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'>)¶

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)¶

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)¶

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)¶

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_smarts(args)¶

Validate that the argument is a valid smarts

Note

This function can be used to directly create argparse typing for list of smarts or single smarts string.

eqopts.add_argument(
FLAG_SMARTS, action=’append’, type=parserutils.type_smarts, help=’Define smarts’)

Parameters

args (str, list) – The argument to validate

Return type

str, list

Returns

The validated smarts list or string

Raises

argparse.ArgumentTypeError – If the argument is not a valid smarts raise exception

schrodinger.application.matsci.parserutils.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

schrodinger.application.matsci.parserutils.type_negative_float(arg)¶

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)¶

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)¶

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_exclusive_percent(arg)¶

Validate that the argument is a percent, but neither zero nor 100

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

schrodinger.application.matsci.parserutils.type_nonpositive_float(arg)¶

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)¶

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)¶

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)¶

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_msj(arg, return_msj=False)¶

Validate that the argument is a valid MSJ file.

Parameters

arg (str) – the argument to validate
return_msj (bool) – Whether to return arg or msj object

Raises

argparse.ArgumentTypeError – if the given argument is not a valid MSJ

Return type

str or sea.Map

Returns

the str-ed argument or MSJ object

schrodinger.application.matsci.parserutils.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

schrodinger.application.matsci.parserutils.get_trj_dir_name(st)¶

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_csv_file(arg)¶

Validate that the argument is a CSV file.

Parameters: arg (str) – the argument to validate
Raises: argparse.ArgumentTypeError – if the given argument is not a CSV file
Return type: str
Returns: the validated argument

schrodinger.application.matsci.parserutils.type_out_file(arg)¶

Validate that the argument is a *.out file (intended to use for Jaguar output file)

Parameters: arg (str) – the argument to validate
Raises: argparse.ArgumentTypeError – if the argument is not a *.out file
Return type: str
Returns: the validated argument

schrodinger.application.matsci.parserutils.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

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)¶

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)¶

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)¶

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)¶

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_toml_file(arg)¶

Validate that the argument is a toml file.

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

schrodinger.application.matsci.parserutils.type_structure_file(arg)¶

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_element(value)¶

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.get_forcefield_typer(opls5_ok)¶

Get a validator that will validate a force field name while forcing OPLS5 to be allowed (or not allowed) regardless of MS_USE_OPLS5 feature flag state

Usage::

parser.add_argument(: A_FLAG, type=get_forcefield_typer(True|False)

Parameters: opls5_ok (bool or None) – If True then ignore the MS_USE_OPLS5 feature flag and whether OPLS5 is available depends only on the OPLS5_SELECTABLE feature flag. If False then ignore MS_USE_OPLS5 and OPLS5 will not be available regardless of OPLS5_SELECTABLE. If None then OPLS5 will be available if and only if both OPLS5_SELECTABLE and MS_USE_OPLS5 are enabled.

See type_forcefield for documentation of return values and exceptions raised by the returned function

schrodinger.application.matsci.parserutils.is_opls5_not_matsci_allowed(opls5_ok)¶

Check if OPLS5 is specifically not allowed by a MatSci setting. The state of the company-wide OPLS5_SELECTABLE setting is ignored.

Parameters: opls5_ok (bool or None) – If True, OPLS5 will be allowed, if False, OPLS5 will not be allowed. Both bool settings override the state of the MS_USE_OPLS5 feature flag. The default value of None obeys MS_USE_OPLS5.
Return type: bool
Returns: True if OPLS5 is not allowed due to a MatSci setting, False if no MatSci setting disallows it

schrodinger.application.matsci.parserutils.type_forcefield(value, opls5_ok=None)¶

Validate that the argument is a valid force field name

This accepts any valid name (OPLS3, OPLS3e, OPLS4, etc) for force field #16

Parameters

value (str) – The argument to validate
opls5_ok (bool or None) – If True then ignore the MS_USE_OPLS5 feature flag and whether OPLS5 is available depends only on the OPLS5_SELECTABLE feature flag. If False then ignore MS_USE_OPLS5 and OPLS5 will not be available regardless of OPLS5_SELECTABLE. If None then OPLS5 will be available if and only if both OPLS5_SELECTABLE and MS_USE_OPLS5 are enabled.

