Package org.openscience.cdk.qsar.descriptors.molecular

Class JPlogPDescriptor.JPlogPCalculator

java.lang.Object
org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator
Enclosing class:
JPlogPDescriptor
protected class JPlogPDescriptor.JPlogPCalculator extends Object
The class that calculated the logP according to the JPlogP method described in: Journal of Cheminformatics 2018 10:61 https://doi.org/10.1186/s13321-018-0316-5 This is lower level access and should normally be obtained through the descriptor above.
Author:
Jeffrey

  • Constructor Details

    • JPlogPCalculator

      public JPlogPCalculator(Object[] params)
      Initialises the required coefficients for the trained model from the paper.

    • JPlogPCalculator

      public JPlogPCalculator()

  • Method Details

    • calcLogP

      protected Double calcLogP(IAtomContainer struct)
      Given a structure in the correct configuration (explicit H and aromatised) it will return the logP as a Double or if it is out of domain (encounters an unknown atomtype) it will return Double.NaN
      Parameters:
      struct - the structure to calculate it must have explicit H and be aromatised.
      Returns:
      The calculated logP as a Double

    • getMappedHologram

      public Map<Integer,Integer> getMappedHologram(IAtomContainer struct)
      Used in Training the model
      Parameters:
      struct -
      Returns:
      Map representing the Hologram of the given structure

    • getHydrogenSpecial

      protected int getHydrogenSpecial(IAtom atom)
      Determines and returns the SS (subsection) portion of the atomtype integer for a Hydrogen Atom
      Parameters:
      atom -
      Returns:
      the final 2 digits for the given atom

    • getDefaultSpecial

      protected int getDefaultSpecial(IAtom atom)
      Determines and returns the SS (subsection) portion of the atomtype integer for a "Default" ie not C,N,O,H,F Atom
      Parameters:
      atom -
      Returns:
      the final 2 digits for the given atom

    • getFluorineSpecial

      protected int getFluorineSpecial(IAtom atom)
      Determines and returns the SS (subsection) portion of the atomtype integer for a Fluorine Atom
      Parameters:
      atom -
      Returns:
      the final 2 digits for the given atom

    • getOxygenSpecial

      protected int getOxygenSpecial(IAtom atom)
      Determines and returns the SS (subsection) portion of the atomtype integer for an Oxygen Atom
      Parameters:
      atom -
      Returns:
      the final 2 digits for the given atom

    • getNitrogenSpecial

      protected int getNitrogenSpecial(IAtom atom)
      Determines and returns the SS (subsection) portion of the atomtype integer for a Nitrogen Atom
      Parameters:
      atom -
      Returns:
      the final 2 digits for the given atom

    • getCarbonSpecial

      protected int getCarbonSpecial(IAtom atom)
      Determines and returns the SS (subsection) portion of the atomtype integer for a Carbon Atom
      Parameters:
      atom -
      Returns:
      the final 2 digits for the given atom

    • checkAlphaCarbonyl

      protected boolean checkAlphaCarbonyl(IAtom atom, String symbol)
      Should be called from the carbonyl oxygen
      Parameters:
      atom -
      symbol -
      Returns:
      true if there is an atom of sybmol alpha to the carbonyl

    • boundTo

      protected boolean boundTo(IAtom atom, String symbol)
      Parameters:
      atom -
      symbol -
      Returns:
      true if the atom has a bond to an atom of the given symbol

    • getNumMoreElectronegativethanCarbon

      protected double getNumMoreElectronegativethanCarbon(IAtom atom)
      Parameters:
      atom -
      Returns:
      bond order for electron withdrawing atoms from the given atom ie =O = 2

    • electronWithdrawing

      protected boolean electronWithdrawing(IAtom atom)
      Parameters:
      atom -
      Returns:
      true if the atom is considered electron withdrawing relative to carbon (N,O,S,F,Cl,Br,I)

    • nonHNeighbours

      protected int nonHNeighbours(IAtom atom)
      Parameters:
      atom -
      Returns:
      number of heavy atoms bound to the atom

    • getPolarBondArray

      protected int[] getPolarBondArray(IAtom atom)
      Parameters:
      atom -
      Returns:
      in array of bond information to polar atoms array form is [single, aromatic, double, triple]

    • isPolar

      protected boolean isPolar(IAtom atom)
      Parameters:
      atom -
      Returns:
      true if atom is a "polar atom" (O,N,S,P)

    • doubleBondHetero

      protected boolean doubleBondHetero(IAtom atom)
      Parameters:
      atom -
      Returns:
      true if atom is doublebonded to a heteroatom (polar atom)

    • carbonylConjugated

      protected boolean carbonylConjugated(IAtom atom)
      Parameters:
      atom -
      Returns:
      true if atom is singly bonded to a carbonyl

    • nextToAromatic

      protected boolean nextToAromatic(IAtom atom)
      Parameters:
      atom -
      Returns:
      true if single bonded to an aromatic atom

    • getCoeffs

      public Map<Integer,Double> getCoeffs()

    • setCoeffs

      public void setCoeffs(Map<Integer,Double> coeffs)