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=True)¶

Get a validator that will validate a force field name while forcing OPLS5 to be allowed (or not allowed)

Usage::

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

Parameters:: opls5_ok (bool) – If True then OPLS5 will be available, if False it will not

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

schrodinger.application.matsci.parserutils.type_forcefield(value, opls5_ok=True)¶

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) – If True then OPLS5 will be available. If False it will not.

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, opls5_ok=True)¶

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 it will not.

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=True)¶

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) – If True OPLS5 will be available. If False, it will not.
Return type:: str
Returns:: A full sentence describing the valid force field names

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

Bases: 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: _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, length=None)¶

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)
length (int or None) – if given, specifies that only this number of values is allowed

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, length=None)¶

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)
length (int or None) – if given, specifies that only this number of values is allowed

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, length=None)¶

Validate that the argument is a integer list separated by comma

Parameters:

value (str) – string containing numbers separated by commas
length (int or None) – if given, specifies that only this number of values is allowed

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: 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: 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: 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=True)¶

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 it will not be

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, opls5_ok=False)¶

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
opls5_ok (bool) – If True then OPLS5 will be available, if False it will not. Since Macromodel does not support OPLS5, the default is False.

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