schrodinger.application.matsci.parserutils module¶

Utilities for working with argument parsers

schrodinger.application.matsci.parserutils.type_ranged_num(arg, top=None, bottom=0.0, top_allowed=False, bottom_allowed=False, typer=<class 'float'>)[source]¶

Validate that the argument is a number over a given range. By default, it is (0, +inf)

Note: This function can be used to directly create argparse typing for

numbers within a specified range using a lambda function such as:

eqopts.add_argument(: FLAG_TEMP, action=’store’, type=lambda x:parserutils.type_ranged_num(x, top=423, bottom=273), metavar=’KELVIN’, help=’Simulation temperature for MD equilibration step’)

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.

Return type

float or int

Returns

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

Raises

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

schrodinger.application.matsci.parserutils.type_ranged_int(*args, **kwargs)[source]¶

Validate that the argument is an int over a given range

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

schrodinger.application.matsci.parserutils.get_ranged_int_typer(bottom_allowed=True, top_allowed=True, **kwargs)[source]¶

Get a validator that will validate an integer over a custom range

Usage::

parser.add_argument(: A_FLAG, type=get_ranged_int_typer(bottom=4, top=12, bottom_allowed=False))

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

schrodinger.application.matsci.parserutils.get_ranged_float_typer(bottom_allowed=True, top_allowed=True, **kwargs)[source]¶

Get a validator that will validate a float over a custom range

Usage::

parser.add_argument(: A_FLAG, type=get_ranged_float_typer(bottom=-5.0, top=5.0, top_allowed=False))

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

schrodinger.application.matsci.parserutils.type_positive_float(arg)[source]¶

Validate that the argument is a positive float

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

schrodinger.application.matsci.parserutils.type_negative_float(arg)[source]¶

Validate that the argument is a negative float

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

schrodinger.application.matsci.parserutils.type_positive_int(arg)[source]¶

Validate that the argument is a positive int

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

schrodinger.application.matsci.parserutils.type_nonnegative_int(arg)[source]¶

Validate that the argument is a nonnegative int

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

schrodinger.application.matsci.parserutils.type_nonpositive_float(arg)[source]¶

Validate that the argument is a nonpositive float

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

schrodinger.application.matsci.parserutils.type_nonzero_percent(arg)[source]¶

Validate that the argument is a percent but not zero

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

schrodinger.application.matsci.parserutils.type_random_seed(arg, seed_min=0, seed_max=2147483647)[source]¶

Validate that the argument is a valid random seed value. If a random value is requested, that value is generated and returned.

Parameters

arg (str) – The argument to validate
seed_min (int) – The minimum allowed random number seed
seed_max (int) – The maximum allowed random number seed

Return type

int

Returns

The random seed

Raises

argparse.ArgumentTypeError – If the argument is not RANDOM_SEED_RANDOM or an integer

schrodinger.application.matsci.parserutils.type_file(arg)[source]¶

Validate that the argument is an existing filename

Parameters: arg (str or unicode) – The argument to validate
Return type: str
Returns: The str-ed argument
Raises: argparse.ArgumentTypeError – If the given filename does not exist

schrodinger.application.matsci.parserutils.type_nonnegative_float(arg)[source]¶

Validate that the argument is a nonnegative float

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

schrodinger.application.matsci.parserutils.get_trj_dir_name(st)[source]¶

Get the trajectory directory name from the given structure.

Parameters: st (schrodinger.structure.Structure) – the structure
Return type: str or None
Returns: the trajectory directory name or None if there isn’t one

schrodinger.application.matsci.parserutils.type_cms_file(arg, ensure_trj=False)[source]¶

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

Raises

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

Return type

str

Returns

the str-ed argument

schrodinger.application.matsci.parserutils.type_xyz_file(arg)[source]¶

Validate that the argument is an existing filename with xyz extension and can be converted into sdf format.

Parameters

arg (The argument to validate) – str

Returns

str

Return type

The validated argument

Raises

argparse.ArgumentTypeError – If the given filename does not exist
argparse.ArgumentTypeError – If the given filename does not have xyz as file extension.
argparse.ArgumentTypeError – If the given filename cannot be converted

schrodinger.application.matsci.parserutils.type_cms_with_trj(arg)[source]¶

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

Parameters: arg (str or unicode) – the argument to validate
Return type: str
Returns: the str-ed argument

schrodinger.application.matsci.parserutils.type_json_file(arg)[source]¶

Validate that the argument is a json file.

