pestifer.tasks.desolvate module

Desolvate task for the Pestifer framework. This is normally used as part of the pestifer desolvate command to process existing DCD files. This task is responsible for generating an index file and a PSF file from a given PSF and PDB file, and then pruning a DCD file based on the generated index. It inherits from the BaseTask class and uses the VMD scripter to create the necessary scripts for processing.

Usage is described in the desolvate documentation.

class pestifer.tasks.desolvate.DesolvateTask(specs: dict = None, **kwargs)

Bases: VMDTask

DesolvateTask class for processing DCD files and generating index and PSF files.

do() → int

This a stub method that should be overridden by subclasses. It is intended to be the main method that performs the task’s operations. Subclasses should implement this method to define the specific behavior of the task. This method is called when the task is executed.

do_dcd_prune()

Prune a DCD file based on the generated index file. This method uses the catdcd command to create a new DCD file that contains only the atoms corresponding to the indices specified in the index file. The new DCD file is created with a specified stride, and the original DCD files are concatenated into the new DCD file.

do_idx_psf_gen()

Generate an index file and a PSF file from the given PSF and PDB files. This method uses the VMD scripter to create a script that performs the necessary operations to generate the index file and the PSF file based on the specified selection criteria. The generated script is then executed to produce the output files.

This is not a pipelined task (for now)