pestifer.objs.orient module¶

This class allows the user to orient a coordinate set along a specified axis and optionally align it with a reference atom. The orientation is performed using the VMD orient command, which computes the principal axes of the coordinate set and aligns it with the specified axis.

class pestifer.objs.orient.Orient(*args, axis: str, refatom: str | None = None)[source]¶

Bases: BaseObj

A class for handling orientation of a coordinate set in VMD.

axis: 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.

refatom: str | None¶

class pestifer.objs.orient.OrientList(initlist: Iterable[T] = ())[source]¶

Bases: BaseObjList[Orient]

A class for handling a list of Orient objects. This class inherits from BaseObjList and provides methods to write Tcl commands for each Orient object in the list.

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