Monomer

class Monomer(monomerName, fromUni=False)[source]

Bases: object

Create a Monomer MDAnalysis Universe from the provided PDB filepath.

Remarks:: Polymer.dihedral_solver(), Polymer.dist(), Polymer.shuffle() and Polymer.shuffler() rely on connectivity information. If your input file does not contain connectivity information (e.g. CONECT records in a pdb), these may not work as intended.

Use MDAnalysis Universe.copy() to create a new MDAnalysis Universe that is an exact copy of this one containing the polymer. Deepcopy is not used as it can be problematic with open file sockets.

Returns:: A new Polymer that is an exact copy of this polymer
Return type:: Polymer

classmethod monomer_from_u(universe: Universe) → Monomer[source]

Create Monomer from an MDAnalysis Universe

Parameters:: universe (mda.Universe) – _description_
Returns:: _description_
Return type:: Monomer

select_atoms(selection: str) → AtomGroup[source]

Selection method that selects atoms from the monomer’s MDAnalysis Universe by leveraging the MDAnalysis atom selection. MDAnalysis atom selection string, for more information on supported atom selection formats see

Parameters:: selection (str) – MDAnalysis atom selection string, for more information on supported atom selection formats see MDAnalysis Atom selection language <https://userguide.mdanalysis.org/stable/selections.html>
Returns:: An MDAnalysis AtomGroup containing only the selected atoms
Return type:: mda.AtomGroup