schrodinger.application.matsci.jobutils module¶

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

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

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

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

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 or schrodinger.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

schrodinger.application.matsci.jobutils.determine_source_path(backend=None, job=None)¶

Determine 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

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).

Return type

str

Returns

The directory that is the source path. Will be either the OrigLaunchDir property of the job or the current directory if not running under job control.

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.

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 or schrodinger.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

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

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.

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

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

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

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.

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.

schrodinger.application.matsci.jobutils.add_save_desmond_files_parser_argument(parser)¶

Add a SAVE_FLAG argument to the parser

Parameters: parser (argparse.ArgumentParser) – The parser to add this argument to

schrodinger.application.matsci.jobutils.add_compress_subjobs_parser_argument(parser, help=None)¶

Add a FLAG_COMPRESS_SUBJOBS argument to the parser

Parameters: 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

schrodinger.application.matsci.jobutils.add_traj_analysis_parser_arguments(parser)¶

Add trajectory analysis parser arguments/

Parameters: parser (argparse.ArgumentParser) – The parser to add this argument to

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.

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

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.

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

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_jobhosts()¶

Return the job hosts from backend or command line.

Return type: None or list of tuple
Rparam: the hosts or None

schrodinger.application.matsci.jobutils.get_jobhost()¶

Return the first job hosts from backend or command line.

Return type: list or None
Rparam: the first host or None

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 workflow_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 workflow_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 workflow_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

schrodinger.application.matsci.jobutils module¶

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