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.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_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)¶