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-
__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-
__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