Bonds

class sknano.core.atoms.Bonds(topolist=None, parent=None)

Bases: sknano.core.atoms.mixins.TopologyCollection

Base class for collection of atom Bonds.

Parameters:

• topolist ({None, sequence, Bonds}, optional) – if not None, then a list of Bond objects
• parent (Parent Molecule, if any.) –

Attributes

Nbonds	Number of Bonds in Bonds.
Ntypes	Number of unique Topology.types.
atom_ids	list of atom_ids.
bonds	ndarray of bonds.
fmtstr	Format string.
ids	list of ids.
lengths	An alias for Bonds.bonds.
mean	An alias for TopologyCollection.mean_measure.
mean_bond	Mean bond length.
mean_length	An alias for Bonds.mean_bond.
mean_measure	Mean measure.
measures	ndarray of measures.
parent	Parent Molecule, if any.
statistics	Bond stats.
strains	ndarray of strains.
types	list of types.
unique	Return new TopologyCollection object containing the set of unique Topologys.
unit_vectors	ndarray of unit_vectors.
vectors	ndarray of vectors.

Methods

append(item)
clear()
compute_strains(reference)	Return ndarray of topology measure strains.
copy()
count(item)
extend(other)
index(item, *args)
insert(i, item)
pop([i])
remove(item)
reverse()
sort([key, reverse])
todict()	Return dict of constructor parameters.