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4d20b62 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 | # Copyright 2025 ByteDance and/or its affiliates.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
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"
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