Class VanDerWaals
- java.lang.Object
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- com.actelion.research.chem.forcefield.mmff.VanDerWaals
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- All Implemented Interfaces:
EnergyTerm
public class VanDerWaals extends java.lang.Object implements EnergyTerm
Nonbonded van der Waals energy term class. This energy term represents the van der Waals interaction between two atoms A1..A2 which are in a 1,X (X > 3) relationship. A cutoff (default: 100.0 angstrom) can be set to skip computation of van der Waals interactions between atoms separated by distances larger than the cutoff.
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Constructor Summary
Constructors Constructor Description VanDerWaals(Tables table, MMFFMolecule mol, int a1, int a2)
Construct a new van der Waals 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<VanDerWaals>
findIn(Tables table, MMFFMolecule mol, Separation sep, double nonbondedCutoff)
Finds all van der Waals energy terms in the current molecule.double
getEnergy(double[] pos)
Calculates the van der Waals 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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VanDerWaals
public VanDerWaals(Tables table, MMFFMolecule mol, int a1, int a2)
Construct a new van der Waals 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.
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Method Detail
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getEnergy
public double getEnergy(double[] pos)
Calculates the van der Waals 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<VanDerWaals> findIn(Tables table, MMFFMolecule mol, Separation sep, double nonbondedCutoff)
Finds all van der Waals energy terms in the current molecule.- Parameters:
table
- The tables object.mol
- The molecule to search for van der Waals forces.sep
- The separations table for molecule mol.- Returns:
- The van der Waals energy terms for this molecule.
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