Shameless Claude modification constants added #374
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Define modification format constants in alphabase.constants.modification: - SEPARATOR, MOD_SITE_SEPARATOR - ANY_N_TERM, ANY_C_TERM, PROTEIN_N_TERM, PROTEIN_C_TERM - ANY_N_TERM_SPECIFIC, ANY_C_TERM_SPECIFIC, PROTEIN_N_TERM_SPECIFIC, PROTEIN_C_TERM_SPECIFIC Replace hardcoded ";" with SEPARATOR across 12 files. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
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Pull request overview
This PR introduces modification format constants to improve code maintainability by replacing hardcoded string literals with named constants. The changes define separators and terminal modification site constants in alphabase.constants.modification, then apply them consistently across the codebase.
- Adds
SEPARATOR,MOD_SITE_SEPARATOR, andMOD_TERM_SEPARATORconstants for delimiters - Adds constants for terminal modification sites (
ANY_N_TERM,ANY_C_TERM,PROTEIN_N_TERM,PROTEIN_C_TERM) and their AA-specific variants - Replaces hardcoded string literals (
;,@,^,"Any_N-term", etc.) with these constants across 15 files
Reviewed changes
Copilot reviewed 15 out of 15 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| alphabase/constants/modification.py | Defines all new modification format constants with documentation |
| alphabase/spectral_library/translate.py | Uses SEPARATOR and MOD_SITE_SEPARATOR for parsing modifications |
| alphabase/smiles/peptide.py | Uses SEPARATOR for splitting modification strings |
| alphabase/smiles/adding_smiles.py | Uses MOD_SITE_SEPARATOR and MOD_TERM_SEPARATOR for parsing PTM format |
| alphabase/psm_reader/utils.py | Uses SEPARATOR and MOD_SITE_SEPARATOR throughout utility functions |
| alphabase/psm_reader/sage_reader.py | Uses all separator constants for modification translation |
| alphabase/psm_reader/pfind_reader.py | Uses terminal site constants and separators for pFind format conversion |
| alphabase/psm_reader/msfragger_reader.py | Uses terminal constants and separators for MSFragger parsing |
| alphabase/psm_reader/modification_mapper.py | Uses PROTEIN_N_TERM constant for modification mapping |
| alphabase/psm_reader/maxquant_reader.py | Uses SEPARATOR for joining modification lists |
| alphabase/psm_reader/alphapept_reader.py | Uses SEPARATOR for joining parsed modifications |
| alphabase/protein/fasta.py | Uses all constants for FASTA processing and modification handling |
| alphabase/peptide/precursor.py | Uses SEPARATOR for splitting modification strings |
| alphabase/peptide/mass_calc.py | Uses SEPARATOR for mass calculations |
| alphabase/peptide/fragment.py | Uses SEPARATOR for fragment ion calculations |
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mschwoer
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Dec 8, 2025
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Changes were made with a script generated by an AI, not directly
should I be more worried not or less :-D
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| # Modification format constants | ||
| #: Separator between multiple values (e.g., "Phospho@S;Oxidation@M", "prot1;prot2") | ||
| SEPARATOR: str = ";" |
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could this name be more specific?
| #: Separator for AA-specific terminal mods (e.g., "Q^Any_N-term") | ||
| MOD_TERM_SEPARATOR: str = "^" | ||
| #: Any N-terminal modification site | ||
| ANY_N_TERM: str = "Any_N-term" |
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could these be gathered in ConstantsClasses?
e.g. TerminalKeys.ANY_C_TERM ?
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Changes were made with a script generated by an AI, not directly
Summary
alphabase.constants.modification:SEPARATOR(;) - separator between multiple valuesMOD_SITE_SEPARATOR(@) - separator between mod name and siteMOD_TERM_SEPARATOR(^) - separator for AA-specific terminal modsANY_N_TERM,ANY_C_TERM,PROTEIN_N_TERM,PROTEIN_C_TERM- terminal site constantsANY_N_TERM_SPECIFIC,ANY_C_TERM_SPECIFIC,PROTEIN_N_TERM_SPECIFIC,PROTEIN_C_TERM_SPECIFIC- AA-specific terminal constants