drugforge.data.util.utils

Functions

cdd_to_schema(cdd_csv[, out_json, out_csv])	Convert a CDD-downloaded and filtered CSV file into a JSON file containing
cdd_to_schema_pair(cdd_csv[, out_json, out_csv])	Convert a CDD-downloaded and filtered CSV file into a JSON file containing an EnantiomerPairList.
cdd_to_schema_v2(cdd_csv, target_prop[, ...])	Convert a CDD-downloaded and filtered CSV file into a JSON file containing a list[ExperimentalCompoundData].
check_empty_dataframe(df[, logger, fail, ...])
check_filelist_has_elements(filelist[, tag])	Check that a glob or list of files actually contains some elements - if not, raise an error.
check_name_length_and_truncate(name[, ...])
combine_files(paths, output_file)
construct_regex_function(pat[, fail_val, ...])	Construct a function that searches for the given regex pattern, either returning fail_val or raising an error if no match is found.
download_file(url, path)	Download a file and save it locally.
extract_compounds_from_filenames(fn_list, ...)	Extract a list of (xtal, compound_id) from fn_list.
filter_molecules_dataframe(mol_df[, ...])	Filter a dataframe of molecules to retain those specified.
get_path_string(module)	Get the absolute path as a string to an imported module.
get_sdf_fn_from_dataset(dataset, fragalysis_dir)
is_valid_smiles(smiles)
parse_fluorescence_data_cdd(mol_df[, ...])	Filter a dataframe of molecules to retain those specified. Required columns are:
seqres_to_res_list(seqres_str)	https://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#SEQRES :Parameters: seqres_str
strip_smiles_salts(smiles)	Strip salts from a SMILES string.