pestifer.util.namdrestart module

Defines the NAMDConfig class for parsing NAMD config files and the make_namd_restart() function for the NAMD restart task.

class pestifer.util.namdrestart.NAMDConfig(configfile: Path | str)[source]

Bases: object

A class for parsing NAMD configuration files. This class reads a NAMD config file, extracts commands and variable assignments, and allows for modification of the configuration by replacing variable assignments and commands.

Parameters:

configfile (str) – The path to the NAMD configuration file to be parsed. The file should exist and be readable.

backresolve_lines()[source]

Back-resolve variable assignments in the lines of the NAMD configuration.

replace_command(commandname: str, args: list[str])[source]

Replace a command in the NAMD configuration with a new command and its arguments.

Parameters:

  • commandname (str) – The name of the command to be replaced. The command name is case-insensitive.

  • args (list) – A list of arguments to be passed to the command. The arguments can include variable references (starting with $). If an argument starts with $, it is treated as a variable reference and will be back-resolved to its value.

var_backresolve(oldvarname: str, newvarval: str)[source]

Back-resolve a variable assignment in the NAMD configuration.

write(filename: Path | str)[source]

Write the NAMD configuration to a file.

Parameters:

filename (str) – The name of the file to which the NAMD configuration will be written. If the file already exists, it will be overwritten.

pestifer.util.namdrestart.make_namd_restart_subcommand(args: Namespace)[source]

Create a NAMD restart configuration file based on an existing NAMD log file and configuration file.

Parameters:

args (argparse.Namespace) –

The command-line arguments parsed by argparse. It should contain the following attributes:

  • namd_log: The path to the NAMD log file.

  • config: The path to the NAMD configuration file.

  • new_base: The new base name for the output files.

  • run: The number of time steps to run. If run is 0, the script will not run any new time steps.

  • slurm: The path to the SLURM script file, if applicable.