opencadd.structure.core.Structure.add_TopologyAttr

Structure.add_TopologyAttr(topologyattr, values=None)

Add a new topology attribute to the Universe

Adding a TopologyAttribute to the Universe makes it available to all AtomGroups etc throughout the Universe.

Parameters

• topologyattr (TopologyAttr or string) – Either a MDAnalysis TopologyAttr object or the name of a possible topology attribute.

• values (np.ndarray, optional) – If initiating an attribute from a string, the initial values to use. If not supplied, the new TopologyAttribute will have empty or zero values.

Example

For example to add bfactors to a Universe:

>>> u.add_TopologyAttr('bfactors')
>>> u.atoms.bfactors
array([ 0.,  0.,  0., ...,  0.,  0.,  0.])

Changed in version 0.17.0: Can now also add TopologyAttrs with a string of the name of the attribute to add (eg ‘charges’), can also supply initial values using values keyword.

Changed in version 1.1.0: Now warns when adding bfactors to a Universe with existing tempfactors, or adding tempfactors to a Universe with existing bfactors. In version 2.0, MDAnalysis will stop treating tempfactors and bfactors as separate attributes. Instead, they will be aliases of the same attribute.