pestifer.tasks.solvate module¶
Definition of the SolvateTask class for solvating a molecular structure.
This class is a descendant of the BaseTask class and is used to solvate a molecular structure
using the VMD solvate and autoionize packages.
It generates a solvated PDB and PSF file, optionally adding ions based on specified salt concentration and ion types.
The task can also handle cubic or rectangular boxes for solvation based on the provided specifications.
The task reads the input PDB and PSF files, calculates the bounding box for the solvation,
and generates the necessary Tcl commands to perform the solvation and ionization.
The resulting solvated structure is saved with the specified basename, and the state is updated with the new PSF, PDB, and XSC files.
Usage is described in the solvate documentation.