pestifer.subcommands.desolvate module

The desolvate subcommand. This subcommand allows a user to specify a system state plus a trajectory which will then be converted to a solvent-free state and trajectory. The state is represented minimally by a PDB, PSF, and XSC file, and the trajectory can be a list of one or more DCD files, ordered chronologically. The user can specify the exact collection atoms to keep using the –keepatsel option; by default, this is “protein or glycan or lipid”.

Example:

$ pestifer desolvate --psf input.psf --pdb input.pdb --dcd-infiles input1.dcd input2.dcd

This will create the new PSF file dry.psf and a single DCD file concatentating the inputs, called dry.dcd, by default. The output file names can be specified using the –psf-outfile and –dcd-outfile options.

desolvate invokes both VMD to create an atom index file and generate the stripped psf file, and catdcd to process the trajectory files. The atom index file name will be dry.idx by default, but can be specified using the –idx-outfile option.

class pestifer.subcommands.desolvate.DesolvateSubcommand(name: str = 'desolvate', aliases: list = <factory>, log_file: str = 'pestifer_diagnostics.log', short_help: str = 'desolvate a system', long_help: str = 'Remove solvent molecules from a solvated system.', func_returns_type: type = <class 'dict'>, parser: argparse.ArgumentParser = None)

Bases: Subcommand

add_subparser(subparsers)

Adds the subcommand parser to the given subparsers. Subclasses declare arguments here, after a super().add_subparser() call.

static func(args: Namespace, **kwargs)

the function that executes the subcommand. Subclasses must implement this method.

func_returns_type

alias of dict

long_help: str = 'Remove solvent molecules from a solvated system.'

description

name: str = 'desolvate'

subcommand name

short_help: str = 'desolvate a system'

help string