schrodinger.application.desmond.cmj

Module cmj

This module provides fundamental facilities for writing a multisim driver script, for writing multisim concrete stage classes, and for dealing with protocol files.

Functions

[hide private]

_print(loglevel, msg)

print_tonull(msg)

print_silent(msg)

print_quiet(msg)

print_verbose(msg)

print_debug(msg)

is_restartable_version(version_string)

build_stages(stage_list, out_fname=None, stage_state=[])

build_stagelinks(stage_list)

probe_checkpoint(fname, indent="")

escape_string(s)

append_stage(cmj_fname, stage_type, cfg_file=None, jobname=None, dir=None, compress=None, parameter={})

msj2sea(fname, msj_content=None)
Parses a file as specified by 'fname' or a string given by 'msj_content' (if both are given, the former will be ignored), and returns a 'sea.Map' object that represents the stage settings with a structure like the following: stage = [ { <stage 1 settings> } { <stage 2 settings> } { <stage 3 settings> } ...

msj2sea_full(fname, msj_content=None, pset="")

parse_msj(fname, msj_content=None, pset="")
`sea.macro_dict' must be set properly before calling this function.

write_msj(stage_list, fname=None, to_str=True)
Given a list of stages, writes out a .msj file of the name `fname'.

write_sea2msj(stage_list, fname=None, to_str=True)

_collect_inputfile_from_file_list(list_, fname_list)

_collect_inputfile_from_file_map(map, fname_list)

_collect_inputfile_from_list(list_, fname_list)

_collect_inputfile_from_map(map, fname_list)

collect_inputfile(stage_list)
Returns a list of file names.

validate_asl_expr(stage_list)
Validates all ASL expressions that start with the "asl:" prefix.

reg_checking(name, func)

Variables

[hide private]

VERSION = "3.8.5.19"

QUEUE = None
hash(x)

ENGINE = None
hash(x)

LOGLEVEL = ["silent", "quiet", "verbose", "debug",]

GENERAL_LOGLEVEL = "quiet"

PACKAGE_SUFFIX = ".tgz"

CHECKPOINT_SUFFIX = "-multisim_checkpoint"

CHECKPOINT_FNAME = "$MASTERJOBNAME"+ CHECKPOINT_SUFFIX

last_logtime = None
hash(x)

PARAM = None
hash(x)

_operator = {}

fname = "my_test.msj"

begin_time = time.time()

end_time = time.time()

Function Details

[hide private]

msj2sea(fname, msj_content=None)


Parses a file as specified by 'fname' or a string given by 'msj_content' (if both are given, the former will be ignored),
and returns a 'sea.Map' object that represents the stage settings with a structure like the following:
  stage = [
     { <stage 1 settings> }
     { <stage 2 settings> }
     { <stage 3 settings> }
     ...
  ]
Each stage's name can be accessed in this way: raw.stage[1].__NAME__, where 'raw' is the returned 'sea.Map' object.

write_msj(stage_list, fname=None, to_str=True)

Given a list of stages, writes out a .msj file of the name `fname'. If 'to_str' is True, a string will be returned. The returned string contains the contents of the .msj file. If 'to_str' is False and not file name is provided, then this function does nothing.