Merge branch 'pc_new_1' into development

Conflicts:
	config.sh

6 files changed, 150 insertions, 23 deletions

diff --git a/ambit_descriptors.yaml b/ambit_descriptors.yaml
new file mode 100644
index 0000000..1e2c347
--- /dev/null
+++ b/ambit_descriptors.yaml
@@ -0,0 +1,124 @@
+--- 
+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 87b19b7..8ece62e 100755
--- a/config.sh
+++ b/config.sh
@@ -34,17 +34,16 @@ RUBY_CONF="$OT_PREFIX/.sh_ruby_ot"
 REDIS_CONF="$OT_PREFIX/.sh_redis_ot"
 NGINX_CONF="$OT_PREFIX/.sh_nginx_ot"
 OB_CONF="$OT_PREFIX/.sh_OB_ot"
-KL_CONF="$OT_PREFIX/.sh_R_ot"
+R_CONF="$OT_PREFIX/.sh_R_ot"
 
 RUBY_VER="ruby-enterprise-$RUBY_NUM_VER"
 OB_VER="openbabel-$OB_NUM_VER"
-KL_VER="$KL_NUM_VER"
 REDIS_VER="$REDIS_NUM_VER"
 
 RUBY_DEST="$OT_PREFIX/$RUBY_VER"
 OB_DEST="$OT_PREFIX/$OB_VER"
 OB_DEST_BINDINGS="$OT_PREFIX/openbabel-ruby-install"
-KL_DEST="$OT_PREFIX/r-packages"
+R_DEST="$OT_PREFIX/r-packages"
 NGINX_DEST="$OT_PREFIX/nginx"
 REDIS_DEST="$OT_PREFIX/redis-$REDIS_VER"
 
diff --git a/install b/install
index a486660..b0422b5 100755
--- a/install
+++ b/install
@@ -19,19 +19,19 @@ if [ -f "$HOME/.opentox-ui.sh" ]
 then
   mv -v --backup=numbered $HOME/.opentox-ui.sh $HOME/.opentox-ui.sh$DATE
 else
-  echo "$HOME/.opentox-ui.sh does not found (nothing to backup)."
+  echo "$HOME/.opentox-ui.sh not found (nothing to backup)."
 fi
 if [ -d "$HOME/.opentox" ]
 then
   mv -v --backup=numbered -T $HOME/.opentox $HOME/.opentox$DATE
 else
-  echo "$HOME/.opentox does not found (nothing to backup)."
+  echo "$HOME/.opentox not found (nothing to backup)."
 fi
 if [ -d "$HOME/opentox-ruby" ]
 then
   mv -v --backup=numbered -T $HOME/opentox-ruby $HOME/opentox-ruby$DATE
 else
-  echo "$HOME/opentox-ruby does not found (nothing to backup)."
+  echo "$HOME/opentox-ruby not found (nothing to backup)."
 fi 
 LOG="$HOME/tmp/`basename $0`-log.txt"
 . "./utils.sh"
diff --git a/kernlab.sh b/kernlab.sh
index 511874b..aad125d 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -32,37 +32,34 @@ echo
 echo "Kernlab ('$LOG')."
 
 R_DONE=false
-mkdir "$KL_DEST" >/dev/null 2>&1
-if [ ! -d "$KL_DEST" ]; then
-  echo "Install directory '$KL_DEST' is not available! Aborting..."
+mkdir "$R_DEST" >/dev/null 2>&1
+if [ ! -d "$R_DEST" ]; then
+  echo "Install directory '$R_DEST' is not available! Aborting..."
   exit 1
 else
-  if ! rmdir "$KL_DEST" >/dev/null 2>&1; then # if not empty this will fail
+  if ! rmdir "$R_DEST" >/dev/null 2>&1; then # if not empty this will fail
     R_DONE=true
   else
-    mkdir "$KL_DEST" >/dev/null 2>&1
+    mkdir "$R_DEST" >/dev/null 2>&1
   fi
 fi
 
 
 if ! $R_DONE; then
-  cd $HOME/tmp
-  URI="http://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_$KL_VER.tar.gz"
-  cmd="$WGET $URI" && run_cmd "$cmd" "Download"
-
-  export R_LIBS="$KL_DEST" # To install non-global
-  cmd="$R CMD INSTALL kernlab_$KL_VER.tar.gz" && run_cmd "$cmd" "Install"
+  export R_LIBS="$R_DEST" # To install non-global
+  cmd="$R CMD BATCH packs.R" && run_cmd "$cmd" "R packages"
+  eval "$cmd"
 fi
 
 
-if [ ! -f $KL_CONF ]; then
+if [ ! -f $R_CONF ]; then
 
-  echo "if echo \"\$R_LIBS\" | grep -v \"$KL_DEST\">/dev/null 2>&1; then export R_LIBS=\"$KL_DEST\"; fi" >> "$KL_CONF"
-  echo "if ! [ -d \"$KL_DEST\" ]; then echo \"\$0: '$KL_DEST' is not a directory!\"; fi" >> "$KL_CONF"
-  echo "R package destination has been stored in '$KL_CONF'."
+  echo "if echo \"\$R_LIBS\" | grep -v \"$R_DEST\">/dev/null 2>&1; then export R_LIBS=\"$R_DEST\"; fi" >> "$R_CONF"
+  echo "if ! [ -d \"$R_DEST\" ]; then echo \"\$0: '$R_DEST' is not a directory!\"; fi" >> "$R_CONF"
+  echo "R package destination has been stored in '$R_CONF'."
 
-  if ! grep "$KL_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then
-    echo ". \"$KL_CONF\"" >> $OT_UI_CONF
+  if ! grep "$R_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then
+    echo ". \"$R_CONF\"" >> $OT_UI_CONF
   fi
 
 fi
diff --git a/opentox-ruby.sh b/opentox-ruby.sh
index 9705682..64ac93a 100755
--- a/opentox-ruby.sh
+++ b/opentox-ruby.sh
@@ -73,6 +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"
 
 if [ "$OT_BRANCH" = "development" ] || expr match "$OT_BRANCH" "release"; then
   mkdir -p $WWW_DEST/opentox >>$LOG 2>&1
diff --git a/packs.R b/packs.R
new file mode 100644
index 0000000..b6b1930
--- /dev/null
+++ b/packs.R
@@ -0,0 +1,6 @@
+# CRAN package installer for opentox-ruby
+# AM, 2012
+
+# 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"))