pestifer.tasks.manipulate module

Definition of the ManipulateTask class for performing coordinate manipulations. This class is a descendant of the BaseTask class and is used for manipulating molecular coordinates.

Usage is described in the manipulate documentation.

class pestifer.tasks.manipulate.ManipulateTask(specs: dict = None, **kwargs)

Bases: BaseTask

ManipulateTask class for performing coordinate manipulations.

coormods()

Perform coordinate modifications based on the specifications provided in the task. This method retrieves the coordinate modifications from the object manager, iterates through the specified object types and their corresponding lists, and applies the modifications using the VMD scripter. It writes the modified coordinates to a PDB file and saves the state with the updated coordinates. The method returns 0 on success or a non-zero error code on failure.

do() → int

Execute the manipulate task.

provision(packet=None)

Provision the task with necessary resources. This method is called to set up the task with the required resources and context. It can be overridden by subclasses to provide additional provisioning logic.

Parameters:

packet (dict, optional) – A dictionary of provisions to be used for the task. If not provided, the existing provisions will be used.