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Diffstat (limited to 'lib/unique_descriptors.rb')
| -rw-r--r-- | lib/unique_descriptors.rb | 120 |
1 files changed, 0 insertions, 120 deletions
diff --git a/lib/unique_descriptors.rb b/lib/unique_descriptors.rb deleted file mode 100644 index fc10cd4..0000000 --- a/lib/unique_descriptors.rb +++ /dev/null @@ -1,120 +0,0 @@ -# set of non redundant descriptors, faster algorithms are preferred -# TODO: -# select logP algorithm -# select l5 algorithm -# use smarts matcher for atom counts -# check correlations -UNIQUEDESCRIPTORS = [ - "Openbabel.abonds", #Number of aromatic bonds - "Openbabel.atoms", #Number of atoms - "Openbabel.bonds", #Number of bonds - "Openbabel.dbonds", #Number of double bonds - "Openbabel.HBA1", #Number of Hydrogen Bond Acceptors 1 (JoelLib) - "Openbabel.HBA2", #Number of Hydrogen Bond Acceptors 2 (JoelLib) - "Openbabel.HBD", #Number of Hydrogen Bond Donors (JoelLib) - #"Openbabe..L5", #Lipinski Rule of Five# TODO Openbabel.L5 returns nil, investigate!!! - "Openbabel.logP", #octanol/water partition coefficient - "Openbabel.MP", #Melting point - "Openbabel.MR", #molar refractivity - "Openbabel.MW", #Molecular Weight filter - "Openbabel.nF", #Number of Fluorine Atoms - "Openbabel.sbonds", #Number of single bonds - "Openbabel.tbonds", #Number of triple bonds - "Openbabel.TPSA", #topological polar surface area - "Cdk.ALOGP", #Calculates atom additive logP and molar refractivity values as described by Ghose and Crippen and - "Cdk.APol", #Descriptor that calculates the sum of the atomic polarizabilities (including implicit hydrogens). - "Cdk.AcidicGroupCount", #Returns the number of acidic groups. - #"Cdk.AminoAcidCount", #Returns the number of amino acids found in the system - #"Cdk.AromaticAtomsCount", #Descriptor based on the number of aromatic atoms of a molecule. - #"Cdk.AromaticBondsCount", #Descriptor based on the number of aromatic bonds of a molecule. - #"Cdk.AtomCount", #Descriptor based on the number of atoms of a certain element type. - "Cdk.AutocorrelationCharge", #The Moreau-Broto autocorrelation descriptors using partial charges - "Cdk.AutocorrelationMass", #The Moreau-Broto autocorrelation descriptors using atomic weight - "Cdk.AutocorrelationPolarizability", #The Moreau-Broto autocorrelation descriptors using polarizability - "Cdk.BCUT", #Eigenvalue based descriptor noted for its utility in chemical diversity described by Pearlman et al. . - "Cdk.BPol", #Descriptor that calculates the sum of the absolute value of the difference between atomic polarizabilities of all bonded atoms in the molecule (including implicit hydrogens). - "Cdk.BasicGroupCount", #Returns the number of basic groups. - #"Cdk.BondCount", #Descriptor based on the number of bonds of a certain bond order. - "Cdk.CPSA", #A variety of descriptors combining surface area and partial charge information - "Cdk.CarbonTypes", #Characterizes the carbon connectivity in terms of hybridization - "Cdk.ChiChain", #Evaluates the Kier & Hall Chi chain indices of orders 3,4,5 and 6 - "Cdk.ChiCluster", #Evaluates the Kier & Hall Chi cluster indices of orders 3,4,5,6 and 7 - "Cdk.ChiPathCluster", #Evaluates the Kier & Hall Chi path cluster indices of orders 4,5 and 6 - "Cdk.ChiPath", #Evaluates the Kier & Hall Chi path indices of orders 0,1,2,3,4,5,6 and 7 - "Cdk.EccentricConnectivityIndex", #A topological descriptor combining distance and adjacency information. - "Cdk.FMF", #Descriptor characterizing molecular complexity in terms of its Murcko framework - "Cdk.FragmentComplexity", #Class that returns the complexity of a system. The complexity is defined as @cdk.cite{Nilakantan06} - "Cdk.GravitationalIndex", #Descriptor characterizing the mass distribution of the molecule. - #"Cdk.HBondAcceptorCount", #Descriptor that calculates the number of hydrogen bond acceptors. - #"Cdk.HBondDonorCount", #Descriptor that calculates the number of hydrogen bond donors. - "Cdk.HybridizationRatio", #Characterizes molecular complexity in terms of carbon hybridization states. - # TODO check why the next descriptor is not present in the CDK_DESCRIPTIONS variable. - #"Cdk.IPMolecularLearning", #Descriptor that evaluates the ionization potential. - "Cdk.KappaShapeIndices", #Descriptor that calculates Kier and Hall kappa molecular shape indices. - "Cdk.KierHallSmarts", #Counts the number of occurrences of the E-state fragments - "Cdk.LargestChain", #Returns the number