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.get_forcefield_typer_and_number_getter(opls5_ok)¶

Get a validator that will validate a force field name while forcing OPLS5 to be allowed (or not allowed) regardless of MS_USE_OPLS5 feature flag state

Usage::

parser.add_argument(: A_FLAG, type=get_forcefield_typer_and_number_getter(True|False)

Parameters: opls5_ok (bool or None) – If True then ignore the MS_USE_OPLS5 feature flag and whether OPLS5 is available depends only on the OPLS5_SELECTABLE feature flag. If False then ignore MS_USE_OPLS5 and OPLS5 will not be available regardless of OPLS5_SELECTABLE. If None then OPLS5 will be available if and only if both OPLS5_SELECTABLE and MS_USE_OPLS5 are enabled.

See type_forcefield_and_get_number for documentation of return values and exceptions raised by the returned function

schrodinger.application.matsci.parserutils.type_forcefield_and_get_number(value, opls5_ok=None)¶

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
opls5_ok (bool) – If True, OPLS5 will be allowed, if False, OPLS5 will not be allowed. Both bool settings override the state of the MS_USE_OPLS5 feature flag. The default value of None obeys the feature flag.

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)¶

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(opls5_ok=None)¶

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.

Parameters: opls5_ok (bool or None) – If True then ignore the MS_USE_OPLS5 feature flag and whether OPLS5 is available depends only on the OPLS5_SELECTABLE feature flag. If False then ignore MS_USE_OPLS5 and OPLS5 will not be available regardless of OPLS5_SELECTABLE. If None then OPLS5 will be available if and only if both OPLS5_SELECTABLE and MS_USE_OPLS5 are enabled.
Return type: str
Returns: A full sentence describing the valid force field names

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

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)¶

class schrodinger.application.matsci.parserutils.KeyPairDict¶

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”

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)¶

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.

schrodinger.application.matsci.parserutils.type_keywords_to_dict(value)¶

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(
    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)¶

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(
    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)¶

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)¶

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)¶

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)¶

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)¶

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)¶

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)¶

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)¶

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)¶

Validate ASL.

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

schrodinger.application.matsci.parserutils.type_desmond_cfg(arg)¶

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

schrodinger.application.matsci.parserutils.type_desmond_msj(arg)¶

Validate that the argument is a desmond msj file. MSJ file contains multiple cfg stages.

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

schrodinger.application.matsci.parserutils.type_host(value)¶

Check the format of a host command line argument. These are expected to be in the format of hostname:X.

Parameters: value (str) – The host command line argument to check
Return type: (str, int)
Returns: The hostname and number of subjobs
Raises: argparse.ArgumentTypeError – If the command line argument is not in the correct format.

class schrodinger.application.matsci.parserutils.SubscriptableNameSpace(**kwargs)¶

Bases: argparse.Namespace

Extend the default namespace to allow getting options using “options[flag]”

getNameFromFlag(flag)¶

Get the option variable name from the flag

Parameters: flag (str) – The commandline flag
Return str: The variable name in the parsed options

__contains__(key)¶

Check if the option contains the passed flag or variable name

Parameters: key (str) – The flag or variable name
Return type: bool
Returns: True if the option exists, False otherwise

get(flag, default=None)¶

Get the option value for the flag, or return the default value if the option doesn’t exist

