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.. 
    === UCSF ChimeraX Copyright ===
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    === UCSF ChimeraX Copyright ===

atomic: Atomic structures
=========================

Atomic data, such as molecules read from a Protein Databank file, is managed in C++ data structures
which are made available through the following equivalent Python classes:

 * :class:`.AtomicStructure`
 * :class:`.Atom`
 * :class:`.Bond`
 * :class:`.Residue`
 * :class:`.Chain`, which is based on :class:`.StructureSeq` which is in turn based on :class:`.Sequence`

Also lines between atoms depicting distances or missing segments of a protein backbone are
represented as pseudobonds:

 * :class:`.Pseudobond`
 * :class:`.PseudobondGroup`
 * :class:`.PseudobondManager`

Efficient collections of molecular objects and molecular surfaces are also available

.. toctree::
   :maxdepth: 1

Atomic data classes
-------------------

.. automodule:: chimerax.atomic.structure
    :members:
    :inherited-members:
    :show-inheritance:

.. automodule:: chimerax.atomic.molobject
    :members:
    :show-inheritance:

.. automodule:: chimerax.atomic.cymol
    :members:
    :exclude-members: contextmanager, suppress_alt_loc_change_notifications
    :show-inheritance:

.. automodule:: chimerax.atomic.molarray
    :members:
    :member-order: bysource
    :special-members: __len__, __iter__, __getitem__, __or__, __and__, __sub__
    :show-inheritance:

.. automodule:: chimerax.atomic.pbgroup
    :members:
    :show-inheritance:

.. automodule:: chimerax.atomic.molsurf
    :members:
    :show-inheritance:

.. automodule:: chimerax.atomic.args
    :members:
    :show-inheritance:

.. automodule:: chimerax.atomic.struct_edit
    :members:
    :show-inheritance:

Atomic-related UI widgets
-------------------------

.. automodule:: chimerax.atomic.widgets
    :members:
    :show-inheritance: