schrodinger.application.matsci.jobutils module¶
Copyright Schrodinger, LLC. All rights reserved.
-
schrodinger.application.matsci.jobutils.
get_logging_tag
(job, tag='log_tag')¶ Get the logging tag of a job.
Parameters: - job (
schrodinger.job.queue.JobControlJob
) – a job object - tag (str) – the job attribute containing the info.
Returns: the logging tag
Return type: str
- job (
-
schrodinger.application.matsci.jobutils.
add_outfile_to_backend
(file_fn, backend=None, set_structure_output=False, stream=False)¶ Add output file to the backend.
Parameters: - file_fn (str) – Filename
- backend (
schrodinger.job._Backend
or None) – Backend handle. If None, a backend will be checked for. If no backend is found, nothing will be done. - set_structure_output (bool) – If True, set this structure as output
- stream (bool) – If True, stream the file to the submission host
-
schrodinger.application.matsci.jobutils.
log_structures_found
(qjob, structure_files, log, jobstates_for_logging=None)¶ Log structures info for a job.
Parameters: - qjob (
schrodinger.job.queue.JobControlJob
) – The subjob to find structures - structure_files (dict) – Keys are subjobs, values are sets of structure file names
- log (callable) – function(msg) writes msg to log file
- jobstates_for_logging (None or list of str) – Log info for subjobs in these states
- qjob (
-
schrodinger.application.matsci.jobutils.
run_jobdj_and_add_files
(jobdj, log, expect_exts=None, exclude_exts=None, jobdj_dir='.')¶ Run the subjobs currently queued up in the jobdj, adding their files to the current backend for copying back to the job directory and locating the expected structure output file for each job.
Parameters: - jobdj (
schrodinger.job.queue.JobDJ
) – The JobDJ with queued up jobs to run - log (callable) – function(msg) writes msg to log file
- expect_exts (None or list of str) – The expected extensions of the output files
- exclude_exts (None or list of str) – The output files found with the excluded extensions are not copied back to the original job directory or documented into logger
- jobdj_dir (str) – jobdj_dir is the relative path from where the backend is created to where the jobdj is created. Using /scr/user/jobname/subdir1/subdir2 as an example, normally backend and jobdj are created in /scr/user/jobname/, and thus jobdj_dir by default is os.curdir. If the jobdj is created inside /scr/user/jobname/subdir1/, the jobdj_dir is subdir1 as backend is created in /scr/user/jobname/. In this example, the backend is in /scr/user/jobname/, jobdj is in /scr/user/jobname/subdir1, and the subjob can run in /scr/user/jobname/subdir1/subdir2. (subjob.getCommandDir() gives subdir2)
Return type: list
Returns: A list of structure output file names, sorted alphabetically
- jobdj (
-
schrodinger.application.matsci.jobutils.
finalize_subjob
(subjob, backend, structure_files, structure_extensions, log, exclude_exts=None, jobdj_dir='.')¶ Mark subjob output and log files for copying back to the job directory, and find the structure output file if there is one
Parameters: - subjob (
schrodinger.job.queue.JobControlJob
or None) – The subjob to mark files from - backend (
schrodinger.job.jobcontrol._Backend
or None) – The current backend or None if there isn’t one - structure_files (dict) – If an output structure file is found, it will be added to this dict. Keys are subjobs, values are sets of structure file names
- structure_extensions (list of str) – The expected extension of the structure files
- log (function) – function(msg) writes msg to log file
- exclude_exts (None or list of str) – The output files found with the excluded extensions are not copied back to the original job directory or documented into logger
- jobdj_dir (str) – jobdj_dir is the relative path from where the backend is created to where the jobdj is created. Using /scr/user/jobname/subdir1/subdir2 as an example, normally backend and jobdj are created in /scr/user/jobname/, and thus jobdj_dir by default is os.curdir. If the jobdj is created inside /scr/user/jobname/subdir1/, the jobdj_dir is subdir1 as backend is created in /scr/user/jobname/. In this example, the backend is in /scr/user/jobname/, jobdj is in /scr/user/jobname/subdir1, and the subjob can run in /scr/user/jobname/subdir1/subdir2. (subjob.getCommandDir() gives subdir2)
Return type: bool
Returns: True if the job has completed, False if not
- subjob (
-
schrodinger.application.matsci.jobutils.
add_subjob_files_to_backend
(subjob, path=None, backend=None, exclude_exts=None)¶ Add all the output and log files from a subjob to the backend of this job so that they get copied back to the original job directory.
