From f2e816fe31e492e28252e780e4be608269564e94 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Mon, 20 Feb 2012 14:48:38 +0100 Subject: Added keys for JOElib descriptors --- opentox-ruby.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/opentox-ruby.sh b/opentox-ruby.sh index 64ac93a..380dc3d 100755 --- a/opentox-ruby.sh +++ b/opentox-ruby.sh @@ -74,6 +74,7 @@ $GIT checkout aa-$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" +cmd="cp jl_keys.yaml $HOME/.opentox/config/" && run_cmd "$cmd" "JOELib" if [ "$OT_BRANCH" = "development" ] || expr match "$OT_BRANCH" "release"; then mkdir -p $WWW_DEST/opentox >>$LOG 2>&1 -- cgit v1.2.3 From 66f2631bdf18bffe4e7600c74e121e2c2b76f705 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Mon, 20 Feb 2012 16:31:35 +0100 Subject: Added keys file --- jl_keys.yaml | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 jl_keys.yaml 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" +] -- cgit v1.2.3 From 1684c349afa0ed169e1def2eb5c70f0948a209f4 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Tue, 3 Apr 2012 16:47:23 +0200 Subject: First commit --- ambit_descriptors.yaml | 124 -------------- config.sh | 4 +- jl_keys.yaml | 38 ----- pc_descriptors.yaml | 432 +++++++++++++++++++++++++++++++++++++++++++++++++ 4 files changed, 434 insertions(+), 164 deletions(-) delete mode 100644 ambit_descriptors.yaml delete mode 100644 jl_keys.yaml create mode 100644 pc_descriptors.yaml diff --git a/ambit_descriptors.yaml b/ambit_descriptors.yaml deleted file mode 100644 index 1e2c347..0000000 --- a/ambit_descriptors.yaml +++ /dev/null @@ -1,124 +0,0 @@ ---- -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 8ece62e..ff93e45 100755 --- a/config.sh +++ b/config.sh @@ -22,8 +22,8 @@ REDIS_NUM_VER="2.4.4" # 4) Server settings. NGINX_SERVERNAME="toxcreate3.in-silico.ch" WWW_DEST="$OT_PREFIX/www" -NGINX_PORT="" # set to empty string ("") for port 80 otherwise set to port *using colon* e.g. ":8080" -OHM_PORT="6379" # set to port (no colon) +NGINX_PORT=":8082" # set to empty string ("") for port 80 otherwise set to port *using colon* e.g. ":8080" +OHM_PORT="6382" # set to port (no colon) # Done. 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/pc_descriptors.yaml b/pc_descriptors.yaml new file mode 100644 index 0000000..e6fd7df --- /dev/null +++ b/pc_descriptors.yaml @@ -0,0 +1,432 @@ +--- + +# 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" -- cgit v1.2.3 From 8b4eecca7381c8c6fa4e941227058054e40dedf2 Mon Sep 17 00:00:00 2001 From: David Vorgrimmler Date: Fri, 20 Apr 2012 11:52:31 +0200 Subject: Added new config file(pc) / R package (validation) --- opentox-ruby.sh | 3 +-- packs.R | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/opentox-ruby.sh b/opentox-ruby.sh index 380dc3d..f080373 100755 --- a/opentox-ruby.sh +++ b/opentox-ruby.sh @@ -73,8 +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" -cmd="cp jl_keys.yaml $HOME/.opentox/config/" && run_cmd "$cmd" "JOELib" +cmd="cp pc_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 index b6b1930..d89c94b 100644 --- a/packs.R +++ b/packs.R @@ -3,4 +3,4 @@ # 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")) +install.packages(c("caret", "doMC", "e1071", "foreach", "iterators", "kernlab", "multicore", "plyr", "reshape", "randomForest", "RANN", "TunePareto")) -- cgit v1.2.3 From 718b4687a9ea071aa3650a3f6e6b82829193496a Mon Sep 17 00:00:00 2001 From: David Vorgrimmler Date: Fri, 20 Apr 2012 15:50:23 +0200 Subject: Set config.sh to default values. --- config.