Parameters: arg (str or unicode) – the argument to validate
Raises: argparse.ArgumentTypeError – if the given argument is not a json file
Return type: str
Returns: the str-ed argument

schrodinger.application.matsci.parserutils.type_yaml_file(arg)[source]¶

Validate that the argument is a yaml file.

Parameters: arg (str or unicode) – the argument to validate
Raises: argparse.ArgumentTypeError – if the given argument is not a yaml file
Return type: str
Returns: the str-ed argument

schrodinger.application.matsci.parserutils.type_yaml_str(arg)[source]¶

Load the arg as a yaml string.

Parameters: arg (str or unicode) – the argument to validate
Raises: argparse.ArgumentTypeError – if the given argument is not in yaml format
Return type: dict
Returns: loaded yaml string

schrodinger.application.matsci.parserutils.type_structure_file(arg)[source]¶

Validate that the argument is a structure file that can be read by StructureReader.

Parameters: arg (str or unicode) – the argument to validate
Raises: argparse.ArgumentTypeError – if the given argument is not a readable structure file
Return type: str
Returns: the str-ed argument

schrodinger.application.matsci.parserutils.type_periodic_structure_file(arg)[source]¶

Validate that the argument is a periodic structure file (priority is chorus followed by pdb).

Parameters: arg (str or unicode) – the argument to validate
Raises: argparse.ArgumentTypeError – if the given argument is not a periodic structure file
Return type: str
Returns: the str-ed argument

schrodinger.application.matsci.parserutils.type_element(value)[source]¶

Validate that the argument is a valid atomic atymbol

Parameters: value (str) – The argument to validate
Return type: str
Returns: The validated argument
Raises: argparse.ArgumentTypeError – If the argument is not a valid atomic symbol

schrodinger.application.matsci.parserutils.type_forcefield(value)[source]¶

Validate that the argument is a valid force field name

This accepts both OPLS3 and OPLS3e for force field #16

Parameters: value (str) – The argument to validate
Return type: str
Returns: The canonical force field name
Raises: argparse.ArgumentTypeError – If the argument is not a valid atomic symbol

schrodinger.application.matsci.parserutils.type_forcefield_and_get_number(value)[source]¶

Validate that the argument is a valid force field name and returns both the canonical force field name and number.

This accepts both OPLS3 and OPLS3e for force field #16

Parameters: value (str) – The argument to validate
Return type: str, int
Returns: The canonical force field name and the corresponding force field int
Raises: argparse.ArgumentTypeError – If the argument is not a valid atomic symbol

schrodinger.application.matsci.parserutils.type_desmond_ensemble(value)[source]¶

Validate that the argument is a valid desmond ensemble

Parameters: value (str) – The argument to validate
Return type: str
Returns: The validated argument
Raises: argparse.ArgumentTypeError – If the argument is not a valid desmond ensemble

schrodinger.application.matsci.parserutils.valid_forcefield_info()[source]¶

Get an informative sentence that can be included in help messages that indicate the valid force field names.

Note that these are the default names and type_forcefield will accept many variants of them, including OPLS3 for OPLS3E.

Return type: str
Returns: A full sentence describing the valid force field names

class schrodinger.application.matsci.parserutils.NoArgCustomAction(*args, **kwargs)[source]¶

Bases: argparse.Action

An action that allows giving an argparse flag a custom action so that the flag does not require an argument

One possible use is the implementation of a flag like ‘-doc’ which immediately performs an action when it is found on the command line - such as printing out detailed documentation and then exiting. This avoids the user having to specify any other flags even if they are marked as required.

__init__(*args, **kwargs)[source]¶: Initialize self. See help(type(self)) for accurate signature.

class schrodinger.application.matsci.parserutils.KeyPairDict[source]¶

Bases: dict

This is a subclass of dict so that the {a:b} can be displayed as “a=b” (e.g, as the help message”

__contains__(key, /)¶: True if the dictionary has the specified key, else False.

__init__(*args, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

__len__()¶: Return len(self).

clear() → None. Remove all items from D.¶

copy() → a shallow copy of D¶

fromkeys(value=None, /)¶: Create a new dictionary with keys from iterable and values set to value.

get(key, default=None, /)¶: Return the value for key if key is in the dictionary, else default.

items() → a set-like object providing a view on D’s items¶

keys() → a set-like object providing a view on D’s keys¶

pop(k[, d]) → v, remove specified key and return the corresponding value.¶: If key is not found, d is returned if given, otherwise KeyError is raised

popitem()¶

Remove and return a (key, value) pair as a 2-tuple.

