svm validation, tensorflow mp2d pa predictions, r results removed, cleanup

1 files changed, 20 insertions, 0 deletions

diff --git a/scripts/pa-fingerprints.rb b/scripts/pa-fingerprints.rb
new file mode 100755
index 0000000..344ba86
--- /dev/null
+++ b/scripts/pa-fingerprints.rb
@@ -0,0 +1,20 @@
+#!/usr/bin/env ruby
+require_relative "../../lazar/lib/lazar.rb"
+training_fingerprints = `sed -n '1p' data/mutagenicity-fingerprints.csv`.chomp.split(",")
+training_fingerprints.pop
+puts training_fingerprints.join(",")
+training_fingerprints.shift
+
+File.readlines(File.join("pyrrolizidine-alkaloids","lazar","pa-smiles.csv")).each_with_index do |line,i|
+  if i > 0
+    (id,smiles) = line.chomp.split(",")
+    c = Compound.new(smiles)
+    out = [c.smiles]
+    fp = c.fingerprint
+    training_fingerprints.each do |frag|
+      fp.include?(frag) ? out << 1 : out << 0
+    end
+    puts out.join(",")
+  end
+end
+