============
Geometry API
============

Classes
=======

``AngleMonitor`` class
----------------------

.. autoclass:: moldesign.AngleMonitor
    :members:
    :undoc-members:
    :show-inheritance:

``DihedralMonitor`` class
-------------------------

.. autoclass:: moldesign.DihedralMonitor
    :members:
    :undoc-members:
    :show-inheritance:

``DistanceMonitor`` class
-------------------------

.. autoclass:: moldesign.DistanceMonitor
    :members:
    :undoc-members:
    :show-inheritance:

Functions
=========

``angle`` function
------------------

.. autofunction:: moldesign.angle

``angle_gradient`` function
---------------------------

.. autofunction:: moldesign.angle_gradient

``dihedral`` function
---------------------

.. autofunction:: moldesign.dihedral

``dihedral_gradient`` function
------------------------------

.. autofunction:: moldesign.dihedral_gradient

``distance`` function
---------------------

.. autofunction:: moldesign.distance

``distance_gradient`` function
------------------------------

.. autofunction:: moldesign.distance_gradient

``set_angle`` function
----------------------

.. autofunction:: moldesign.set_angle

``set_dihedral`` function
-------------------------

.. autofunction:: moldesign.set_dihedral

``set_distance`` function
-------------------------

.. autofunction:: moldesign.set_distance

Unexported API
==============

``AngleConstraint`` class
-------------------------

.. autoclass:: moldesign.geom.AngleConstraint
    :members:
    :undoc-members:
    :show-inheritance:

``DihedralConstraint`` class
----------------------------

.. autoclass:: moldesign.geom.DihedralConstraint
    :members:
    :undoc-members:
    :show-inheritance:

``DistanceConstraint`` class
----------------------------

.. autoclass:: moldesign.geom.DistanceConstraint
    :members:
    :undoc-members:
    :show-inheritance:

``FixedCoordinate`` class
-------------------------

.. autoclass:: moldesign.geom.FixedCoordinate
    :members:
    :undoc-members:
    :show-inheritance:

``FixedPosition`` class
-----------------------

.. autoclass:: moldesign.geom.FixedPosition
    :members:
    :undoc-members:
    :show-inheritance:

``GeometryConstraint`` class
----------------------------

.. autoclass:: moldesign.geom.GeometryConstraint
    :members:
    :undoc-members:
    :show-inheritance:

``MolecularSymmetry`` class
---------------------------

.. autoclass:: moldesign.geom.MolecularSymmetry
    :members:
    :undoc-members:
    :show-inheritance:

``Monitor`` class
-----------------

.. autoclass:: moldesign.geom.Monitor
    :members:
    :undoc-members:
    :show-inheritance:

``SymmetryElement`` class
-------------------------

.. autoclass:: moldesign.geom.SymmetryElement
    :members:
    :undoc-members:
    :show-inheritance:

``apply_4x4_transform`` function
--------------------------------

.. autofunction:: moldesign.geom.apply_4x4_transform

``get_symmetry`` function
-------------------------

.. autofunction:: moldesign.geom.get_symmetry

``improper_axis_from_matrix`` function
--------------------------------------

.. autofunction:: moldesign.geom.improper_axis_from_matrix

``normalized`` function
-----------------------

.. autofunction:: moldesign.geom.normalized

``perpendicular`` function
--------------------------

.. autofunction:: moldesign.geom.perpendicular

``safe_arccos`` function
------------------------

.. autofunction:: moldesign.geom.safe_arccos

``shake_positions`` function
----------------------------

.. autofunction:: moldesign.geom.shake_positions

``sub_angles`` function
-----------------------

.. autofunction:: moldesign.geom.sub_angles