data_management.generate_molecules
==================================

.. py:module:: data_management.generate_molecules

.. autoapi-nested-parse::

   This script will read each molecule file in the provided directory
   and generate a C++ source file with commands to make each molecule.

   Usage
   -----

   ::

      usage: generate_molecules.py [-h] [--ang2au ANG2AU] [-r] [-a ATOMS_DIR] molecule_dir src_dir
      
      positional arguments:
        molecule_dir          Data directory for molecule files. If combined with the "-r" flag, this directory will be recursively searched.
        src_dir               Destination directory for generated source files.
      
      options:
        -h, --help            show this help message and exit
        --ang2au ANG2AU       Ratio of angstroms to atomic units. (Default: 1.8897161646320724)
        -r, --recursive       Toggle on recursive search through molecule_dir directory. Default OFF.
        -a ATOMS_DIR, --atoms_dir ATOMS_DIR
                              The path to where ElementNames.txt can be found.

   This script creates the following files based on the include and source
   directories given. The directories are not created by this script and must
   be present before running it.

   ::

      +---src
      |       load_molecules.cpp



Classes
-------

.. autoapisummary::

   data_management.generate_molecules.Molecule


Functions
---------

.. autoapisummary::

   data_management.generate_molecules._parse_molecules_xyz
   data_management.generate_molecules._parse_molecules
   data_management.generate_molecules._write_load_molecules
   data_management.generate_molecules.main
   data_management.generate_molecules.parse_args


Module Contents
---------------

.. py:class:: Molecule

   Representation of a molecule.
       


   .. py:attribute:: carts
      :value: []



   .. py:attribute:: atoms
      :value: []



   .. py:method:: add_atom(Z: int, carts: list) -> None

      Adds an atom at the specified cartesian coordinates.

      :param Z: Atomic number
      :type Z: int
      :param carts: Cartesian coordinates
      :type carts: list of float



   .. py:method:: __repr__() -> str

      Text representation of the molecule.

      :return: Text representation of the molecule
      :rtype: str



   .. py:method:: cxxify(tab: str = '    ') -> str

      C++ representation of the molecule.

      :param indent: The current indentation
      :type indent: str

      :param tab: The current tab character, defaults to "    "
      :type tab: str, optional

      :return: C++ string representing the molecule
      :rtype: str



.. py:function:: _parse_molecules_xyz(filepaths: list, sym2Z: dict, ang2au: float) -> Molecule

   Parses an XYZ formatted molecule file.

   :param file_name: Full paths to molecule files.
   :type file_name: list of str

   :param sym2Z: Mapping from lowercased atomic symbols to atomic numbers
   :type sym2Z: dict

   :param ang2au: Ratio of angstroms to atomic units
   :type ang2au: float

   :return: Molecule parsed from file.
   :rtype: Molecule


.. py:function:: _parse_molecules(filepaths: list, sym2Z: dict, ang2au: float, extension: str = '.xyz') -> dict

   Parse molecule files of the specified format.

   :param filepaths: Full paths to molecule files.
   :type filepaths: list of str

   :param sym2Z: Mapping from lowercased atomic symbols to atomic numbers
   :type sym2Z: dict

   :param ang2au: Ratio of angstroms to atomic units
   :type ang2au: float

   :param extension: File format extension to parse, defaults to ".xyz"
   :type extension: str, optional

   :raises RuntimeError: Unsupported atomic density file format.

   :return: Collection of molecules
   :rtype: dict of Molecule


.. py:function:: _write_load_molecules(src_dir: str, mols: dict, tab: str = '    ') -> None

   Write the load_molecules.cpp file with all parsed molecules.

   :param src_dir: ``src`` directory to write load_molecules.cpp to
   :type src_dir: str

   :param mols: Dictionary of names to :class:Molecule
   :type mols: dict of str to :class:Molecule

   :param tab: String representing a tab character
   :type tab: str


.. py:function:: main(args: argparse.Namespace) -> None

   Entry point function to generate atomic density files.

   :param args: Command line argument namespace
   :type args: Namespace


.. py:function:: parse_args() -> argparse.Namespace

   Parse command line arguments.

   :return: Values of command line arguments.
   :rtype: Namespace