Pairs are returned in LIFO (last-in, first-out) order. Raises KeyError if the dict is empty.

setdefault(key, default=None, /)¶

Insert key with a value of default if key is not in the dictionary.

Return the value for key if key is in the dictionary, else default.

update([E, ]**F) → None. Update D from dict/iterable E and F.¶: If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]

values() → an object providing a view on D’s values¶

class schrodinger.application.matsci.parserutils.StoreDictKeyPair(option_strings, dest, nargs=None, const=None, default=None, type=None, choices=None, required=False, help=None, metavar=None)[source]¶

Bases: argparse._StoreAction

This is the action used with nargs=”+” and values=’KEYWORD=VALUE KEYWORD=VALUE’

By default nargs=”+” and action=’store’ save the multiple values “k1=v1 k2=v2” as list. With this StoreDictKeyPair as the action, “k1=v1 k2=v2” will be stored as {k1:v1, k2:v2} in the options.

__init__(option_strings, dest, nargs=None, const=None, default=None, type=None, choices=None, required=False, help=None, metavar=None)¶: Initialize self. See help(type(self)) for accurate signature.

schrodinger.application.matsci.parserutils.type_keywords_to_dict(value)[source]¶

Convert a string of ‘keyword=value keyword=value …’ to a dictionary keyed by keyword. Values are the keyword values.

Note

When calling parser.add_argument for the flag that uses this function, do not use “nargs=+”. That will result in the return value from this function being placed as an item in a list. Instead, do not use nargs at all and simply use “action=’store’”. All of the keyword=value pairs will then be passed into this function as a single string. Example:

parser.add_argument(
jobutils.FLAG_KEYWORDS, action=’store’, metavar=’KEYWORD=VALUE KEYWORD=VALUE …’, type=parserutils.type_keywords_to_dict, help=’Jaguar keywords given as a space-separated keyword=value ‘

‘ pairs’

)

will result in options.keyword = the dictionary returned by this function

Parameters

value (str) – The argument to validate

Return type

dict

Returns

A dictionary with keywords as key keyword values as values

Raises

argparse.ArgumentTypeError – If the argument is not a valid keyword string

schrodinger.application.matsci.parserutils.type_keywords_to_string(value)[source]¶

Validate the format of a string of ‘keyword=value keyword=value …’

Note

When calling parser.add_argument for the flag that uses this function, do not use “nargs=+”. That will result in the return value from this function being placed as an item in a list. Instead, do not use nargs at all and simply use “action=’store’”. All of the keyword=value pairs will then be passed into this function as a single string. Example:

parser.add_argument(
jobutils.FLAG_KEYWORDS, action=’store’, metavar=’KEYWORD=VALUE KEYWORD=VALUE …’, type=parserutils.type_keywords_to_string, help=’Jaguar keywords given as a space-separated keyword=value ‘

‘ pairs’

)

will result in options.keyword = the string returned by this function

Parameters

value (str) – The argument to validate

Return type

string

Returns

The original command line string

Raises

argparse.ArgumentTypeError – If the argument is not a valid keyword string

schrodinger.application.matsci.parserutils.type_num_list(value, delimiter=', ', typer=<class 'float'>, bottom=None, bottom_allowed=False)[source]¶

Validate that the argument is a list of numbers separated by the delimiter

Parameters

value (str) – string containing numbers separated by delimiter
delimiter (str) – the char to split the input value
typer (callable) – Should be one of the built-in float or int functions and defines the type of the value returned from this function.
bottom (float or int) – The lower limit of the allowed range
bottom_allowed (bool) – Whether arg may take the bottom value or not (whether the bottom limit is inclusive or exclusive)

Return type

list

Returns

The validated argument converted to a list of numbers

Raises

argparse.ArgumentTypeError – If the argument is not a valid list of numbers

schrodinger.application.matsci.parserutils.type_num_comma_list(value, typer=<class 'float'>, bottom=None, bottom_allowed=False)[source]¶

