Class AngleBend
- java.lang.Object
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- com.actelion.research.chem.forcefield.mmff.AngleBend
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- All Implemented Interfaces:
EnergyTerm
public class AngleBend extends java.lang.Object implements EnergyTerm
Angle bending energy term class. This energy term represents the angle bending energy associated with three bonded atoms A1--A2--A3 with an angle at A2.
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Constructor Summary
Constructors Constructor Description AngleBend(Tables table, MMFFMolecule mol, int a1, int a2, int a3)
Construct a new angle bend 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<AngleBend>
findIn(Tables t, MMFFMolecule mol)
Helper function that builds a list of AngleBends for a molecule.double
getEnergy(double[] pos)
Calculates the angle energy.void
getGradient(double[] pos, double[] grad)
Calculates the gradient and adds it to the gradients array.
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Constructor Detail
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AngleBend
public AngleBend(Tables table, MMFFMolecule mol, int a1, int a2, int a3)
Construct a new angle bend 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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getEnergy
public double getEnergy(double[] pos)
Calculates the angle 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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findIn
public static java.util.List<AngleBend> findIn(Tables t, MMFFMolecule mol)
Helper function that builds a list of AngleBends for a molecule.- Parameters:
t
- The tables object.mol
- The molecule to generate angles for.- Returns:
- Am array of AngleBends.
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