protected class JPlogPDescriptor.JPlogPCalculator extends Object
Constructor and Description |
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JPlogPCalculator() |
JPlogPCalculator(Object[] params)
Initialises the required coefficients for the trained model from the paper.
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Modifier and Type | Method and Description |
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protected boolean |
boundTo(IAtom atom,
String symbol) |
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
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protected boolean |
carbonylConjugated(IAtom atom) |
protected boolean |
checkAlphaCarbonyl(IAtom atom,
String symbol)
Should be called from the carbonyl oxygen
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protected boolean |
doubleBondHetero(IAtom atom) |
protected boolean |
electronWithdrawing(IAtom atom) |
protected int |
getCarbonSpecial(IAtom atom)
Determines and returns the SS (subsection) portion of the atomtype integer for a Carbon Atom
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Map<Integer,Double> |
getCoeffs() |
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
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protected int |
getFluorineSpecial(IAtom atom)
Determines and returns the SS (subsection) portion of the atomtype integer for a Fluorine Atom
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protected int |
getHydrogenSpecial(IAtom atom)
Determines and returns the SS (subsection) portion of the atomtype integer for a Hydrogen Atom
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Map<Integer,Integer> |
getMappedHologram(IAtomContainer struct)
Used in Training the model
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protected int |
getNitrogenSpecial(IAtom atom)
Determines and returns the SS (subsection) portion of the atomtype integer for a Nitrogen Atom
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protected double |
getNumMoreElectronegativethanCarbon(IAtom atom) |
protected int |
getOxygenSpecial(IAtom atom)
Determines and returns the SS (subsection) portion of the atomtype integer for an Oxygen Atom
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protected int[] |
getPolarBondArray(IAtom atom) |
protected boolean |
isPolar(IAtom atom) |
protected boolean |
nextToAromatic(IAtom atom) |
protected int |
nonHNeighbours(IAtom atom) |
void |
setCoeffs(Map<Integer,Double> coeffs) |
public JPlogPCalculator(Object[] params)
public JPlogPCalculator()
protected Double calcLogP(IAtomContainer struct)
struct
- the structure to calculate it must have explicit H and be aromatised.public Map<Integer,Integer> getMappedHologram(IAtomContainer struct)
struct
- protected int getHydrogenSpecial(IAtom atom)
atom
- protected int getDefaultSpecial(IAtom atom)
atom
- protected int getFluorineSpecial(IAtom atom)
atom
- protected int getOxygenSpecial(IAtom atom)
atom
- protected int getNitrogenSpecial(IAtom atom)
atom
- protected int getCarbonSpecial(IAtom atom)
atom
- protected boolean checkAlphaCarbonyl(IAtom atom, String symbol)
atom
- symbol
- protected boolean boundTo(IAtom atom, String symbol)
atom
- symbol
- protected double getNumMoreElectronegativethanCarbon(IAtom atom)
atom
- protected boolean electronWithdrawing(IAtom atom)
atom
- protected int nonHNeighbours(IAtom atom)
atom
- protected int[] getPolarBondArray(IAtom atom)
atom
- protected boolean isPolar(IAtom atom)
atom
- protected boolean doubleBondHetero(IAtom atom)
atom
- protected boolean carbonylConjugated(IAtom atom)
atom
- protected boolean nextToAromatic(IAtom atom)
atom
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