Package schrodinger :: Package application :: Package mopac :: Module mopac_startup

Module mopac_startup

Startup driver for running semiempirical calculations (i.e. MOPAC)

Functions

_do_license_checks(parsed_args)
Do license checking.

_get_EXTERNAL_files(infiles, keywords)
Look for EXTERNAL specification in MOPAC input files and cmdline flags to indicate files which need to be registered as additional input files.

_get_input_files(parsed_args)
Return set of input files that need to be registered with jobcontrol and/or copied to the work directory.

_get_output_files(parsed_args)
Return set of output files expected from this workflow.

_register_input_files(jsb, infiles)
Register input files with job specification.

_register_output_files(jsb, outfiles)
Register output files with job specification.

_get_job_params()
Return the jobcontrol launch parameters

_get_job_spec(cmdline, infiles, outfiles, licenses, jobname)
Return the jobcontrol job specification

_run_backend(args)
Launch backend process under jobcontrol

main(args)
Startup driver for running MOPAC

Variables

[hide private]

_external_re = re.compile(r'(?i)EXTERNAL\s*=\s*(\S+)')

__package__ = 'schrodinger.application.mopac'

Function Details

[hide private]

_do_license_checks(parsed_args)

Do license checking. Note that this is a convenience check so that users get immediate feedback if they lack licenses. It is not meant for security; more rigorous checks are done in the backends.

Parameters:

parsed_args (ParsedArgs object) - parsed cmdline arguments
@return list of tuples of required license tokens

_get_EXTERNAL_files(infiles, keywords)

Look for EXTERNAL specification in MOPAC input files and cmdline flags to indicate files which need to be registered as additional input files.

Parameters:

infiles (list) - known input file paths
keywords (str) - string of additional MOPAC keywords from cmdline

Returns:

set of input file names

_get_input_files(parsed_args)

Return set of input files that need to be registered with jobcontrol and/or copied to the work directory.

Parameters:

parsed_args (ParsedArgs object) - parsed cmdline arguments

Returns:

set of input file names

_get_output_files(parsed_args)

Return set of output files expected from this workflow.

Currently all output files are registered on-the-fly in the backend scripts. Hopefully this can be improved in the future to make the API more clearly defined.

Parameters:

parsed_args (ParsedArgs object) - parsed cmdline arguments

Returns:

set of output file names

_register_input_files(jsb, infiles)

Parameters:

jsb (schrodinger.job.launchapi.JobSpecificationArgsBuilder) - jobcontrol job specification builder instance
infiles (set of strings) - input file names

_register_output_files(jsb, outfiles)

Parameters:

jsb (schrodinger.job.launchapi.JobSpecificationArgsBuilder) - jobcontrol job specification builder instance
outfiles (list of strings) - output file names

_get_job_params()

Return the jobcontrol launch parameters

Parameters:

parsed_args (ParsedArgs object) - parsed cmdline arguments

_get_job_spec(cmdline, infiles, outfiles, licenses, jobname)

Return the jobcontrol job specification

Parameters:

cmdline (str) - cmdline to launch under jobcontrol
infiles (list) - list of input files to register
outfiles (list) - list of (known) output files to register
licenses (list of tuples)
jobname (str) - name of job
@return schrodinger.job.launchapi.JobSpecification

_run_backend(args)

Launch backend process under jobcontrol

Parameters:

args (list) - cmdline arguments

main(args)

Startup driver for running MOPAC

Parameters:

args (list) - cmdline arguments