OpenMM
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:

List of all members.

Public Member Functions

def getOriginWeights
 getOriginWeights(self) -> Vec3 const &
def getXWeights
 getXWeights(self) -> Vec3 const &
def getYWeights
 getYWeights(self) -> Vec3 const &
def getLocalPosition
 getLocalPosition(self) -> Vec3 const &
def __init__
 __init__(self, particle1, particle2, particle3, originWeights, xWeights, yWeights, localPosition) -> LocalCoordinatesSite __init__(self, other) -> LocalCoordinatesSite

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__(self, particle1, particle2, particle3, originWeights, xWeights, yWeights, localPosition) -> LocalCoordinatesSite __init__(self, other) -> LocalCoordinatesSite

Create a new LocalCoordinatesSite virtual site.

Parameters:
particle1(int) the index of the first particle
particle2(int) the index of the second particle
particle3(int) the index of the third particle
originWeights(Vec3) the weight factors for the three particles when computing the origin location
xWeights(Vec3) the weight factors for the three particles when computing xdir
yWeights(Vec3) the weight factors for the three particles when computing ydir
localPosition(Vec3) the position of the virtual site in the local coordinate system

Member Function Documentation

def getLocalPosition (   self)

getLocalPosition(self) -> Vec3 const &

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

def getOriginWeights (   self)

getOriginWeights(self) -> Vec3 const &

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

def getXWeights (   self)

getXWeights(self) -> Vec3 const &

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

def getYWeights (   self)

getYWeights(self) -> Vec3 const &

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


Member Data Documentation


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