schrodinger.livedesign.cmdline module

Runs core suite functionality hooked up to bluebird-chem used in LiveDesign. This command line utility is exclusively for testing/debugging purposes.

schrodinger.livedesign.cmdline.read_file(input_file: str) Tuple[str, schrodinger.rdkit_extensions.Format]

Read a file and return the contents and the format

schrodinger.livedesign.cmdline.process_input(func: Callable, input_files: List[str])

Iterate through input files, passing their contents/format to a given callable which should log all relevant output to the console

schrodinger.livedesign.cmdline.log_info(header: str, data)

Log data to the console via readable JSON

schrodinger.livedesign.cmdline.check_config(config_file: str)

Validate a given preprocessor configuration JSON


Function to validate preprocessor config, logging all output to the console


Function to run registration, logging all output to the console

schrodinger.livedesign.cmdline.entity_registration(data: str, fmt: schrodinger.rdkit_extensions.Format, args, options)

Run the registration process for a given input string, logging all output registration data to the console


Run format conversion, logging the output to the console


Run the image generation endpoint code, logging each image to the console

schrodinger.livedesign.cmdline.display_image(mol_input: str, fallback_entity: Optional[schrodinger.livedesign.entity_type.EntityClass] = None)

Generate an image and log it to the console

schrodinger.livedesign.cmdline.has_fingerprint_match(target: str, query: str, substructure_options: Optional[schrodinger.rdkit.substructure.QueryOptions] = None) bool

Mimic LiveDesign SSS fingerprints filtering logic before evaluating a substructure match

  • target – molecule to find substructure matches in

  • query – substructure molecule on which to find matches

  • substructure_options – substructure matching options

schrodinger.livedesign.cmdline.similarity_fp_score(mol1: str, mol2: str) Optional[float]

Mimic LiveDesign SSS similarity score reporting


Mimic the Substructure Search Service, logging substructure/subsequence matching, as well as similarity scores


Log a multiple sequence alignment as would be shown in the sequence viewer for the given chain across input files; additionally, debug log annotations