diff options
author | Andreas Maunz <andreas@maunz.de> | 2013-02-17 16:21:37 +0100 |
---|---|---|
committer | Andreas Maunz <andreas@maunz.de> | 2013-02-17 16:21:37 +0100 |
commit | 2743068f2930fed2b2d64c0eba6e33f63634ed7a (patch) | |
tree | e449fcdb59c716432f15c750360b03ccfc997d94 | |
parent | 04303b88d749a10a481ece22812c9a360ee30904 (diff) | |
parent | 58f25b5b123331ac5480f34073a63e430370e0dc (diff) |
Merge branch 'development' of github.com:opentox/install into development
-rwxr-xr-x | 4store-install | 5 | ||||
-rwxr-xr-x | base-install | 4 | ||||
-rwxr-xr-x | config.sh | 13 | ||||
-rw-r--r-- | debian.list | 2 | ||||
-rwxr-xr-x | install | 3 | ||||
-rw-r--r-- | jl_keys.yaml | 38 | ||||
-rw-r--r-- | ot-tools-user.sh | 32 | ||||
-rw-r--r-- | pc_descriptors.yaml | 432 | ||||
-rw-r--r-- | ubuntu.list | 3 |
9 files changed, 40 insertions, 492 deletions
diff --git a/4store-install b/4store-install index 8b78d41..3e310ed 100755 --- a/4store-install +++ b/4store-install @@ -10,12 +10,13 @@ DIR=`pwd` 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 "git make" +check_utils "git make tar wget" # Build cd $OT_PREFIX/tmp/ ([ -d $SELF ] && cd $SELF && cmd="$GIT pull" && run_cmd "$cmd" "Git pull") || (cmd="$GIT clone https://github.com/garlik/$SELF" && run_cmd "$cmd" "Git clone") cd $SELF +cmd="$GIT checkout -b ist c3d8593c39dc04a39e272f729e486c1576f6aeba" && run_cmd "$cmd" "checkout to particular commit" cmd="./autogen.sh" && run_cmd "$cmd" "Autogen" export FST=$OT_PREFIX/4S cmd="./configure --prefix=$FST --exec-prefix=$FST --with-storage-path=$FST/var/lib --with-config-file=$FST/$SELF.conf -with-http-log=$FST/log CFLAGS=-O2 CPPFLAGS=-O3" && run_cmd "$cmd" "Configure" @@ -25,7 +26,7 @@ cmd="make install" && run_cmd "$cmd" "Make Install" # Config echo "if echo \"\$LD_LIBRARY_PATH\" | grep -v \"$FST/lib\">/dev/null 2>&1; then export LD_LIBRARY_PATH=\"\$LD_LIBRARY_PATH:$FST/lib\"; fi" >> "$FST_CONF" -if ! cat "$OT_DEFAULT_CONF" | grep "four_store">/dev/null 2>&1; then echo '$four_store = { :uri => "http://localhost:9088", :user => "", :password => "" }' >> $OT_DEFAULT_CONF; fi +if ! cat "$OT_DEFAULT_CONF" | grep "four_store">/dev/null 2>&1; then echo '$four_store = { :uri => "http://localhost:9088", :user => "user", :password => "pw" }' >> $OT_DEFAULT_CONF; fi echo "$SELF configuration stored in '$FST_CONF'." if ! grep "$FST_CONF" $OT_UI_CONF >/dev/null 2>&1; then diff --git a/base-install b/base-install index 444d7f9..44abffd 100755 --- a/base-install +++ b/base-install @@ -28,6 +28,7 @@ if ! cat "/etc/apt/sources.list" | grep "$REDLAND_DEB">/dev/null 2>&1; then fi sudo $APTITUDE update -y >/dev/null 2>&1 +sudo $APTITUDE upgrade -y >/dev/null 2>&1 DISTRIB_INFO=$(cat /proc/version) @@ -37,6 +38,7 @@ case "$DISTRIB_INFO" in *) PACK_LIST="debian.list";; esac +sudo $APTITUDE update -y >/dev/null 2>&1 sudo $DPKG --set-selections < "$PACK_LIST" sudo $APT_GET -y --force-yes -u dselect-upgrade @@ -44,6 +46,8 @@ if [ ! -f $JAVA_CONF ]; then if [ ! -d "$OT_JAVA_HOME" ]; then echo "Directory '$OT_JAVA_HOME' does not exist! Aborting..." + echo "Please check if openjdk-6-jdk has been installed properly." + echo "You may need to set the OT_JAVA_HOME variable in config.sh to the correct path on your system." exit 1 fi @@ -18,9 +18,16 @@ OT_JAVA_HOME="/usr/lib/jvm/java-6-openjdk" OB_NUM_VER="2.3.1" RAPTOR2_NUM_VER="2.0.8" RASQAL_NUM_VER="0.9.29" +REDIS_NUM_VER="2.4.4" RUBY_NUM_VER="1.9.3-p194" +FOUR_STORE_VER="4store-v1.1.5" +REDIS_URL="http://redis.googlecode.com/files" REDLAND_DWL="http://download.librdf.org" REDLAND_APT_KEY="http://purl.org/net/dajobe/gnupg.asc" +FOUR_STORE_URL="http://4store.org/download" + +# 4) Server settings. +OHM_PORT="6379" # set to