Parameters

flag (str) – The flag to get the option for
default (Any) – The default value

Return Any

The option value or default value

copy()¶

Return a copy of this namespace

Return SubscriptableNameSpace: A copy of this namespace

extract_dict(*flags)¶

Extract the options for the passed flags and return a dict containing them

Parameters: flags (tuple) – The flags to extract options for
Return type: dict
Returns: The extracted options

class schrodinger.application.matsci.parserutils.DriverParser(*args, add_help=False, formatter_class=<class 'argparse.ArgumentDefaultsHelpFormatter'>, allow_abbrev=False, **kwargs)¶

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, add_help=False, formatter_class=<class 'argparse.ArgumentDefaultsHelpFormatter'>, allow_abbrev=False, **kwargs)¶: Accepts all arguments normally given for an ArgumentParser

parse_args(args=None, namespace=None)¶

Overwrite parent method to use SubscriptableNameSpace as default namespace

Parameters

args (list or None) – List of commandline arguments
namespace (None or argparse.Namespace) – The namespace to use. Uses SubscriptableNameSpace by default

Return argparse.Namespace

The parsed commandline arguments

set_defaults(**defaults)¶

Overwrite parent method to set defaults only for arguments that have been added to the parser

Parameters: defaults (dict) – Dict mapping arguments to their default values

error(message, *args, **kwargs)¶: Overwrite to store the error message.

schrodinger.application.matsci.parserutils.modify_help_message(parser, flag, msg)¶

Modify the help message of an existing parser argument

Parameters

parser (DriverParser) – The populated parser
flag (str) – The flag whose help message should be modified
msg (str) – The new help message

Raises

ValueError – If the flag is not recognized by the parser

schrodinger.application.matsci.parserutils.parse_keyword_list(options, exit_on_error=True, logger=None, validate=False)¶

Adds keystring and keydict properties to the argparse options object that are the list of keyword arguments turned into, respectively, a string or a dictionary. Valid keyword syntax is checked for.

Typical usage:

parserutils.add_keyword_parser_argument(parser) options = parser.parse_args(args) parserutils.parse_keyword_list(options) print options.keystring, options.keydict

Parameters

options (argparse.Namespace) – The parser Namespace object with a keywords attribute
exit_on_error (bool) – True if the ValueError for keyword syntax should result in a message being printed and sys.exit() being called, False if the error should just be raised.
logger (logging.Logger) – The logger to use for recording error messages, otherwise they’ll be printed.
validate (bool) – Whether keywords/values not recognized by Jaguar should be considered an error.

Raises

ValueError – If an invalid keyword pair syntax is detected and handle_error is False

:raises schrodinger.application.jaguar.validation.JaguarKeywordException: if validate=True, exit_on_error=False and an invalid Jaguar keyword/value has been used.

schrodinger.application.matsci.parserutils.get_stripped_defaults(adict)¶

Remove dashes in the beginning of the keys. Used with ArgumentParser.

Parameters: adict (dict{string:any}) – Dictionary of defaults
Return type: dict{string:any}
Returns: Dictionary of defaults with dashed stripped from the keys

schrodinger.application.matsci.parserutils.argparser_set_defaults(parser, defaults)¶

Set default values to the arguments already present in the parser. Note that, parser.set_defaults contaminates namespace with the arguments that might be absent from the parser.

Parameters

parser (argparse.ArgumentParser) – The parser to set defaults
defaults (dict{string:any}) – Dictionary of the defaults

class schrodinger.application.matsci.parserutils.PhysicalFlag(name, unit, default)¶

Bases: schrodinger.application.matsci.parserutils.PhysicalFlag

namedtuple containing the information needed to create an argument flag for a physical property.

Variables

name (str) – The name of the physical property being flagged
unit (str) – The displayed units of the physical property (e.g., ‘K’ for temperature)
default – The default value to use for the given physical flag. If None, a default value will be chosen for you.

schrodinger.application.matsci.parserutils.add_physical_arguments(parser, flags)¶

Add physical arguments to the parser

Parameters

parser (argparse.ArgumentParser) – The parser to add arguments to
flags (list(PhysicalFlag)) – List of physical flags to add to the parser. Each element should be an instance of the PhysicalFlag namedtuple.