Validate that the argument is a list of numbers separated by comma

Parameters

value (str) – string containing numbers separated by commas
typer (callable) – Should be one of the built-in float or int functions and defines the type of the value returned from this function.
bottom (float or int) – The lower limit of the allowed range
bottom_allowed (bool) – Whether arg may take the bottom value or not (whether the bottom limit is inclusive or exclusive)

Return type

list

Returns

The validated argument positive integers coverted to list

Raises

argparse.ArgumentTypeError – If the argument is not a valid list of floats

schrodinger.application.matsci.parserutils.type_num_colon_list(value, typer=<class 'float'>, bottom=None, bottom_allowed=False)[source]¶

Validate that the argument is a list of numbers separated by colon

Parameters

value (str) – string containing numbers separated by colon
typer (callable) – Should be one of the built-in float or int functions and defines the type of the value returned from this function.
bottom (float or int) – The lower limit of the allowed range
bottom_allowed (bool) – Whether arg may take the bottom value or not (whether the bottom limit is inclusive or exclusive)

Return type

list

Returns

The validated argument positive integers coverted to list

Raises

argparse.ArgumentTypeError – If the argument is not a valid list of floats

schrodinger.application.matsci.parserutils.type_float_comma_list(value)[source]¶

Validate that the argument is a float list separated by comma

Parameters: value (str) – string containing numbers separated by commas
Return type: list
Returns: The validated argument positive integers converted to list
Raises: argparse.ArgumentTypeError – If the argument is not a valid list of floats

schrodinger.application.matsci.parserutils.type_nonnegative_float_comma_list(value)[source]¶

Validate that the argument is a nonnegative float list separated by comma

Parameters: value (str) – string containing numbers separated by commas
Return type: list
Returns: The validated argument positive integers converted to list
Raises: argparse.ArgumentTypeError – If the argument is not a valid list of floats

schrodinger.application.matsci.parserutils.type_positive_integer_comma_list(value)[source]¶

Validate that the argument is a integer list separated by comma

Parameters: value (str) – string containing numbers separated by commas
Return type: list
Returns: The validated argument positive integers coverted to list
Raises: argparse.ArgumentTypeError – If the argument is not a valid list of positive integers

schrodinger.application.matsci.parserutils.type_element_comma_list(value)[source]¶

Validate that the argument is a element separated by comma

Return type: list
Returns: The validated argument list of element symbols
Raises: argparse.ArgumentTypeError – If the argument is not a valid list of strings

schrodinger.application.matsci.parserutils.type_percentage(value)[source]¶

Validate that the argument is a percentage between 0 and 100

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

schrodinger.application.matsci.parserutils.type_asl(asl)[source]¶

Validate ASL.

Return type: str
Returns: ASL
Raises: argparse.ArgumentTypeError – If ASL is not valid

schrodinger.application.matsci.parserutils.type_desmond_cfg(arg)[source]¶

Validate that the argument is a desmond CFG file.

Parameters: arg (str or unicode) – the argument to validate
Raises: argparse.ArgumentTypeError – if the given argument is not a readable CFG file
Return type: str
Returns: the str-ed argument

class schrodinger.application.matsci.parserutils.DriverParser(*args, **kwargs)[source]¶

Bases: argparse.ArgumentParser

Subclass that shows driver usage relative to python/scripts or python/common directories and adds a help argument by default

__init__(*args, **kwargs)[source]¶: Accepts all arguments normally given for an ArgumentParser

add_argument(dest, ..., name=value, ...)¶: add_argument(option_string, option_string, …, name=value, …)

add_argument_group(*args, **kwargs)¶

add_mutually_exclusive_group(**kwargs)¶

add_subparsers(**kwargs)¶

convert_arg_line_to_args(arg_line)¶

error(message: string)¶

Prints a usage message incorporating the message to stderr and exits.

If you override this in a subclass, it should not return – it should either exit or raise an exception.

exit(status=0, message=None)¶

format_help()¶

format_usage()¶

get_default(dest)¶

parse_args(args=None, namespace=None)¶

parse_intermixed_args(args=None, namespace=None)¶

parse_known_args(args=None, namespace=None)¶

parse_known_intermixed_args(args=None, namespace=None)¶

print_help(file=None)¶

print_usage(file=None)¶

register(registry_name, value, object)¶

set_defaults(**kwargs)¶

schrodinger.application.matsci.parserutils module¶

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