SpeciesGroup

Synopsis

SpeciesGroup is a class template for classes that describes covalent groups within a Species of molecule.

A SpeciesGroup<N> object describes a covalent group of N atoms. Such an object has integer identifiers for the N atoms in the group and an integer group type identifier. The atoms in the group are identified by integer indices that identify the position of each atom within a molecule by an integer greater than or equal to 0 and less than the number of atoms in a molecule of that species.

See also

Simp::SpeciesGroup

Text Representation

The text representation of a species SpeciesGroup<N> is as follows

atomId1 atomId2 ... atomIdN groupTypeId

where atomId1, ..., atomIdN are integer identifiers for the n atoms, and groupTypId is an identifier for the type of group (i.e., the type of bond, angle, or dihedral potential).

For example, a SpeciesGroup<2> with the text representation

4    5    1

represents a bond that connects that 4th and 5th atoms in each molecule of the species with a bond of bond type id 1.