fairmd.lipids.auxiliary.mollib module

Auxiliary module for molecule handling in FMDL.

Includes elements assigneer functions that help Molecule to define brutto formula from existing mapping files and element guesser.

fairmd.lipids.auxiliary.mollib.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’, …

fairmd.lipids.auxiliary.mollib.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

fairmd.lipids.auxiliary.mollib.get_tails_of_lipid(lipid: Lipid) → set[str][source]

Get the tails of a lipid molecule.

Parameters:

lipid – Lipid molecule

Returns:

List of tails (str-s)