Metadata-Version: 2.1
Name: glypy
Version: 0.12.7
Summary: A Glycoinformatics Toolkit
Home-page: https://github.com/mobiusklein/glypy
Maintainer: Joshua Klein
Maintainer-email: jaklein@bu.edu
License: UNKNOWN
Description: glypy Glycan Analysis and Glycoinformatics Library for Python
        -------------------------------------------------------------
        
        |https://img.shields.io/travis/mobiusklein/glypy.svg| |Documentation
        Status|
        
        
        Glycobiology is the study of the biological functions, properties, and
        structures of carbohydrate biomolecules, also called *glycans*. These
        large, tree-like molecules are complex, having a wide variety of
        building blocks as well as modifications and substitutions on those
        building blocks.
        
        `glypy` is a Python library providing code for reading, writing, and
        manipulating glycan structures, glycan compositions, monosaccharides, and
        their substituents. It also includes interfaces to popular glycan structure
        databases, `GlyTouCan <https://glytoucan.org/>`_ and `UnicarbKB <http://www.unicarbkb.org/>`_
        using `SPARQL` queries and an RDF-object mapper.
        
        Example Use Cases
        ~~~~~~~~~~~~~~~~~
        
        1. Traverse structures using either canonical or residue-level rule
           ordering.
        2. Operate on monosaccharide and substituents as nodes and bonds as
           edges.
        3. Add, remove, and modify these structures to alter glycan properties.
        4. Identify substructures and motifs, classifying glycans.
        5. Evaluate structural similarities with one of several ordering and
           comparator methods.
        6. Plot tree structures with MatPlotLib, rendering using a configurable
           symbol nomenclature, such as SNFG, CFG, or IUPAC. Layout using vector
           graphics for lossless scaling.
        7. Calculate the mass of a native or derivatized glycan.
        8. Generate glycosidic and cross ring cleavage fragments for a
           collection of glycan structures for performing MS/MS database search.
        9. Perform substructure similarity searches with exact ordering or
           topological comparison and exact or fuzzy per-residue matching to
           classify a structure as an N-linked glycan.
        10. Annotate MS spectra with glycan structures, labeling which peaks
            matched a database entry.
        11. Download all N-Glycans from `GlyTouCan <https://glytoucan.org/>`__
        12. Find all glycans in a list which contain a particular subtree, or
            find common subtrees in a database of glycans, performing treelet
            enrichment analysis.
        13. Synthesize all possible glycans using a set of enzymes starting from
            a set of seed structures.
        
        .. |https://img.shields.io/travis/mobiusklein/glypy.svg| image:: https://img.shields.io/travis/mobiusklein/glypy.svg
           :target: https://travis-ci.org/mobiusklein/glypy
        .. |Documentation Status| image:: https://readthedocs.org/projects/glypy/badge/?version=master
           :target: http://glypy.readthedocs.org/en/master/?badge=master
        
        
        Citing
        ~~~~~~
        
        If you use `glypy` in a publication please cite:
        
            Klein, J., & Zaia, J. (2019). glypy - An open source glycoinformatics library.
            Journal of Proteome Research.
            https://doi.org/10.1021/acs.jproteome.9b00367
        
Keywords: glycomics glycan carbohydrate glycoinformatics glypy n-linked o-linked glycosaminoglycan
Platform: UNKNOWN
Provides-Extra: plot
Provides-Extra: glyspace
Provides-Extra: all
