pestifer.subcommands.density_profile module¶
The density-profile subcommand. Computes and plots species-resolved mass-density
profiles (water, lipid, protein, ions) along the bilayer normal z for a membrane
system, from a PSF, a single coordinate frame (PDB or NAMD binary .coor), and
an XSC cell file.
The bilayer midplane is centered at z=0 and bulk solvent is made continuous through
the periodic boundary. For a multicomponent bilayer, --lipid-components adds a
per-lipid-species profile in addition to the total lipid profile.
Example:¶
$ pestifer density-profile --basename my_system --lipid-components
This reads my_system.psf, my_system.coor (or my_system.pdb), and
my_system.xsc and writes my_system-density-profile.png.
- class pestifer.subcommands.density_profile.DensityProfileSubcommand(name: str = 'density-profile', aliases: list = <factory>, log_file: str = 'density-profile.log', short_help: str = 'plot species-resolved density profiles along z', long_help: str = 'Compute and plot water/lipid/protein/ion mass-density profiles along the bilayer normal from a PSF, a coordinate frame, and an XSC.', func_returns_type: type = <class 'bool'>, parser: argparse.ArgumentParser = None)[source]¶
Bases:
Subcommand- add_subparser(subparsers)[source]¶
Adds the subcommand parser to the given subparsers. Subclasses declare arguments here, after a super().add_subparser() call.
- static func(args: Namespace, **kwargs)[source]¶
the function that executes the subcommand. Subclasses must implement this method.