=========
Tools API
=========

Functions
=========

``add_hydrogen`` function
-------------------------

.. autofunction:: moldesign.add_hydrogen

``add_missing_data`` function
-----------------------------

.. autofunction:: moldesign.add_missing_data

``add_water`` function
----------------------

.. autofunction:: moldesign.add_water

``assign_forcefield`` function
------------------------------

.. autofunction:: moldesign.assign_forcefield

``assign_formal_charges`` function
----------------------------------

.. autofunction:: moldesign.assign_formal_charges

``build_assembly`` function
---------------------------

.. autofunction:: moldesign.build_assembly

``build_bdna`` function
-----------------------

.. autofunction:: moldesign.build_bdna

``build_dna_helix`` function
----------------------------

.. autofunction:: moldesign.build_dna_helix

``calc_am1_bcc_charges`` function
---------------------------------

.. autofunction:: moldesign.calc_am1_bcc_charges

``calc_gasteiger_charges`` function
-----------------------------------

.. autofunction:: moldesign.calc_gasteiger_charges

``guess_bond_orders`` function
------------------------------

.. autofunction:: moldesign.guess_bond_orders

``guess_histidine_states`` function
-----------------------------------

.. autofunction:: moldesign.guess_histidine_states

``mutate`` function
-------------------

.. autofunction:: moldesign.mutate

``parameterize`` function
-------------------------

.. autofunction:: moldesign.parameterize

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

``ATNUM_VALENCE_CHARGE`` 
-------------------------

.. autoattribute:: moldesign.tools.ATNUM_VALENCE_CHARGE

``ION_CHARGE`` 
---------------

.. autoattribute:: moldesign.tools.ION_CHARGE