schrodinger.application.phase.shape_screen_reporter.option_utils module¶
Performs parsing and validation of options for generating and using shape screen report databases.
Copyright Schrodinger LLC, All Rights Reserved.
- class schrodinger.application.phase.shape_screen_reporter.option_utils.ClusterBy(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶
Bases:
enum.Enum- features = 1¶
- scaffolds = 2¶
- class schrodinger.application.phase.shape_screen_reporter.option_utils.PageSize(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶
Bases:
enum.Enum- Letter = 1¶
- A4 = 2¶
- schrodinger.application.phase.shape_screen_reporter.option_utils.add_cluster_args(parser)¶
Adds arguments for the “cluster” task.
- Parameters
parser (argparse.ArgumentParser) – Argument parser object.
- schrodinger.application.phase.shape_screen_reporter.option_utils.add_create_args(parser)¶
Adds arguments for the “create” task.
- Parameters
parser (argparse.ArgumentParser) – Argument parser object.
- schrodinger.application.phase.shape_screen_reporter.option_utils.add_export_args(parser)¶
Adds arguments for the “export” task.
- Parameters
parser (argparse.ArgumentParser) – Argument parser object.
- schrodinger.application.phase.shape_screen_reporter.option_utils.add_feature_matching_args(parser, features_required=False)¶
Adds arguments for specifying a list of features to match, positional tolerances and feature type matching rules.
- Parameters
parser (argparse.ArgumentParser) – Argument parser object.
features_required – If True, the help message will indicate that the list of features is required.
- schrodinger.application.phase.shape_screen_reporter.option_utils.add_filter_args(parser)¶
Adds arguments for the “filter” task.
- Parameters
parser (argparse.ArgumentParser) – Argument parser object.
- schrodinger.application.phase.shape_screen_reporter.option_utils.add_print_args(parser)¶
Adds arguments for the “print” task.
- Parameters
parser (argparse.ArgumentParser) – Argument parser object.
- schrodinger.application.phase.shape_screen_reporter.option_utils.check_feature_string(s, expect_number=False)¶
Returns a non-empty error message if s is not a valid pharmacophore feature specification.
- Parameters
s (str) – Pharmacophore feature string
expect_number (bool) – Whether to expect a feature number at the end of s
- Returns
Non-empty error message if s is invalid
- Return type
str
- schrodinger.application.phase.shape_screen_reporter.option_utils.check_permitted_features_string(s)¶
Returns a non-empty error message if s contains any illegal characters.
- Parameters
s (str) – String of permitted feature types
- Returns
Non-empty error message if s is invalid
- Return type
str
- schrodinger.application.phase.shape_screen_reporter.option_utils.get_parser()¶
Creates argparse.ArgumentParser with supported command line options.
- Returns
Argument parser object
- Return type
argparse.ArgumentParser
- schrodinger.application.phase.shape_screen_reporter.option_utils.is_mae_or_sd(filename)¶
Returns True if filename corresponds to a Maestro or SD file.
- Parameters
filename (str) – File name
- Returns
True if filename is a Maestro or SD file
- Return type
bool
- schrodinger.application.phase.shape_screen_reporter.option_utils.is_positive_int(value)¶
Returns True if the provided string can be cast to a positive int.
- Parameters
value (str) – The string to be tested
- Returns
Whether value is a positive int (1, 2, etc.)
- Return type
bool
- schrodinger.application.phase.shape_screen_reporter.option_utils.is_positive_numeric(value)¶
Returns True if the provided string can be cast to a float value > 0.
- Parameters
value (str) – The string to be tested
- Returns
Whether value is a positive numeric
- Return type
bool
- schrodinger.application.phase.shape_screen_reporter.option_utils.parse_feature_rules(rules_string, expect_number=False)¶
Given a comma-delimited string of <feature>:<permitted> pairs, where <feature> may or may not contain a number, and where <permitted> is a string of feature types that <feature> is allowed to match, this function attempts to translate the string into a dictionary and reports any syntax errors it finds.
- Parameters
rules_string (str) – Comma-delimited string of <feature>:<permitted> pairs
expect_number (bool) – Whether to expect a feature number at the end of each feature string
- Returns
tuple of <feature>:<permitted> dictionary and non-empty error message if rules_string is illegal
- Return type
dict{str: float}, str
- schrodinger.application.phase.shape_screen_reporter.option_utils.parse_feature_tol(tol_string, expect_number=False)¶
Given a comma-delimited string of <feature>:<tol> pairs, where <feature> may or may not contain a number, this function attempts to translate the string into a dictionary and reports any syntax errors it finds.
- Parameters
tol_string (str) – Comma-delimited string of <feature>:<tol> pairs
expect_number (bool) – Whether to expect a feature number at the end of each feature string
- Returns
tuple of <feature>:<tol> dictionary and non-empty error message if tol_string is illegal
- Return type
dict{str: float}, float
- schrodinger.application.phase.shape_screen_reporter.option_utils.sanitize_permitted(feature, permitted)¶
Constructs a permitted features string that conforms to the format Phase expects, which is the type of the feature itself, followed by other types it’s allowed to match. For example, if feature is ‘R’ and permitted is ‘HR’, the sanitized permitted features string would be ‘RH’.
- Parameters
feature (str) – Feature type, with or without a trailing number
permitted (str) – String of types feature is allowed to match
- Returns
Sanitized version of permitted
- Return type
str
- schrodinger.application.phase.shape_screen_reporter.option_utils.validate_cluster_args(args)¶
Checks the validity of arguments for “cluster” task.
- Parameters
args (argparser.Namespace) – argparser.Namespace with command line arguments
- Returns
tuple of validity and non-empty error message if not valid
- Return type
bool, str
- schrodinger.application.phase.shape_screen_reporter.option_utils.validate_create_args(args)¶
Checks the validity of arguments for “create” task.
- Parameters
args (argparser.Namespace) – argparser.Namespace with command line arguments
- Returns
tuple of validity and non-empty error message if not valid
- Return type
bool, str
- schrodinger.application.phase.shape_screen_reporter.option_utils.validate_export_args(args)¶
Checks the validity of arguments for “export” task.
- Parameters
args (argparser.Namespace) – argparser.Namespace with command line arguments
- Returns
tuple of validity and non-empty error message if not valid
- Return type
bool, str
- schrodinger.application.phase.shape_screen_reporter.option_utils.validate_feature_matching_args(args)¶
Checks validity of args -features <list>, -tol <dict> and -rules <dict>, where the features in the <dict> specifications are expected to include feature numbers.
- Parameters
args (argparser.Namespace) – argparser.Namespace with command line arguments
- Returns
tuple of validity and non-empty error message if not valid
- Return type
bool, str
- schrodinger.application.phase.shape_screen_reporter.option_utils.validate_filter_args(args)¶
Checks the validity of arguments for “filter” task.
- Parameters
args (argparser.Namespace) – argparser.Namespace with command line arguments
- Returns
tuple of validity and non-empty error message if not valid
- Return type
bool, str
- schrodinger.application.phase.shape_screen_reporter.option_utils.validate_print_args(args)¶
Checks the validity of arguments for “print” task.
- Parameters
args (argparser.Namespace) – argparser.Namespace with command line arguments
- Returns
tuple of validity and non-empty error message if not valid
- Return type
bool, str
- schrodinger.application.phase.shape_screen_reporter.option_utils.validate_args(args)¶
Checks the validity of command line arguments.
- Parameters
args (argparser.Namespace) – argparser.Namespace with command line arguments
- Returns
tuple of validity and non-empty error message if not valid
- Return type
bool, str