schrodinger.job.jobwriter module

Functions for writing job command lists into shell scripts.

exception schrodinger.job.jobwriter.OplsArchiveNotFoundError(opls_dir: str)

Bases: Exception

__init__(opls_dir: str)
Parameters

opls_dir – The path to the OPLS directory containing an archive or the archive itself.

schrodinger.job.jobwriter.write_job_cmd(cmdlist, sh_filename, job_dir, append=False)

Write a shell script that can be used to run the given cmdlist.

Parameters

  • cmdlist (list[str]) – The command the script should run.

  • sh_filename (sh) – The name of the file the script should be written to

  • job_dir (str) – The desired job directory to be used for the command

  • append (bool) – Whether to append to the given file or overwrite it. This is useful for writing a single shell script that launches multiple jobs.

schrodinger.job.jobwriter.cmdlist_to_cmd(cmdlist)

Converts a command list to a command string. Don’t do this if you can possibly avoid it.

Parameters

cmdlist (list) – a list of commands

Returns

str

schrodinger.job.jobwriter.set_sh_file_flags(filename)
schrodinger.job.jobwriter.copy_opls_archive_to_job_dir(opls_dir: str, job_dir: str) → str

Copy the OPLS archive (.opls file) to the job directory if it’s not already there.

Parameters

  • opls_dir – The path to the OPLS directory that contains the archive.

  • job_dir – The path to the job directory

Returns

The base name of the copied archive file.

Raises

OplsArchiveNotFoundError – If the OPLS archive is not found.