pestifer.tasks.cleave module

Definition of the CleaveTask class for cleaving chains in a molecular structure. This class is a descendant of the PsfgenTask class and is used to cleave chains in a molecular structure based on specified cleavage sites. It reads the cleavage sites from the task specifications, updates the base molecule to a state that can be reproduced by an inferential psfgen call, and then performs the cleavage operation. The resulting structure is then processed by the psfgen method, and the final result is saved as a PSF file.

Usage is described in the cleave documentation.

class pestifer.tasks.cleave.CleaveTask(specs: dict = None, **kwargs)

Bases: PsfgenTask

CleaveTask class for cleaving chains in a molecular structure. This class inherits from the PsfgenTask class and is used to cleave chains in a molecular structure based on specified cleavage sites. Because cleaving chains is a topological operation, psfgen is required, and the system’s PSF file is updated.

Cleavage sites are listed in the sites entry of the task specifications.

Example

tasks:
  - (prior tasks...)
  - cleave:
      sites:
        - A:10-11
        - B:5-6
  - (subsequent tasks...)

do()

Execute the cleave task. This method reads the cleavage sites from the task specifications, updates the base molecule to a state that can be reproduced by an inferential psfgen call, and then performs the cleavage operation(s). The resulting structure is then processed by the psfgen method, and the final result is saved as a PSF/PDB fileset.