Note: subjob log files are added as output files instead of log files. They will not be streamed back to the original job directory but instead copied back at the end of this job like a normal output file.
Parameters: - subjob (
schrodinger.job.jobcontrol.Job
orschrodinger.job.queue.JobControlJob
) – The subjob to add files from. - path (str) – The path to the subjob directory from where the backend is created
if it was not run in the same directory as this job. Use
FROM_SUBJOB
to get the subjob directory from a JobControlJob object - this will be ignored if subjob is a Job object. - backend (
schrodinger.job.jobcontrol._Backend
) – The backend if one exists - exclude_exts (None or list of str) – The output files found with the excluded extensions are not copied back to the original job directory or documented into logger
- subjob (
-
schrodinger.application.matsci.jobutils.
set_source_path
(struct, backend=None, job=None, path=None)¶ Set the source path property to the original job directory. This is obtained from the job control Job object for this process. If no Job object is found, the current directory is used.
Parameters: - struct (
schrodinger.structure.Structure
) – The structure to set the property on. Note that property setting works properly on both Structure and Cms objects. - backend (
schrodinger.job.jobcontrol._Backend
) – The job control backend. Will be used to obtain the job object if no job is supplied. If neither backend or job are supplied, the backend will be obtained from job control (if one exists). - job (
schrodinger.job.jobcontrol.Job
) – The job control job for this process. If not supplied, will be obtained from the backend (if one exists). - path (str) – Manually set this path to the source directory, overriding all other options
Return type: str
Returns: The directory set as the source path. Will be either the OrigLaunchDir property of the job or the current directory if not running under job control.
- struct (
-
schrodinger.application.matsci.jobutils.
get_source_path
(source, existence_check=True)¶ Get the source path to the original job directory
Parameters: - source (
schrodinger.structure.Structure
orschrodinger.project.ProjectRow
) – Either the ProjectRow or the structure to obtain the source information from. If a structure, can be either a Structure or a Cms object. - existence_check (bool) – If True (default), a blank string will be returned if the source path does not exist. If False, the path is returned regardless of whether it exists or not.
Return type: str
Returns: The original job directory or a blank string if none is found
- source (
-
schrodinger.application.matsci.jobutils.
get_file_path
(struct, prop)¶ Get the path of the file defined by source path and property name
Parameters: - struct (
schrodinger.structure.Structure
) – The structure whose property is checked - prop (str) – property pointing to a file
Returns: path of the file if found
Return type: str or None
- struct (
-
schrodinger.application.matsci.jobutils.
fix_jaguar_file_links
(struct, subdir=None)¶ Change the Jaguar file link properties to point to the original job directory instead of the subjob directory
Parameters: - struct (schrodinger.structure.Structure) – The structure to fix
- subdir (str) – The subdirectory for these files in the main job directory
-
schrodinger.application.matsci.jobutils.
prepare_job_spec_builder
(argv, program_name, default_jobname, input_fn=None, set_driver_reserves_cores=False, schrodinger_product=None)¶ Prepare generic job specification builder. If set_driver_reserves_cores script (driver) is set to True, script is expected to use all the cores (cpus), similar to umbrella mode in multisim. For an example see stress-strain driver. For all other cases (such as in opto/hopping/amorphous) keep set_driver_reserves_cores to False.
Parameters: - argv (list) – The list of command line arguments, including the script name at [0], similar to that returned by sys.argv
- program_name (str) – Program name
- default_jobname (str) – Default job name
- input_fn (str) – Input filename
- set_driver_reserves_cores (bool) – If True, enable launchapi.setDriverReservesCores
- schrodinger_product (str) – A product directory to search for the script/executable. This should be the name of a directory under SCHRODINGER without the trailing version (i.e. the “-v*” part).
Return type: launchapi.JobSpecificationArgsBuilder
Returns: Job specification builder object
-
schrodinger.application.matsci.jobutils.
add_folder_to_job_builder
(job_builder, folder_path)¶ Add folder (trajectory folder) to job directory.
Parameters: - job_builder (
launchapi.JobSpecificationArgsBuilder
) – Job specification builder object. - folder_path (str) – Full path to the folder that needs to copied.
- job_builder (
-
schrodinger.application.matsci.jobutils.
get_stripped_defaults
(adict)¶ Remove dashes in the beginning of the keys. Used with ArgumentParser.