of atoms in the largest chain - "Cdk.LargestPiSystem", #Returns the number of atoms in the largest pi chain - "Cdk.LengthOverBreadth", #Calculates the ratio of length to breadth. - "Cdk.LongestAliphaticChain", #Returns the number of atoms in the longest aliphatic chain - "Cdk.MDE", #Evaluate molecular distance edge descriptors for C, N and O - #"Cdk.MannholdLogP", #Descriptor that calculates the LogP based on a simple equation using the number of carbons and hetero atoms . - "Cdk.MomentOfInertia", #Descriptor that calculates the principal moments of inertia and ratios of the principal moments. Als calculates the radius of gyration. - "Cdk.PetitjeanNumber", #Descriptor that calculates the Petitjean Number of a molecule. - "Cdk.PetitjeanShapeIndex", #The topological and geometric shape indices described Petitjean and Bath et al. respectively. Both measure the anisotropy in a molecule. - "Cdk.RotatableBondsCount", #Descriptor that calculates the number of nonrotatable bonds on a molecule. - #"Cdk.RuleOfFive", #This Class contains a method that returns the number failures of the Lipinski's Rule Of Five. - #"Cdk.TPSA", #Calculation of topological polar surface area based on fragment contributions . - "Cdk.VABC", #Describes the volume of a molecule. - "Cdk.VAdjMa", #Descriptor that calculates the vertex adjacency information of a molecule. - "Cdk.WHIM", #Holistic descriptors described by Todeschini et al . - #"Cdk.Weight", #Descriptor based on the weight of atoms of a certain element type. If no element is specified, the returned value is the Molecular Weight - "Cdk.WeightedPath", #The weighted path (molecular ID) descriptors described by Randic. They characterize molecular branching. - "Cdk.WienerNumbers", #This class calculates Wiener path number and Wiener polarity number. - "Cdk.XLogP", #Prediction of logP based on the atom-type method called XLogP. - "Cdk.ZagrebIndex", #The sum of the squared atom degrees of all heavy atoms. - "Joelib.count.NumberOfS", #no description available - "Joelib.count.NumberOfP", #no description available - "Joelib.count.NumberOfO", #no description available - "Joelib.count.NumberOfN", #no description available - #"Joeli#.count.AromaticBonds", #no description available - "Joelib.count.NumberOfI", #no description available - "Joelib.count.NumberOfF", #no description available - "Joelib.count.NumberOfC", #no description available - "Joelib.count.NumberOfB", #no description available - "Joelib.count.HydrophobicGroups", #no description available - #"Joelib.KierShape3", #no description available - #"Joelib.KierShape2", #no description available - #"Joelib.KierShape1", #no description available - #"Joelib.count.AcidicGroups", #no description available - "Joelib.count.AliphaticOHGroups", #no description available - #"Joelib.count.NumberOfAtoms", #no description available - "Joelib.TopologicalRadius", #no description available - "Joelib.GeometricalShapeCoefficient", #no description available - #"Joelib.MolecularWeight", #no description available - "Joelib.FractionRotatableBonds", #no description available - #"Joeli..count.HBD2", #no description available - #"Joelib.count.HBD1", #no description available - "Joelib.LogP", #no description available - "Joelib.GraphShapeCoefficient", #no description available - "Joelib.count.BasicGroups", #no description available - #"Joelib.count.RotatableBonds", #no description available - "Joelib.count.HeavyBonds", #no description available - "Joelib.PolarSurfaceArea", #no description available - #"Joelib.ZagrebIndex1", #no description available - "Joelib.GeometricalRadius", #no description available - "Joelib.count.SO2Groups", #no description available - "Joelib.count.AromaticOHGroups", #no description available - "Joelib.GeometricalDiameter", #no description available - #"Joelib.MolarRefractivity", #no description available - "Joelib.count.NumberOfCl", #no description available - "Joelib.count.OSOGroups", #no description available - "Joelib.count.NumberOfBr", #no description available - "Joelib.count.NO2Groups", #no description available - "Joelib.count.HeteroCycles", #no description available - #"Joelib.count.HBA2", #no description available - #"Joelib.count.HBA1", #no description available - #"Joelib.count.NumberOfBonds", #no description available - "Joelib.count.SOGroups", #no description available - "Joelib.TopologicalDiameter", #no description available - "Joelib.count.NumberOfHal", #no description available -] |