schrodinger.application.phase.packages.conformer_reader module

Conformer structure reader, which extracts blocks of conformers from the given input based on perception options.

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class schrodinger.application.phase.packages.conformer_reader.ConformerReaderOptions(args, preferred_subset)

Bases: object

class schrodinger.application.phase.packages.conformer_reader.ConformerReader(source, options)

Bases: object

getConformers()

Yields the next block of contiguous conformers in the source.

Returns:block of contiguous conformers
Return type:list(structure.Structure)
schrodinger.application.phase.packages.conformer_reader.add_file_options(parser)

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
Returns:Argument group object
Return type:argparse._ArgumentGroup
schrodinger.application.phase.packages.conformer_reader.add_confgen_options(parser, refine)

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
Returns:

Argument group object
Return type:

argparse._ArgumentGroup
schrodinger.application.phase.packages.conformer_reader.add_standard_confgen_options(argument_group, refine)

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
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
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
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