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remove smiles prediction #289

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merged 2 commits into from
Dec 11, 2024
Merged

remove smiles prediction #289

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752655c
remove smiles prediction
CunliangGeng Dec 4, 2024
47d60db
remove smiles from BGC and AntismashBGCLoader
CunliangGeng Dec 6, 2024
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362 changes: 0 additions & 362 deletions src/nplinker/genomics/aa_pred.py
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22 changes: 0 additions & 22 deletions src/nplinker/genomics/bgc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,9 +2,7 @@
import logging
from typing import TYPE_CHECKING
from typing import Any
from deprecated import deprecated
from nplinker.strain import Strain
from .aa_pred import predict_aa


if TYPE_CHECKING:
Expand Down Expand Up @@ -240,23 +238,3 @@ def _to_string(value: Any) -> str:
else:
formatted_value = str(value)
return formatted_value

# CG: why not providing whole product but only amino acid as product monomer?
# this property is not used in NPLinker core business.
@property
@deprecated(version="2.0.0", reason="This method will be removed soon")
def aa_predictions(self) -> list:
"""Amino acids as predicted monomers of product.

Returns:
list of dicts with key as amino acid and value as prediction
probability.
"""
# Load aa predictions and cache them
self._aa_predictions = None
if self._aa_predictions is None:
self._aa_predictions = {}
if self.antismash_file is not None:
for p in predict_aa(self.antismash_file):
self._aa_predictions[p[0]] = p[1]
return [self._aa_predictions]
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