LocalCoordinatesSite Class Reference

This is a VirtualSite that uses the locations of three other particles to compute a local coordinate system, then places the virtual site at a fixed location in that coordinate system. More...

Inheritance diagram for LocalCoordinatesSite:

Public Member Functions
def	getOriginWeights
	getOriginWeights(LocalCoordinatesSite self) -> Vec3 const & More...
def	getXWeights
	getXWeights(LocalCoordinatesSite self) -> Vec3 const & More...
def	getYWeights
	getYWeights(LocalCoordinatesSite self) -> Vec3 const & More...
def	getLocalPosition
	getLocalPosition(LocalCoordinatesSite self) -> Vec3 const & More...
def	__init__
	init(OpenMM::LocalCoordinatesSite self, int particle1, int particle2, int particle3, Vec3 const & originWeights, Vec3 const & xWeights, Vec3 const & yWeights, Vec3 const & localPosition) -> LocalCoordinatesSite init(OpenMM::LocalCoordinatesSite self, LocalCoordinatesSite other) -> LocalCoordinatesSite More...
def	__del__
	del(OpenMM::LocalCoordinatesSite self) More...
Public Member Functions inherited from VirtualSite
def	__init__
def	__del__
	del(OpenMM::VirtualSite self) More...
def	getNumParticles
	getNumParticles(VirtualSite self) -> int More...
def	getParticle
	getParticle(VirtualSite self, int particle) -> int More...

Public Attributes
	this

Detailed Description

This is a VirtualSite that uses the locations of three other particles to compute a local coordinate system, then places the virtual site at a fixed location in that coordinate system.

The origin of the coordinate system and the directions of its x and y axes are each specified as a weighted sum of the locations of the three particles:

origin = w₁r₁ + w₂r₂ + w₃r₃

xdir = w₁r₁ + w₂r₂ + w₃r₃

ydir = w₁r₁ + w₂r₂ + w₃r₃

For the origin, the three weights must add to one. For example if (w₁, w₂, w₃) = (1.0, 0.0, 0.0), the origin of the local coordinate system is at the location of particle 1. For xdir and ydir, the weights must add to zero. For excample, if (w₁, w₂, w₃) = (-1.0, 0.5, 0.5), the x axis points from particle 1 toward the midpoint between particles 2 and 3.

The z direction is computed as zdir = xdir x ydir. To ensure the axes are all orthogonal, ydir is then recomputed as ydir = zdir x xdir. All three axis vectors are then normalized, and the virtual site location is set to

origin + x*xdir + y*ydir + z*zdir

Constructor & Destructor Documentation

def __init__	(		self,
			args
	)

init(OpenMM::LocalCoordinatesSite self, int particle1, int particle2, int particle3, Vec3 const & originWeights, Vec3 const & xWeights, Vec3 const & yWeights, Vec3 const & localPosition) -> LocalCoordinatesSite init(OpenMM::LocalCoordinatesSite self, LocalCoordinatesSite other) -> LocalCoordinatesSite

Create a new LocalCoordinatesSite virtual site.

Parameters

particle1	the index of the first particle
particle2	the index of the second particle
particle3	the index of the third particle
originWeights	the weight factors for the three particles when computing the origin location
xWeights	the weight factors for the three particles when computing xdir
yWeights	the weight factors for the three particles when computing ydir
localPosition	the position of the virtual site in the local coordinate system

References simtk.openmm.openmm.stripUnits().

def __del__

(

self

)

del(OpenMM::LocalCoordinatesSite self)

References simtk.openmm.openmm.stripUnits().

Member Function Documentation

def getLocalPosition	(		self,
			args
	)

getLocalPosition(LocalCoordinatesSite self) -> Vec3 const &

Get the position of the virtual site in the local coordinate system.

References simtk.openmm.openmm.stripUnits().

def getOriginWeights	(		self,
			args
	)

getOriginWeights(LocalCoordinatesSite self) -> Vec3 const &

Get the weight factors for the three particles when computing the origin location.

References simtk.openmm.openmm.stripUnits().

def getXWeights	(		self,
			args
	)

getXWeights(LocalCoordinatesSite self) -> Vec3 const &

Get the weight factors for the three particles when computing xdir.

References simtk.openmm.openmm.stripUnits().

def getYWeights	(		self,
			args
	)

getYWeights(LocalCoordinatesSite self) -> Vec3 const &

Get the weight factors for the three particles when computing ydir.

References simtk.openmm.openmm.stripUnits().

Member Data Documentation

this

Referenced by System.__init__().

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The documentation for this class was generated from the following file:

• openmm.py