DatabankLib.settings.elements module

Elements assigneer functions.

Helps Molecule to define brutto formula from existing mapping files and element guesser.

DatabankLib.settings.elements.uname2element(mapping_name: str) → str[source]

Guess element name from universal atom name.

Parameters:

mapping_name – name of the mapping, e.g. ‘M_C1’, ‘M_G’

Raises:

KeyError – if element cannot be determined from mapping name

Returns:

element name, e.g. ‘C’, ‘N’, …

DatabankLib.settings.elements.guess_elements(system: System, u: Universe) → None[source]

Assign elements to atoms in the MDAnalysis Universe based on the system’s composition.

Parameters:

  • system (System) – Databank System object

  • u (mda.Universe) – MDAnalysis Universe object