Merge branch 'release/v3.2.0'v4.0.0

10 files changed, 468 insertions, 147 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/base-install.sh b/base-install.sh
index aed094c..66bb539 100644
--- a/base-install.sh
+++ b/base-install.sh
@@ -36,18 +36,7 @@ echo
 echo "Updating index"
 sudo $APTITUDE update -y >/dev/null 2>&1
 
-echo
-echo "Checking installation:"
-pack_arr=""
-for p in $packs; do
-  if [ "un" != `$DPKG -l "$p" 2>/dev/null | tail -1 | awk -F " " '{print $1}'` ]; then
-     printf "%50s%30s\n" "'$p'" "Y"
-  else
-     printf "%50s%30s\n" "'$p'" "N"
-    pack_arr="$pack_arr $p"
-  fi
-done
-
+pack_arr=$packs
 if [ -n "$pack_arr" ]; then
   echo 
   echo "Checking availablity:"
@@ -70,12 +59,9 @@ fi
 
 echo
 if [ -n "$pack_arr" ]; then 
-  echo "Installing missing packages:"
+  cmd="sudo $APTITUDE -y install $pack_arr" && run_cmd "$cmd" "Installing packages"
 fi
 
-for p in $pack_arr; do
-  cmd="sudo $APTITUDE -y install $p" && run_cmd "$cmd" "$p"
-done
 
 if [ ! -f $JAVA_CONF ]; then
 
diff --git a/config.sh b/config.sh
index 8ece62e..b8228c9 100755
--- a/config.sh
+++ b/config.sh
@@ -12,9 +12,10 @@ OT_BRANCH="development"     # Maturity              (development -you need SSH k
 # 2) Where all binaries are installed.
 OT_PREFIX="$HOME/opentox-ruby"
 OT_JAVA_HOME="/usr/lib/jvm/java-6-openjdk"
+# USE THIS FOR 64BIT: OT_JAVA_HOME="/usr/lib/jvm/java-6-openjdk-amd64"
 
 # 3) What versions to install.
-RUBY_NUM_VER="1.8.7-2011.03"
+RUBY_NUM_VER="1.8.7-2012.02"
 OB_NUM_VER="2.2.3"
 KL_NUM_VER="0.9-11"
 REDIS_NUM_VER="2.4.4"
diff --git a/opentox-ruby.sh b/opentox-ruby.sh
index 64ac93a..f080373 100755
--- a/opentox-ruby.sh
+++ b/opentox-ruby.sh
@@ -73,7 +73,7 @@ $GIT checkout aa-$OT_INSTALL.yaml  >>$LOG 2>&1
 
 cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,;s,NGINX_PORT,$NGINX_PORT,;s,OHM_PORT,$OHM_PORT,\" production.yaml > $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 1"
 cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,;s,NGINX_PORT,$NGINX_PORT,;s,OHM_PORT,$OHM_PORT,\" aa-$OT_INSTALL.yaml >> $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 2"
-cmd="cp ambit_descriptors.yaml $HOME/.opentox/config/" && run_cmd "$cmd" "Ambit"
+cmd="cp pc_descriptors.yaml $HOME/.opentox/config/" && run_cmd "$cmd" "Ambit"
 
 if [ "$OT_BRANCH" = "development" ] || expr match "$OT_BRANCH" "release"; then
   mkdir -p $WWW_DEST/opentox >>$LOG 2>&1
diff --git a/opentox-webservices.sh b/opentox-webservices.sh
index 88f864c..f9a85e2 100755
--- a/opentox-webservices.sh
+++ b/opentox-webservices.sh
@@ -60,8 +60,8 @@ done
 # fminer etc
 cmd="test -f $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config present"
 cd "$WWW_DEST/opentox/algorithm" >>$LOG 2>&1
-cmd="$GIT submodule init" && run_cmd "$cmd" "Fminer Init"
-cmd="$GIT submodule update" && run_cmd "$cmd" "Fminer Update"
+cmd="$GIT submodule init" && run_cmd "$cmd" "Submodules init"
+cmd="$GIT submodule update" && run_cmd "$cmd" "Submodules update"
 cd "libfminer/libbbrc">>$LOG 2>&1
 $GIT checkout $OT_BRANCH>>$LOG 2>&1
 $GIT pull >>$LOG 2>&1
@@ -83,6 +83,10 @@ cd - >>$LOG 2>&1
 cd "last-utils">>$LOG 2>&1
 $GIT checkout $OT_BRANCH>>$LOG 2>&1
 $GIT pull >>$LOG 2>&1
+cd - >>$LOG 2>&1
+cd "bbrc-sample">>$LOG 2>&1
+$GIT checkout $OT_BRANCH>>$LOG 2>&1
+$GIT pull >>$LOG 2>&1
 
