The structural package
======================

The `structural` package contains modules for dealing with molecular structures - it is the functional core that performs the real action behind most of the methods that are available in the `Molecule` class's methods. 
This includes operations such as computing angles, rotating around bonds, and assembling molecules together.

The `structural` package is divided into several submodules, each of which is described below.

Basic structural operations
---------------------------

The `base` module contains the basic structural operations that are used by the other modules.

.. dropdown:: Basic structural operations
      
   .. automodule:: buildamol.structural.base
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Inferring Structural Properties
-------------------------------

The `infer` module contains methods for inferring structural properties from a molecule's atoms and connectivity.
Among these are connections, or atom labels.

.. dropdown:: Inferential structural operations
      
   .. automodule:: buildamol.structural.infer
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.. dropdown:: SMILES
      
      .. automodule:: buildamol.structural.smiles
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Reactivities
------------

The `reactivity` module contains methods for defining reactivities of atom groups (i.e. functional groups) in a molecule in order to guide connectivity between fragments.
These reactivities can be used in conjunction with the `Reaction` class to define how molecules should react with each other. They are the successors of the older `FunctionalGroup` classes.

.. dropdown:: Reactivities
      
   .. automodule:: buildamol.structural.reactivity
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Molecular Geometries
--------------------

The `geometry` module contains methods to place atoms in a molecule in a specific geometry.
Defined are the basic geometries: linear, trigonal planar, tetrahedral, trigonal bipyramidal, and octahedral.

.. dropdown:: Molecular Geometries
      
   .. automodule:: buildamol.structural.geometry
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Functional Groups
-----------------

.. important::

   Functional groups have now been superseded by the more general `Reactivity` classes! Please refer to the `Reactivity` tutorial for more information.

The `groups` module contains methods for describing functional groups in a molecule in order to guide connectivity between fragments.

.. dropdown:: Functional Groups
      
   .. automodule:: buildamol.structural.groups
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Graph Neighborhood in Molecular Structures
------------------------------------------

In order to infer the neighborhoods from connectivity information in molecules, the `neighbors` module defines a `Neighborhood` class that can be used to infer the neighborhoods of atoms in a molecule.

.. dropdown:: Graph Neighborhood in Molecular Structures
      
   .. automodule:: buildamol.structural.neighbors
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Assembling Molecules
--------------------

In order to assemble two molecules together there are two modules that are used: `stitch` and `patch`.
The `patch` module defines a `patch` function and corresponding `Patcher` class that can be used to assemble two molecules together using
a `patch` (i.e. a `Linkage` with internal coordinates). The `stitch` module defines a `stitch` function and corresponding `Stitcher` class that can be used to assemble two molecules together using a `recipe` (i.e. a `Linkage` without internal coordinates).


.. tab-set::

   .. tab-item:: patch module

      .. automodule:: buildamol.structural.patch
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   .. tab-item:: stitch module

      .. automodule:: buildamol.structural.stitch
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   .. tab-item:: connector module

      .. automodule:: buildamol.structural.connector
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