pestifer.objs.substitution module¶

A Substitution is a user-specified modification in which a sequence of one or more contiguous residues are replaced by a new sequence of one or more residues.

class pestifer.objs.substitution.Substitution(*args, chainID: str, resid1: ResID, resid2: ResID, subseq: str)[source]¶

Bases: BaseObj

A class for handling substitutions

chainID: str¶

model_config = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'frozen': False}¶: Configuration for pydantic.BaseModel.

model_post_init(context: Any, /) → None¶

This function is meant to behave like a BaseModel method to initialize private attributes.

It takes context as an argument since that’s what pydantic-core passes when calling it.

Parameters:

self – The BaseModel instance.
context – The context.

resid1: ResID¶

resid2: ResID¶

shortcode() → str[source]¶

subseq: str¶

class pestifer.objs.substitution.SubstitutionList(initlist: Iterable[T] = ())[source]¶

Bases: BaseObjList[Substitution]

A list of Substitution objects. This class is used to manage a collection of Substitution objects.

describe()[source]¶: Abstract method to describe the contents of the BaseObjList. Subclasses should implement this method to provide a meaningful description.