Package schrodinger :: Package application :: Package jaguar :: Module file_logger

Module file_logger

General classes and functions related to output files, in particular when running under jobcontrol.

Classes

FileLogger
Class to store names of output files and archive them so that a single file can be registered with jobcontrol and returned from the work directory to the user.

Functions

[hide private]

register_file(fname, archive=False)
Convenience wrapper for FileLogger.register_file() when using "with FileLogger:" context management.

launch_path()
Get the path from which the job was launched.

relative_path()
return the path to the cwd, relative to a launch directory If the cwd the same as the launch directory the path is returned as an empty string (does not contain '.')

set_structure_file(fname)
Register the file fname as the output structure file with jobcontrol, assumes the file fname, is in the cwd.

copy_file(fname)
Copy the file fname running under jobcontrol to the launch dir.

transfer_subjob_files(jobbe, job_id, do_recover=False, archive=False)
Copy files held in a job record from the working dir to the launch dir associated with a jobcontrol backend.

slugify(mystr)
Transform a string to a valid file and job name

make_outmaefile(outmaefile, infiles, status, write_jname=False)
Collect output CTs from Jaguar jobs into a single .mae file

make_smapfile(outmaefile, smapfile)
Write a .smap file containing the associations between CT index numbers in the outmaefile, and .vib, .vis, .spm files.

Variables

[hide private]

LEGIT_CHARS = 'abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTU...

SUFFICES_NOT_ARCHIVED = ('.hosts', '.nodes', '.mpinodes', '.di...

JNAME = 's_j_jname'

_filelogger = None
hash(x)

__package__ = 'schrodinger.application.jaguar'

Function Details

[hide private]

register_file(fname, archive=False)

Convenience wrapper for FileLogger.register_file() when using "with FileLogger:" context management. See FileLogger docstring for more details.

launch_path()

Get the path from which the job was launched. if its a local job it will be the cwd.

transfer_subjob_files(jobbe, job_id, do_recover=False, archive=False)

Copy files held in a job record from the working dir to the launch dir associated with a jobcontrol backend. This function can handle jobs launched in subdirectories.

Parameters:

jobbe (schrodinger.job.jobcontrol._Backend) - The Backend object for the current job.
job_id (jobcontrol.Job.JobID) - jobcontrol job id
do_recover (bool) - if False, update the .recover file
archive (bool) - if True, the file is registered as an archive file.

make_outmaefile(outmaefile, infiles, status, write_jname=False)

Collect output CTs from Jaguar jobs into a single .mae file

Parameters:

outmaefile (str) - name of output .mae file
infiles (list of strs) - subjob input files, including suffix, e.g. mol1.in
status (dictionary) - status of each subjob indexed by filename

make_smapfile(outmaefile, smapfile)

Write a .smap file containing the associations between CT index numbers in the outmaefile, and .vib, .vis, .spm files. This function relies on CT's in the .mae file having a property 's_j_jname' (stored in JNAME) which maps to the name of the .vib etc file.

Variables Details

[hide private]

LEGIT_CHARS

Value:

'abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789._-'

SUFFICES_NOT_ARCHIVED

Value:

('.hosts', '.nodes', '.mpinodes', '.diag')