tfep.potentials.gromacs.GmxTraj

class tfep.potentials.gromacs.GmxTraj(*args, executable_path=None, **kwargs)

Bases: CLITool

The traj subprogram of gmx from the GROMACS suite.

The executable path variable only specifies the path to the gmx executable. The class takes care of adding the “traj” subprogram after “gmx” so it does not have to be passed when the command is instantiated.

Relative file paths must be relative to the working directory used for executing the command (i.e., they are not converted to absolute paths before changing the working directory). This is to enable executing multiple instances of the command in parallel in different working directories.

Parameters:

• executable_path (str, optional) – The executable path associated to the instance of the command. If this is not specified, the EXECUTABLE_PATH class variable is used instead.

• traj_file_path (str) – Path to the input .trr file.

• tpr_file_path (str) – Path to input .tpr file.

• force_xvg_file_path (str) – Path to output .xvg file holding the forces.

• full_precision (bool, optional) – Whether to save the output in full precision or always single.

__init__(*args, executable_path=None, **kwargs)

Methods

__init__(*args[, executable_path])
to_subprocess()	Convert the command to a list that can be run with the subprocess module.

Attributes

EXECUTABLE_PATH
SUBPROGRAM
executable_path	The path to the command executable to run.
force_xvg_file_path	A generic command line key-value option.
full_precision	A generic command line flag option.
tpr_file_path	A generic command line key-value option.
traj_file_path	A generic command line key-value option.

property executable_path

The path to the command executable to run.

to_subprocess()

Convert the command to a list that can be run with the subprocess module.

Returns:

subprocess_cmd – The command in subprocess format. For example ['grep', '-v'].

Return type:

List[str]