From 0ddd04c32280e6fd166a52fa6da653df24aabf99 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Wed, 23 Nov 2016 15:10:58 +0000
Subject: added delog10;generalized mmol2-log10

---
 lib/overwrite.rb       |  5 +++++
 scripts/mmol2-log10.rb | 19 +++++++++++++------
 2 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/lib/overwrite.rb b/lib/overwrite.rb
index d0422ee..31d30c9 100644
--- a/lib/overwrite.rb
+++ b/lib/overwrite.rb
@@ -28,6 +28,11 @@ class Float
   def signif(n)
     Float("%.#{n}g" % self)
   end
+
+  # converts -10 logarithmized values back
+  def delog10
+    10**(-1*self)
+  end
 end
 
 module Enumerable
diff --git a/scripts/mmol2-log10.rb b/scripts/mmol2-log10.rb
index ec0fdf5..188d8cb 100755
--- a/scripts/mmol2-log10.rb
+++ b/scripts/mmol2-log10.rb
@@ -1,22 +1,29 @@
 #!/usr/bin/env ruby
 require_relative '../lib/lazar'
 include OpenTox
-newfile = ARGV[0].sub(/.csv/,"_log10.csv") 
+
+newfile = ARGV[0].sub(/.csv/,"_log10.csv")
 p newfile
 CSV.open(newfile, "wb") do |csv|
   i = 1
   CSV.read(ARGV[0]).each do |line|
-    smi,mmol = line
+    type,mmol = line
     if i == 1
-      csv << [smi, "-log10(#{mmol})"]
+      csv << [type, "-log10(#{mmol})"]
+      @type = type
     else
       if mmol.numeric?
-        c = Compound.from_smiles smi
+        if @type =~ /smiles/i
+          c = Compound.from_smiles type
+        elsif @type =~ /inchi/i
+          c = Compound.from_inchi type
+        else
+          p "Unknown type '#{@type}' at line #{i}."
+        end
         mmol = -Math.log10(mmol.to_f)
-        csv << [smi, mmol]
+        csv << [type, mmol]
       else
         p "Line #{i}: '#{mmol}' is not a numeric value."
-        #csv << [smi, ""]
       end
     end
     i += 1
-- 
cgit v1.2.3


From e111369ce5564f159b3f5f85c92afdd22352eaa1 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Thu, 24 Nov 2016 07:16:54 +0000
Subject: always convert to SMILES

---
 scripts/mmol2-log10.rb | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/scripts/mmol2-log10.rb b/scripts/mmol2-log10.rb
index 188d8cb..ff4af2a 100755
--- a/scripts/mmol2-log10.rb
+++ b/scripts/mmol2-log10.rb
@@ -9,16 +9,17 @@ CSV.open(newfile, "wb") do |csv|
   CSV.read(ARGV[0]).each do |line|
     type,mmol = line
     if i == 1
-      csv << [type, "-log10(#{mmol})"]
       @type = type
+      csv << ["SMILES", "-log10(#{mmol})"]
     else
       if mmol.numeric?
         if @type =~ /smiles/i
           c = Compound.from_smiles type
         elsif @type =~ /inchi/i
           c = Compound.from_inchi type
+          type = c.smiles
         else
-          p "Unknown type '#{@type}' at line #{i}."
+          p "Unknown type '#{type}' at line 1."
         end
         mmol = -Math.log10(mmol.to_f)
         csv << [type, mmol]
-- 
cgit v1.2.3