Package ffx.openmm
Class LocalCoordinatesSite
java.lang.Object
ffx.openmm.VirtualSite
ffx.openmm.LocalCoordinatesSite
This is a VirtualSite that computes the particle location based on a local coordinate system.
The site is placed at a fixed position relative to a local coordinate system defined by
other particles. This is useful for representing sites like lone pairs or pi-electron
centers that have well-defined positions relative to the molecular framework.
The local coordinate system is defined by an origin and two direction vectors (x and y axes). Each of these is specified as a weighted average of particle positions. The z axis is taken to be the cross product of the x and y axes.
-
Field Summary
Fields inherited from class ffx.openmm.VirtualSite
pointer -
Constructor Summary
ConstructorsConstructorDescriptionLocalCoordinatesSite(int particle1, int particle2, int particle3, edu.uiowa.jopenmm.OpenMM_Vec3 originWeights, edu.uiowa.jopenmm.OpenMM_Vec3 xdir, edu.uiowa.jopenmm.OpenMM_Vec3 ydir, edu.uiowa.jopenmm.OpenMM_Vec3 localPosition) Create a LocalCoordinatesSite using specific particles and vectors to define the coordinate system.LocalCoordinatesSite(com.sun.jna.ptr.PointerByReference originWeights, com.sun.jna.ptr.PointerByReference xWeights, com.sun.jna.ptr.PointerByReference yWeights, com.sun.jna.ptr.PointerByReference zWeights, edu.uiowa.jopenmm.OpenMM_Vec3 localPosition) Create a LocalCoordinatesSite using weighted averages to define the coordinate system. -
Method Summary
Modifier and TypeMethodDescriptionvoiddestroy()Destroy the virtual site.edu.uiowa.jopenmm.OpenMM_Vec3Get the position of the virtual site in the local coordinate system.voidgetOriginWeights(com.sun.jna.ptr.PointerByReference weights) Get the weights used for computing the origin of the local coordinate system.voidgetXWeights(com.sun.jna.ptr.PointerByReference weights) Get the weights used for computing the x direction of the local coordinate system.voidgetYWeights(com.sun.jna.ptr.PointerByReference weights) Get the weights used for computing the y direction of the local coordinate system.Methods inherited from class ffx.openmm.VirtualSite
getNumParticles, getParticle, getPointer
-
Constructor Details
-
LocalCoordinatesSite
public LocalCoordinatesSite(com.sun.jna.ptr.PointerByReference originWeights, com.sun.jna.ptr.PointerByReference xWeights, com.sun.jna.ptr.PointerByReference yWeights, com.sun.jna.ptr.PointerByReference zWeights, edu.uiowa.jopenmm.OpenMM_Vec3 localPosition) Create a LocalCoordinatesSite using weighted averages to define the coordinate system.- Parameters:
originWeights- The weights for computing the origin as a weighted average of particle positions.xWeights- The weights for computing the x direction as a weighted average of particle positions.yWeights- The weights for computing the y direction as a weighted average of particle positions.zWeights- The weights for computing the z direction as a weighted average of particle positions.localPosition- The position of the virtual site in the local coordinate system.
-
LocalCoordinatesSite
public LocalCoordinatesSite(int particle1, int particle2, int particle3, edu.uiowa.jopenmm.OpenMM_Vec3 originWeights, edu.uiowa.jopenmm.OpenMM_Vec3 xdir, edu.uiowa.jopenmm.OpenMM_Vec3 ydir, edu.uiowa.jopenmm.OpenMM_Vec3 localPosition) Create a LocalCoordinatesSite using specific particles and vectors to define the coordinate system.- Parameters:
particle1- The index of the first particle.particle2- The index of the second particle.particle3- The index of the third particle.originWeights- The weights for the origin calculation.xdir- The x direction vector.ydir- The y direction vector.localPosition- The position of the virtual site in the local coordinate system.
-
-
Method Details
-
destroy
public void destroy()Destroy the virtual site.- Specified by:
destroyin classVirtualSite
-
getLocalPosition
public edu.uiowa.jopenmm.OpenMM_Vec3 getLocalPosition()Get the position of the virtual site in the local coordinate system.- Returns:
- The local position of the virtual site.
-
getOriginWeights
public void getOriginWeights(com.sun.jna.ptr.PointerByReference weights) Get the weights used for computing the origin of the local coordinate system.- Parameters:
weights- The weights for the origin calculation (output).
-
getXWeights
public void getXWeights(com.sun.jna.ptr.PointerByReference weights) Get the weights used for computing the x direction of the local coordinate system.- Parameters:
weights- The weights for the x direction calculation (output).
-
getYWeights
public void getYWeights(com.sun.jna.ptr.PointerByReference weights) Get the weights used for computing the y direction of the local coordinate system.- Parameters:
weights- The weights for the y direction calculation (output).
-