Class OutOfPlane
- java.lang.Object
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- com.actelion.research.chem.forcefield.mmff.OutOfPlane
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- All Implemented Interfaces:
EnergyTerm
public class OutOfPlane extends java.lang.Object implements EnergyTerm
Out of plane energy term class. This energy term represents the out of plane energy associated with four atoms: A1 / A2--AC \ A3 Where AC is the central atom and A1, A2 and A3 are each connected to AC.
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Constructor Summary
Constructors Constructor Description OutOfPlane(Tables table, MMFFMolecule mol, int ac, int a1, int a2, int a3)
Construct a new out of plane energy term.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
equals(int ac, int a1, int a2, int a3)
Checks if this OutOfPlane's atoms are the same as a given set of 4 atoms, it checks all possible permutations of a1, a2 and a3.boolean
exactly(int ac, int a1, int a2, int a3)
Checks if this OutOfPlane term is exactly equal to a given set of four atoms.static java.util.List<OutOfPlane>
findIn(MMFFMolecule mol)
static java.util.List<OutOfPlane>
findIn(Tables t, MMFFMolecule mol)
Finds all out of plane angles in the current molecule.double
getEnergy(double[] pos)
Calculates the out of plane energy.void
getGradient(double[] pos, double[] grad)
Calculates the gradient and adds it to the gradients array.double
getKoop()
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Constructor Detail
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OutOfPlane
public OutOfPlane(Tables table, MMFFMolecule mol, int ac, int a1, int a2, int a3)
Construct a new out of plane energy term.- Parameters:
table
- The tables parameter object.mol
- The molecule.a1
- Index of atom 1 in mol.a2
- Index of atom 2 (the central atom) in mol.a3
- Index of atom 3 in mol.
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Method Detail
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getKoop
public double getKoop()
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getEnergy
public double getEnergy(double[] pos)
Calculates the out of plane energy.- Specified by:
getEnergy
in interfaceEnergyTerm
- Parameters:
pos
- The atoms current positions array.- Returns:
- The energy.
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getGradient
public void getGradient(double[] pos, double[] grad)
Calculates the gradient and adds it to the gradients array.- Specified by:
getGradient
in interfaceEnergyTerm
- Parameters:
pos
- The atoms current positions array.grad
- the atoms current gradients array.
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equals
public boolean equals(int ac, int a1, int a2, int a3)
Checks if this OutOfPlane's atoms are the same as a given set of 4 atoms, it checks all possible permutations of a1, a2 and a3.- Parameters:
ac
- The central atom.a1
- Neighbouring atom 1.a2
- Neighbouring atom 2.a3
- Neighbouring atom 3.- Returns:
- True if this OutOfPlane has the same permutation of neighbouring atoms as those provided.
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exactly
public boolean exactly(int ac, int a1, int a2, int a3)
Checks if this OutOfPlane term is exactly equal to a given set of four atoms.- Parameters:
ac
- The central atom.a1
- Neighbouring atom 1.a2
- Neighbouring atom 2.a3
- Neighbouring atom 3.- Returns:
- True if the out of plane atoms are the same as the provided atoms.
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findIn
public static java.util.List<OutOfPlane> findIn(Tables t, MMFFMolecule mol)
Finds all out of plane angles in the current molecule.- Parameters:
t
- The tables parameter object.mol
- The molecule to search in.- Returns:
- An array of OutOfPlane angles.
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findIn
public static java.util.List<OutOfPlane> findIn(MMFFMolecule mol)
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