Topology

class sknano.core.atoms.Topology(*atoms, size, id=0, type=0, parent=None, check_operands=True)[source] [edit on github][source]

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:

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()[source] [edit on github][source]

Compute topological measure from Topology.atoms.

compute_strain(m0)[source] [edit on github][source]

Compute topological strain in Topology.measure.

Parameters:m0 (float) –
Returns:
Return type:float
rotate(**kwargs)[source] [edit on github][source]

Rotate the Topology by rotating the atoms.

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

Return dict of constructor parameters.