config-help

Because it imports the class Yclept from Ycleptic, Pestifer has a built-in, interactive, command-line system for help generating YAML-format input configuration files available through the config-help subcommand.

$ pestifer config-help
Help on user-provided configuration file format
   charmmff ->
   psfgen ->
   namd2 ->
   title
   paths ->
   tasks ->
   .. up
   ! quit
pestifer-help:

This command ends at a prompt (pestifer-help:) that allows you to drill down into the help system. The help system is organized around the topics that are allowed in a config file, which appear in the list above. Any item with an arrow after it can be drilled down into. Double-dot (..) takes you up, and bang (!) quits. For example, in the case above, if you type tasks, you will get a list of the tasks that can be performed in a config file:

pestifer-help: tasks

tasks:
    Specifies the tasks to be performed serially in a pestifer run

base|tasks
    restart ->
    psfgen ->
    ligate ->
    mdplot ->
    cleave ->
    domainswap ->
    solvate ->
    desolvate ->
    ring_check ->
    make_membrane_system ->
    md ->
    manipulate ->
    terminate ->
    .. up
    ! quit
pestifer-help:

Continuing to drill down is easy – just add the next directive to the interactive-help command line:

pestifer-help: make_membrane_system

make_membrane_system:
    Parameters controlling packmol to generate a membrane system with an
      embedded protein

base|tasks->make_membrane_system
    bilayer ->
    embed ->
    .. up
    ! quit
pestifer-help: bilayer

bilayer:
   Parameters controlling bilayer generation

base|tasks->make_membrane_system->bilayer
   prebuilt ->
   lipids
   lipid_conformers
   mole_fractions
   patch_nlipids ->
   composition ->
   half_mid_zgap
   solvents
   solvent_mole_fractions
   solvent_to_lipid_ratio
   SAPL
   dims
   npatch
   solution_gcc
   cation
   anion
   salt_con
   nloop
   nloop_all
   tolerance
   seed
   relaxation_protocols ->
   .. up
   ! quit