Class TorsionAngle
- java.lang.Object
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- com.actelion.research.chem.forcefield.mmff.TorsionAngle
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- All Implemented Interfaces:
EnergyTerm
public class TorsionAngle extends java.lang.Object implements EnergyTerm
Torsional Angle energy term class. This energy term represents the energy associated with the torsional angle formed by four atoms A1..A4: A1 \ A2--A3 \ A4
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Constructor Summary
Constructors Constructor Description TorsionAngle(Tables table, MMFFMolecule mol, int a1, int a2, int a3, int a4)
Construct a new torsion angle energy term.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static java.util.List<TorsionAngle>
findIn(Tables t, MMFFMolecule mol)
Helper function that builds a list of TorsionAngles for a molecule.double
getEnergy(double[] pos)
Calculates the torsional energy.void
getGradient(double[] pos, double[] grad)
Calculates the gradient and adds it to the gradients array.boolean
nonZero()
Checks that at least one of the constants is non-zero.
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Constructor Detail
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TorsionAngle
public TorsionAngle(Tables table, MMFFMolecule mol, int a1, int a2, int a3, int a4)
Construct a new torsion angle energy term.- Parameters:
table
- The tables parameter object.mol
- The molecule.a1
- Index of atom 1 in mol.a2
- Index of atom 2 in mol.a3
- Index of atom 3 in mol.a4
- Index of atom 4 in mol.
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Method Detail
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getEnergy
public double getEnergy(double[] pos)
Calculates the torsional 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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nonZero
public boolean nonZero()
Checks that at least one of the constants is non-zero.- Returns:
- True if any constant is non-zero, false otherwise.
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findIn
public static java.util.List<TorsionAngle> findIn(Tables t, MMFFMolecule mol)
Helper function that builds a list of TorsionAngles for a molecule.- Parameters:
t
- The tables object.mol
- The molecule to generate torsions for.- Returns:
- Am array of TorsionAngle.
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