Optimize ProForma proteoform generation#204
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Co-authored-by: Copilot <copilot@github.com>
…tive Co-authored-by: Copilot <copilot@github.com>
mobiusklein
reviewed
May 7, 2026
mobiusklein
reviewed
May 7, 2026
mobiusklein
reviewed
May 7, 2026
mobiusklein
reviewed
May 7, 2026
mobiusklein
reviewed
May 7, 2026
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| def generate(self): | ||
| seen = set() | ||
| for slots in self._build_modification_iter(): |
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When you have multiple modifications per position, _build_modification_iter produces a lot of redundant configurations. These are unlikely to be in the use-case you have in mind, but in the future if that becomes important, this is probably another place to tune.
mobiusklein
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Thank you for reviewing this issue in detail. Your solutions look good, especially the place where I was being wasteful with nested find_positions calls.
Co-authored-by: Copilot <copilot@github.com>
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This should preserve the functionality but improve speed by up to 50%.
One change is the addition of a
deepcopyparameter that is disabled by default, assuming that the output ofProteoformCombinatorwill rarely be additionally modified.