Package schrodinger :: Package application :: Package desmond :: Package packages :: Module cui

Module cui

Common command-line interface for Desmond scripts

Classes

LazyParser
Some argument parsers are so slow, e.g., the msys parser.

CommandLine
Use this class to define common command line arguments such input cms file, input trajectory, output file base name, trajectory slicing option, and so on.

Functions

[hide private]

info(message)

warn(message)

error(message, exit_code=1, should_exit=True)

list of str

all_fnames_in_dir(dname)
Returns all regular files under the given directory, including those in subdirectories.

jc_reg_input(builder, fname)
Register an input file for jobcontrol to transfer.

jc_reg_output(builder, fname)
Preregister an output file for jobcontrol to transfer.

jc_backend_reg_output(fname)
Register (on the fly) an output file for jobcontrol to transfer.

_parse_slice(s)

_cms_only(s)

_msys_cms(s)

_read_mae(s)

_parse_trj(s)

_parse_out(s)

_validate_asl(value)

Variables

[hide private]

REQUIRE_CMS_ONLY = 1

REQUIRE_MSYS_CMS = 2

REQUIRE_TRJ = 4

REQUIRE_OUT = 8

OPTIONAL_TRJ = 16

SLICE_TRJ = 32

REF_MAE = 64

REF_FRAME = 128

JC = 256

__package__ = 'schrodinger.application.desmond.packages'

Function Details

[hide private]

all_fnames_in_dir(dname)

Returns all regular files under the given directory, including those in subdirectories.

Parameters:

dname (str) - Path of the directory

Returns: list of str

jc_reg_input(builder, fname)

Parameters:

builder (launchapi.JobSpecificationArgsBuilder) - You can get a builder by calling CommandLine.get_job_spec.
fname (str) - Input file name to be transferred by jobcontrol. The file can be a directory, and in this case all regular files under this directory will be transferred. If fname contains a relative path, the relative path will be preserved on the host.

jc_reg_output(builder, fname)

Preregister an output file for jobcontrol to transfer.

Parameters:

builder (launchapi.JobSpecificationArgsBuilder) - You can get a builder by calling CommandLine.get_job_spec.
fname (str) - Input file name to be transferred by jobcontrol. The file can be a directory.

jc_backend_reg_output(fname)

Parameters:

fname (str) - Output file name to be transferred by jobcontrol. The file can be a directory.