Repository navigation
feat: N-terminal acetylation flag + D-amino Wave 2 guidance in presynth QC (#41) - #42
Merged
Merged
Conversation
…presynth QC - SynthQC gains n_acetylation_recommended/n_acetylation_reason fields: when interior trypsin sites exist, flag recommends Nα-Ac at zero synthesis cost to block aminopeptidase entry (Creighton 1993; Dhankhar et al. 2023) - SynthQC gains wave2_d_substitutions list: up to 3 most-N-terminal interior K/R sites yield D-Lys/D-Arg substitution guidance for Wave 2 synthesis (expected t½ gain 3–10×; Wade et al. 1990 PNAS) - Both guidance flags appended AFTER synthesis_difficulty is computed (zero synthesis cost — must not inflate difficulty rating) - to_dict() exposes all three new fields - WET_LAB_HANDOFF.md: two new rows in the QC flags table - 10 new tests in TestWave2Guidance; full 954-test suite green
…K/R, 1-indexed positions, empty seq) - HIGH: lock in that a C-terminal-only K/R does NOT trigger N-acetylation flags (regression guard) - MEDIUM: assert 1-indexed position strings in wave2_d_substitutions for RRWQWRMKKLG - MEDIUM: empty-sequence smoke test (parallel to TestCTerminalAmidation) - LOW: fix misleading comment in interior-trypsin-sites test - LOW: assert n_acetylation_reason is non-empty and contains "acetylat"
4 tasks
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
n_acetylation_recommendedflag to SynthQC: when interior trypsin sites exist, recommend N-terminal acetylation (Ac-) at zero synthesis cost to block aminopeptidase entrywave2_d_substitutionsguidance list: for each interior K/R trypsin cleavage site, provide specific D-Lys/D-Arg substitution instructions for Wave 2 synthesis (expected t½ gain: 3–10×)Scientific basis
Implementation note
Both new flags are appended after
synthesis_difficultyis computed — neither N-terminal acetylation nor Wave 2 D-substitution incurs any Wave 1 synthesis cost, so they must not inflate the difficulty rating.Test plan