added no enzyme query for the use of fasta sequence itself for peptid…#598
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YukiMatsuzawa merged 2 commits intomasterfrom Jul 10, 2025
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Pull Request Overview
Adds support for a “no enzyme” option by defining it in the enzyme resource file and updating the digestion logic to return the intact protein when specified.
- Introduce a new
<enzyme>entry with title “No enzyme” and specificity-in enzymes.xml - Update
GetDigestedPeptideSequencesto handle empty/null cleavage lists and the"-"indicator by returning the full protein as a single peptide
Reviewed Changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.
| File | Description |
|---|---|
| src/Common/CommonStandard/Proteomics/Resources/enzymes.xml | Added a “No enzyme” entry with specificity - to allow full-protein queries without cleavage |
| src/Common/CommonStandard/Proteomics/Function/ProteinDigestion.cs | Added early return for empty/null cleavage sites and special case for "-" to yield full-length peptide |
Comments suppressed due to low confidence (1)
src/Common/CommonStandard/Proteomics/Function/ProteinDigestion.cs:27
- Consider adding a unit test to verify that the method returns the full protein sequence as a single peptide when using the no-enzyme indicator (
"-").
if (cleavagesites.Count == 1 && cleavagesites[0] == "-") {
src/Common/CommonStandard/Proteomics/Function/ProteinDigestion.cs
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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