schrodinger.application.phase.packages.conformer_reader module¶
Conformer structure reader, which extracts blocks of conformers from the given input based on perception options.
Copyright Schrodinger LLC, All Rights Reserved.
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class
schrodinger.application.phase.packages.conformer_reader.
ConformerReaderOptions
(args, preferred_subset)¶ Bases:
object
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__init__
(args, preferred_subset)¶ Initializes command line options used to read conformer blocks.
Parameters: args (argparser.Namespace) – argparser.Namespace with command line options
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class
schrodinger.application.phase.packages.conformer_reader.
ConformerReader
(source, options)¶ Bases:
object
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__init__
(source, options)¶ Initializes…
Parameters: - source (str) – conformer structure input source
- options (ConformerReaderOptions) – reader options derived from command line options
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close
()¶
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getConformers
()¶ Yields blocks of conformers read (or derived) from the source.
Yield: Conformer structures. Ytype: list(structure.Structure)
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schrodinger.application.phase.packages.conformer_reader.
add_file_options
(parser, create_group=True)¶ Adds file screening options to the provided parser and returns the argument group object that holds those options.
Parameters: - parser (argparser.ArgumentParser) – Argument parser object
- create_group (bool) – Create a new argument group and put file screening options into that group.
Returns: Argument group object
Return type: argparse._ArgumentGroup
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schrodinger.application.phase.packages.conformer_reader.
add_confgen_options
(parser, refine, default_conf_sample_name='rapid')¶ Adds conformer generation options to the provided parser and returns the argument group object that holds those options.
Parameters: - parser (argparser.ArgumentParser) – Argument parser object
- refine (bool) – Flag to add -refine as mutually exclusive option to -flex
- default_conf_sample_name (str) – Name of the conformer sampling method to be used by default (for help string only).
Returns: Argument group object
Return type: argparse._ArgumentGroup
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schrodinger.application.phase.packages.conformer_reader.
add_standard_confgen_options
(argument_group, refine, default_conf_sample_name='rapid')¶ Adds standard conformer generation options to the provided argument group.
Parameters: - argument_group (argparser._ArgumentGroup) – Argument group object
- refine (bool) – Set to True if argument_group supports -refine flag
- default_conf_sample_name (str) – Name of the conformer sampling method to be used by default (for help string only).
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schrodinger.application.phase.packages.conformer_reader.
get_confgen_options
(args)¶ Creates conformer generation options from the supplied parser.
Parameters: args (argparse.Namespace) – Command line arguments. Returned: Conformer generation options Return type: PhpConfOptions
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schrodinger.application.phase.packages.conformer_reader.
validate_confgen_conflicts
(args)¶ Checks options for conflicts between file options and confgen options not detected by ArgumentParser.parse_args and returns an informative error message if a conflict is found.
Parameters: args (argparser.Namespace) – argparser.Namespace with command line options Returns: tuple of validity and error message if a conflict is found Return type: bool, str
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schrodinger.application.phase.packages.conformer_reader.
validate_confgen_nddo
(args)¶ Checks for illegal use of -nddo flag.
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
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schrodinger.application.phase.packages.conformer_reader.
validate_title_option
(args)¶ Checks for illegal values of -title flag.
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