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⚡ Optimize calculate_tm to avoid string slicing #101

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⚡ Optimize calculate_tm to avoid string slicing #101

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9c3be46
Optimize calculate_tm loop to avoid string slicing
google-labs-jules[bot] Jan 26, 2026
b6353f9
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 26, 2026
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14 changes: 10 additions & 4 deletions src/amplifyp/melting.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,13 @@
"CC": (-8000, -19.9),
}

# Optimization: Pre-compute tuple keys for faster lookup in loops
# zip(seq, seq[1:]) produces tuples of characters, e.g. ('A', 'A')
_NN_THERMO_DATA_TUPLE: Final[dict[tuple[str, str], tuple[float, float]]] = {
tuple(k): v
for k, v in NN_THERMO_DATA.items() # type: ignore[misc]
}


def calculate_tm(
primer: Primer, settings: TMSettings = GLOBAL_TM_SETTINGS
Expand Down Expand Up @@ -122,10 +129,9 @@ def calculate_tm(
ds += 4.1

# Nearest neighbor steps
for i in range(n - 1):
dinuc = seq[i : i + 2]
if dinuc in NN_THERMO_DATA:
val = NN_THERMO_DATA[dinuc]
for dinuc in zip(seq, seq[1:]):
if dinuc in _NN_THERMO_DATA_TUPLE:
val = _NN_THERMO_DATA_TUPLE[dinuc]
dh += val[0]
ds += val[1]
else:
Expand Down
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