 cd "$DIR"
 
diff --git a/ot-tools-root.sh b/ot-tools-root.sh
index 064ea29..9198f83 100644
--- a/ot-tools-root.sh
+++ b/ot-tools-root.sh
@@ -32,6 +32,12 @@ otupdate() {
     return 1
   fi
   cd -
+  cd $HOME/opentox-ruby/www/opentox/algorithm/bbrc-sample
+  if ! git pull; then
+    echo "Error! Pull for Bbrc-Sample failed."
+    return 1
+  fi
+  cd -
   cd opentox-ruby
   LINK_DIR=`gem which opentox-ruby | sed 's/\/opentox-ruby.rb//'`
   if [ -h $LINK_DIR ]; then 
diff --git a/ot-tools-user.sh b/ot-tools-user.sh
index 57c6c00..49278a1 100644
--- a/ot-tools-user.sh
+++ b/ot-tools-user.sh
@@ -32,6 +32,12 @@ otupdate() {
     return 1
   fi
   cd -
+  cd $HOME/opentox-ruby/www/opentox/algorithm/bbrc-sample
+  if ! git pull; then
+    echo "Error! Pull for Bbrc-Sample failed."
+    return 1
+  fi
+  cd -
   cd opentox-ruby
   LINK_DIR=`gem which opentox-ruby | sed 's/\/opentox-ruby.rb//'`
   if [ -h $LINK_DIR ]; then 
@@ -52,8 +58,8 @@ otupdate() {
 otstart() {
   otconfig
   otkill
-  bash -c "nohup redis-server $HOME/opentox-ruby/redis-*/redis.conf >/dev/null 2>&1 &"
-  bash -c "nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &"
+  nice bash -c "nohup redis-server $HOME/opentox-ruby/redis-*/redis.conf >/dev/null 2>&1 &"
+  nice bash -c "nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &"
   sleep 2
   if ! pgrep -u $USER nginx>/dev/null 2>&1; then echo "Failed to start nginx."; fi
   if ! pgrep -u $USER redis-server>/dev/null 2>&1; then echo "Failed to start redis."; fi
@@ -81,3 +87,11 @@ otkill() {
   for p in `pgrep -u $USER R 2>/dev/null`; do kill -9 $p; done
 }
 
+# Check the server
+otcheck() {
+  check_service=`cat $HOME/.opentox/config/production.yaml  | grep opentox-algorithm | sed 's/.*\s//g' | sed 's/"//g'`
+  if [ -z "`curl -v $check_service 2>&1 | grep '200 OK'`" ]; then
+    otstart
+  fi
+}
+
diff --git a/packs.R b/packs.R
index b6b1930..d89c94b 100644
--- a/packs.R
+++ b/packs.R
@@ -3,4 +3,4 @@
 
 # set mirror to avoid questioning the user
 options(repos="http://mirrors.softliste.de/cran")
-install.packages(c("caret", "doMC", "e1071", "foreach", "iterators", "kernlab", "multicore", "plyr", "reshape", "randomForest", "RANN"))
+install.packages(c("caret", "doMC", "e1071", "foreach", "iterators", "kernlab", "multicore", "plyr", "reshape", "randomForest", "RANN", "TunePareto"))
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/ruby.sh b/ruby.sh
index 2e53384..8f96604 100755
--- a/ruby.sh
+++ b/ruby.sh
@@ -44,6 +44,8 @@ if [ ! $RUBY_DONE ]; then
     cmd="$WGET $URI" && run_cmd "$cmd" "Download"
     cmd="tar xzf $RUBY_VER.tar.gz" && run_cmd "$cmd" "Unpack"
   fi
+  # Fix Bug
+  sed -i '1672s/__memalign/\ volatile\ __memalign/g' $HOME/tmp/$RUBY_VER/source/distro/google-perftools-1.7/src/tcmalloc.cc
   cmd="sh $HOME/tmp/$RUBY_VER/installer  --dont-install-useful-gems --no-dev-docs --auto=$RUBY_DEST" && run_cmd "$cmd" "Install"
 fi