obsolete data and java directories deleted

1 files changed, 38 insertions, 0 deletions

diff --git a/bin/sdf2csv.rb b/bin/sdf2csv.rb
new file mode 100755
index 0000000..ba31fad
--- /dev/null
+++ b/bin/sdf2csv.rb
@@ -0,0 +1,38 @@
+#!/usr/bin/env ruby
+require_relative "../lib/compound"
+
+read_result = false
+sdf = ""
+feature_name = ""
+compound = nil
+features = {}
+table = [["ID","SMILES"]]
+
+File.readlines(ARGV[0]).each do |line|
+  if line.match %r{\$\$\$\$}
+    sdf << line
+    id = sdf.split("\n").first.chomp
+    compound = Compound.from_sdf sdf
+    row = [id,compound.smiles]
+    features.each do |f,v|
+      table[0] << f unless table[0].include? f
+      row[table[0].index(f)] = v
+    end
+    table << row
+    sdf = ""
+    features = {}
+  elsif line.match(/^>\s+</)
+    feature_name = line.match(/^>\s+<(.*)>/)[1]
+    read_result = true
+  else
+    if read_result
+      value = line.chomp
+      features[feature_name] = value
+      read_result = false
+    else
+      sdf << line
+    end
+  end
+end
+
+table.each{|row| puts row.join(",")}