Class JPlogPDescriptor.JPlogPCalculator
java.lang.Object
org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator
- Enclosing class:
- JPlogPDescriptor
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
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Constructor Summary
ConstructorsConstructorDescriptionJPlogPCalculator
(Object[] params) Initialises the required coefficients for the trained model from the paper. -
Method Summary
Modifier and TypeMethodDescriptionprotected boolean
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.NaNprotected boolean
carbonylConjugated
(IAtom atom) protected boolean
checkAlphaCarbonyl
(IAtom atom, String symbol) Should be called from the carbonyl oxygenprotected 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 Atomprotected 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 Atomprotected int
getFluorineSpecial
(IAtom atom) Determines and returns the SS (subsection) portion of the atomtype integer for a Fluorine Atomprotected int
getHydrogenSpecial
(IAtom atom) Determines and returns the SS (subsection) portion of the atomtype integer for a Hydrogen AtomgetMappedHologram
(IAtomContainer struct) Used in Training the modelprotected int
getNitrogenSpecial
(IAtom atom) Determines and returns the SS (subsection) portion of the atomtype integer for a Nitrogen Atomprotected double
protected int
getOxygenSpecial
(IAtom atom) Determines and returns the SS (subsection) portion of the atomtype integer for an Oxygen Atomprotected int[]
getPolarBondArray
(IAtom atom) protected boolean
protected boolean
nextToAromatic
(IAtom atom) protected int
nonHNeighbours
(IAtom atom) void
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Constructor Details
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JPlogPCalculator
Initialises the required coefficients for the trained model from the paper. -
JPlogPCalculator
public JPlogPCalculator()
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Method Details
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calcLogP
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
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getMappedHologram
Used in Training the model- Parameters:
struct
-- Returns:
- Map representing the Hologram of the given structure
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getHydrogenSpecial
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
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getDefaultSpecial
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
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getFluorineSpecial
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
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getOxygenSpecial
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
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getNitrogenSpecial
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
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getCarbonSpecial
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
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checkAlphaCarbonyl
Should be called from the carbonyl oxygen- Parameters:
atom
-symbol
-- Returns:
- true if there is an atom of sybmol alpha to the carbonyl
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boundTo
- Parameters:
atom
-symbol
-- Returns:
- true if the atom has a bond to an atom of the given symbol
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getNumMoreElectronegativethanCarbon
- Parameters:
atom
-- Returns:
- bond order for electron withdrawing atoms from the given atom ie =O = 2
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electronWithdrawing
- Parameters:
atom
-- Returns:
- true if the atom is considered electron withdrawing relative to carbon (N,O,S,F,Cl,Br,I)
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nonHNeighbours
- Parameters:
atom
-- Returns:
- number of heavy atoms bound to the atom
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getPolarBondArray
- Parameters:
atom
-- Returns:
- in array of bond information to polar atoms array form is [single, aromatic, double, triple]
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isPolar
- Parameters:
atom
-- Returns:
- true if atom is a "polar atom" (O,N,S,P)
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doubleBondHetero
- Parameters:
atom
-- Returns:
- true if atom is doublebonded to a heteroatom (polar atom)
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carbonylConjugated
- Parameters:
atom
-- Returns:
- true if atom is singly bonded to a carbonyl
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nextToAromatic
- Parameters:
atom
-- Returns:
- true if single bonded to an aromatic atom
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getCoeffs
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setCoeffs
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