Added ambit_descriptors.yaml

2 files changed, 125 insertions, 0 deletions

diff --git a/ambit_descriptors.yaml b/ambit_descriptors.yaml
new file mode 100644
index 0000000..19e66f9
--- /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: "electronic"
+  :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/opentox-ruby.sh b/opentox-ruby.sh
index ec7f5c2..d53d5ba 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