diff options
-rw-r--r-- | ambit_descriptors.yaml | 124 | ||||
-rwxr-xr-x | config.sh | 5 | ||||
-rwxr-xr-x | install | 6 | ||||
-rwxr-xr-x | kernlab.sh | 31 | ||||
-rwxr-xr-x | opentox-ruby.sh | 1 | ||||
-rw-r--r-- | packs.R | 6 |
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" @@ -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" @@ -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 $0`-log.txt" . "./utils.sh" @@ -32,37 +32,34 @@ echo echo "Kernlab ('$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 @@ -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")) |