Bond

class sknano.core.atoms.mixins.Bond(*args, order=None, **kwargs)[source] [edit on github][source]

Bases: sknano.core.atoms.mixins.Topology

Class representation of bond between 2 Atom objects.

Parameters:
  • end (origin,) –
  • parent (Parent Molecule, if any.) –
  • id (int) –
  • order ({1, 2, 3, 5}) –

Attributes

atom1 An alias for origin.
atom2 An alias for end.
atom_ids Topology.atoms ids.
atoms Atoms in TopologyCollection.
bond An alias for TopologyCollection.measure.
centroid centroid of Topology.atoms.
end Atom 2 in Bond.
fmtstr Format string.
length An alias for TopologyCollection.measure.
measure Measure of topology.
order Bond order.
origin Atom 1 in Bond.
strain Strain in measure.
unit_vector Bond unit_vector.
vector Bond Vector.

Methods

compute_measure() Bond length.
compute_strain(m0) Compute topological strain in Topology.measure.
partner(atom) Return Atom bonded to atom.
rotate(**kwargs) Rotate the Topology by rotating the atoms.
todict() Return dict of constructor parameters.

Attributes Summary

atom1 An alias for origin.
atom2 An alias for end.
bond An alias for TopologyCollection.measure.
end Atom 2 in Bond.
length An alias for TopologyCollection.measure.
order Bond order.
origin Atom 1 in Bond.
unit_vector Bond unit_vector.
vector Bond Vector.

Methods Summary

compute_measure() Bond length.
partner(atom) Return Atom bonded to atom.
todict() Return dict of constructor parameters.

Attributes Documentation

atom1

An alias for origin.

atom2

An alias for end.

bond

An alias for TopologyCollection.measure.

end

Atom 2 in Bond.

length

An alias for TopologyCollection.measure.

order

Bond order.

origin

Atom 1 in Bond.

unit_vector

Bond unit_vector.

vector

Bond Vector.

Bond Vector points from Bond.origin to Bond.end.

Note

Accounts for periodic boundary conditions if a Crystal3DLattice is assigned to the atoms.

Methods Documentation

compute_measure()[source] [edit on github][source]

Bond length.

partner(atom)[source] [edit on github][source]

Return Atom bonded to atom.

todict()[source] [edit on github][source]

Return dict of constructor parameters.