py2opsin package

Submodules

py2opsin.py2opsin module

py2opsin.py2opsin.pkg_fopen(fname)
py2opsin.py2opsin.py2opsin(chemical_name: str | list, output_format: Literal['SMILES', 'ExtendedSMILES', 'CML', 'InChI', 'StdInChI', 'StdInChIKey'] = 'SMILES', allow_acid: bool = False, allow_radicals: bool = False, allow_bad_stereo: bool = False, wildcard_radicals: bool = False, jar_fpath: str = 'default', tmp_fpath: str = 'py2opsin_temp_input.txt') → str

Simple passthrough to opsin, returning results as Python strings.

Parameters:

  • chemical_name (str, list) – IUPAC name of chemical as string, or list of strings.

  • output_format (str, optional) – One of “SMILES”, “ExtendedSMILES”, “CML”, “InChI”, “StdInChI”, or “StdInChIKey”. Defaults to “SMILES”.

  • allow_acid (bool, optional) – Allow interpretation of acids. Defaults to False.

  • allow_radicals (bool, optional) – Enable radical interpretation. Defaults to False.

  • allow_bad_stereo (bool, optional) – Allow OPSIN to ignore uninterpreatable stereochem. Defaults to False.

  • wildcard_radicals (bool, optional) – Output radicals as wildcards. Defaults to False.

  • jar_fpath (str, optional) – Filepath to OPSIN jar file. Defaults to “default”, which causes py2opsin to use its included jar.

  • tmp_fpath (str, optional) – Name for temporary file used for calling OPSIN. Defaults to “py2opsin_temp_input.txt”. When multiprocessing, set this to a unique name for each process.

Returns:

Species in requested format, or False if not found or an error ocurred. List of strings if input is list.

Return type:

str

Module contents