From de001bb0b9acb4b145449bf8ff75049a784b3173 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Tue, 24 Jul 2012 16:09:30 +0200 Subject: config files --- ambit_descriptors.yaml | 124 ++++++++++++++ jl_keys.yaml | 38 +++++ pc_descriptors.yaml | 432 ------------------------------------------------- 3 files changed, 162 insertions(+), 432 deletions(-) create mode 100644 ambit_descriptors.yaml create mode 100644 jl_keys.yaml delete mode 100644 pc_descriptors.yaml 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/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" +] diff --git a/pc_descriptors.yaml b/pc_descriptors.yaml deleted file mode 100644 index e6fd7df..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" -- cgit v1.2.3