From 063acd4dc63e9287287cc1ff78fff2064ff74e4f Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 7 Apr 2016 17:39:14 +0200
Subject: initial ambit import

---
 lib/dataset.rb      |  1 -
 lib/feature.rb      |  1 +
 lib/lazar.rb        |  3 ++-
 lib/nanoparticle.rb | 17 +++++++++++++++++
 lib/opentox.rb      |  1 +
 5 files changed, 21 insertions(+), 2 deletions(-)
 create mode 100644 lib/nanoparticle.rb

(limited to 'lib')

diff --git a/lib/dataset.rb b/lib/dataset.rb
index 5d8aeaf..2e48626 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -9,7 +9,6 @@ module OpenTox
     field :feature_ids, type: Array, default: []
     field :compound_ids, type: Array, default: []
     field :data_entries, type: Array, default: []
-    field :source, type: String
 
     # Readers
 
diff --git a/lib/feature.rb b/lib/feature.rb
index b58946b..f13a3fb 100644
--- a/lib/feature.rb
+++ b/lib/feature.rb
@@ -6,6 +6,7 @@ module OpenTox
     field :numeric, type: Boolean
     field :measured, type: Boolean
     field :calculated, type: Boolean
+    field :unit, type: String
   end
 
   # Feature for categorical variables
diff --git a/lib/lazar.rb b/lib/lazar.rb
index a28ba3a..39dd8fa 100644
--- a/lib/lazar.rb
+++ b/lib/lazar.rb
@@ -61,7 +61,7 @@ suppressPackageStartupMessages({
 "
 
 # OpenTox classes and includes
-CLASSES = ["Feature","Compound","Dataset","Validation","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment"]# Algorithm and Models are modules
+CLASSES = ["Feature","Compound","Dataset","Validation","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment","Nanoparticle"]# Algorithm and Models are modules
 
 [ # be aware of the require sequence as it affects class/method overwrites
   "overwrite.rb",
@@ -71,6 +71,7 @@ CLASSES = ["Feature","Compound","Dataset","Validation","CrossValidation","LeaveO
   "feature.rb",
   "physchem.rb",
   "compound.rb",
+  "nanoparticle.rb",
   "dataset.rb",
   "algorithm.rb",
   "model.rb",
diff --git a/lib/nanoparticle.rb b/lib/nanoparticle.rb
new file mode 100644
index 0000000..3783ece
--- /dev/null
+++ b/lib/nanoparticle.rb
@@ -0,0 +1,17 @@
+module OpenTox
+
+  class Nanoparticle
+    include OpenTox
+
+    field :particle_id, type: String
+    field :core, type: String
+    field :coatings, type: Array
+
+    #field :physchem_descriptors, type: Hash, default: {}
+    #field :toxicities, type: Hash, default: {}
+    field :features, type: Hash, default: {}
+
+  end
+end
+
+
diff --git a/lib/opentox.rb b/lib/opentox.rb
index 186c87a..cc18cc6 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -13,6 +13,7 @@ module OpenTox
       include Mongoid::Timestamps
       store_in collection: klass.downcase.pluralize
       field :name,  type: String
+      field :source,  type: String
       field :warnings, type: Array, default: []
     end
     OpenTox.const_set klass,c
-- 
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