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Pydoc: module xplorInit

xplorInit

python interface intialization script this should not normally be modified by users. this executes in module "xplor" Builtin Methods: from xplorWrap.XplorWrap: command(string,names) - call XplorWrap.command(). shell() - invoke the XPLOR interpreter Useful members: simulation: an instance of xplorSimulation.XplorSimulation which represents the atomic structure state within XPLOR. wrap: an instance of xplorWrap.XplorWrap interp: the top-level pyInterp.PyInterp object

Functions

callerName() -> str: Return the calling function's name.

execfile(filename, globals=None, locals=None)

fastCommand(c, r=()): call xplorWrap.XplorWrap.fastCommand

help()

parseArguments(options=[], cmdline='', description='[no description provided]', usageString='', allowExtraOptions=False, minArgs=None, maxArgs=None): process extra Xplor-NIH command-line arguments.

Mistyped options will be detected.

Options can be specified using the options argument as a sequence of strings
without leading dash(es). On the command-line options start with a single or
double dash. Option can have zero or more arguments, the number of which is
specified by a number separated by a colon from the option name (if omitted,
the number defaults to 0. Alternatively, the elements of the options argument
can be tuples with 3 elements: option name, sequence of argument
descriptions (or None), and a description. If there is a single option
argument, it may be specified as a string. For option arguments the literal
character sequence %q% is converted to a single quote. Thus, it is
not possible to pass this sequence as an option argument.

If allowExtraOptions is True, extra options will be allowed, and not treated
as errors.

Options present on the command-line but which are not specified in the
options argument will cause an error.

The return value is (optlist,args), where
  optlist is [(option, arg1, arg2..), ...]
  and args are the remaining command-line arguments after options have
  been parsed.

example:
  (optlist,args) = parseArguments(["help-script","outfile:1"])

The cmdline, description and usageString arguments are used to generate
output when the following options are specified:

    --help-cmdline  - prints the program name (as deduced from argv[0]),
                      followed by the cmdline argument.
    --help-description - print the description string with newline characters
                         replaced with spaces.
    --help-script      - print a usage string build from the cmdline,
                         description and usageString arguments.
    --help             - same as --help-script
    --help-all         - print common Xplor-NIH command-line options after
                         --help-script output
    --output-rst       - the usage string printed using --help-script
                         normally has its reStructedText markup stripped
                         with the rst2txt facility. If this option is
                         placed first, the markup is preserved.
    --pdf              - in a similar fashion to the --output-rst option,
                         if this option is placed before --help-script, the
                         reStructuredText help string is converted to PDF
                         and displayed in a separate window. This option
                         has the side-effect of setting the module-global
                         variable outputPDF to True (otherwise it is False).

For each of these options after printing the string, exit() is called.

The number of non-option arguments can be bracketed using the minArgs and
maxArgs parameters.

pyConfigFile(name): return the full path of a .xplornih configuration file whose filename
is name

rcDir(): return the path of the Xplor-NIH configuration directory.

If the directory does not exist, create it

rcPyDir(): return the path of the Xplor-NIH configuration directory.

If the directory does not exist, create it

requireVersion(vStr, raiseException=True): Returns True if the current Xplor-NIH version is less than
that specified in vStr. If raiseException=True, an exception is
raised.

writeConsole(msg): write a message to the user's console - file descriptor number 9.
This is stdout from where the xplor command is typed.

writeExitMessage()

Data
		LD_LIBPATH_VAR = 'LD_LIBRARY_PATH' XPLOR_DIR = '/home/schwitrs/xplor' allowStartupFailures = 1 arg1 = '-w' argN = 'publicIVM' argv = ['xplorDoc', '-w', 'xplor', 'ivm', 'monteCarlo', 'trace', 'trajFile', 'selectLogic', 'selectTools', 'xplorInit', 'vmdInter', 'checkWrap', 'hybridMC', 'atomAction', 'potCosAngleRatio', 'rdcPotTools', 'simulationTools', 'shapePotTools', 'pck2xplor', 'protocol', ...] cnt = 1 e = '.' env = environ({'ARCH': 'Linux_x86_64', 'NUM_THREADS': ...home/schwitrs/lib/Linux_x86_64::/usr/local/lib'}) exitMessage = '' k = 'orig_LD_LIBRARY_PATH' lineBuffering = True newPath = '/home/schwitrs/lib/Linux_x86_64:/home/schwitrs/lib/Linux_x86_64::/usr/local/lib' newargv = ['xplorDoc', '-w', 'xplor', 'ivm', 'monteCarlo', 'trace', 'trajFile', 'selectLogic', 'selectTools', 'xplorInit', 'vmdInter', 'checkWrap', 'hybridMC', 'atomAction', 'potCosAngleRatio', 'rdcPotTools', 'simulationTools', 'shapePotTools', 'pck2xplor', 'protocol', ...] numProcs = 1 out = 'stderr' p_comm = <socketComm.Comm object> p_host0 = '' p_numProcs = 1 p_port = 9064 p_processID = 0 paths = ['/home/schwitrs/lib/Linux_x86_64', '/home/schwitrs/lib/Linux_x86_64', '', '/usr/local/lib'] progName = '/home/schwitrs/bzr-repo/xplor-python3/bin/xplor' scriptName = 'publicIVM' tmp = ['/home/schwitrs/bzr-repo/xplor-python3/bin.Linux_x86_64', '/home/schwitrs/xplor/bin.Linux_x86_64', '/home/schwitrs/xplor/python', '/home/schwitrs/xplor/python/bin.Linux_x86_64', '/home/schwitrs/xplor/python/bin.Linux_x86_64/lib/python3.11', '/home/schwitrs/xplor/python/bin.Linux_x86_64/lib/python3.11/lib-dynload', '/home/schwitrs/xplor/python/bin.Linux_x86_64/lib/python3.11/site-packages', '/home/schwitrs/.xplornih/python', '/home/schwitrs/.xplornih/python', '.'] varName = 'XPLOR_NOLINEBUFFER' wrap = <xplorWrap.XplorWrap; proxy of <Swig Object of type 'XplorWrap *' at 0x7fe0bb9a2cd0> >