Merge branch 'development' of https://github.com/opentox/install into development

8 files changed, 487 insertions, 142 deletions

diff --git a/ambit_descriptors.yaml b/ambit_descriptors.yaml
deleted file mode 100644
index 1e2c347..0000000
--- a/ambit_descriptors.yaml
+++ /dev/null
@@ -1,124 +0,0 @@
---- 
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor: 
-  :category: "geometrical"
-  :name: "Length Over Breadth"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor: 
-  :category: "topological"
-  :name: "Kier & Hall SMARTS"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor: 
-  :category: "topological"
-  :name: "Fragment Complexity"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor: 
-  :category: "electronic"
-  :name: "Atomic Polarizabilities"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor: 
-  :category: "constitutional"
-  :name: "Largest Chain"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor: 
-  :category: "topological"
-  :name: "Chi Path Indices"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor: 
-  :category: "topological"
-  :name: "Petitjean Number"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor: 
-  :category: "constitutional"
-  :name: "Longest Aliphatic Chain"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor: 
-  :category: "topological"
-  :name: "Kier and Hall kappa molecular shape indices"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor: 
-  :category: "constitutional"
-  :name: "Aromatic Bonds Count"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor: 
-  :category: "cpsa"
-  :name: "Charged Partial Surface Areas"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor: 
-  :category: "topological"
-  :name: "Vertex adjacency information magnitude"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass: 
-  :category: "topological"
-  :name: "Moreau-Broto Autocorrelation (mass) descriptors"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor: 
-  :category: "constitutional"
-  :name: "Lipinski's Rule of Five"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor: 
-  :category: "geometrical"
-  :name: "Gravitational Index"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor: 
-  :category: "topological"
-  :name: "Wiener Numbers"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor: 
-  :category: "topological"
-  :name: "Chi Path-Cluster Indices"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor: 
-  :category: "constitutional"
-  :name: "Atoms Count"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor: 
-  :category: "geometrical"
-  :name: "Moments of Inertia"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor: 
-  :category: "topological"
-  :name: "Carbon Types"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability: 
-  :category: "topological"
-  :name: "Moreau-Broto Autocorrelation (polarizability) descriptors"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor: 
-  :category: "topological"
-  :name: "Eccentric Connectivity Index"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor: 
-  :category: "hybrid"
-  :name: "BCUT"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor: 
-  :category: "constitutional"
-  :name: "Aromatic Atoms Count"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor: 
-  :category: "hybrid"
-  :name: "WHIM"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor: 
-  :category: "constitutional"
-  :name: "ALogP"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor: 
-  :category: "constitutional"
-  :name: "XLogP"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor: 
-  :category: "topological"
-  :name: "Petitjean Number"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor: 
-  :category: "topological"
-  :name: "Molecular Distance Edge"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor: 
-  :category: "topological"
