diff options
author | David Vorgrimmler <vorgrimmlerdavid@gmx.de> | 2012-04-20 15:51:22 +0200 |
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committer | David Vorgrimmler <vorgrimmlerdavid@gmx.de> | 2012-04-20 15:51:22 +0200 |
commit | 3673d175b95ac3d675f52c19951a9cb6d16a11e7 (patch) | |
tree | 44ce30baa47ee02ae16a3a01863e882f57de6d81 | |
parent | d7c43e8399c64acbc02ce31eb756a347137f0e2c (diff) | |
parent | 718b4687a9ea071aa3650a3f6e6b82829193496a (diff) |
Merge branch 'pc_unified_from_jl' into development
-rw-r--r-- | ambit_descriptors.yaml | 124 | ||||
-rwxr-xr-x | opentox-ruby.sh | 2 | ||||
-rw-r--r-- | packs.R | 2 | ||||
-rw-r--r-- | pc_descriptors.yaml | 432 |
4 files changed, 434 insertions, 126 deletions
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/opentox-ruby.sh b/opentox-ruby.sh index 64ac93a..f080373 100755 --- a/opentox-ruby.sh +++ b/opentox-ruby.sh @@ -73,7 +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 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 @@ -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")) 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" |