JPlogPDescriptor.JPlogPCalculator (cdk 2.7.1 API)

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 Summary

Constructors
Constructor and Description

JPlogPCalculator()

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

Constructors
Constructor and Description
`JPlogPCalculator()`
`JPlogPCalculator(Object[] params)` Initialises the required coefficients for the trained model from the paper.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`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
`protected boolean`	`carbonylConjugated(IAtom atom)`
`protected boolean`	`checkAlphaCarbonyl(IAtom atom, String symbol)` Should be called from the carbonyl oxygen
`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
`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
`protected int`	`getFluorineSpecial(IAtom atom)` Determines and returns the SS (subsection) portion of the atomtype integer for a Fluorine Atom
`protected int`	`getHydrogenSpecial(IAtom atom)` Determines and returns the SS (subsection) portion of the atomtype integer for a Hydrogen Atom
`Map<Integer,Integer>`	`getMappedHologram(IAtomContainer struct)` Used in Training the model
`protected int`	`getNitrogenSpecial(IAtom atom)` Determines and returns the SS (subsection) portion of the atomtype integer for a Nitrogen Atom
`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
`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)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - JPlogPCalculator
```
public JPlogPCalculator(Object[] params)
```
    Initialises the required coefficients for the trained model from the paper.
  - JPlogPCalculator
```
public JPlogPCalculator()
```
- Method Detail
  - 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)
```

Class JPlogPDescriptor.JPlogPCalculator

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

JPlogPCalculator

JPlogPCalculator

Method Detail

calcLogP

getMappedHologram

getHydrogenSpecial

getDefaultSpecial

getFluorineSpecial

getOxygenSpecial

getNitrogenSpecial

getCarbonSpecial

checkAlphaCarbonyl

boundTo

getNumMoreElectronegativethanCarbon

electronWithdrawing

nonHNeighbours

getPolarBondArray

isPolar

doubleBondHetero

carbonylConjugated

nextToAromatic

getCoeffs

setCoeffs