Spaces:
Sleeping
Sleeping
File size: 9,538 Bytes
ce7bf5b |
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 |
# Copyright Generate Biomedicines, Inc.
#
# 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.
"""Standard residue names for polymers of different types (e.g., L- or D-amino acid proteins,
mixed-chirality proteins, DNA/RNA, etc.)
"""
from enum import Enum
class polymerType(Enum):
LPROT = 0
DPROT = 1
LDPROT = 2
DNA = 3
RNA = 4
def polymer_type_name(ptype: polymerType):
if ptype == polymerType.LPROT:
return "polypeptide(L)"
elif ptype == polymerType.DPROT:
return "polypeptide(D)"
elif ptype == polymerType.LDPROT:
return "polypeptide(L,D)"
elif ptype == polymerType.DNA:
return "polydeoxyribonucleotide"
elif ptype == polymerType.RNA:
return "polyribonucleotide"
else:
raise Exception(f"unknown polymer type {ptype}")
_res3 = [[] for _ in range(len(polymerType))]
_res1 = [[] for _ in range(len(polymerType))]
_res_to_idx = [dict() for _ in range(len(polymerType))]
_unk_idx = [set() for _ in range(len(polymerType))]
_gap_idx = [set() for _ in range(len(polymerType))]
_stp_idx = [set() for _ in range(len(polymerType))]
def _add_residue(ptype: polymerType, res3, res1):
if isinstance(ptype, list):
for pt, r3, r1 in zip(ptype, res3, res1):
_add_residue(pt, r3, r1)
else:
_res_to_idx[ptype.value][res3] = len(_res3[ptype.value])
# single-letter code is ambiguous, so take the first residue when going from single-letter code to index
if res1 not in _res_to_idx[ptype.value]:
_res_to_idx[ptype.value][res1] = _res_to_idx[ptype.value][res3]
_res3[ptype.value].append(res3)
_res1[ptype.value].append(res1)
if res3 == "---":
_gap_idx[ptype.value].add(_res_to_idx[ptype.value][res3])
elif res3 == "UNK":
_unk_idx[ptype.value].add(_res_to_idx[ptype.value][res3])
elif res3 == "STP":
_stp_idx[ptype.value].add(_res_to_idx[ptype.value][res3])
def num_tokens(ptype=polymerType.LPROT):
return len(_res3[ptype.value])
def num_known_molecular_tokens(ptype=polymerType.LPROT):
return sum(
[
not is_punctuation_index(idx) and not is_unknown(idx)
for idx in range(len(_res3[ptype.value]))
]
)
def res_to_index(res: str, ptype=polymerType.LPROT):
return _res_to_idx[ptype.value].get(res, next(iter(_unk_idx[ptype.value])))
def index_to_single(idx: int, ptype=polymerType.LPROT):
return _res1[ptype.value][idx]
def index_to_triple(idx: int, ptype=polymerType.LPROT):
return _res3[ptype.value][idx]
def to_single(res: str, ptype=polymerType.LPROT):
return index_to_single(res_to_index(res, ptype))
def to_triple(res: str, ptype=polymerType.LPROT):
return index_to_triple(res_to_index(res, ptype))
def is_gap_index(idx: int, ptype=polymerType.LPROT):
return idx in _gap_idx[ptype.value]
def is_stop_index(idx: int, ptype=polymerType.LPROT):
return idx in _stp_idx[ptype.value]
def is_unknown(res: str, ptype=polymerType.LPROT):
return is_unknown_index(res_to_index(res, ptype), ptype)
def is_unknown_index(idx: int, ptype=polymerType.LPROT):
return idx in _unk_idx[ptype.value]
def is_polymer_residue(res: str, ptype: polymerType):
if ptype is None:
# determine if this is a polymer residue for any known polymer
for ptype in polymerType:
if res in _res_to_idx[ptype.value]:
return True
return False
return res in _res_to_idx[ptype.value]
def is_punctuation_index(idx: int, ptype=polymerType.LPROT):
return is_gap_index(idx, ptype) or is_stop_index(idx, ptype)
def is_canonical(res: str, ptype=polymerType.LPROT):
if ptype == polymerType.LPROT or ptype == polymerType.DPROT:
idx = res_to_index(res, ptype)
return (idx < 20) and (idx >= 0)
elif ptype == polymerType.LDPROT:
return is_canonical(res, polymerType.LPROT) or is_canonical(
mirror_amino_acid(res), polymerType.DPROT
)
raise Exception(f"do not known how to deal with polymer type {ptype}")
def canonical_amino_acids(ptype=polymerType.LPROT):
canonicals = []
for aa in _res3[ptype.value]:
if is_canonical(aa, ptype):
canonicals.append(aa)
return canonicals