-  :name: "Chi Chain Indices"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor: 
-  :category: "constitutional"
-  :name: "Bonds Count"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor: 
-  :category: "constitutional"
-  :name: "Mannhold LogP"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor: 
-  :category: "electronic"
-  :name: "Bond Polarizabilities"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge: 
-  :category: "topological"
-  :name: "Moreau-Broto Autocorrelation (charge) descriptors"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor: 
-  :category: "topological"
-  :name: "Zagreb Index"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor: 
-  :category: "topological"
-  :name: "Chi Cluster Indices"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor: 
-  :category: "constitutional"
-  :name: "Rotatable Bonds Count"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor: 
-  :category: "topological"
-  :name: "Topological Polar Surface Area"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor: 
-  :category: "electronic"
-  :name: "Hydrogen Bond Donors"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor: 
-  :category: "electronic"
-  :name: "Hydrogen Bond Acceptors"
-http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor: 
-  :category: "constitutional"
-  :name: "Largest Pi Chain"
diff --git a/config.sh b/config.sh
index 8ca0d2e..3d062af 100755
--- a/config.sh
+++ b/config.sh
@@ -41,7 +41,6 @@ RASQAL_VER="rasqal-$RASQAL_NUM_VER"
 OB_DEST="$OT_PREFIX/$OB_VER"
 OB_DEST_BINDINGS="$OT_PREFIX/openbabel-ruby-install"
 RUBY_DWL="http://ftp.ruby-lang.org/pub/ruby/1.9"
-RUBY_DIR="$HOME/.rbenv/versions/$RUBY_NUM_VER"
 RAPTOR2_DWL="$REDLAND_DWL/source/$RAPTOR2_VER.tar.gz"
 RASQAL_DWL="$REDLAND_DWL/source/$RASQAL_VER.tar.gz"
 REDLAND_DEB="$REDLAND_DWL/binaries/$OT_DIST/unstable"
diff --git a/debian.list b/debian.list
index 73be6d9..b10234d 100644
--- a/debian.list
+++ b/debian.list
@@ -6,10 +6,9 @@ cmake install
 curl install
 libavahi-glib-dev install
 libavahi-client-dev install
+libcairo2-dev install
 libglib2.0-dev install
 libgsl0-dev install
-libopenbabel4 install
-libopenbabel-dev install
 libopenssl-ruby install
 libpcre3-dev install
 libraptor1-dev install
diff --git a/install b/install
index 7561732..c8f335f 100755
--- a/install
+++ b/install
@@ -41,6 +41,7 @@ echo
 [ -f $OT_DEFAULT_CONF ] || (cmd="echo '\$aa = { :uri => nil }' > $OT_DEFAULT_CONF" && run_cmd "$cmd" "default.rb => $HOME/.opentox/config")
 
 . ./base-install # Debian specific; disable this for others.
+./openbabel-install # Download, compile and build openbabel. Install to OT_PREFIX
 ./raptor2-install # Download, compile and build raptor2. Install to OT_PREFIX.
 ./rasqal-install # Download, compile and build rasqal. Install to OT_PREFIX.
 ./4store-install # Download, compile and build 4store. Install to OT_PREFIX.
@@ -56,7 +57,7 @@ if ! grep "rbenv" $OT_UI_CONF >/dev/null 2>&1 ; then
   echo 'if ! echo "$PATH" | grep "$HOME/.rbenv/bin">/dev/null 2>&1; then export PATH="$HOME/.rbenv/bin:$PATH"; eval "$(rbenv init -)"; fi' >> $OT_UI_CONF
 fi
 
-[ -f $HOME/.opentox/config/ambit_descriptors.yaml ] || (cmd="cp ambit_descriptors.yaml $HOME/.opentox/config/" && run_cmd "$cmd" "Ambit keys file")
+[ -f $HOME/.opentox/config/pc_descriptors.yaml ] || (cmd="cp pc_descriptors.yaml $HOME/.opentox/config/" && run_cmd "$cmd" "Pc descriptor file")
 [ -f $HOME/.opentox/config/jl_keys.yaml ] || (cmd="cp jl_keys.yaml $HOME/.opentox/config/" && run_cmd "$cmd" "Joelib keys file")
 [ -f $OT_TOOLS_CONF ] || (cmd="cp ot-tools-user.sh $OT_TOOLS_CONF" && run_cmd "$cmd" "ot-tools.sh => $HOME/.opentox)")
 
diff --git a/openbabel-install b/openbabel-install
new file mode 100755
index 0000000..5f183c5
--- /dev/null
+++ b/openbabel-install
@@ -0,0 +1,47 @@
+#!/bin/sh
+
+# Installs 4store on Debian and compatible systems.
