miniworld.utils.data_refactoring

This file just contains the test data generation.

Functions

AF_Results_filtering([file_path, ...])	Input : AF results folder path Output : None
AF_Results_json_filtering(json_file_path[, ...])	Input : AF results json path, plddt_filtering (float) Output : plddt_filtered (np.array) [It is index of filtered seq]
AF_Results_json_viewer(file_path)	Input : AF results json path Output : None
PDB_parsing_from_pt(PDB_file[, IS_LABEL, source])	Input : PDB file path, IS_LABEL (bool) Output : Protein object
STRING_refactoring([rank_num])
a3m_pickling(a3m_folder[, saving_directory])	Input : a3m folder path Output : None
check_hhr_loaded(hhr_folder, saved_dir)
get_ID_to_source_dict(sources_path_list[, ...])	Input : sources directory path, saving directory path(.txt) Output : ID_to_source_dict (dictionary)
get_csv()
get_hash_dict(msa_folder_path[, saving_path])
get_query_from_a3m(a3m_file_path)
gzip_files()	It's just for convenience.
hhr_dir_rerefactoring([hhr_dir, saving_dir])
hhr_file_rerefactoring(hhr_file_path, saving_dir)
hhr_refactoring(hhr_folder[, saving_directory])	Input : hhr folder path Output : None
mmcif_Full_sequence_parsing(mmcif_file[, output])	Input : mmcif file path Output : Full Sequence
mmcif_full_sequence(mmcif_folder[, ...])	Input : mmcif folder path Output : None
mmcif_line_parser(line[, loop_])	Parses a single line from an mmCIF file..
mmcif_loop_parser(lines_split_by_sharp, ...)	CAUTION !!! mmcif is not well-sturctured file.
mmcif_parsing(mmcif_file[, IS_LABEL])	Input : mmcif file path (~.cif or ~.cif.gz) Output : Protein object
mmcif_pickling(mmcif_folder[, saving_directory])	Input : mmcif folder path Output : None
pdb_Sampling([output_path])
pdb_pickling(pdb_folder[, saving_directory])	Input : pdb folder path Output : None
print_hhr_pt([file_path])
protein_to_template(protein[, position, ...])	Input : Protein object, position (torch.Tensor) Output : ProteinTemplate object This function is used when Alphafold output is used as template.
refactoring_hhr_file(original_hhr_file[, ...])	Input : original hhr file path Do : Refactoring hhr file and save it Output : None
test_a3m()
test_a3m_file(file_path)