Package schrodinger :: Package application :: Package jaguar :: Module input

Module input

Functions and classes for reading and creating Jaguar input files.

It allows setting and querying of keyword values in Jaguar input &gen sections and also provides an interface to some of the mmjag library.

The JaguarInput class also provides for the running of jobs.

Classes

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JaguarInput
A class for specifying Jaguar input.

GenOptions
A class to convert keyword value pairs defined in a single string into a data structure, and allow them to be converted back into a string.

Functions

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launch_file(input, wait=False, save=False, disp=None, **kwargs)
Launch a Jaguar job from the Jaguar input file 'input'.

read(filename, index=1, **kwargs)
Create and return a JaguarInput object from a Jaguar .in file or a maestro .mae file.

get_name_file(input)
Get the input filename and jobname, given either the input filename or the jobname.

split_structure_files(files)
Given a list of structure (.in or .mae) files, split all .mae files into individual structures and write them back to disk with new names.

Variables

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__cvs_version__ = "$Revision: 1.40 $"

_version = "$Revision: 1.40 $"

logger = schrodinger.utils.log.get_logger("schrodinger.jaguar....

Function Details

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launch_file(input, wait=False, save=False, disp=None, **kwargs)


Launch a Jaguar job from the Jaguar input file 'input'. Returns a
jobcontrol.Job object.

Arguments

wait (bool)
    Do not return until the job is complete.

save (bool)
    Set to True to save the scratch directory.

disp (str)
    Set to a valid jobcontrol disposition.

read(filename, index=1, **kwargs)


Create and return a JaguarInput object from a Jaguar .in file or a
maestro .mae file. Additional keyword args are passed on to the
JaguarInput constructor.

Parameters

filename (str)
    Can be a Jaguar input .in file, Maestro structure .mae file, or the
    basename of a file of one of these types.

index (int)
    The index of the structure to use for an .mae input file.

kwargs (additional keyword arguments)
    All keyword arguments are passed on to the JaguarInput constructor.

get_name_file(input)

Get the input filename and jobname, given either the input filename or the jobname.

Return a tuple of (jobname, filename).

split_structure_files(files)

Given a list of structure (.in or .mae) files, split all .mae files into individual structures and write them back to disk with new names.

Return the list of structure files, each of which contains a single structure. Any split mae files are named with either the entry ID (if available) or the source file basename with an index suffix.

Variables Details

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logger

Value:

schrodinger.utils.log.get_logger("schrodinger.jaguar.input")