles
+      mw = key.molecular_weight
+      weight = Compound.from_smiles(compound).mmol_to_mg(prediction[:value], mw)
       endpoint = "#{model.endpoint.gsub('_', ' ')} (#{model.species})"
       if prediction[:confidence] == "measured"
         type = ""
-        pred = prediction[:value].numeric? ? "#{prediction[:value].round(3)} (#{model.unit})" : prediction[:value]
+        pred = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % weight} (mg/kg_bw/day)" : prediction[:value]
         confidence = "measured activity"
       elsif prediction[:neighbors].size > 0
         type = model.model.class.to_s.match("Classification") ? "Classification" : "Regression"
-        pred = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} #{model.unit}" : prediction[:value]
+        pred = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} #{model.unit} | #{'%.2e' % weight} (mg/kg_bw/day)" : prediction[:value]
         confidence = prediction[:confidence]
       else
         type = ""
diff --git a/views/batch.haml b/views/batch.haml
index ec987c4..f593188 100644
--- a/views/batch.haml
+++ b/views/batch.haml
@@ -18,6 +18,7 @@
       / key = compound, values = array of arrays with model, prediction
       - @batch.each do |key, values|
         - compound = key
+        - mw = compound.molecular_weight
         %tr
           %td{:style=>"vertical-align:top;"}
             %p= compound.svg
@@ -34,7 +35,7 @@
                 %p
                 / TODO fix scientific notation from database
                 %b Measured activity:
-                = prediction[:value].numeric? ? "#{prediction[:value].round(3)} (#{model.unit})" : prediction[:value]
+                = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
                 %p Compound is part of the training dataset
               - elsif prediction[:neighbors].size > 0
                 %p
@@ -44,7 +45,7 @@
                 %br
                 %b Prediction:
                 / TODO scientific notation
-                = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit})" : prediction[:value]
+                = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
                 %br
                 / TODO probability
                 %b Confidence:
diff --git a/views/neighbors.haml b/views/neighbors.haml
index a741b45..4a1f3ea 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -65,9 +65,11 @@
                       /%a.btn.btn-link{:href => "#details#{j+1}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(neighbor[0].to_s)}/details"), :id=>"link#{j+1}#{count}"}}
                       %p= Compound.find(neighbor[0]).svg
                       %p= Compound.find(neighbor[0]).smiles
+                    - c = Compound.find(neighbor[0])
+                    - mw = c.molecular_weight
                     / Measured Activity
-                    %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
-                      = (type == "Regression") ? neighbor[2].collect{|n| '%.2e' % n + " (#{@models[j].unit})"}.join("</br>") : neighbor[2].join(", ")
+                    %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;white-space:nowrap;"}
+                      = (type == "Regression") ? neighbor[2].collect{|n| weight = c.mmol_to_mg(n, mw); '%.2e' % n + " (#{@models[j].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : neighbor[2].join(", ")
                     / Similarity
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
                       / TODO differentiate between no neighbors found and compound found in dataset, display neighbors for compounds in dataset?
diff --git a/views/prediction.haml b/views/prediction.haml
index ef0c5db..11d542e 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -18,6 +18,7 @@
           %td{:id=>"compound", :style=>"vertical-align:top;"}
             %p= @compound.svg
             %p= @compound.smiles
+          - mw = @compound.molecular_weight
           - @model_types = {}
           - @dbhit = {}
           - @predictions.each_with_index do |prediction,i|
@@ -32,7 +33,7 @@
                 %p
                 / TODO fix scientific notation from database
                 %b Measured activity:
-                = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit})" : prediction[:value]
+                = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
                 %p Compound is part of the training dataset
               - elsif prediction[:neighbors].size > 0
                 %p
@@ -41,8 +42,7 @@
                 = type
                 %br
                 %b Prediction:
-                / TODO scientific notation
-                = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{@models[i].unit})" : prediction[:value]
+                = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
                 / TODO update description
                 / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", data: {toggle:"popover", placement:"left", html:"true", content:"LAZAR calculates searches the training dataset for similar compounds (neighbors) and calculates the prediction from their measured activities. LAZAR calculates predictions using <ul><li>a majority vote (weighted by compound similarity) for<br /><b>classification</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'>original publication</a>) </li><li>a local QSAR model based on neighbors for<br /><b>regression</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'</h>original publication</a>) </li></ul>Please keep in mind that predictions are based on the measured activities of neighbors."}}
                 %br