+# Author: Andreas Maunz
+
+DIR=`pwd`
+
+# Boot
+. ./utils.sh || (echo "Utils could not be loaded, check opentox-ui.sh." 1>&2 && exit 1)
+SELF=$(basename $0 -install)
+check_log $SELF
+[ "`id -u`" = "0" ] && echo "This script must not be run as root" 1>&2 && exit 1
+check_utils "wget cmake tar"
+
+# Build
+cd $OT_PREFIX/tmp/
+mkdir $SELF 2>/dev/null
+cd $SELF
+cmd="$WGET http://downloads.sourceforge.net/project/openbabel/openbabel/$OB_NUM_VER/openbabel-$OB_NUM_VER.tar.gz" && run_cmd "$cmd" "Download"
+cmd="$TAR zxf $OB_VER.tar.gz $OB_VER"  && run_cmd "$cmd" "Unpack"
+mkdir build 2>/dev/null 
+cd build
+cmd="$CMAKE ../$OB_VER -DCMAKE_INSTALL_PREFIX=$OB_DEST" && run_cmd "$cmd" "Cmake"
+cmd="make -j2" && run_cmd "$cmd" "Make"
+cmd="make install" && run_cmd "$cmd" "Make Install"
+
+# Config
+if [ ! -f "$OB_CONF" ]; then
+  echo "if echo \"\$PATH\" | grep -v \"$OB_DEST\">/dev/null 2>&1; then export PATH=\"$OB_DEST/bin:\$PATH\"; fi" >> "$OB_CONF"
+  echo "if echo \"\$PKG_CONFIG_PATH\" | grep -v \"$OB_DEST/lib/pkgconfig\">/dev/null 2>&1; then export PKG_CONFIG_PATH=\"$OB_DEST/lib/pkgconfig:\$PKG_CONFIG_PATH\"; fi" >> "$OB_CONF"
+  echo "if echo \"\$LD_LIBRARY_PATH\" | grep -v \"$OB_DEST\">/dev/null 2>&1; then export LD_LIBRARY_PATH=\"$OB_DEST/lib:\$LD_LIBRARY_PATH\"; fi" >> "$OB_CONF"
+  echo "if ! [ -d \"$OB_DEST\" ]; then echo \"\$0: '$OB_DEST' is not a directory!\"; fi" >> "$OB_CONF"
+  echo "if [ -z \"\$BABEL_LIBDIR\" ]; then export BABEL_LIBDIR=\"$OB_DEST/lib/openbabel/$OB_NUM_VER\"; fi" >> "$OB_CONF"
+  echo "if ! [ -d \"\$BABEL_LIBDIR\" ]; then echo \"\$0: '\$BABEL_LIBDIR' is not a directory!\"; fi" >> "$OB_CONF"
+  echo "if [ -z \"\$BABEL_DATADIR\" ]; then export BABEL_DATADIR=\"$OB_DEST/share/openbabel/$OB_NUM_VER\"; fi" >> "$OB_CONF"
+  echo "if ! [ -d \"\$BABEL_DATADIR\" ]; then echo \"\$0: '\$BABEL_DATADIR' is not a directory!\"; fi" >> "$OB_CONF"
+
+  echo "Openbabel configuration has been stored in '$OB_CONF'."
+  if ! grep "$OB_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then
+    echo ". \"$OB_CONF\"" >> $OT_UI_CONF
+  fi
+fi
+
+notify
+
+# return to wd
+cd $DIR
diff --git a/pc_descriptors.yaml b/pc_descriptors.yaml
new file mode 100644
index 0000000..e6fd7df
--- /dev/null
+++ b/pc_descriptors.yaml
@@ -0,0 +1,432 @@
+--- 
+
+# cdk
+
+LengthOverBreadthDescriptor: 
+  :pc_type: "geometrical"
+  :lib: "cdk"
+  :name: "Length Over Breadth"
+
+KierHallSmartsDescriptor:
+  :pc_type: "topological"
+  :lib: "cdk"
+  :name: "Kier & Hall SMARTS"
+
+FragmentComplexityDescriptor:
+  :pc_type: "topological"
+  :lib: "cdk"
+  :name: "Fragment Complexity"
+
+APolDescriptor:
+  :pc_type: "electronic"
+  :lib: "cdk"
+  :name: "Atomic Polarizabilities"
+
+LargestChainDescriptor:
+  :pc_type: "constitutional"
+  :lib: "cdk"
+  :name: "Largest Chain"
+
+ChiPathDescriptor:
+  :pc_type: "topological"
+  :lib: "cdk"