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/config.sh b/config.sh index ff93e45..8ece62e 100755 --- a/config.sh +++ b/config.sh @@ -22,8 +22,8 @@ REDIS_NUM_VER="2.4.4" # 4) Server settings. NGINX_SERVERNAME="toxcreate3.in-silico.ch" WWW_DEST="$OT_PREFIX/www" -NGINX_PORT=":8082" # set to empty string ("") for port 80 otherwise set to port *using colon* e.g. ":8080" -OHM_PORT="6382" # set to port (no colon) +NGINX_PORT="" # set to empty string ("") for port 80 otherwise set to port *using colon* e.g. ":8080" +OHM_PORT="6379" # set to port (no colon) # Done. -- cgit v1.2.3 From b5f9186a72cb2dc107e65e5d50baa57d42f7658d Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Thu, 24 May 2012 11:18:36 +0200 Subject: Added otcheck and nice --- ot-tools-user.sh | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/ot-tools-user.sh b/ot-tools-user.sh index 57c6c00..b002db6 100644 --- a/ot-tools-user.sh +++ b/ot-tools-user.sh @@ -52,8 +52,8 @@ otupdate() { otstart() { otconfig otkill - bash -c "nohup redis-server $HOME/opentox-ruby/redis-*/redis.conf >/dev/null 2>&1 &" - bash -c "nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &" + nice bash -c "nohup redis-server $HOME/opentox-ruby/redis-*/redis.conf >/dev/null 2>&1 &" + nice bash -c "nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &" sleep 2 if ! pgrep -u $USER nginx>/dev/null 2>&1; then echo "Failed to start nginx."; fi if ! pgrep -u $USER redis-server>/dev/null 2>&1; then echo "Failed to start redis."; fi @@ -81,3 +81,11 @@ otkill() { for p in `pgrep -u $USER R 2>/dev/null`; do kill -9 $p; done } +# Check the server +otcheck() { + check_service=`cat $HOME/.opentox/config/production.yaml | grep opentox-algorithm | sed 's/.*\s//g' | sed 's/"//g'` + if [ -z "`curl -v $check_service 2>&1 | grep '200 OK'`" ]; then + otstart + fi +} + -- cgit v1.2.3 From 4d26a300f51d698c3558a89f7919caa92955321c Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Fri, 25 May 2012 13:32:55 +0200 Subject: Adjusted Ruby + Java Package hint --- base-install.sh | 18 ++---------------- config.sh | 3 ++- ruby.sh | 2 ++ 3 files changed, 6 insertions(+), 17 deletions(-) diff --git a/base-install.sh b/base-install.sh index aed094c..66bb539 100644 --- a/base-install.sh +++ b/base-install.sh @@ -36,18 +36,7 @@ echo echo "Updating index" sudo $APTITUDE update -y >/dev/null 2>&1 -echo -echo "Checking installation:" -pack_arr="" -for p in $packs; do - if [ "un" != `$DPKG -l "$p" 2>/dev/null | tail -1 | awk -F " " '{print $1}'` ]; then - printf "%50s%30s\n" "'$p'" "Y" - else - printf "%50s%30s\n" "'$p'" "N" - pack_arr="$pack_arr $p" - fi -done - +pack_arr=$packs if [ -n "$pack_arr" ]; then echo echo "Checking availablity:" @@ -70,12 +59,9 @@ fi echo if [ -n "$pack_arr" ]; then - echo "Installing missing packages:" + cmd="sudo $APTITUDE -y install $pack_arr" && run_cmd "$cmd" "Installing packages" fi -for p in $pack_arr; do - cmd="sudo $APTITUDE -y install $p" && run_cmd "$cmd" "$p" -done if [ ! -f $JAVA_CONF ]; then diff --git a/config.sh b/config.sh index 8ece62e..b8228c9 100755 --- a/config.sh +++ b/config.sh @@ -12,9 +12,10 @@ OT_BRANCH="development" # Maturity (development -you need SSH k # 2) Where all binaries are installed. OT_PREFIX="$HOME/opentox-ruby" OT_JAVA_HOME="/usr/lib/jvm/java-6-openjdk" +# USE THIS FOR 64BIT: OT_JAVA_HOME="/usr/lib/jvm/java-6-openjdk-amd64" # 3) What versions to install. -RUBY_NUM_VER="1.8.7-2011.03" +RUBY_NUM_VER="1.8.7-2012.02" OB_NUM_VER="2.2.3" KL_NUM_VER="0.9-11" REDIS_NUM_VER="2.4.4" diff --git a/ruby.sh b/ruby.sh index 2e53384..8f96604 100755 --- a/ruby.sh +++ b/ruby.sh @@ -44,6 +44,8 @@ if [ ! $RUBY_DONE ]; then cmd="$WGET $URI" && run_cmd "$cmd" "Download" cmd="tar xzf $RUBY_VER.tar.gz" && run_cmd "$cmd" "Unpack" fi + # Fix Bug + sed -i '1672s/__memalign/\ volatile\ __memalign/g' $HOME/tmp/$RUBY_VER/source/distro/google-perftools-1.7/src/tcmalloc.cc cmd="sh $HOME/tmp/$RUBY_VER/installer --dont-install-useful-gems --no-dev-docs --auto=$RUBY_DEST" && run_cmd "$cmd" "Install" fi -- cgit v1.2.3 From 365ad4e93288b96233e38c6bc732c197315d41cf Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Thu, 21 Jun 2012 13:46:19 +0200 Subject: Support for bbrc-sample --- opentox-webservices.sh | 8 ++++++-- ot-tools-root.sh | 6 ++++++ ot-tools-user.sh | 6 ++++++ 3 files changed, 18 insertions(+), 2 deletions(-) diff --git a/opentox-webservices.sh b/opentox-webservices.sh index 88f864c..f9a85e2 100755 --- a/opentox-webservices.sh +++ b/opentox-webservices.sh @@ -60,8 +60,8 @@ done # fminer etc cmd="test -f $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config present" cd "$WWW_DEST/opentox/algorithm" >>$LOG 2>&1 -cmd="$GIT submodule init" && run_cmd "$cmd" "Fminer Init" -cmd="$GIT submodule update" && run_cmd "$cmd" "Fminer Update" +cmd="$GIT submodule init" && run_cmd "$cmd" "Submodules init" +cmd="$GIT submodule update" && run_cmd "$cmd" "Submodules update" cd "libfminer/libbbrc">>$LOG 2>&1 $GIT checkout $OT_BRANCH>>$LOG 2>&1 $GIT pull >>$LOG 2>&1 @@ -83,6 +83,10 @@ cd - >>$LOG 2>&1 cd "last-utils">>$LOG 2>&1 $GIT checkout $OT_BRANCH>>$LOG 2>&1 $GIT pull >>$LOG 2>&1 +cd - >>$LOG 2>&1 +cd "bbrc-sample">>$LOG 2>&1 +$GIT checkout $OT_BRANCH>>$LOG 2>&1 +$GIT pull >>$LOG 2>&1 cd "$DIR" diff --git a/ot-tools-root.sh b/ot-tools-root.sh index 064ea29..9198f83 100644 --- a/ot-tools-root.sh +++ b/ot-tools-root.sh @@ -32,6 +32,12 @@ otupdate() { return 1 fi cd - + cd $HOME/opentox-ruby/www/opentox/algorithm/bbrc-sample + if ! git pull; then + echo "Error! Pull for Bbrc-Sample failed." + return 1 + fi + cd - cd opentox-ruby LINK_DIR=`gem which opentox-ruby | sed 's/\/opentox-ruby.rb//'` if [ -h $LINK_DIR ]; then diff --git a/ot-tools-user.sh b/ot-tools-user.sh index b002db6..49278a1 100644 --- a/ot-tools-user.sh +++ b/ot-tools-user.sh @@ -32,6 +32,12 @@ otupdate() { return 1 fi cd - + cd $HOME/opentox-ruby/www/opentox/algorithm/bbrc-sample + if ! git pull; then + echo "Error! Pull for Bbrc-Sample failed." + return 1 + fi + cd - cd opentox-ruby LINK_DIR=`gem which opentox-ruby | sed 's/\/opentox-ruby.rb//'` if [ -h $LINK_DIR ]; then -- cgit v1.2.3