port (no colon) # Done. @@ -31,6 +38,7 @@ OB_CONF="$HOME/.opentox/OB.sh" R_CONF="$HOME/.opentox/R.sh" RAPTOR2_CONF="$HOME/.opentox/RAPTOR2.sh" RASQAL_CONF="$HOME/.opentox/RASQAL.sh" +REDIS_CONF="$HOME/.opentox/REDIS.sh" OT_UI_CONF="$HOME/.opentox/opentox-ui.sh" OT_TOOLS_CONF="$HOME/.opentox/ot-tools.sh" OT_DEFAULT_CONF="$HOME/.opentox/config/default.rb" @@ -38,10 +46,15 @@ OT_DEFAULT_CONF="$HOME/.opentox/config/default.rb" OB_VER="openbabel-$OB_NUM_VER" RAPTOR2_VER="raptor2-$RAPTOR2_NUM_VER" RASQAL_VER="rasqal-$RASQAL_NUM_VER" +REDIS_VER="redis-$REDIS_NUM_VER" OB_DEST="$OT_PREFIX/$OB_VER" OB_DEST_BINDINGS="$OT_PREFIX/openbabel-ruby-install" R_DEST="$OT_PREFIX/r-packages" RUBY_DWL="http://ftp.ruby-lang.org/pub/ruby/1.9" RAPTOR2_DWL="$REDLAND_DWL/source/$RAPTOR2_VER.tar.gz" RASQAL_DWL="$REDLAND_DWL/source/$RASQAL_VER.tar.gz" +REDIS_DWL="$REDIS_URL/$REDIS_VER.tar.gz" +REDIS_DIR="$OT_PREFIX/$REDIS_VER" +REDIS_SERVER_CONF="$REDIS_DIR/redis.conf" REDLAND_DEB="$REDLAND_DWL/binaries/$OT_DIST/unstable" +FOUR_STORE_DWL="$FOUR_STORE_URL/$FOUR_STORE_VER.tar.gz" diff --git a/debian.list b/debian.list index b10234d..e5af5b5 100644 --- a/debian.list +++ b/debian.list @@ -4,6 +4,7 @@ avahi-daemon install build-essential install cmake install curl install +gnuplot install libavahi-glib-dev install libavahi-client-dev install libcairo2-dev install @@ -22,3 +23,4 @@ openjdk-6-jdk install r-base-dev install r-base install uuid-dev install +xsltproc install @@ -71,11 +71,8 @@ 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/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") - # Install global ruby version . ./utils.sh install_ruby global diff --git a/jl_keys.yaml b/jl_keys.yaml deleted file mode 100644 index 22f26ae..0000000 --- a/jl_keys.yaml +++ /dev/null @@ -1,38 +0,0 @@ -[ - "joelib2.feature.types.FractionRotatableBonds", - "joelib2.feature.types.GeometricalDiameter", - "joelib2.feature.types.GeometricalRadius", - "joelib2.feature.types.GeometricalShapeCoefficient", - "joelib2.feature.types.GraphShapeCoefficient", - "joelib2.feature.types.KierShape1", - "joelib2.feature.types.KierShape2", - "joelib2.feature.types.KierShape3", - "joelib2.feature.types.LogP", - "joelib2.feature.types.MolarRefractivity", - "joelib2.feature.types.MolecularWeight", - "joelib2.feature.types.PolarSurfaceArea", - "joelib2.feature.types.FractionRotatableBonds", - "joelib2.feature.types.RotatableBonds", - "joelib2.feature.types.TopologicalDiameter", - "joelib2.feature.types.TopologicalRadius", - "joelib2.feature.types.ZagrebIndex1", - "joelib2.feature.types.count.AcidicGroups", - "joelib2.feature.types.count.AliphaticOHGroups", - "joelib2.feature.types.count.AromaticBonds", - "joelib2.feature.types.count.AromaticOHGroups", - "joelib2.feature.types.count.BasicGroups", - "joelib2.feature.types.count.HBA1", - "joelib2.feature.types.count.HBA2", - "joelib2.feature.types.count.HBD1", - "joelib2.feature.types.count.HBD2", - "joelib2.feature.types.count.HeavyBonds", - "joelib2.feature.types.count.HeteroCycles", - "joelib2.feature.types.count.HydrophobicGroups", - "joelib2.feature.types.count.NO2Groups", - "joelib2.feature.types.count.NumberOfAtoms", - "joelib2.feature.types.count.NumberOfBonds", - "joelib2.feature.types.count.NumberOfHal", - "joelib2.feature.types.count.OSOGroups", - "joelib2.feature.types.count.SO2Groups", - "joelib2.feature.types.count.OSOGroups" -] diff --git a/ot-tools-user.sh b/ot-tools-user.sh index bb036ef..47f0f66 100644 --- a/ot-tools-user.sh +++ b/ot-tools-user.sh @@ -27,9 +27,9 @@ start_unicorn() { # @example start_unicorn algorithm 8081 start_4s() { nice bash -c "nohup $OT_PREFIX/4S/bin/4s-backend $1 >/dev/null 2>&1 &"; - sleep 0.5; + sleep 2; nice