+  :name: "Chi Path Indices"
+
+PetitjeanNumberDescriptor:
+  :pc_type: "topological"
+  :lib: "cdk"
+  :name: "Petitjean Number"
+
+LongestAliphaticChainDescriptor:
+  :pc_type: "constitutional"
+  :lib: "cdk"
+  :name: "Longest Aliphatic Chain"
+
+KappaShapeIndicesDescriptor:
+  :pc_type: "topological"
+  :lib: "cdk"
+  :name: "Kier and Hall kappa molecular shape indices"
+
+AromaticBondsCountDescriptor:
+  :pc_type: "constitutional"
+  :lib: "cdk"
+  :name: "Aromatic Bonds Count"
+
+CPSADescriptor:
+  :pc_type: "cpsa"
+  :lib: "cdk"
+  :name: "Charged Partial Surface Areas"
+
+VAdjMaDescriptor:
+  :pc_type: "topological"
+  :lib: "cdk"
+  :name: "Vertex adjacency information magnitude"
+
+AutocorrelationDescriptorMass:
+  :pc_type: "topological"
+  :lib: "cdk"
+  :name: "Moreau-Broto Autocorrelation (mass) descriptors"
+
+RuleOfFiveDescriptor:
+  :pc_type: "constitutional"
+  :lib: "cdk"
+  :name: "Lipinski's Rule of Five"
+
+GravitationalIndexDescriptor:
+  :pc_type: "geometrical"
+  :lib: "cdk"
+  :name: "Gravitational Index"
+
+WienerNumbersDescriptor:
+  :pc_type: "topological"
+  :lib: "cdk"
+  :name: "Wiener Numbers"
+
+ChiPathClusterDescriptor:
+  :pc_type: "topological"
+  :lib: "cdk"
+  :name: "Chi Path-Cluster Indices"
+
+AtomCountDescriptor:
+  :pc_type: "constitutional"
+  :lib: "cdk"
+  :name: "Atoms Count"
+
+MomentOfInertiaDescriptor:
+  :pc_type: "geometrical"
+  :lib: "cdk"
+  :name: "Moments of Inertia"
+
+CarbonTypesDescriptor:
+  :pc_type: "topological"
+  :lib: "cdk"
+  :name: "Carbon Types"
+
+AutocorrelationDescriptorPolarizability:
+  :pc_type: "topological"
+  :lib: "cdk"
+  :name: "Moreau-Broto Autocorrelation (polarizability) descriptors"
+
+EccentricConnectivityIndexDescriptor:
+  :pc_type: "topological"
+  :lib: "cdk"
+  :name: "Eccentric Connectivity Index"
+
+BCUTDescriptor:
+  :pc_type: "hybrid"
+  :lib: "cdk"
+  :name: "BCUT"
+
+AromaticAtomsCountDescriptor:
+  :pc_type: "constitutional"
+  :lib: "cdk"
+  :name: "Aromatic Atoms Count"
+
+WHIMDescriptor:
+  :pc_type: "hybrid"
+  :lib: "cdk"
+  :name: "WHIM"
+
+ALOGPDescriptor:
+  :pc_type: "constitutional"
+  :lib: "cdk"
+  :name: "ALogP"
+
+XLogPDescriptor:
+  :pc_type: "constitutional"
+  :lib: "cdk"
+  :name: "XLogP"
+
+PetitjeanShapeIndexDescriptor:
+  :pc_type: "topological"
+  :lib: "cdk"
+  :name: "Petitjean Number"
+
+MDEDescriptor:
+  :pc_type: "topological"
+  :lib: "cdk"
+  :name: "Molecular Distance Edge"
+
+ChiChainDescriptor:
+  :pc_type: "topological"
+  :lib: "cdk"
+  :name: "Chi Chain Indices"
+
+BondCountDescriptor:
+  :pc_type: "constitutional"
+  :lib: "cdk"
+  :name: "Bonds Count"
+
+MannholdLogPDescriptor:
+  :pc_type: "constitutional"
+  :lib: "cdk"
+  :name: "Mannhold LogP"
+
+BPolDescriptor:
+  :pc_type: "electronic"
+  :lib: "cdk"
+  :name: "Bond Polarizabilities"
+
+AutocorrelationDescriptorCharge:
+  :pc_type: "topological"
+  :lib: "cdk"
+  :name: "Moreau-Broto Autocorrelation (charge) descriptors"
+
+ZagrebIndexDescriptor:
+  :pc_type: "topological"
+  :lib: "cdk"
+  :name: "Zagreb Index"
+
+ChiClusterDescriptor:
+  :pc_type: "topological"
+  :lib: "cdk"
+  :name: "Chi Cluster Indices"
+
+RotatableBondsCountDescriptor:
+  :pc_type: "constitutional"
+  :lib: "cdk"
+  :name: "Rotatable Bonds Count"
+
+TPSADescriptor:
+  :pc_type: "topological"
+  :lib: "cdk"
+  :name: "Topological Polar Surface Area"
+
+HBondDonorCountDescriptor:
+  :pc_type: "electronic"
+  :lib: "cdk"
+  :name: "Hydrogen Bond Donors"
+
+HBondAcceptorCountDescriptor:
+  :pc_type: "electronic"
+  :lib: "cdk"
+  :name: "Hydrogen Bond Acceptors"
+
+LargestPiSystemDescriptor:
+  :pc_type: "constitutional"
+  :lib: "cdk"
+  :name: "Largest Pi Chain"
+
+
+# joelib
+
+
+HBA2:
+  :pc_type: "electronic"
+  :lib: "joelib"
+  :name: "Hydrogen Bond Acceptors 2"
+MolarRefractivity:
+  :pc_type: "constitutional"
+  :lib: "joelib"
+  :name: "Molar Refractivity"
+KierShape3:
+  :pc_type: "topological"
+  :lib: "joelib"
+  :name: "Kier Shape 3"
+SO2Groups:
+  :pc_type: "constitutional"
+  :lib: "joelib"
+  :name: "SO2 Groups"
+MolecularWeight:
+  :pc_type: "constitutional"
+  :lib: "joelib"
+  :name: "Molecular Weight"
+LogP:
+  :pc_type: "constitutional"
+  :lib: "joelib"
+  :name: "Log P"
+OSOGroups:
+  :pc_type: "constitutional"
+  :lib: "joelib"
+  :name: "OSO Groups"
+AromaticOHGroups:
+  :pc_type: "constitutional"
+  :lib: "joelib"
+  :name: "Aromatic OH Groups"
+AromaticBonds:
+  :pc_type: "constitutional"
+  :lib: "joelib"
+  :name: "Aromatic Bonds"
+AcidicGroups:
+  :pc_type: "constitutional"
+  :lib: "joelib"
+  :name: "Acidic Groups"
+GraphShapeCoefficient:
+  :pc_type: "topological"
+  :lib: "joelib"
+  :name: "Graph Shape Coefficient"
+GeometricalShapeCoefficient:
+  :pc_type: "topological"
+  :lib: "joelib"
+  :name: "Geometrical Shape Coefficient"
+ZagrebIndex1:
+  :pc_type: "topological"
+  :lib: "joelib"
+  :name: "Zagreb Index1"
+TopologicalRadius:
+  :pc_type: "topological"
+  :lib: "joelib"
+  :name: "Topological Radius"
+GeometricalDiameter:
+  :pc_type: "geometrical"
+  :lib: "joelib"
+  :name: "Geometrical Diameter"
+FractionRotatableBonds:
+  :pc_type: "constitutional"
+  :lib: "joelib"
+  :name: "Fraction Rotatable Bonds"
+NumberOfAtoms:
+  :pc_type: "constitutional"
+  :lib: "joelib"
+  :name: "Number Of Atoms"
+HeteroCycles:
+  :pc_type: "constitutional"
+  :lib: "joelib"
+  :name: "Hetero Cycles"
+RotatableBonds:
+  :pc_type: "constitutional"
+  :lib: "joelib"
+  :name: "Rotatable Bonds"
+BasicGroups:
+  :pc_type: "constitutional"
+  :lib: "joelib"
+  :name: "Basic Groups"
+TopologicalDiameter:
+  :pc_type: "topological"
+  :lib: "joelib"
+  :name: "Topological Diameter"
+NumberOfBonds:
+  :pc_type: "constitutional"
