Skip to content

Add opt-in support for chimeric ProForma parsing#210

Open
josiehong wants to merge 1 commit into
levitsky:masterfrom
josiehong:feature/chimeric-proforma
Open

Add opt-in support for chimeric ProForma parsing#210
josiehong wants to merge 1 commit into
levitsky:masterfrom
josiehong:feature/chimeric-proforma

Conversation

@josiehong

@josiehong josiehong commented Jun 12, 2026

Copy link
Copy Markdown

Adds opt-in parsing support for chimeric ProForma strings using chimeric=True related to #209.

This keeps the default single-sequence behavior unchanged while allowing top-level + to separate chimeric peptidoform components when explicitly requested.

Changes

  • Add chimeric option to Parser, proforma.parse, and ProForma.parse.
  • Return a list of parse results / ProForma objects when chimeric=True.
  • Share fixed modifications, isotope labels, and peptidoform names across chimeric components.
  • Preserve the current default behavior for +, with an error message suggesting chimeric=True.
  • Add tests for opt-in parsing, shared metadata, empty components, charge/adduct boundaries, and shared fixed modifications.
  • Document chimeric parsing and component-wise use with existing downstream APIs.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant