Module startup

Classes and functions used by the Glide startup script.

Classes

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GlideStartupError
Glide startup exception class.

GlideStartup
This class implements the overall, high-level logic of the startup script.

StartupInterface
Interface for Glide jobs with helper functions needed for startup.

DockingJob
Docking job subclass with an implementation of StartupInterface.

GridgenJob
Gridgen job subclass with an implementation of StartupInterface.

CombinedJob
Combined job class; mainly an aggregate of a DockingJob and a GridgenJob which delegates to each subclass and combines the results.

GlideLauncher
Base class for launching Glide jobs.

SerialLauncher

DriverLauncher

EnvAction
Arparse action class that, in addition to "store_true", sets SCHRODINGER_GLIDE_<dest>=1 in the environment.

PrintKeywordsActionFactory
Generate an Action object that prints the list of Glide keywords and exits as soon as the command-line option is processed.

PrintKeywordsAction
Arparse action class that prints the Glide keyword list and exits as soon as the command-line option is processed.

Functions

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parse_args(args=None)

get_startup_parser()
Return and ArgumentParser object that knows only the arguments that are used by glide_startup but not by glide_driver.

print_keywords(jobtypes)
Print the keywords for the given jobtypes to stdout and exit.

get_driver_args(args=None)

get_data_files()
Return the set of data files from CWD or the user's Schrodinger data directory that exist and need to be registered as inputs.

_get_data_file(basename)
Return a set with the path to an optional data file, which may be found in the CWD or in the glide user data directory.

to_list(obj)

get_glide_job(input_filename, extra_keywords)

get_launcher(job, options)

jobhost_is_localhost()

setup_valgrind_suppressions_env_var()

get_use_cons_labels(section)
Return the set of constraint labels used in a given section (a dict with the USE_CONS keyword.

running_under_wscore()

Variables

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logger = log.get_output_logger("glide_startup")

DATA_FILES = ['badat.dat', 'badat_2005.dat', 'confunc.dat', 'e...

REQUIRED_GRID_EXTS = set(['.csc', '.grd', '.gsc', '.save', '.s...

OPTIONAL_GRID_EXTS = set(['.cons', '.gxvol', '_h2o.maegz'])

DEBUG = None
hash(x)

__package__ = 'schrodinger.application.glide.packages'

Function Details

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_get_data_file(basename)

Return a set with the path to an optional data file, which may be found in the CWD or in the glide user data directory. The set may be empty.

Variables Details

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DATA_FILES

Value:

['badat.dat',
 'badat_2005.dat',
 'confunc.dat',
 'element.lis',
 'grid.pts',
 'iangmap.20000to302',
 'metalradii.def',
 'ptype.def',
...

REQUIRED_GRID_EXTS

Value:

set(['.csc',
     '.grd',
     '.gsc',
     '.save',
     '.site',
     '.vdwc',
     '_coul2.fld',
     '_greedy.save',
...