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These are the classes that are required to make new polymer chemistry definitions that model the chemical structure of a polymer.
Model for specifying the acido-basic behaviour of a chemical group of either a Monomer object or of a Modif object | |
Model for refining the acido-basic behaviour of a chemical group of either a Monomer object or of a Modif object | |
List of Coordinates allocated instances | |
The localization of a sequence region in a Polymer Sequence | |
The specification about how CrossLinker objects are represented | |
Sophisticated abstractions to work with formulas | |
Abstractions to work with entities that have masses (base class Ponderable) and that can be ionized | |
Ionization rule | |
Models an isotope | |
Collection of Isotopes and associated methods to access them in various ways | |
Features basic handling of IsotopicData | |
Handles IsotopicData from the IsoSpec element data tables directly from the library's data. These are the reference, pristine, unmodified, isotopic data | |
Handles a peculiar kind of IsotopicData that cannot be handled with the other handlers | |
Handles user-defined IsotopicData | |
Abstractions to work with chemical modifications | |
The specification about how Modif objects are represented | |
Abstractions to work with monomers | |
The specification about how Monomer objects are represented | |
Abstractions to work with an oligomer molecule (peptide , for example) | |
Model for specifying the acido-basic properties of a chemical entity | |
File reader for the pKa, pH, pI data XML file. | |
Abstractions to work with a polymer molecule (protein or saccharide , for example) | |
Abstraction for any chemical entity having a monoisotopic and an average mass | |
Abstractions to work with a simple sequence of Monomers |