Raises

argparse.ArgumentTypeError – If an argument is not recognized as a physical argument.

schrodinger.application.matsci.parserutils.add_restart_parser_arguments(parser)¶

Add restart arguments to the parser

Parameters: parser (argparse.ArgumentParser) – The parser to add arguments to

schrodinger.application.matsci.parserutils.add_keyword_parser_argument(parser, keyword_flags=None, default='', arghelp=None, action='store')¶

Add a keyword argument to the parser

Parameters

parser (argparse.ArgumentParser) – The parser to add this argument to
keyword_flags (None or list of str) – the customized flags for this argument
default (str or None) – The customized default values for this argument
arghelp (str or None) – The customized help message for this argument
action (argparse.Action or str) – The customized action for this argument or the standard ones: ‘store’, ‘store_true’, ‘store_false’, ‘append’ and so on.

schrodinger.application.matsci.parserutils.add_save_desmond_files_parser_argument(parser)¶

Add a SAVE_FLAG argument to the parser

Parameters: parser (argparse.ArgumentParser) – The parser to add this argument to

schrodinger.application.matsci.parserutils.add_compress_subjobs_parser_argument(parser, help=None)¶

Add a FLAG_COMPRESS_SUBJOBS argument to the parser

Parameters: parser (argparse.ArgumentParser) – The parser to add this argument to

schrodinger.application.matsci.parserutils.add_desmond_parser_arguments(parser, args, defaults=None, time_use_ps=False, opls5_ok=None)¶

Add desmond related arguments to the parser

Parameters

parser (argparse.ArgumentParser) – The parser to add this argument to
args (list) – List of arguments to add to the parser
defaults (dict or None) – Default values for the arguments
time_use_ps (bool) – If true use pico-second for time else nanosecond
opls5_ok (bool) – If True, OPLS5 will be allowed, if False, OPLS5 will not be allowed. Both bool settings override the state of the MS_USE_OPLS5 feature flag. The default value of None obeys the feature flag.

schrodinger.application.matsci.parserutils.add_cg_forcefield_parser_arguments(parser, local_path, defaults=None)¶

Add desmond related arguments to the parser

Parameters

parser (argparse.ArgumentParser) – The parser to add the arguments to
local_path (str) – We can search for CG forcefield files in either an “installed” directory or a “local” directory. This argument is the location of the “local” directory.
defaults (dict) – Default values for the arguments

schrodinger.application.matsci.parserutils.add_traj_analysis_parser_arguments(parser, trj_optional=False)¶

Add trajectory analysis parser arguments/

Parameters

parser (argparse.ArgumentParser) – The parser to add this argument to
trj_optional (bool) – Whether trajectory is optional

schrodinger.application.matsci.parserutils.add_random_seed_parser_argument(parser, additional_args=(), help='Seed for random number generator.')¶

Add the command line flag for the random number seed

Parameters

parser (argparse.ArgumentParser) – The parser to add this argument to
additional_args (tuple) – Arguments that should also be accepted in addition to FLAG_RANDOM_SEED
help (str) – The help string to show for random seed. The default string will be used if nothing is supplied.

schrodinger.application.matsci.parserutils.add_conformational_search_to_parser(parser, seed_min=0, seed_max=2147483647)¶

Add flags related to the conformational search to the parser.

Parameters

parser (argparse.ArgumentParser) – The parser to add this argument to
seed_min (int) – The minimum allowed random number seed
seed_max (int) – The maximum allowed random number seed

schrodinger.application.matsci.parserutils.add_tpp_parser_argument(parser)¶

Add a FLAG_TPP argument to the parser

Parameters: parser (argparse.ArgumentParser) – The parser to add this argument to

schrodinger.application.matsci.parserutils.add_out_rep_parser_argument(parser)¶

Add a FLAG_OUT_REP argument to the parser

Parameters: parser (argparse.ArgumentParser) – The parser to add this argument to

schrodinger.application.matsci.parserutils.add_dedup_geom_eps_parser_argument(parser)¶

