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| import functools |
| import logging |
| from pathlib import Path |
| from typing import Union |
|
|
| from protenix.data.ccd import ( |
| _connect_inter_residue, |
| add_inter_residue_bonds, |
| biotite_load_ccd_cif, |
| get_ccd_ref_info, |
| get_component_atom_array, |
| get_component_rdkit_mol, |
| res_names_to_sequence, |
| ) |
| from protenix.data.substructure_perms import get_substructure_perms |
|
|
| from pxdesign.configs.configs_data import data_configs |
| from pxdesign.data.constants import MOL_TYPE_MAP, STD_DESIGN |
|
|
| logger = logging.getLogger(__name__) |
|
|
| COMPONENTS_FILE = data_configs["ccd_components_file"] |
| RKDIT_MOL_PKL = Path(data_configs["ccd_components_rdkit_mol_file"]) |
|
|
|
|
| @functools.lru_cache(maxsize=None) |
| def get_one_letter_code(ccd_code: str) -> Union[str, None]: |
| """get one_letter_code from CCD components file. |
| |
| normal return is one letter: ALA --> A, DT --> T |
| unknown protein: X |
| unknown DNA or RNA: N |
| other unknown: None |
| some ccd_code will return more than one letter: |
| eg: XXY --> THG |
| |
| Args: |
| ccd_code (str): _description_ |
| |
| Returns: |
| str: one letter code |
| """ |
| ccd_cif = biotite_load_ccd_cif() |
| design_dic = {"xpb": "j"} |
| if ccd_code not in ccd_cif: |
| return None |
| if ccd_code in design_dic.keys(): |
| return design_dic[ccd_code] |
| one = ccd_cif[ccd_code]["chem_comp"]["one_letter_code"].as_item() |
| if one == "?": |
| return None |
| else: |
| return one |
|
|
|
|
| @functools.lru_cache(maxsize=None) |
| def get_mol_type(ccd_code: str) -> str: |
| """get mol_type from CCD components file. |
| |
| based on _chem_comp.type |
| http://mmcif.rcsb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.type.html |
| |
| not use _chem_comp.pdbx_type, because it is not consistent with _chem_comp.type |
| e.g. ccd 000 --> _chem_comp.type="NON-POLYMER" _chem_comp.pdbx_type="ATOMP" |
| https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v5_next.dic/Items/_struct_asym.pdbx_type.html |
| |
| Args: |
| ccd_code (str): ccd code |
| |
| Returns: |
| str: mol_type, one of {"protein", "rna", "dna", "ligand"} |
| """ |
| ccd_cif = biotite_load_ccd_cif() |
|
|
| if ccd_code in STD_DESIGN: |
| return MOL_TYPE_MAP[ccd_code] |
|
|
| if ccd_code not in ccd_cif: |
| return "ligand" |
|
|
| link_type = ccd_cif[ccd_code]["chem_comp"]["type"].as_item().upper() |
|
|
| if "PEPTIDE" in link_type and link_type != "PEPTIDE-LIKE": |
| return "protein" |
| if "DNA" in link_type: |
| return "dna" |
| if "RNA" in link_type: |
| return "rna" |
| return "ligand" |
|
|
