Package ffx.openmm

Class VirtualSite

java.lang.Object
ffx.openmm.VirtualSite
Direct Known Subclasses:
LocalCoordinatesSite, OutOfPlaneSite, ThreeParticleAverageSite, TwoParticleAverageSite
public abstract class VirtualSite extends Object
A VirtualSite describes the rules for computing a particle's position based on other particles. This is an abstract class. Subclasses define particular rules. To define a virtual site, create an instance of a VirtualSite subclass and then call setVirtualSite() on the System.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    protected com.sun.jna.ptr.PointerByReference
    pointer
    The pointer is allocated and deallocated by classes that extend VirtualSite.

  • Constructor Summary

    Constructors
    Constructor
    Description
    VirtualSite(com.sun.jna.ptr.PointerByReference pointer)
    Create a VirtualSite from an existing pointer.

  • Method Summary

    Modifier and Type
    Method
    Description
    abstract void
    destroy()
    Destroy the virtual site.
    int
    getNumParticles()
    Get the number of particles this virtual site depends on.
    int
    getParticle(int particle)
    Get the index of a particle this virtual site depends on.
    com.sun.jna.ptr.PointerByReference
    getPointer()
    Get the pointer to the OpenMM VirtualSite.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Field Details

    • pointer

      protected com.sun.jna.ptr.PointerByReference pointer
      The pointer is allocated and deallocated by classes that extend VirtualSite.

  • Constructor Details

    • VirtualSite

      public VirtualSite(com.sun.jna.ptr.PointerByReference pointer)
      Create a VirtualSite from an existing pointer.
      Parameters:
      pointer - The pointer to the OpenMM VirtualSite.

  • Method Details

    • destroy

      public abstract void destroy()
      Destroy the virtual site.

    • getNumParticles

      public int getNumParticles()
      Get the number of particles this virtual site depends on.
      Returns:
      The number of particles.

    • getParticle

      public int getParticle(int particle)
      Get the index of a particle this virtual site depends on.
      Parameters:
      particle - the particle to get (between 0 and getNumParticles())
      Returns:
      the index of the particle in the System

    • getPointer

      public com.sun.jna.ptr.PointerByReference getPointer()
      Get the pointer to the OpenMM VirtualSite.
      Returns:
      The pointer to the OpenMM VirtualSite.