API Reference
=============

.. automodule:: peptacular
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Core
----

Peptacular contains a functional and object-oriented API for working with peptides and proteins. Everything 
can be accessed through the peptacular namespace (```import peptacular as pt```), but for clarity the API is broken down into sections below.


Sequence
~~~~~~~~

Processing
^^^^^^^^^^

.. automodule:: peptacular.sequence.digestion
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.. automodule:: peptacular.sequence.transformations
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.. automodule:: peptacular.sequence.mod_builder
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.. automodule:: peptacular.sequence.subseqs
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.. automodule:: peptacular.sequence.basic
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.. automodule:: peptacular.sequence.combinatoric
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.. automodule:: peptacular.sequence.converters
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Mass/Comp/Isotope/Fragment
^^^^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: peptacular.sequence.isotope
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.. automodule:: peptacular.sequence.mass_funcs
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.. automodule:: peptacular.sequence.fragmentation
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Property
^^^^^^^^

.. automodule:: peptacular.sequence.properties
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Data Classes
~~~~~~~~~~~~

Some of the core data classes used throughout Peptacular.

.. autoclass:: peptacular.annotation.mod.Interval
.. autoclass:: peptacular.annotation.mod.Mod
.. autoclass:: peptacular.annotation.mod.Mods
.. autoclass:: peptacular.spans.Span
.. autoclass:: peptacular.isotope.IsotopicData
.. autoclass:: peptacular.isotope.IsotopeLookup

Data Modules
------------

Peptacular relies on the python tacular package for data on amino acids, modifications, elements, and other
chemical entities, but are accessible from the peptacular namespace.

see https://tacular.readthedocs.io