.. _secstruct_db:

Secondary structure database
============================

Under the hood, `pmlbeta` maintains a database of secondary structures, which is essentially a bunch of backbone
dihedral angle triplets with labels. This is stored in the form of a Python `dict`, mapping string labels to tuples of
floating point numbers.

By default the following are defined:

.. code:: python

    DEFAULT_HELIXTYPES = {
        'Z6M': (126.7, 62.6, 152.7),
        'Z6P': (-126.7, -62.6, -152.7),
        'Z8M': (47.5, 53.5, -104.3),
        'Z8P': (-47.5, -53.5, 104.3),
        'H8M': (76.8, -120.6, 52.7),
        'H8P': (-76.8, 120.6, -52.7),
        'H10M': (-77.5, -51.8, -75.1),
        'H10P': (77.5, 51.8, 75.1),
        'H12M': (92.3, -90.0, 104.6),
        'H12P': (-92.3, 90.0, -104.6),
        'H14M': (-140.3, 66.5, -136.8),
        'H14P': (140.3, -66.5, 136.8),
        'SM': (70.5, 176.2, 168.9),
        'SP': (-70.5, -176.2, -168.9),
        'Straight': (180, 180, 180),
        'Straight alpha': (180, None, 180),
        'Alpha-helix': (-57, None, -47),
        '3_10-helix': (-49, None, -26),
        'P-beta-sheet': (-119, None, 113),
        'AP-beta-sheet': (-139, None, 135),
    }

Corresponding to the following:

+----------------+-----------+-----------+-----------+--------------------------+
| Abbreviation   |   phi     | theta     | psi       | Comments                 |
+================+===========+===========+===========+==========================+
|    Z6M         |   126.7°  |    62.6°  |   152.7°  | from Beke et. al.(2006)  |
+----------------+-----------+-----------+-----------+                          +
|    Z6P         |  -126.7°  |   -62.6°  |  -152.7°  |                          |
+----------------+-----------+-----------+-----------+                          +
|    Z8M         |  47.5°    |   53.5°   |  -104.3°  |                          |
+----------------+-----------+-----------+-----------+                          +
|    Z8P         |  -47.5°   |   -53.5°  |   104.3°  |                          |
+----------------+-----------+-----------+-----------+                          +
|    H8M         |  76.8°    |  -120.6°  |    52.7°  |                          |
+----------------+-----------+-----------+-----------+                          +
|    H8P         |  -76.8°   |   120.6°  |   -52.7°  |                          |
+----------------+-----------+-----------+-----------+                          +
|    H10M        |  -77.5°   |   -51.8°  |   -75.1°  |                          |
+----------------+-----------+-----------+-----------+                          +
|    H10P        |   77.5°   |    51.8°  |    75.1°  |                          |
+----------------+-----------+-----------+-----------+                          +
|    H12M        |   92.3°   |   -90.0°  |   104.6°  |                          |
+----------------+-----------+-----------+-----------+                          +
|    H12P        |   -92.3°  |    90.0°  |  -104.6°  |                          |
+----------------+-----------+-----------+-----------+                          +
|    H14M        |  -140.3°  |    66.5°  |  -136.8°  |                          |
+----------------+-----------+-----------+-----------+                          +
|    H14P        |   140.3°  |   -66.5°  |   136.8°  |                          |
+----------------+-----------+-----------+-----------+                          +
|     SM         |    70.5°  |   176.2°  |   168.9°  |                          |
+----------------+-----------+-----------+-----------+                          +
|     SP         |   -70.5°  |  -176.2°  |  -168.9°  |                          |
+----------------+-----------+-----------+-----------+--------------------------+
|  Straight      |   180°    |   180°    |    180°   |                          |
+----------------+-----------+-----------+-----------+                          +
| Straight alpha |   180°    |   ---     |    180°   |                          |
+----------------+-----------+-----------+-----------+--------------------------+
| Alpha-helix    |    -57°   |   ---     |     -47°  | from PyMOL               |
+----------------+-----------+-----------+-----------+                          +
| P-beta-sheet   |    -119°  |   ---     |     113°  |                          |
+----------------+-----------+-----------+-----------+                          +
| AP-beta-sheet  |    -139°  |   ---     |     135°  |                          |
+----------------+-----------+-----------+-----------+--------------------------+
| 3_10-helix     |    -49°   |   ---     |     -26°  |                          |
+----------------+-----------+-----------+-----------+--------------------------+

Editing this list is possible by the :ref:`corresponding GUI utility <sseditor_gui>`, or by the :ref:`ssdb_\* <ssdb_commands>` commands.

Changes to the secondary structure database are remembered in the next PyMOL session.

Python API documentation
------------------------

.. automodule:: pmlbeta.secstructdb
    :members:
    :noindex: ssdb_add