Add a FLAG_DEDUP_GEOM_EPS argument to the parser

Parameters: parser (argparse.ArgumentParser) – The parser to add this argument to

schrodinger.application.matsci.parserutils.add_mopac_parser_argument(parser)¶

Add a FLAG_MOPAC argument to the parser

Parameters: parser (argparse.ArgumentParser) – The parser to add this argument to

schrodinger.application.matsci.parserutils.add_xtb_parser_argument(parser)¶

Add a FLAG_XTB argument to the parser

Parameters: parser (argparse.ArgumentParser) – The parser to add this argument to

schrodinger.application.matsci.parserutils.add_robust_jaguar_argument(parser)¶

Add a FLAG_ROBUST argument to the parser

Parameters: parser (argparse.ArgumentParser) – The parser to add this argument to

schrodinger.application.matsci.parserutils.add_boltzmann_energy_argument(parser, lowest=True, prop_required=True)¶

Add parser arguments for Boltzmann averaging

Parameters

parser (argparse.ArgumentParser) – The parser to add this argument to
lowest (bool) – Whether to add the -lowest flag
prop_required (bool) – Whether the energy prop flag is required

schrodinger.application.matsci.parserutils.add_max_retries_argument(parser)¶

Add a FLAG_MAX_RETRIES argument to the parser

Parameters: parser (argparse.ArgumentParser) – The parser to add this argument to

schrodinger.application.matsci.parserutils.add_smarts_method_argument(parser, default=SMARTS_METHOD.internal)¶

Add a FLAG_SMARTS_METHOD argument to the parser.

Parameters

parser (argparse.ArgumentParser) – The parser to add this argument to
default (msconst.SMARTS_METHOD) – Default method

schrodinger.application.matsci.parserutils.add_metal_center_element_argument(parser)¶

add an ATOMIC_SYMBOL argument to the parser, for metal center in coordination complex.

Parameters: parser (argparse.ArgumentParser) – The parser to add this argument to

schrodinger.application.matsci.parserutils.add_geom_argument(parser, default_choice=None)¶

add a VSEPR_GEOMETRY argument to the parser, for geometry of coordination complex.

Parameters

parser (argparse.ArgumentParser) – The parser to add this argument to
default_choice (str) – Default geometry to use. Must be in buildcomplex.CMDLINE_GEOMETRIES

schrodinger.application.matsci.parserutils.add_cpu_gpu_host_arguments(parser, required=False, cpu_default=None, gpu_default=None)¶

Add a flags for setting the cpu host and gpu host to the parser.

Parameters

parser (argparse.ArgumentParser) – The parser to add these arguments to
required (bool) – Whether the arguments are required
cpu_default (type_host) – The default value for the cpu host
gpu_default (type_host) – The default value for the gpu host

schrodinger.application.matsci.parserutils.add_jaguar_dict_keywords_flag(parser, default=None, msg=None)¶

Add a flag for keywords to be stored in a keyword/value dict

Parameters

parser (argparse.ArgumentParser) – The parser to add this argument to
default (str) – The default keyword string to use
msg (str) – A custom help message for the flag

schrodinger.application.matsci.parserutils.get_cpu_and_gpu_hosts(options)¶

Get the command line options for the cpu and gpu hosts

Parameters: options (SubscriptableNameSpace) – The command line options
Return type: tuple
Returns: The first item in the tuple is the result for the CPU host, the second is for the GPU host. Each item is either a (hostname, #_procs) tuple or None if that option was not given.

schrodinger.application.matsci.parserutils.get_jobname(options, default_jobname)¶

Gets the job name from the parsed options. If there is no job name, use the default specified in this driver.

Parameters

options (argparse.Namespace) – The parsed command line options
default_jobname (str) – The job name to use if no explicit name is found in options

Returns

The name of the job. Prioritizes the name given in the options, but falls back to a default job name.

Return type

str