Package ffx.potential.terms

Class PiOrbitalTorsionPotentialEnergy

java.lang.Object
ffx.potential.terms.EnergyTerm
ffx.potential.terms.PiOrbitalTorsionPotentialEnergy
public class PiOrbitalTorsionPotentialEnergy extends EnergyTerm
Pi-Orbital Torsion potential energy term using PiOrbitalTorsion instances.

  • Constructor Details

    • PiOrbitalTorsionPotentialEnergy

      public PiOrbitalTorsionPotentialEnergy(String name)
      Create a PiOrbitalTorsionPotentialEnergy with the provided name.
      Parameters:
      name - Name for this term.

    • PiOrbitalTorsionPotentialEnergy

      public PiOrbitalTorsionPotentialEnergy(String name, int forceGroup)
      Create a PiOrbitalTorsionPotentialEnergy with the provided name and force group.
      Parameters:
      name - Name for this term.
      forceGroup - Integer force group identifier.

    • PiOrbitalTorsionPotentialEnergy

      public PiOrbitalTorsionPotentialEnergy(String name, int forceGroup, List<PiOrbitalTorsion> piOrbitalTorsions)
      Create a PiOrbitalTorsionPotentialEnergy initialized with a list of terms and force group.
      Parameters:
      name - Name for this term.
      forceGroup - Force group identifier.
      piOrbitalTorsions - List of PiOrbitalTorsion instances to add (null-safe).

    • PiOrbitalTorsionPotentialEnergy

      public PiOrbitalTorsionPotentialEnergy(String name, Collection<PiOrbitalTorsion> piOrbitalTorsions)
      Create a PiOrbitalTorsionPotentialEnergy initialized with a collection of terms.
      Parameters:
      name - Name for this term (may be null).
      piOrbitalTorsions - Collection of PiOrbitalTorsion instances to add (null-safe).

  • Method Details

    • getNumberOfTerms

      public int getNumberOfTerms()
      Get the number of BondedTerms in this term.
      Specified by:
      getNumberOfTerms in class EnergyTerm
      Returns:
      The number of BondedTerms.

    • getBondedTermsArray

      public BondedTerm[] getBondedTermsArray()
      Get an array of BondedTerms in this term.
      Specified by:
      getBondedTermsArray in class EnergyTerm
      Returns:
      Array of BondedTerms.

    • addPiOrbitalTorsion

      public boolean addPiOrbitalTorsion(PiOrbitalTorsion piOrbitalTorsion)
      Add a PiOrbitalTorsion to this term.
      Parameters:
      piOrbitalTorsion - PiOrbitalTorsion to add (ignored if null).
      Returns:
      true if it was added.

    • addPiOrbitalTorsions

      public boolean addPiOrbitalTorsions(PiOrbitalTorsion[] piOrbitalTorsions)
      Add an array of PiOrbitalTorsions to this term.
      Parameters:
      piOrbitalTorsions - Array of PiOrbitalTorsion instances to add.
      Returns:
      true if they were added.

    • addPiOrbitalTorsions

      public boolean addPiOrbitalTorsions(List<PiOrbitalTorsion> piOrbitalTorsions)
      Add a list of PiOrbitalTorsions to this term.
      Parameters:
      piOrbitalTorsions - List of PiOrbitalTorsion instances to add.
      Returns:
      true if they were added.

    • removePiOrbitalTorsion

      public boolean removePiOrbitalTorsion(PiOrbitalTorsion piOrbitalTorsion)
      Remove a PiOrbitalTorsion from this term.
      Parameters:
      piOrbitalTorsion - PiOrbitalTorsion to remove (ignored if null).
      Returns:
      true if it was present and removed.

    • getPiOrbitalTorsion

      public PiOrbitalTorsion getPiOrbitalTorsion(int index)
      Get the PiOrbitalTorsion at a given index.
      Parameters:
      index - Index in the internal list.
      Returns:
      PiOrbitalTorsion at the specified index.
      Throws:
      IndexOutOfBoundsException - if index is invalid.

    • getPiOrbitalTorsions

      public List<PiOrbitalTorsion> getPiOrbitalTorsions()
      Get an unmodifiable view of the PiOrbitalTorsions in this term.
      Returns:
      Unmodifiable List of PiOrbitalTorsions.

    • getPiOrbitalTorsionArray

      public PiOrbitalTorsion[] getPiOrbitalTorsionArray()
      Get an array of PiOrbitalTorsions in this term.
      Returns:
      Array of PiOrbitalTorsions.

    • getNumberOfPiOrbitalTorsions

      public int getNumberOfPiOrbitalTorsions()
      Get the number of PiOrbitalTorsions in this term.
      Returns:
      The number of PiOrbitalTorsions.

    • setLambda

      public void setLambda(double lambda)
      Set the lambda value for all Pi-Orbital Torsions in this term.
      Parameters:
      lambda - Lambda value to set for all Pi-Orbital Torsions.

    • getdEdL

      public double getdEdL()
      Get the energy contribution from all Pi-Orbital Torsions in this term.
      Returns:
      Total energy from all Pi-Orbital Torsions.

    • getd2EdL2

      public double getd2EdL2()
      Get the energy contribution from all Torsions in this term.
      Returns:
      Total energy from all Pi-Orbital Torsions.

    • getPiOrbitalTorsionEnergyString

      public static String getPiOrbitalTorsionEnergyString()

    • log

      public void log()
      Log the details of Pi-Orbital Torsion interactions.
      Specified by:
      log in class EnergyTerm

    • toPDBString

      public String toPDBString()
      Description copied from class: EnergyTerm
      Get a PDB-style REMARK representation of this energy term.
      Specified by:
      toPDBString in class EnergyTerm
      Returns:
      A PDB REMARK string for this energy term.

    • toString

      public String toString()
      Description copied from class: EnergyTerm
      Get a string representation of this energy term.
      Specified by:
      toString in class EnergyTerm
      Returns:
      A string representation of the energy term.