schrodinger.application.phase.packages.conformer_reader module¶

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

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

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

close()¶

getConformers()¶

Yields blocks of conformers read (or derived) from the source.

Yield: Conformer structures.
Ytype: list(structure.Structure)

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

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

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).

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

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