Package ffx.openmm

Class BondArray

java.lang.Object
ffx.openmm.BondArray
public class BondArray extends Object
Bonds are specified by pairs of integers (the atom indices).

  • Constructor Summary

    Constructors
    Constructor
    Description
    BondArray(int size)
    Create a new bond array.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    append(int i1, int i2)
    Append a bond to the bond array.
    void
    destroy()
    Destroy the bond array.
    void
    get(int index, com.sun.jna.ptr.IntByReference i1, com.sun.jna.ptr.IntByReference i2)
    Get the bond at index.
    void
    get(int index, IntBuffer i1, IntBuffer i2)
    Get the bond at index.
    com.sun.jna.ptr.PointerByReference
    getPointer()
    Get the pointer to the bond array.
    int
    getSize()
    Get the size of the bond array.
    void
    resize(int size)
    Resize the bond array.
    void
    set(int index, int i1, int i2)
    Set the bond at index to i1 and i2.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • BondArray

      public BondArray(int size)
      Create a new bond array.
      Parameters:
      size - The size of the bond array.

  • Method Details

    • append

      public void append(int i1, int i2)
      Append a bond to the bond array.
      Parameters:
      i1 - The first atom index.
      i2 - The second atom index.

    • destroy

      public void destroy()
      Destroy the bond array.

    • get

      public void get(int index, IntBuffer i1, IntBuffer i2)
      Get the bond at index.
      Parameters:
      index - The index of the bond to get.
      i1 - The first atom index.
      i2 - The second atom index.

    • get

      public void get(int index, com.sun.jna.ptr.IntByReference i1, com.sun.jna.ptr.IntByReference i2)
      Get the bond at index.
      Parameters:
      index - The index of the bond to get.
      i1 - The first atom index.
      i2 - The second atom index.

    • getPointer

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

    • getSize

      public int getSize()
      Get the size of the bond array.
      Returns:
      The size of the bond array.

    • resize

      public void resize(int size)
      Resize the bond array.
      Parameters:
      size - The new size of the bond array.

    • set

      public void set(int index, int i1, int i2)
      Set the bond at index to i1 and i2.
      Parameters:
      index - The index of the bond to set.
      i1 - The first atom index.
      i2 - The second atom index.