DummyAtomSite Struct Reference

#include <internalcoordinates.h>

Public Attributes
Index	anchor = MaxIndex
Vector3	position = Vector3::Zero()

Detailed Description

Where a z-matrix over a molecule would need a dummy atom.

A z-matrix cannot describe a linear fragment. With a row's atom, its distance reference and its angle reference in a line, the 180 degree angle pins nothing down, no dihedral measured from that row can be reconstructed, and neither value can be edited: there is no plane to open the angle in and no axis the torsion would turn the atom about. The remedy chemists have always used is a dummy atom set off the axis, which gives those rows a right angle and a plane to be measured against.

Member Data Documentation

anchor

Index anchor = MaxIndex

The atom the dummy belongs beside, and should be bonded to.

position

Vector3 position = Vector3::Zero()

Where the dummy goes: off the linear axis, beside anchor.

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

• internalcoordinates.h