_add_residue([polymerType.LPROT, polymerType.DPROT], ["ALA", "DAL"], ["A", "a"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["CYS", "DCY"], ["C", "c"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["ASP", "DAS"], ["D", "d"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["GLU", "DGL"], ["E", "e"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["PHE", "DPN"], ["F", "f"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["GLY", "GLY"], ["G", "G"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["HIS", "DHI"], ["H", "h"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["ILE", "DIL"], ["I", "i"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["LYS", "DLY"], ["K", "k"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["LEU", "DLE"], ["L", "l"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["MET", "MED"], ["M", "m"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["ASN", "DSG"], ["N", "n"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["PRO", "DPR"], ["P", "p"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["GLN", "DGN"], ["Q", "q"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["ARG", "DAR"], ["R", "r"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["SER", "DSN"], ["S", "s"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["THR", "DTH"], ["T", "t"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["VAL", "DVA"], ["V", "v"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["TRP", "DTR"], ["W", "w"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["TYR", "DTY"], ["Y", "y"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["HSD", "DSD"], ["H", "h"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["HSE", "DSE"], ["H", "h"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["HSC", "DSC"], ["H", "h"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["HSP", "DSP"], ["H", "h"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["MSE", "DMS"], ["M", "m"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["CSO", "DCS"], ["C", "c"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["SEC", "DEC"], ["C", "c"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["CSX", "DCX"], ["C", "c"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["HIP", "DHP"], ["H", "h"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["SEP", "DEP"], ["S", "s"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["TPO", "DTP"], ["T", "t"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["PTR", "DPT"], ["Y", "y"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["UNK", "UNK"], ["X", "X"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["STP", "STP"], ["*", "*"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["---", "---"], ["-", "-"])
_add_residue([polymerType.LPROT, polymerType.DPROT], ["---", "---"], [".", "."])
for grp in [1, 2, 3]:
for tp in [polymerType.LPROT, polymerType.DPROT]:
for idx in range(num_tokens(tp)):
if grp == 1:
if not is_punctuation_index(idx, tp) and (
not is_unknown_index(idx, tp)
):
if _res3[tp.value][idx] not in _res3[polymerType.LDPROT.value]:
_add_residue(
polymerType.LDPROT,
_res3[tp.value][idx],
_res1[tp.value][idx],
)
elif grp == 2:
if is_unknown_index(idx, tp):
if _res3[tp.value][idx] not in _res3[polymerType.LDPROT.value]:
_add_residue(
polymerType.LDPROT,
_res3[tp.value][idx],
_res1[tp.value][idx],
)
elif grp == 3:
if is_punctuation_index(idx, tp):
if _res3[tp.value][idx] not in _res3[polymerType.LDPROT.value]:
_add_residue(
polymerType.LDPROT,
_res3[tp.value][idx],
_res1[tp.value][idx],
)
def mirror_amino_acid(res: str):
idx = mirror_amino_acid_index(res_to_index(res, polymerType.LDPROT))
if len(res) == 1:
return index_to_single(idx)
return index_to_triple(idx)
def mirror_amino_acid_index(idx: int):
N = num_known_molecular_tokens(polymerType.LDPROT)
# if this is an unknown residue or a punctuation mark, return as is
if idx >= N:
return idx
# otherwise, flip chirality
return (idx + N // 2) % N
|