Merge branch 'jl' into modular

Conflicts:
	config.sh
	kernlab.sh
	opentox-ruby.sh

3 files changed, 165 insertions, 3 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/install b/install
index c3cf9a4..7b8a4a8 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/jl_keys.yaml b/jl_keys.yaml
new file mode 100644
index 0000000..22f26ae
--- /dev/null
+++ b/jl_keys.yaml
@@ -0,0 +1,38 @@
+[
+  "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"
+]