Monomer

class Monomer(topology: Topology, junctions: Junctions | List[Junction])[source]

Bases: object

Represents a monomer with its properties in a molecular system.

Parameters:

topology (Topology) – the Topology object used to create this Monomer.
junctions (Union[Junctions, List[Junction]]) – a list of Junction objects or Junctions object containing all Junctions which will be present in this Monomer.

copy() → Monomer[source]

Method to duplicate a Monomer, which leverages the Topology.copy() function.

Raises:

ValueError – if the monomer atom in one of the Polymer’s Junctions is not present.
ValueError – if the residue atom in one of the Polymer’s Junctions is not present.

Returns:

a new Monomer which has the same attributes as this Monomer.

Return type:

Monomer

classmethod from_Polymer(polymer: Polymer) → Monomer[source]

Convert a Polymer object to a Monomer object. Useful for creating Polymeric branches of a set size and converting them back to a Monomer so that they can be polymerised onto another Polymer.

Parameters:

polymer (Polymer) – a Polymer to convert.

Raises:

ValueError – if the monomer atom in one of the Polymer’s Junctions is not present.
ValueError – if the residue atom in one of the Polymer’s Junctions is not present.

Returns:

a new Monomer which has the same attributes (Topology and Junctions) as the provided Polymer.

Return type:

Monomer

classmethod from_dict(data: dict) → Monomer[source]

Create a new Monomer from a dictionary, such as that created with Monomer.to_dict().

The structure of the dictionary is as below: {“topology”: self.topology.to_dict(), “junctions”: self.junctions.to_dict()}

Parameters:: data (dict) – dictionary containing data to make a Monomer, generate with ‘to_dict()’.
Returns:: a new Monomer
Return type:: Monomer

classmethod load(file_path: str) → Monomer[source]

Load a JSON text dump of a Monomer, generated with Monomer.save(), to a new Monomer.

Parameters:: file_path (str) – path to the Monomer JSON dictionary text dump file.
Returns:: a new Monomer
Return type:: Monomer

renumber_atoms(start: int)[source]

Renumber the ids of Atoms in the Topology starting from a given number. Each atom’s new id number is equal to its current id number plus the value of start.

E.g. an atom with and id of 1 renumbered with a start value of 10 will: have a new id of 11.

Parameters:: start (int) – value that will be added to the atom’s existing ids to renumber them.

save(file_path: str)[source]

Save and export the Monomer to a JSON text dump.

Parameters:: file_path (str) – path to and desired name of output file.

to_dict() → dict[source]

Convert this Monomer to a dictionary representation.

The structure of the dictionary is as below: {“topology”: self.topology.to_dict(), “junctions”: self.junctions.to_dict()}

Returns:: a dictionary containing references to the dictionary representations of this Monomer’s Topology and Junctions attributes.
Return type:: dict