Topology

class sknano.core.atoms.mixins.Topology(*atoms, size, id=0, type=0, parent=None, check_operands=True)

Bases: sknano.core.meta.BaseClass, sknano.core.strings.TabulateMixin

Base Atom topology class.

Parameters:

• *atoms –

  list of Atoms or an Atoms object.

• size (int) –
• parent (Parent Molecule, if any.) –
• id (int) –
• type (int) –
• check_operands (bool, optional) –

Raises:

• TypeError – if atoms is not a list of Atom objects or an Atoms object.
• ValueError – if len(atoms) != size.

Attributes

atom_ids	Topology.atoms ids.
atoms	Atoms in TopologyCollection.
centroid	centroid of Topology.atoms.
fmtstr	Format string.
measure	Measure of topology.
strain	Strain in measure.

Methods

compute_measure()	Compute topological measure from Topology.atoms.
compute_strain(m0)	Compute topological strain in Topology.measure.
rotate(**kwargs)	Rotate the Topology by rotating the atoms.
todict()	Return dict of constructor parameters.

Attributes Summary

atom_ids	Topology.atoms ids.
atoms	Atoms in TopologyCollection.
centroid	centroid of Topology.atoms.
measure	Measure of topology.
strain	Strain in measure.

Methods Summary

compute_measure()	Compute topological measure from Topology.atoms.
compute_strain(m0)	Compute topological strain in Topology.measure.
rotate(**kwargs)	Rotate the Topology by rotating the atoms.
todict()	Return dict of constructor parameters.

Attributes Documentation

atom_ids

Topology.atoms ids.

atoms

Atoms in TopologyCollection.

centroid

centroid of Topology.atoms.

measure

Measure of topology.

strain

Strain in measure.

Methods Documentation

compute_measure()

Compute topological measure from Topology.atoms.

compute_strain(m0)

Compute topological strain in Topology.measure.

Parameters:m0 (float) – Returns: Return type:float

rotate(**kwargs)

Rotate the Topology by rotating the atoms.

todict()

Return dict of constructor parameters.