bash -c "nohup $OT_PREFIX/4S/bin/4s-httpd -H localhost -p $2 -s -1 $1 >/dev/null 2>&1 &"; #-D for testing - sleep 0.5; + sleep 1; } @@ -72,8 +72,8 @@ otstart() { "feature") start_unicorn $1 8084;; "model") start_unicorn $1 8085;; "task") start_unicorn $1 8086;; - "validation") #start_unicorn $1 8087;; - echo "$1 not available yet.";; + "validation") start_unicorn $1 8087; + nice bash -c "nohup redis-server $OT_PREFIX/validation/redis-*/redis.conf >/dev/null 2>&1 &";; "4store") start_4s opentox 9088; if ! pgrep -u $USER 4s-backend>/dev/null 2>&1; then echo "Failed to start 4s-backend."; fi if ! pgrep -u $USER 4s-httpd>/dev/null 2>&1; then echo "Failed to start 4s-httpd."; fi;; @@ -83,8 +83,8 @@ otstart() { otstart dataset; otstart feature; otstart model; - otstart task;; - #otstart validation;; + otstart task; + otstart validation;; *) echo "One argument required: [service_name] or 'all'"; echo "usage: otstart [all|algorithm|compound|dataset|feature|model|task|validation|4store]"; return 1;; @@ -132,9 +132,8 @@ otreload() { check_service "model";; "task") reload_unicorn 8086; check_service "task";; - "validation") #reload_unicorn 8087;; - #check_service "validation"; - echo "$1 not available yet.";; + "validation") reload_unicorn 8087; + check_service "validation";; "4store") #killall 4s-httpd >/dev/null 2>&1; #killall 4s-backend >/dev/null 2>&1; #check_service "four_store";; @@ -144,8 +143,8 @@ otreload() { otreload dataset; otreload feature; otreload model; - otreload task;; - #otrelaod validation; + otreload task; + otrelaod validation;; #otreload 4store;; *) echo "One argument required: [service_name] or 'all'"; echo "usage: otreload [all|algorithm|compound|dataset|feature|model|task|validation|4store]"; @@ -176,8 +175,8 @@ otkill() { "feature") kill_unicorn 8084;; "model") kill_unicorn 8085;; "task") kill_unicorn 8086;; - "validation") #kill_unicorn 8087;; - echo "$1 not available yet.";; + "validation") kill_unicorn 8087; + bash -c "redis-cli -p $OHM_PORT shutdown >/dev/null 2>&1";; "4store") killall 4s-httpd >/dev/null 2>&1; killall 4s-backend >/dev/null 2>&1;; "all") otkill algorithm; @@ -186,7 +185,7 @@ otkill() { otkill feature; otkill model; otkill task; - #otkill validation; + otkill validation; otkill 4store;; *) echo "One argument required: [service_name] or 'all'"; echo "usage: otkill [all|algorithm|compound|dataset|feature|model|task|validation|4store]"; @@ -265,8 +264,7 @@ otcheck() { "feature") check_service "feature";; "model") check_service "model";; "task") check_service "task";; - "validation") #check_service "validation";; - echo "$1 not available yet.";; + "validation") check_service "validation";; "4store") check_service "four_store";; "all") otcheck "algorithm"; otcheck "compound"; @@ -274,7 +272,7 @@ otcheck() { otcheck "feature"; otcheck "model"; otcheck "task"; - #otcheck "validation"; + otcheck "validation"; otcheck 4store;; *) echo "One argument required: [service_name] or 'all'"; echo "usage: otcheck [all|algorithm|compound|dataset|feature|model|task|validation|4store]"; diff --git a/pc_descriptors.yaml b/pc_descriptors.yaml deleted file mode 100644 index ba32800..0000000 --- a/pc_descriptors.yaml +++ /dev/null @@ -1,432 +0,0 @@ ---- - -# 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 923759d..e5af5b5 100644 --- a/ubuntu.list +++ b/ubuntu.list @@ -4,8 +4,10 @@ avahi-daemon install build-essential install cmake install curl install +gnuplot install libavahi-glib-dev install libavahi-client-dev install +libcairo2-dev install libglib2.0-dev install libgsl0-dev install libopenssl-ruby install @@ -21,3 +23,4 @@ openjdk-6-jdk install r-base-dev install r-base install uuid-dev install +xsltproc install |