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topdownproteomics / sdk

Software solution for common top-down proteomics tasks
http://www.topdownproteomics.org/
MIT License
9 stars 4 forks source link

Create Chemical Formula API to support ProForma #24

Closed rfellers closed 6 years ago

rfellers commented 6 years ago

ProForma uses the Unimod chemical formula notation and must be supported by the parser and the writer. The group should develop a set of interfaces, concrete implementations, and tests to handle chemical formulas.

rfellers commented 6 years ago

To clarify, the chemical formula only needs to be parsed during validation. It is an open question as to when this specific validation should happen. It could be a high level validation (like checking modification databases for valid IDs) or low level (like checking for a valid floating point value with mass:)