+  :lib: "joelib"
+  :name: "Number Of Bonds"
+NO2Groups:
+  :pc_type: "constitutional"
+  :lib: "joelib"
+  :name: "NO2 Groups"
+HBD1:
+  :pc_type: "electronic"
+  :lib: "joelib"
+  :name: "Hydrogen Bond Donors 1"
+AliphaticOHGroups:
+  :pc_type: "constitutional"
+  :lib: "joelib"
+  :name: "Aliphatic OH Groups"
+HBD2:
+  :pc_type: "electronic"
+  :lib: "joelib"
+  :name: "Hydrogen Bond Donors 2"
+HydrophobicGroups:
+  :pc_type: "constitutional"
+  :lib: "joelib"
+  :name: "Hydrophobic Groups"
+HeavyBonds:
+  :pc_type: "constitutional"
+  :lib: "joelib"
+  :name: "Heavy Bonds"
+KierShape1:
+  :pc_type: "topological"
+  :lib: "joelib"
+  :name: "Kier Shape1"
+NumberOfHal:
+  :pc_type: "constitutional"
+  :lib: "joelib"
+  :name: "Number Of Halogens"
+HBA1:
+  :pc_type: "electronic"
+  :lib: "joelib"
+  :name: "Hydrogen Bond Acceptors 1"
+PolarSurfaceArea:
+  :pc_type: "topological"
+  :lib: "joelib"
+  :name: "Polar Surface Area"
+KierShape2:
+  :pc_type: "topological"
+  :lib: "joelib"
+  :name: "Kier Shape 2"
+GeometricalRadius:
+  :pc_type: "geometrical"
+  :lib: "joelib"
+  :name: "Geometrical Radius"
+
+
+# openbabel
+NumAtoms:       
+  :pc_type: "constitutional"
+  :lib: "openbabel"
+  :name: "Number of atoms"
+NumBonds:       
+  :pc_type: "constitutional"
+  :lib: "openbabel"
+  :name: "Number of bonds"
+NumHvyAtoms:    
+  :pc_type: "constitutional"
+  :lib: "openbabel"
+  :name: "Number of heavy atoms"
+NumResidues:    
+  :pc_type: "constitutional"
+  :lib: "openbabel"
+  :name: "Number of residues"
+NumRotors:      
+  :pc_type: "constitutional"
+  :lib: "openbabel"
+  :name: "Number of rotatable bonds"
+GetEnergy:
+  :pc_type: "constitutional"
+  :lib: "openbabel"
+  :name: "Heat of formation for this molecule (in kcal/mol)"
+GetMolWt:       
+  :pc_type: "constitutional"
+  :lib: "openbabel"
+  :name: "Standard molar mass given by IUPAC atomic masses (amu)"
+GetExactMass:   
+  :pc_type: "constitutional"
+  :lib: "openbabel"
+  :name: "Mass given by isotopes (or most abundant isotope if not specified)"
+GetTotalCharge: 
+  :pc_type: "topological"
+  :lib: "openbabel"
+  :name: "Total charge"
+HBA1:           
+  :pc_type: "electronic"
+  :lib: "openbabel"
+  :name: "Number of hydrogen bond acceptors 1 (JoelLib)"
+HBA2:           
+  :pc_type: "electronic"
+  :lib: "openbabel"
+  :name: "Number of hydrogen bond acceptors 2 (JoelLib)"
+HBD:            
+  :pc_type: "electronic"
+  :lib: "openbabel"
+  :name: "Number of hydrogen bond donors (JoelLib)"
+L5:             
+  :pc_type: "constitutional"
+  :lib: "openbabel"
+  :name: "Lipinski rule of five"
+logP:           
+  :pc_type: "constitutional"
+  :lib: "openbabel"
+  :name: "Octanol/water partition coefficient"
+MR:             
+  :pc_type: "constitutional"
+  :lib: "openbabel"
+  :name: "Molar refractivity"
+MW:             
+  :pc_type: "constitutional"
+  :lib: "openbabel"
+  :name: "Molecular weight"
+nF:             
+  :pc_type: "constitutional"
+  :lib: "openbabel"
+  :name: "Number of fluorine atoms"
+nHal:           
+  :pc_type: "constitutional"
+  :lib: "openbabel"
+  :name: "Number of halogen atoms"
+spinMult:       
+  :pc_type: "electronic"
+  :lib: "openbabel"
+  :name: "Total spin multiplicity"
+TPSA:           
+  :pc_type: "topological"
+  :lib: "openbabel"
+  :name: "Topological polar surface area"
diff --git a/ubuntu.list b/ubuntu.list
index 73be6d9..923759d 100644
--- a/ubuntu.list
+++ b/ubuntu.list
@@ -8,8 +8,6 @@ libavahi-glib-dev install
 libavahi-client-dev install
 libglib2.0-dev install
 libgsl0-dev install
-libopenbabel4 install
-libopenbabel-dev install
 libopenssl-ruby install
 libpcre3-dev install
 libraptor1-dev install
diff --git a/utils.sh b/utils.sh
index b4cceab..5c34539 100755
--- a/utils.sh
+++ b/utils.sh
@@ -79,7 +79,7 @@ install_ruby() {
   if ! $RBENV versions $RUBY_NUM_VER | grep $RUBY_NUM_VER>/dev/null 2>&1; then
     [ -d $OT_PREFIX/tmp ] || mkdir -p $OT_PREFIX/tmp && cd $OT_PREFIX/tmp
     ([ -d $OT_PREFIX/tmp/ruby-$RUBY_NUM_VER ] || $CURL $RUBY_DWL/ruby-$RUBY_NUM_VER.tar.gz 2>/dev/null | $TAR xz) && cd ruby-$RUBY_NUM_VER
-    cmd="./configure --prefix=$RUBY_DIR" && run_cmd "$cmd" "Configure"
+    cmd="./configure --prefix=$HOME/.rbenv/versions/$RUBY_NUM_VER" && run_cmd "$cmd" "Configure"
     cmd="$MAKE -j2" && run_cmd "$cmd" "Make"
     cmd="$MAKE install" && run_cmd "$cmd" "Install"
   fi
@@ -120,20 +120,13 @@ notify() {
   echo
   if ps -o stat= -p $PPID | grep "s" >/dev/null 2>&1; then
     echo "IMPORTANT: How to configure your system if everything went fine:"
-    echo "IMPORTANT: ot-tools are supported for bash shell."
-    echo "IMPORTANT: a) Include '$OT_TOOLS_CONF' in shell startup (e.g. ~/.bashrc)."
-    echo "IMPORTANT: b) Manually source '$OT_TOOLS_CONF' every time."
-    echo "IMPORTANT: The command in both cases: '. $OT_TOOLS_CONF'"
-    echo "IMPORTANT: If you are using another shell please source '$OT_UI_CONF'"
-    echo "IMPORTANT: NOW would be the best time to configure!"
-    echo "Visit 'http://opentox.github.com/General/2012/08/09/install-opentox-development-environment/' for further information (e.g. the usage of ot-tools)."
-    echo
-    echo "Thank you for your attention."
-    echo
+    echo "IMPORTANT: bash shell only: '. $OT_TOOLS_CONF; otconfig' (convenient ot-tools)"
+    echo "IMPORTANT: other shells: '. $OT_UI_CONF' (no ot-tools available)"
+    echo "IMPORTANT: More information: 'http://opentox.github.com/General/2012/08/09/install-opentox-development-environment'"
+    echo "IMPORTANT: Thank you for your attention."
   fi
 }
 
-
 # Force loading configuration from local, if we are installing for the first time
 if [ -z "$OT_PREFIX" ]; then
   . ./config.sh