utils

utils

Utilities for building plugins, shell convenience functions and GROMACS related functions

Attributes

Name	Description
TopologyAtomAddress	Address to an atom in the topology.

Name	Description
check_gmx_version	Check for an existing gromacs installation.
get_gmx_dir	Returns the path to the gromacs installation
get_shell_stdout	Run command in shell and capture stdout.
get_task_directories	create list of subdirectories that match the tasks.
run_gmx	Run GROMACS command in shell.
run_shell_cmd	Run command in shell.
write_gro_at_reaction_time	Write out a gro file from the trajectory (xtc or trr) at the reaction time.
write_reaction_time_marker	Write out a file as marker for the reaction time.

utils.check_gmx_version(config)

Check for an existing gromacs installation.

If PLUMED is meant to be used it additionally checks for the keyword ‘MODIFIED’ or ‘plumed’ in the version name.

If slow growth pairs are used, it checks for gromacs version >= 2023.2

utils.get_gmx_dir(gromacs_alias='gmx', grompp_prefix=None)

Returns the path to the gromacs installation

utils.get_shell_stdout(s)

Run command in shell and capture stdout.

utils.get_task_directories(dir, tasks='all')

create list of subdirectories that match the tasks. If tasks is “all”, all subdirectories are returned.

Name	Type	Description	Default
dir	Path	Directory to search for subdirectories	required
tasks	Union[list[str], str]	List of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories	`'all'`

utils.run_gmx(cmd, cwd=None)

Run GROMACS command in shell.

Adds a ‘-quiet’ flag to the command and checks the return code.

utils.run_shell_cmd(s, cwd=None)

Run command in shell.

utils.write_gro_at_reaction_time(files, time)

Write out a gro file from the trajectory (xtc or trr) at the reaction time.

utils.write_reaction_time_marker(dir, time)

Write out a file as marker for the reaction time.