smith-chem-wisc
Ptm stoichiometry
New PR with changes from PR #797 and more.
Description:
PTM stoichiometry classes created for each structural level (protein group -> protein -> (base) peptide - modification). Probably the most important class to understand is the QuantifiedPeptide class for which an object represents a collection of post-translationally modified variants sharing the same base sequence. This is in contrast with other Peptide classes that represent a peptide with a given full sequence. The QuantifiedProtein class, which stores the QuantifiedPeptide objects, handles peptide-to-protein indexing and obtaining of the modification stoichiometry for the protein. The QuantifiedModification class is primarily a data class, and the QuantifiedProteinGroup class is mostly a container for the different QuantifiedProtein members of the protein group. Lastly, the PositionFrequencyAnalysis class has a method to take a list of (full sequence, protein group list, intensity) tuples and create a collection of QuantifiedProteinGroup objects.