Parameters: adict (dict{string:any}) – Dictionary of defaults Return type: dict{string:any} @rparam: Dictionary of defaults with dashed stripped from the keys
-
schrodinger.application.matsci.jobutils.
argparser_set_defaults
(parser, defaults)¶ Set default values to the arguments already present in the parser. Note that, parser.set_defaults contaminates namespace with the arguments that might be absent from the parser.
Parameters: - parser (
argparse.ArgumentParser
) – The parser to set defaults - defaults (dict{string:any}) – Dictionary of the defaults
- parser (
-
schrodinger.application.matsci.jobutils.
parse_restart_parameters_file
(path)¶ Parse parameters file.
Format of the file: 1st line is driver’s filename 2nd line is original arguments passed to the driver
Parameters: path (str) – Path to the file with original arguments Return type: dict Returns: Dictionary with parsed values
-
schrodinger.application.matsci.jobutils.
write_restart_parameters_file
(driver, args, outpath)¶ Write out original arguments to parameters file and add the file as an output file to any existing jobcontrol backend.
Parameters: - driver (str) – Driver’s filename
- args (list) – Original arguments passed to driver
- outpath (str) – Path to the parameters file to write original arguments
-
schrodinger.application.matsci.jobutils.
get_restart_id_filename
(jobname)¶ For the given restart jobname, return the name of the file containing the job id.
Return type: str Returns: The name of the restart jobid file
-
schrodinger.application.matsci.jobutils.
extract_job_data
(options)¶ Unzip the archive in the current directory. All the error handling is on the caller function.
Parameters: options ( argparse.Namespace
) – The object holding all the option values
-
schrodinger.application.matsci.jobutils.
archive_job_data
(path, files_path)¶ Create a gzipped tar archive in the current directory from the provided list of file paths. All the error handling is on the caller function.
Parameters: - path (files_path) – Path to the new archive to be created
- path – List of files to be archived
-
schrodinger.application.matsci.jobutils.
create_restart_launcher
(script, prog, input_name, output_name, zip_name, options, args)¶
-
schrodinger.application.matsci.jobutils.
create_restart_jobcmd
(driver_path, zip_fn, restart_options, args, default_jobname)¶ Generate command-line list for the job restart.
Parameters: - driver_path (str) – Path to the driver
- zip_fn (str) – Filename of the archive with all restart files
- restart_options (
argparse.Namespace
) – The object holding all the option values - args (list) – List of the arguments passed to the original run
- default_jobname (str) – Default job name
Return type: list
@rparam: List of parameters ready for job submission
-
schrodinger.application.matsci.jobutils.
write_idfile
(jobobj)¶ Store the job id in a file as a signal to the GUI that a new job has been launched.
Parameters: jobobj ( schrodinger.job.jobcontrol.Job
) – The object holding all the option values
-
schrodinger.application.matsci.jobutils.
get_option
(options, flag)¶ Return the option value associated with flag
Parameters: - options (
argparse.Namespace
) – The object holding all the option values - flag (str) – The flag for the desired option.
Return type: any
Returns: The value associated with flag, or None if flag (minus any leading dashes) is not found as a property on options
- options (
-
schrodinger.application.matsci.jobutils.
set_option
(options, flag, value)¶ Set the option value associated with flag
Parameters: - options (
argparse.Namespace
) – The object holding all the option values - flag (str) – The flag for the desired option. If the string starts with a ‘-‘, the ‘-‘ is removed.
- value (any) – The value to set the option.flag value to
- options (
-
schrodinger.application.matsci.jobutils.
add_restart_parser_arguments
(parser)¶ Add restart arguments to the parser
Parameters: parser ( argparse.ArgumentParser
) – The parser to add arguments to
-
schrodinger.application.matsci.jobutils.
get_restart_options
(options)¶ Get the command line options from the -restart_x flags
Return type: tuple Returns: tuple of strings (viewname, incorporation, project, host:cpu, jobname)
-
schrodinger.application.matsci.jobutils.
add_keyword_parser_argument
(parser, keyword_flags=None, default='', arghelp=None, action='store')¶ Add a keyword argument to the parser
Parameters: - parser (
argparse.ArgumentParser
) – The parser to add this argument to - keyword_flags (None or list of str) – the customized flags for this argument
- default (str or None) – The customized default values for this argument
- arghelp (str or None) – The customized help message for this argument
- action (
argparse.Action
or str) – The customized action for this argument or the standard ones: ‘store’, ‘store_true’, ‘store_false’, ‘append’ and so on.
- parser (
-
schrodinger.application.matsci.jobutils.
parse_keyword_list
(options, exit_on_error=True, logger=None, validate=False)¶ Adds keystring and keydict properties to the argparse options object that are the list of keyword arguments turned into, respectively, a string or a dictionary. Valid keyword syntax is checked for.
Typical usage:
jobutils.add_keyword_parser_argument(parser) options = parser.parse_args(args) jobutils.parse_keyword_list(options) print options.keystring, options.keydict
Parameters: - options (
argparse.Namespace
) – The parser Namespace object with a keywords attribute - exit_on_error (bool) – True if the ValueError for keyword syntax should result in a message being printed and sys.exit() being called, False if the error should just be raised.
- logger (
logging.Logger
) – The logger to use for recording error messages, otherwise they’ll be printed. - validate (bool) – Whether keywords/values not recognized by Jaguar should be considered an error.
Raises: ValueError – If an invalid keyword pair syntax is detected and handle_error is False
- :raises
schrodinger.application.jaguar.validation.JaguarKeywordException
- if validate=True, exit_on_error=False and an invalid Jaguar keyword/value has been used.
- options (
-
schrodinger.application.matsci.jobutils.
add_save_desmond_files_parser_argument
(parser)¶ Add a
SAVE_FLAG
argument to the parserParameters: parser ( argparse.ArgumentParser
) – The parser to add this argument to
-
schrodinger.application.matsci.jobutils.
add_desmond_parser_arguments
(parser, args, defaults=None)¶ Add desmond related arguments to the parser
Parameters: - parser (
argparse.ArgumentParser
) – The parser to add this argument to - args (list) – List of arguments to add to the parser
- defaults (dict or None) – Default values for the arguments
- parser (
-
schrodinger.application.matsci.jobutils.
add_random_seed_parser_argument
(parser, additional_args=(), help='Seed for the random number generator used in simulations.')¶ Add the command line flag for the random number seed
Parameters: - parser (
argparse.ArgumentParser
) – The parser to add this argument to - additional_args (tuple) – Arguments that should also be accepted in addition to FLAG_RANDOM_SEED
- help (str) – The help string to show for random seed. The default string will be used if nothing is supplied.
- parser (
-
schrodinger.application.matsci.jobutils.
seed_random_number_generator
(options, log=None)¶ Seed the random number generator based on the command line options. If there is no seed in the command line options, a random value is used.
Parameters: - options (
argparse.Namespace
) – The command line options from argparse. Note that passing in None for options will have the same affect as if the seed flag does not exist on options (i.e. a random value will be generated). - log (function) – A function to log the seed value. Should take a single str argument.
Return type: int
Returns: The seed used for the generator
- options (
-
schrodinger.application.matsci.jobutils.
check_license
(panel=None, token=94, name='', as_validator=False)¶ Check if a valid token exists. If called from Maestro, also check out and hold a MATERIALSCIENCE_MAIN token.
Parameters: - panel (schrodinger.ui.qt.appframework.AppFramework) – panel to use to put up an error dialog if no license
- token (
schrodinger.utils.license
constant) – A token type from the schrodinger.utils.license module, such as MATERIALSCIENCE_MAIN or MATERIALSCIENCE_GA - name (str) – The user-identifiable name for the token - used for error messages. If not provided, the string used in the license module for this token (if one exists) will be used.
- as_validator (bool) – If True, this function will work as an AF2 validation method. Instead of posting a dialog or printing a message for a failed license check, it will return (False, error_message).
Return type: bool or (bool, str)
Returns: True if valid license exists. If no valid license exists, False will be returned by default, but (False, msg) will be returned if as_validator=True. Note that (False, msg) evalutes to True so must be handled by the calling routine as not a boolean if as_validator=True.
-
schrodinger.application.matsci.jobutils.
create_run_dir
(panel, jobname)¶ Create a subdirectory to run a job in, asking the user and removing existing directories if needed.
Parameters: - panel (schrodinger.ui.qt.appframework.AppFramework) – panel to use to put up an error dialog if no license
- jobname (str) – The name of the job. The directory will be jobname + _dir
Return type: str or None
Returns: The path to the directory or None if an existing directory was found and the user elected not to remove it
-
schrodinger.application.matsci.jobutils.
string_to_value
(string)¶ Change a text string from a file to a value. Converts string values of special Python tokens such as True, False or None to the Python tokens. Converts numbers to int or float if possible.
Parameters: string (str) – The string to convert Returns: string converted to, in order of preference: [True|False|None], int, float, or input type
-
schrodinger.application.matsci.jobutils.
working_directory
(path)¶ A context manager which changes the working directory to the given path, and then changes it back to its previous value on exit.
-
class
schrodinger.application.matsci.jobutils.
StringCleaner
(extra_replacement_pairs=None, separator='-')¶ Bases:
object
Manages the cleaning of strings.
-
__init__
(extra_replacement_pairs=None, separator='-')¶ Populate an instance with some defaults. The replacement dictionary needs to be set such that the most specific replacements occur last. This is because the replacements should be done in a certain order, for example (‘C:’, ‘’) should be done before (‘:’, ‘’) and (‘’, ‘’), and because people tend to append to an iterable rather than prepend we will traverse the iterable backwards.
Parameters: - extra_replacement_pairs (list of tuples) – each tuple in this list contains a single replacement pair, i.e. a single substring to be replaced and a single substring to replace it.
- separator (str) – in the case of non-unique strings this is the string that separates the non-unique part from the number of times used which is the unique part.
-
cleanAndUniquify
(input_str, clear_prev=False, max_len=100)¶ Shorten if necessary, replace certain characters in an input string and then uniquify the string by comparing with a dictionary of previous names and number of times used.
Parameters: - input_str (str) – the input string we want cleaned and uniqified
- clear_prev (bool) – specify if the dictionary of previous names should first be cleared
- max_len (int) – maximum length of the input_str allowed, otherwise it will be shortened to the max_len value
Return type: str
Returns: the input string now cleaned and uniquified
-
-
schrodinger.application.matsci.jobutils.
clean_string
(string, default='title')¶ Cleans the given string by removing special characters to make it acceptable for a file name. If the string is blank, it will be replaced by the value of default.
Parameters: - string (str) – The string to clean.
- default (str) – The name to use if string is blank
Return type: str
Returns: A string usable as a filename
-
schrodinger.application.matsci.jobutils.
zip_and_set_incorporation
(zipname, filelist)¶ Zip up all the requested files and set the resulting archive as the job control backend structure output file (if runnning under job control).
Parameters: - zipname (str) – The name of the archive to create
- filelist (list) – Each item in filelist is the name of a file to add to file zipname
-
schrodinger.application.matsci.jobutils.
escape_dollars_for_cmdline
(pattern)¶ Make sure $ are escaped in the given pattern for command lines
Parameters: pattern (str) – A string to modify Return type: str Returns: pattern with a in front of $
-
class
schrodinger.application.matsci.jobutils.
CellRunInfo
(structs, basename, replicate, multiple_cells, component=None, repeat_unit_info=None)¶ Bases:
object
Holds the information for the run for a single cell
-
__init__
(structs, basename, replicate, multiple_cells, component=None, repeat_unit_info=None)¶ Create a CellRunInfo object
Parameters: - structs (list) – The list of structures to include in the cell
- basename (str) – The generic basename for job files. This will be modified based on the value of replicate, component and multiple_cells to form the base name for files for this specific cell.
- replicate (int) – Which replicate this is for - 1-based
- multiple_cells (bool) – Whether there will be multiple replicates of this cell
- component (int or None) – The structure number this cell is for, or None if this is a mixed structure cell
- repeat_unit_info (list or None) – Each item of the list is a tuple. The first item of the list is the sequence of monomer one-letter codes that give the repeat unit sequence. The second item is a tag to be added to the polymer name for that sequence (used for enumerated sequences)
-
-
class
schrodinger.application.matsci.jobutils.
MultijobDriver
(runlist, options, args, log, remote_script, default_jobname, basename=None)¶ Bases:
object
Resubmit the driver as subjobs
-
COMPOSITION_FLAG
= '-composition'¶
-
COMPOSITION_FLAG_SHORT
= '-c'¶
-
__init__
(runlist, options, args, log, remote_script, default_jobname, basename=None)¶ Create multiple cells in parallel running a subjob for each cell. Zip up the resulting cms files into a jobname.zip file and set it as the structure output file to be incorporated.
Parameters: - runlist (list of
CellRunInfo
) – Each item of runlist will generate a subjob and a single cell - options (
argparse.Namespace
) – The command line options - args (iterable) – The command line arguments as passed in by sys
- log (function) – function(msg) writes msg to log file
- remote_script (string) – the dir and name for driver to resubmit
- default_jobname (string) – Default job name
- basename (str or None) – The generic basename defined from inputfile.
- runlist (list of
-
remove_flag
(args, flag, and_value=False)¶ Remove a flag from the comand line flags
Parameters: - args (list) – The list of command line arguments
- flag (str) – The flag to remove
- and_value (bool) – Also remove the value associated with the flag - it is assumed that this is the following list item
-
replace_value
(args, old_value, new_value)¶ Replace the list item with value=old_value with the new value
Parameters: - args (list) – The list of command line arguments
- old_value (str) – The value to replace
- new_value (str) – The value to replace old_value with
-
multijob_driver
(runlist, options, args, basename, log, remote_script)¶ Create multiple cells in parallel running a subjob for each cell. Zip up the resulting cms files into a jobname.zip file and set it as the structure output file to be incorporated.
Parameters: - runlist (list of
CellRunInfo
) – Each item of runlist will generate a subjob and a single cell - options (
argparse.Namespace
) – The command line options - args (iterable) – The command line arguments as passed in by sys
- basename (str) – The zipped .zip or . maegz filename for all job files.
- log (function) – function(msg) writes msg to log file
- remote_script (string) – the dir and name for driver to resubmit
- runlist (list of
-
-
schrodinger.application.matsci.jobutils.
get_jobname
(default_jobname)¶ Return a the jobname from backend, command line (-NAMEJOB / environment), DEFAULT_JOBNAME
Parameters: default_jobname (str) – default_jobname of the current module Return type: string Returns: Jobname
-
schrodinger.application.matsci.jobutils.
get_procs
()¶ Get number of processors from backend or command-line arguments.
Return type: int Returns: Number of processors
-
schrodinger.application.matsci.jobutils.
memory_usage_psutil
()¶ return the memory usage in MB
Return type: float Rparam: memory usage in MB
-
schrodinger.application.matsci.jobutils.
get_size_of
(an_object, size_unit='megabytes')¶ Return the size of an object in size_unit. The object can be any type of object. All built-in objects will return correct results, but this does not have to hold true for third-party extensions as it is implementation specific.
Parameters: an_object (any type of python object) – Returns: the size of an object in size_unit Return type: float
-
schrodinger.application.matsci.jobutils.
get_jobhost_name
()¶ Return the job host name from backend or command line.
Return type: str or None Rparam: the host name
-
schrodinger.application.matsci.jobutils.
is_hostname_known
(hostname)¶ Check whether hostname is defined in the host file.
Parameters: hostname (str) – the hostname to check against Return type: bool Rparam: True, if the hostname is defined in the host file
-
schrodinger.application.matsci.jobutils.
is_jobhost_gpu_available
()¶ Check whether the gpu is available on the host. First check SUBHOST, if defined. Then, check HOST, if defined. At last, check localhost.
Return type: bool Rparam: True means gpu is available.
-
schrodinger.application.matsci.jobutils.
add_zipfile_to_backend
(adir)¶ Add a zip file of the given directory to the job backend.
Parameters: adir (str) – the directory
-
schrodinger.application.matsci.jobutils.
get_backend_first_host
()¶ Get backend first host.
Return type: str, int Returns: host, number of processors
-
schrodinger.application.matsci.jobutils.
write_cms_with_wam
(cms_model, filename, wam_type)¶ Write the cms model to a file with the provided WAM property
Parameters: - cms_model (cms.Cms) – The cms model to write to file
- filename (str) – The cms path
- wam_type (int) – One of the enums defined in workspace_action_menu.h
-
schrodinger.application.matsci.jobutils.
add_wam_to_cms
(filename, wam_type)¶ Rewrite the cms with the WAM type added
Parameters: - filename (str) – The cms path
- wam_type (int) – One of the enums defined in workspace_action_menu.h
-
schrodinger.application.matsci.jobutils.
write_mae_with_wam
(struct, filename, wam_type=None)¶ Parameters: - struct (structure.Structure) – The structure to write to file
- filename (str) – The mae path
- wam_type (int) – One of the enums defined in workspace_action_menu.h
Raises: ValueError – If the file path is not for a Maestro file
-
schrodinger.application.matsci.jobutils.
set_smart_distribution_from_environ
(jobq)¶ Set smart distribution of the queue to on/off based on the environment variable.
Parameters: jobq ( schrodinger.job.queue.JobDJ
) – The JobDJ object