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

schrodinger.livedesign.cmdline.run_check_config(args)

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

schrodinger.livedesign.cmdline.run_registration(args)

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

schrodinger.livedesign.cmdline.run_format_convert(args)

Run format conversion, logging the output to the console

schrodinger.livedesign.cmdline.run_image_generation(args)

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

schrodinger.livedesign.cmdline.to_image_bytes(mol_input, image_fmt, fallback_entity=None)

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.write_image_to_file(mol_input: str, outfile: str)

Write an image to a file

schrodinger.livedesign.cmdline.has_LD_substructure_fp_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

Parameters

• target – molecule to find substructure matches in

• query – substructure molecule on which to find matches

• substructure_options – substructure matching options

schrodinger.livedesign.cmdline.get_LD_similarity_score(mol1: str, mol2: str) → float

Mimic LiveDesign SSS similarity score reporting

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

Mimic LiveDesign SSS substructure matching with fingerprint filtering

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

Mimic how LiveDesign performs filtering in a LiveReport

schrodinger.livedesign.cmdline.run_search_service(args)

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

schrodinger.livedesign.cmdline.run_multiple_sequence_alignment(args)

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

schrodinger.livedesign.cmdline.main(argv=None)