Package schrodinger :: Package application :: Package matsci :: Module parserutils

Module parserutils

Utilities for working with argument parsers

Functions

float or int

type_ranged_num(arg, top=None, bottom=0.0, top_allowed=False, bottom_allowed=False, typer=<type 'float'>)
Validate that the argument is a number over a given range.

type_ranged_int(*args, **kwargs)
Validate that the argument is an int over a given range

type_positive_float(arg)
Validate that the argument is a positive float

type_positive_int(arg)
Validate that the argument is a positive int

type_nonnegative_int(arg)
Validate that the argument is a nonnegative int

str

type_file(arg)
Validate that the argument is an existing filename

type_nonnegative_float(arg)
Validate that the argument is a nonnegative float

str or None

get_trj_dir_name(st)
Get the trajectory directory name from the given structure.

str

type_cms_file(arg, ensure_trj=False)
Validate that the argument is a cms file.

str

type_cms_with_trj(arg)
Validate that the argument is a cms file with trajectory information.

str

type_json_file(arg)
Validate that the argument is a json file.

Variables

[hide private]

OLD_TRJ_END = '-out.idx'

NEW_TRJ_END = '_trj'

__package__ = 'schrodinger.application.matsci'

Function Details

[hide private]

type_ranged_num(arg, top=None, bottom=0.0, top_allowed=False, bottom_allowed=False, typer=<type 'float'>)

Validate that the argument is a number over a given range.

Parameters:

arg (str) - The argument to validate
top (float or int) - The upper limit of the allowed range
bottom (float or int) - The lower limit of the allowed range
top_allowed (bool) - Whether arg may take the top value or not (whether the upper limit is inclusive or exclusive)
bottom_allowed (bool) - Whether arg may take the bottom value or not (whether the bottom limit is inclusive or exclusive)
typer (callable) - Should be one of the built-in float or int functions and defines the type of the value returned from this function.

Returns: float or int

The argument converted to a float or int, depending on the value of the typer keyword argument

@raise argparse.ArgumentTypeError: If the argument cannot be converted to a ranged floating point number in the given range

type_ranged_int(*args, **kwargs)

Validate that the argument is an int over a given range

see type_ranged_num for documentation of arguments, return values and exceptions raised

type_positive_float(arg)

Validate that the argument is a positive float

see type_ranged_num for documentation of arguments, return values and exceptions raised

type_positive_int(arg)

Validate that the argument is a positive int

see type_ranged_num for documentation of arguments, return values and exceptions raised

type_nonnegative_int(arg)

Validate that the argument is a nonnegative int

see type_ranged_num for documentation of arguments, return values and exceptions raised

type_file(arg)

Validate that the argument is an existing filename

Parameters:

arg (str or unicode) - The argument to validate

Returns: str

The str-ed argument

@raise argparse.ArgumentTypeError: If the given filename does not exist

type_nonnegative_float(arg)

Validate that the argument is a nonnegative float

see type_ranged_num for documentation of arguments, return values and exceptions raised

get_trj_dir_name(st)

Get the trajectory directory name from the given structure.

Parameters:

st (schrodinger.structure.Structure) - the structure

Returns: str or None

the trajectory directory name or None if there isn't one

type_cms_file(arg, ensure_trj=False)

Validate that the argument is a cms file.

Parameters:

arg (str or unicode) - the argument to validate
ensure_trj (bool) - ensure that the cms file has trajectory information, for example is a Desmond output file

Returns: str

the str-ed argument

Raises:

argparse.ArgumentTypeError - if the given argument is not a cms file

type_cms_with_trj(arg)

Validate that the argument is a cms file with trajectory information.

Parameters:

arg (str or unicode) - the argument to validate

Returns: str

the str-ed argument

type_json_file(arg)

Validate that the argument is a json file.

Parameters:

arg (str or unicode) - the argument to validate

Returns: str

the str-ed argument

Raises:

argparse.ArgumentTypeError - if the given argument is not a json file